3,931 Matching Annotations
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    1. racial achievement gap

      The difference in performance (for example on standardized tests) between minority students and white students.

    2. gateway courses

      Classes that students are required to take before taking more advanced courses in the field.

    3. snowballing effect

      A process that may start small, but build on itself becoming larger and more serious.

    4. discipline

      A specific branch of knowledge.

    5. interactive engagement approaches

      Teaching strategies in which students are challenged to think about the material on their own and with other students, while the instructor acts as a guide.

    6. residual

      Amount left unexplained by other variables.

    7. SE

      Standard Error: A measure of how far away the mean of your data is likely to be from the true mean of the population.

    8. Error bars

      A graphical representation (usually lines through a point on the graph that run parallel to one of the axes) showing the amount of uncertainty there is in the location of that point

    9. grand mean

      The mean of the mean of several sub-samples.

    10. z scores

      A z-score is a measure of the number of standard deviations above or below the average score a raw, individual score is.

    11. SD

      Standard deviation: a statistical way of measuring the amount of variation in data.

      It can be used to quantify how far an individual's data is from the average data.

    12. continuous

      Continuous variables have an infinite number of possible values.

    13. negative relation

      A condition in which when the value of one variable goes up, the value of the other variable goes down.

    14. moderation effect

      Moderating variables are variables that affect the direction of strength of a relationship between dependent and independent variables (in this case, the level of endorsement of stereotype threat is the moderating variable).

      A moderating effect is the result of the influence of a moderating variable.

    15. SOM

      Supporting Online Materials (typically located at the end of the article)

    16. main

      A main effect is the effect of one independent variable (in this case gender) on the dependent variable (in this case beginning-of-semester FMCE scores), and ignores the effects of other independent variables.

    17. as a function of

      A function defines one variable in terms of another.

      Defining y "as a function of" x means that y varies based on the level of x.

    18. values affirmation

      An intervention in which people reflect on and write about the beliefs and values (for example: family, integrity...) that are important in their life

    19. psychological threat

      Any outside force (real or perceived) that challenges a person's values, beliefs or sense of self

      Stereotype (or identity) threat is a subset of psychological threat in which a person feels they will be judged according to common prejudices about some aspect of their identity (for example: race, ethnicity or gender)

    20. identity threat

      A situation in which a person feels they will be judged according to common, negative prejudices about a larger group in which they belong (for example: ethnic group or gender)

    21. standardized test

      Any form of an exam that requires all people taking the test to answer the same questions and is scored the same way in all cases, so that comparisons can be made between all people who take the test. These are typically multiple choice tests taken by large populations of students (for example: all 8th grade students in the US)

    22. distribution

      The frequency of occurrence of some measure (for example: how many students got As, Bs, Cs, Ds, and Fs)

    23. cumulative exam

      Test on all material covered during the course

    24. outcome measure

      Tools used to assess a subject's performance.

    25. nationally normed standardized test

      A standardized test that is given across the country so that an average performance can be determined for the country.

    26. condition

      Assigned group, either the intervention group or the control group

    27. recitation

      A meeting of a subset of students from a larger lecture course in which students can ask questions, get clarification on lecture topics and may solve additional problems or take quizzes (typically required with very large college courses).

    28. self-relevant

      Related to an individual's sense of identity

    29. control group

      The subjects that do not receive treatment

    30. pedagogical

      Related to teaching

    31. evaluative stress

      Fear and anxiety caused by the thought of having to take an exam

    32. theoretically motivated

      Based on a hypothesis that may have been supported in laboratory experiments, but has not been shown to work in practice

    33. fear of being devalued based on a group identity

      Stereotype threat or identity threat

    34. cognitive

      Perception, attention, learning, memory and problem solving

    35. instructional methods

      Ways that course material is taught, such as through context-rich problems

    36. social-psychological

      The effect of the presence or imagined presence of others on someone's thoughts, feelings and behaviors

    37. context-rich problems

      Short scenarios that give the student a real-world situation in which to apply their knowledge

    38. curricular materials

      Educational resources that can be incorporated into a teacher's lessons

    39. interactive techniques

      Activities in which the student participates (as opposed to passively listening to a lecture)

    40. conceptual mastery

      Understanding the main ideas that make up the field

    1. acridines

      An organic molecule that is not naturally found in cells, as they are substituted derivatives of the parent ring.

      Acridines used to be used in some dyes and many have antiseptic properties, but usage largely stopped as acridines are also a skin irritant.

    2. genetic recombination

      The exchange of genetic material between two different organisms. In the case of T4 bacteriophage, this is done by infecting a single E. coli cell with multiple phages. The phage genomes then recombine and produce new variants.

    3. rII locus

      A locus is a specific location or section of genetic material. The rII locus is one of three loci composing the genetic material of bacteriophage T4 (described below).

    4. chemically induced mutations

      Chemically induced mutations occur when a scientist uses chemicals to alter a DNA sequence.

    5. messenger RNA

      A class of RNA that acts as a messenger of genetic information, delivering the code from DNA to a ribosome where it is translated into amino acids, eventually resulting in a polypeptide or protein.

    6. Gamow's

      George Gamow (1904-1968) was a theoretical physicist. He was so curious about the natural world that he was often in contact with scientific giants outside of physics, like Crick. Despite his inexperience in chemistry and biology, Gamow learned about these fields and ultimately influenced their progress. Gamow is just one of many historical examples of an outside, "non-expert" perspective having a profound influence on a difficult problem.

    7. a sequence of 20 or more things is determined by a sequence of four things of a different type.

      That is, a specific sequence of bases encodes a specific sequence of amino acids. Within this code, which is used by all living organisms, there are only four kinds of bases and 20 kinds of amino acids.

    8. bases

      Here, bases refer to the chemical pendants—side groups of molecules—that are found on the backbone of nucleotides. Nucleotides consist of a sugar called deoxyribose, a phosphate group, and one of five bases.

      An example of a base is guanine.

    1. fidelity

      How specifically an enzyme carries out its function. We can say that Cas13b has high fidelity because it produced very few off-targets in the knockdown experiment (see Figures 1E, 1F, and 1G).

    2. structure-guided protein engineering

      When researchers want to modify a protein to improve a particular feature, they can use the knowledge of the protein's 3D structure to identify and modify key amino acids in the sequence.

    3. coverage

      When you sequence a genome, you do it in pieces rather than in a single, continuous stretch. This is similar to cutting the genome up and then putting it back together again, like a puzzle. Each base may be read multiple times and be a part of multiple sequences—comparing pieces to see where they overlap is how the full genome is reconstructed. The number of times a base is read is called the "coverage," and higher coverage leads to a more accurate sequence.

    4. adeno-associated viral (AAV) vectors

      Adeno-associated virus (AAV) is a human virus that is present in 80% - 90% of the adult population but does not cause any disease. This virus has been extensively used as a biomolecular tool because it is small and has low risk of genome integration and causing unwanted mutations.

    5. the ClinVar database

      ClinVar is an archive that collects data about the relationship between gene variants and phenotypes. It contains more than 400,000 records.

      ClinVar is free to use—try looking up information about AVPR2. Search for AVPR2 to find out more about the 878G>A mutation that the authors looked at.

    6. Fanconi anemia

      Fanconi anemia (FA) is a rare genetic condition resulted from nonfunctional DNA repair mechanisms.

      Because DNA repair is vital for every cell in the body, all organs are affected when repair mechanisms don't function properly. Organs that contain frequently dividing cells (such as skin) are the most affected. People with Fanconi anemia have bone marrow defects, organ abnormalities, and an increased risk of some cancers.

    7. FANCC

      FANCC codes for a protein involved in the Fanconi anemia (FA) disease pathway.

      This pathway is activated when the cell DNA gets damaged. The FANCC protein is a part of a complex responsible for recognizing this DNA damage and activating repair mechanisms.

    8. PPIB

      Stands for, Peptidylprolyl Isomerase B (also known as Cyclophilin B), which codes for a protein that regulates protein folding in the cytoplasmic reticulum. Some mutations of PPIB result in impaired bone development.

    9. orthologs

      Paralogs are genes that originate from gene duplication which could have occurred in an ancestral species. With time, paralogs can acquire specific functions.

      Orthologs are genes that originate from an ancestral gene through speciation event.

      For instance, ADAR1 genes from human and chimpanzee are orthologs, whereas human ADAR1 and ADAR2 genes are paralogs.

      Image credit: https://www3.beacon-center.org/blog/2015/03/23/beacon-researchers-at-work-same-behavior-same-genes/

    10. DNA base editors, consisting of a fusion between Cas9 nickase and cytidine deaminase, can mediate efficient cytidine-to-uridine conversions within a target window and substantially reduce the formation of double-strand break–induced indels

      DNA base editing is a technique which allows precise conversion of one nucleotide into another without any template sequence.

      A base editor is a fusion protein made up of a protein that recognizes specific DNA sequences (for example, Cas9), and a deaminase that can convert one amino acid to another (i.e., cytidine [C] to uridine [U] or adenosine [A] to inosine [I]).

      Because of the geometry of the proteins, this conversion can only happen in a certain range of nucleotides, called the target window.

    11. frame shifts

      Genes are transcribed into proteins by codons, which are made up of sequences of three amino acids. Mutations that occur in numbers divisible by three will not affect the reading frame, but those not divisible by three will cause a shift in the reading frame. Generally, a mutation in-frame will not disrupt the protein function and can be handled by the cell. A frame-shift mutation will completely inactivate a protein and can be very detrimental to cellular function in some cases.

      For example:

      Original sequence: THE CAT WAS RED

      Frame shift mutation: ATH ECA TWA SRE D

      Non-frame shift mutation: THE BIG CAT WAS RED

    12. Cpf1

      Cpf1 is a nuclease that is analogous to Cas9.

      Cpf1 differs from Cas9 in a number of ways. The most important one is that when Cpf1 cuts DNA, it leaves overhangs. It also requires different PAM sequences, which are short sequences that help the system distinguish self DNA from non-self DNA.

      Cfp1 has the potential to be more accurate than Cas9, and can sometimes be used when there are no sequences that Cas9 can use as a target.

    13. Precise nucleic acid–editing technologies

      These techniques allow researchers to modify a chosen nucleic acid sequence.

      The most widely used technologies are TALENs (transcription activator-like effector nucleases), ZFNs (zinc finger nucleases) and CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9).

      CRISPR is the most popular since it can be programmed to new sequences using a guide RNA, whereas other tools must be engineered at the protein level, which is difficult and time consuming. The focus of this paper is a variation of CRISPR that uses Cas13.

    1. despite high interaction dissimilarity across communities

      Although the exact behaviors between species differed between different locations, the networks for all of the areas shared common traits.

    2. modular

      Organized into distinct, independent groups

    3. perturbations

      A deviation or disturbance from the norm.

  2. May 2019
    1. dispersal

      To distribute throughout an area.

    2. biotic factors

      Living parts of an ecosystem

    3. Abiotic factors

      Non-living parts of an ecosystem

    4. supergeneralist

      A species that interacts with multiple groups of species in ecological networks

    5. insular

      From an island

    6. frugivores

      An animal that eats fruit

    7. archipelago

      A group of islands

    8. Anthropocene

      The current geological age where human activity is the dominant influence on climate change and the environment.

    1. tribopair

      Refers to the components in a friction system. Here, the DLC coated ball and the graphene-plus-nanodiamonds constitute the tribopair.

    2. energetic barriers

      The minimum energy needed to overcome the attractive forces between atoms at the sliding interface is referred to as energertic barriers.

    3. dispersive interlayer interactions

      This force occurs due to the out of plane interaction between adjacent graphene layers.

    4. van der Waals forces

      A general term used to describe the intermolecular forces of attraction between molecules.

      See more from Khan Academy

    5. dangling bonds

      An unsatisfied valence of an immobilized atom.

    6. transmission electron microscopy (TEM)

      TEM is an imaging technique capable of generating high resolution (nanometer scale) images of a sample.

    7. dry nitrogen

      Nitrogen gas with no water vapor.

    1. lucrative


    2. gender gap

      Another term for the "gender achievement gap" in which men outperform women in the same field

    3. modal grades

      The "mode" refers to the number that occurs most frequently in a set.

      The "modal grade" is the course grade that occurred most frequently.

    4. double-blind study

      An experiment in which neither the participants nor the experimenters know which group the each participant is assigned to until after the data is analyzed.

    5. randomized

      Participants are equally likely to end up in any of the test conditions.

      In this case, participants are equally likely to end up in the control group and the values affirmation test group.

    6. gender achievement gap

      The difference in test scores, course performance and job prospects between men and women in the same field

    7. psychological intervention

      Any activities used to modify behavior, emotional state, or feelings

    8. effect size

      Statistical measure of the strength of the relationship between two variables

    9. interaction

      Interaction effects occur when the effect of one variable depends on another variable

      In this case, the effect of the intervention (values affirmation or control) depended on the student gender (male or female).

    1. polygenic

      Referring to traits that are controlled by two or more genes at different places on different chromosomes.

    2. synteny

      When two or more genomic regions are derived from a single ancestor.

    3. directional selection

      Type of natural selection where one phenotype is favored over others. This causes the frequency of alleles to shift in the direction of that phenotype.

    4. Introgressive hybridization

      Movement of gene from one species into the gene pool of another species by the repeated crossing of a hybrid with one of its parents.

  3. Apr 2019
    1. heterozygotes

      An individual that has two different forms of a particular gene on homologous chromosomes.

    2. homozygous

      Referring to a particular gene in which all of the alternative forms of that gene are identical on homologous chromosomes.

    3. missense mutation

      Where a single nucleotide base is changed which results in a different amino acid.

    4. phenotype

      Observable characteristics of an individual.

    5. single-nucleotide polymorphism

      Refers to a variation in a single base pair within a DNA sequence.

    6. intrinsic transcriptional activity

      An essential copying of DNA into RNA, the first step of gene expression.

    7. genome-wide fixation index

      Measure of the genetic differences in and among populations due to genetic structure.

    8. selection differential analysis

      Measures the difference between the average genetic value of selected organisms and the average genetic value of all the organisms in the population.

    9. multiple regression

      Used to explain the relationship between a dependent variable and one or more independent variables.

    10. heritable

      Referring to traits that are transmissible from parent to offspring.

    11. taxa

      Groups of one or more populations.

    12. phylogenetic

      Referring to the study of the evolutionary history and relationships of various biological species.

    13. speciation

      The formation of new species.

    14. haplotypes

      Groups of genes inherited from a single parent.

    15. genomic analysis

      The process of measuring or comparing features such as DNA sequences, variation of structures, gene functions, or gene expression.

    16. adaptive radiation

      Event in which a lineage rapidly diversifies into more species with different adaptations. These events lead to speciation.

    17. morphological

      Relating to the structure or form of living organisms.

    18. character displacement

      When two competing species overlap in habitat, natural selection may drive one population to use resources that are not used by individuals of the other population. This allows two similar species to coexist.

    19. Ecological

      Describing a branch of biology that deals with relationships and interactions among organisms and the environment.

    1. an order of magnitude

      About 10 times. Let's say zeolites (a conventional adsorbent) could adsorb 2 liters, then MOF-801 could adsorb an order of magnitude greater—that is, 20 liters.

    2. noncondensables

      Gases that cannot easily be turned into liquids. In this case, noncondensables refers to the gases present in air which are mainly dioxygen, dinitrogen, and argon.

    3. global horizontal irradiation

      The amount of solar light received by a horizontal surface on Earth.

    4. solar absorptance of 0.91

      The fraction of the sun radiation that penetrates the surface. A solar absorptance of 0.91 means that 91% of the sun's radiation penetrates the material and is converted to heat.

    5. face-centered cubic topology

      Describes the 3D geometry of the MOF. MOF-801 is constituted of a repetition of cubes having one cluster in each corner and each center of the faces. Figure 1B shows one of these small cubes constituting the repeating unit of the MOF.

    6. diurnal

      During the day. It is the opposite of nocturnal, which means during the night.

    7. porosity

      The ratio of the cavities' volume to the total volume of the material. MOFs are made of microscopic crystals, which are responsible for the presence of these cavities. Porosity can range from 0 to 1, a porosity of 0 meaning that there are no cavities within the structure.

    8. microcrystalline

      Made of atoms and molecules arranged in a highly ordered microscopic structure that extends in every direction.

    9. 1 sun

      Unit of light intensity corresponding to 1000 watts per square meter. For reference, if you stood one meter away from a standard 60-watt light bulb, the light intensity would be equal to about 4.8 watts per square meter.

    10. [Zr6O4(OH)4(fumarate)6]

      The chemical composition of MOF-801. This specific MOF is based on zirconium (Zr) metal ions linked together by fumarate molecules, which are small organic compounds made of carbon, oxygen, and hydrogen.

    1. wear debris

      Wear is the progressive loss of materials from contacting surfaces relative in motion. The wear process results in generation of debris—or particles—of various size, shape, color distributions, and chemical composition.

    2. mechanical strength

      Refers to the material's resistance to failure by fracture or deformation when a load is applied.

    3. sp3/sp2 bonded carbon

      Hybridization is the combining or mixing up of atomic orbitals (an expected region of electron density around an atom) to form new hybrid orbitals that have geometries suitable to form bonds. Electrons can be found in s, p, d and f orbitals. When an s orbital combines with three p orbitals, it results in four sp3 hybridized orbitals. Similarly, the combination of an s orbital with two p orbitals gives rise to three sp2 hybrid orbitals.

      Learn more about hybrid orbitals with these videos from Khan Academy.

    4. defects

      Perfect crystal is an idealization and in real materials, atom arrangements do not follow perfect crystalline patterns. Crystal defects can be due to missing atoms, introduction of an impurity atom, broken crystal pattern along fault lines or due to the joining of distinct crystal planes.

    5. incommensurability

      Misaligned or misfit.

    6. highly oriented pyrolytic graphite (HOPG)

      A high purity graphite material with high degree of preferred crystallographic orientation.

    7. macroscopic

      Relating to the large-scale, likely visible to the human eye.

    8. nanoscale

      Refers to dimensions less than 100 nanometers (where one nanometer is one billionth of a meter).

    9. mesoscopic

      This region is an intermediate between atomic and macroscopic scales.

    10. coefficient of friction

      The ratio of the frictional resistance force to the normal force. When two objects are in contact, the force which presses the surfaces together is called normal force.

    11. nanoscrolls

      A nanomaterial structure with a spiral wrapped geometry.

    12. diamondlike carbon (DLC)

      A carbon material that exhibits many of the desirable properties of the diamond material.

    13. graphene

      The building block of graphite, which is used in pencil tips. Graphene is a one atom thick layer of carbon atoms arranged in a hexagonal lattice (atoms are arranged at the corners of a hexagon). The thickness of graphene is one million times less than that of a single human hair. Graphene is the world's first two dimensional material and the 2010 Nobel prize in Physics was awarded for its discovery.

      Source: Wikimedia

    14. superlubricity

      The state of near-zero friction at the sliding interfaces of two contacting solid surfaces is called superlubricity. In superlubric regimes, the extent of physical and/or chemical interactions is extremely small and hence the surfaces can slide over one another without causing much friction.

    15. quasi-2D ordered

      Quasicrystals are materials with perfect long-range order, but with no three-dimensional translational periodicity of crystals.

    1. phylogenetic

      Referring to the study of the evolutionary history and relationships of various biological species.

    2. morphological

      Relating to the structure or form of living organisms.

    3. interspecific competition

      Individuals of different species compete for the same resources.

    4. adaptive radiations

      Events in which a lineage rapidly diversifies into more species with different adaptations. These events lead to speciation.

    5. speciation

      The formation of new species.

    6. heritability

      A statistic that describes how much variation of a specific trait can be attributed to genetics. With these finches, it's a measure of how well differences in beak genes account for differences in beak sizes.

    7. natural selection

      Process that describes how species adapt to their environment. The organisms that are best adapted tend to survive and reproduce.

    8. ecological

      Describing a branch of biology that deals with relationships and interactions among organisms and the environment.

    9. character displacement

      When two competing species overlap in habitat, natural selection may drive one population to use resources that are not used by individuals of the other population. This allows two similar species to coexist.

    1. polarity of the NAO

      Polarity means to have two opposite or contradictory tendencies or aspects. In this case, the North Atlantic Oscillation (NAO) has both a warm phase and a cool phase, and convection (ocean mixing) differs between these conditions.

    2. 500-mb height of the atmosphere

      This 500-mb height (mb stands for millibar, which is a unit for measuring air pressure) is the typical height presented in weather maps. Since most weather occurs roughly around this height in the atmosphere, looking at 500-mb maps of the sky makes it possible to more accurately predict weather events.

    3. El Ñino

      What causes El Niño, how can it affect you, and why is it so hard to predict? Find out in this video from National Geographic:


    4. altimetric

      Altimetry is a technique for measuring the height of the surface below the altimeter. Satellites do this by sending a radar pulse to the surface of Earth. The time it takes for the pulse to bounce off the surface and return to the satellite is used to measure height, or altitude. Combined with precise satellite location data, such satellite measurements yield sea-surface heights.

    5. TOPEX/Poseidon

      Launched in 1992 as a joint mission of the U.S. and French space agencies, TOPEX/Poseidon was the first major oceanographic research satellite in space. It's goal was to map the topography of the ocean surface.

    6. sea-level pressure

      The sea-level pressure is the atmospheric pressure at a given location in the ocean. Because pressure and temperature are correlated, changes in temperature that result from climate change can, in turn, change sea-level pressure. 

    7. convection and/or subduction

      Convection is the movement of a fluid due to changes in density, where more dense waters sink and less dense waters rise. Subduction is the term for the downwards movement of a substance, in this case when one water mass moves below another.

    8. coupled air-sea general circulation model

      To accurately predict conditions on Earth, models of ocean currents and circulation are connected, or coupled, with models of atmospheric, ocean, and sea ice dynamics.

    9. anthropogenic

      Caused or influenced by human activities.

    10. basin-scale forcings

      The mechanisms causing ocean temperatures to increase are likely the same for every ocean.

      Examples include the radiative forcings from volcanic aerosols, stratospheric ozone depletion, greenhouse gases, and solar variability.

    11. statistically significant,

      The likelihood that a relationship between two or more variables is caused by something other than random chance. The data suggest there is a real difference in the temperature values between 1955-59 and 1970-74, as well as between 1970-74 and 1988-92.

    12. Student's t test

      A statistical test to compare the means of two groups.

      For more information visit: http://www.biostathandbook.com/twosamplettest.html

    13. subarctic

      Ocean regions between latitudes 50°N and 70°N are subarctic.

      In subarctic oceans, there is a large range of temperature variation through the year, with cold winters and moderately warm summers. These latitudes also experience deep ocean mixing due to strong winter storms.

    14. pentads

      A series of 5 years. The later two pentads refers to the periods 1988-1992 and 1970-1974.

    15. Mediterranean Outflow

      The North Atlantic has different water masses with distinctive temperature, salinity, and densities.

      The Mediterranean Outflowoccurs at the region where the Mediterranean Sea meets the Atlantic, and has a different enough density to be distinct as it's own water mass.

      This figure shows some of the water masses in the Atlantic Ocean from Antarctica (60°S) to the Northern Arctic Ocean (70°N). Image Source: http://www.atmosedu.com/Geol390/Life/OceanCirculation.html

    16. Pacific Decadal Oscillation

      The Pacific Decadal Oscillation (PDO) is typically thought of as a long-lived El Niño-like pattern of Pacific climate variability. Areas of the Pacific Ocean go through alternating patterns of warming and cooling every 10 to 30 years. 

      For more information and to see a time series of PDO variability, visit: https://www.ncdc.noaa.gov/teleconnections/pdo/

    17. oscillation

      The repetitive variation of a measurement over time, such as how temperature varies around a central value over time. 

    18. quasi-bidecadal changes

      Occurring roughly every two decades.

    19. positive correlation

      A relationship between two variables such that their values increase or decrease together. As time increases, the heat content of these basins also increases, suggesting these variables are positively correlated.

    20. standard error

      The measure of the statistical accuracy of an estimate. One of the most common measures is standard deviation, which can be presented as error bars (showing a margin of error) on a graph.

    21. standard depth levels

      Oceanographers typically measure distinct depth levels in the ocean, with more measurements taken in the surface ocean than in the deep ocean.

      For the upper 100m, measurements are taken every 5m in depth (i.e., 0m, 5m, 10m, 15m, 20m, etc.). Between 100m and 500m, measurements are taken every 25m (100m, 125m, 150m, 175m, etc.). From 500m to 2000m those measurements are every 50m (500m, 550m, 600m, 650m, etc.). For depths greater than 2000m, then data is collected in increments of 100m (2000m, 2100m, 2200m, 2300m, etc.).

    22. anomaly

      An anomaly is something that deviates from what is standard, normal, or expected. Here, the authors examine how temperature varies from expected values.

    1. founder effects

      The long-lasting and persistent effects of reduced genetic diversity due to the small number of individuals that initially colonized a certain environment.

    2. enterotypes

      A classification of living organisms, similar to ecosystems, based on their bacteriological ecosystem. They are identifiable constellations of intestinal bacteria, biological communities of microorganisms in the gut. Dr. Peer Bork discovered three human gut types in April 2011: Bacteroides, Prevotella and Ruminococcus.

    3. biclustering

      A technique that identifies and clusters groups, specifically for two separate clusters.

    4. ulcerative colitis

      Chronic intestinal disease characterized by flares of inflammation of the innermost lining of the large intestine and rectum. Symptoms such as diarrhea, abdominal cramps, and bloody stools may occur alternating with quiescent (inactive/dormant) periods. Patients with ulcerative colitis are at an increased risk of developing colon cancer.

    5. Bristol stool scale

      A diagnostic tool used to classify human faeces into seven categories based on its shape, texture, and consistency. The chart allows patients with gastrointestinal symptoms to describe their bowel movements without needed to provide a sample.

      Learn more about BSS from this article in The Conversation: https://theconversation.com/what-the-consistency-of-your-poo-says-about-your-health-65106

    6. generalized linear model analysis

      A statistical model used to describe associations between multiple independent and dependent variables. The goal is the optimal linear combination of parameters to explain an observation.

    7. alpha-diversity

      Alpha-diversity is a measurement of the diversity within a single community/ecosystem. In this study, the researchers found that all of the 69 factors correlated with both the average species diversity and abundance in all samples.

      Check out this video to learn more about alpha-diversity in the context of the microbiome.

    8. microbiome

      The combined genetic information of microorganisms, such as bacteria and viruses, that are found in a specific environment.

    1. 2',3' hydroxyls on the sugar.

      Hydroxyls are -OH groups and are found on the sugar ribose on the 2nd and 3rd carbon. In RNA, only one chemical unit in the entire strand has a hydroxyl on both the 2nd and 3rd (2' and 3') carbon.

      Check out this image to identify the hydroxyls found on 2nd and 3rd carbon.

    2. poly (U,C)

      Crick defines poly(Y, Z) as a DNA strand with equal amounts of two bases "Y" and "Z" in random order. Here, Poly(U, C) is then a strand of genetic material with equal amounts of uracil and cytosine in random order.

    3. polynucleotide

      Poly means many, and a nucleotide is the building block of genetic material. Therefore, a polynucleotide is a chain of many nucleotides—or one strand of genetic material.

    4. polyphenylalanine

      Poly means many and phenylalanine is a specific amino acid. Therefore, polyphenylalanine is a chain of many phenylalanine residues.

    5. carboxyl end

      The carboxyl end refers to the carboxylic acid group exposed on the protein chain. (Remember the analogy of kids lined up holding hands? This is in the Glossary annotation of "amino end.")

    6. codon

      A set of nucleotide bases which codes for one amino acid.

    7. mutagens

      An agent that changes one base into another either by chemical methods or radiation. Acridine is not a mutagen since it does not modify existing bases in DNA, but rather adds or deletes bases.

    8. bacteriophage T4

      Bacteriophage is a type of virus that infects bacteria. The T4 bacteriophage is a specific bacteriophage that infects E coli. Bacteriophages, like living organisms, have genetic material.

    9. hemoglobins

      The iron-rich proteins in our red blood cells that transport oxygen from our lungs to the rest of our body.

    10. Watson

      James Watson (1928 - ) co-discovered the structure of DNA with Francis Crick (the author of this paper).


    11. cistron

      A section of DNA or RNA that codes for a specific chain of amino acids (or 'polypeptide chain'). Cistron is another word for gene. As such, it's not normally used much nowadays.

    12. Beadle

      George Beadle (1903-1989) was a Nobel Prize winning scientist credited with discovering the inherent connection between genes (DNA) and enzymes (proteins).


    1. Type VI CRISPR-Cas systems

      CRISPR is a family of DNA sequences that are part of the immune system of bacteria. CRISPR enzymes detect specific viral DNA or RNA sequences, and can cleave the invading sequences and destroy them. Recently, researchers have begun to use CRISPR as a highly accurate tool for detecting specific DNA sequences in their research.

      Type VI CRISPR-Cas systems are those that involve the protein Cas13, which can cut RNA molecules.

    2. ortholog

      Genes in different species that can be traced to a common ancestral DNA sequence.

      There are many different Cas9 and Cas13 orthologs from different bacterial organisms. As engineers, the researchers test many of them as they will have different levels of activity in mammalian cells (as compared to bacterial) and some might not work at all.

    3. nonhomologous end joining (NHEJ)

      When both strands of DNA are cut, a cell can repair the DNA by rejoining the two strands. Nonhomologous end joining is one way this repair can happen, and it does not require homologous (similar) sequences.

      Because the sequences do not have to be homologous, this process is imprecise and can result in deletions or insertions.

    4. homology-directed repair (HDR)

      A process of precise DNA editing in which a cell uses homologous (similar) sequences as a template to repair DNA.

      This method is more precise than nonhomologous end joining (NHEJ), but takes more time. It's also generally less efficient and does not operate on non-dividing cell types like neurons.

    5. catalytically inactive

      The job of enzymes is to make chemical reactions happen faster. An enzyme that is catalytically inactive does not accelerate chemical reactions.

      Cas13 catalyzes the cleavage (cutting) of RNA molecules. This is an important function of the bacterial immune system, where Cas13 helps protect the organism from invading RNA.

      To use Cas13 for RNA editing, the researchers created a catalytically inactive enzyme (dCas13) that can be used to target RNA without cutting it and allowing for recruitment of other enzymes to the RNA.

    6. endogenous editing of transcripts

      RNA editing happens in the cell after DNA has been transcribed (RNA molecules have been synthesized from a using a DNA sequence as a template). This editing is usually insertion, deletion, or substitution of bases. The most common type of RNA editing is the substitution of adenosine to inosine, which functionally reads as guanosine (facilitated by the ADAR family of enzymes). Essentially, this reads as an A to G base change.

    7. Endogenous

      Native to a system (i.e. not the result of changes by external factors). Endogenous targeting here means the normal target sites for the ADAR protein in the cell.

    8. cloned

      Cloning means to insert a gene, a gene fragment, or an accessory sequence into a vector. Vectors are vehicles that carry DNA into a cell and exist as a plasmid in the nucleus,

      When the vector is multiplied in a cell or in a cell-free system, many copies of this fragment (clones) are generated.

    1. energy homeostasis

      Refers to energy balance, in which an organism's energy intake (food) and outflow (energy expenditure) is coordinated to achieve no overall energy surplus or deficit.

    1. basal

      Normal or minimum level

    2. pontine

      Refers to the group of nucleus present in the pons of the brain.

      Pons is a brain region that links medulla and the mid-brain.

    3. sympathoadrenal

      Relates to both sympathetic nervous system and the adrenal medulla.