5,090 Matching Annotations
  1. Jun 2019
    1. quantitative

      Refers to the measurement of quantities, a countable amount of something. For example: A baby weighs 7 pounds and 4 ounces.

    2. qualitative

      Refers to the measurement of qualities, a describable trait of something. For example: The girl has brown eyes.

    3. phenotype

      Here, referring to the physical characteristics of the neurons.

    4. peptide putative transmitters

      Widely accepted class of neurotransmitters.

      Read more about the different neurotransmitters here.

    5. Neurotransmitters

      A chemical that is released by brain cells called neurons. These chemicals aid in communication or passing messages between neurons.

    6. veratridine

      Drug that increases the influx of sodium into the cell.

    7. mutability

      The ability to change.

      For example, think of a caterpillar, which has the ability to change to butterfly.

    8. thermoregulation

      Maintaining the body’s temperature within the normal limits.

    9. basal

      Normal or minimum level.

    1. translational

      Research that can be useful to prevent or treat disease

    2. developmental

      Relating to the growth of the individual.

    3. subsequent

      Following.

    4. cocaine-induced

      The response prompted by cocaine.

    5. nicotine-induced

      Response prompted by nicotine.

    6. risk

      Prone to; susceptible.

    7. pretreatment

      Treatment received prior to something in advance

    8. assessed

      Evaluate; measure.

    9. administered

      Given.

    10. prompted

      Pushed; urged; required.

    11. diminished

      Reduced.

    12. endpoints

      Outcome

    13. long-term synaptic potentiation

      Strengthening of synapses between neurons

    14. prenatal

      before birth; during pregnancy

    15. phenocopied

      mimicked; acted similarly

    16. transient

      only for a short time

    17. baseline

      normal

    18. facilitation

      help; make the process easy

    19. variant

      modified

    20. ERK/MAPK

      signaling pathways that help in gene regulation

    21. phosphorylates

      adding phosphate residues

    22. concurrent

      happening at the same time

    23. Hypoacetylated

      not enough acetylation

    24. deacetylase

      removal of acetyl groups

    25. hyperacetylation

      increase or excessive acetylation

    26. promoter

      DNA sequences that define where the transcription should start in a gene

    27. disinhibits

      restrain

    28. simulate

      prompt or trigger

    29. psychostimulants

      drugs that cause an increased behavioral or motor response

    30. robust

      widely used

    31. behavioral paradigm

      a model designed to perform behavioral experiments

    32. acetylation

      Process by which acetyl groups are added to preferred residues in a protein.

      For instance, acetyl groups are added to lysine residues in a protein structure

    33. histone

      components of chromatin that helps in gene regulation

    34. chromatin

      DNA + histone

    35. FosB

      it is one of the transcription factors that help in gene expression

    36. transcription

      the process by which a copy of genetic information is made from DNA to RNA

    37. synaptic

      A synapse is a space between the neurons that allows passage of electric or chemical signals between the neurons.

      Anything that occurs between synapses is referred to as synaptic

    38. plasticity

      the ability of the neurons (brain cells) to change and learn new things by changing their synaptic strength

    39. spiny neurons

      Medium sized neurons that have dendritic branches

    40. inhibitory

      slowing down, hold back, restrain, negatively affecting a response

    41. GABAergic

      neurons that contain inhibitory neurotransmitter, GABA

    42. prefrontal cortex

      Part of the frontal cortex in the brain. Its function includes planning, organization, and decision making

    43. amygdala

      A brain region present in the temporal lobe. It is almond In shape. It plays an important role in emotions.

      Eg. When we see a lion, we immediately run due to fear. The fear response is due to the amygdala.

    44. ventral tegmental area

      A brain region in the midbrain. Serves as a center for the origin of dopaminergic neurons

    45. glutamatergic

      neurons that can modulate (or alter or modify) the neurotransmitter, glutamate. Glutamate is an excitatory neurotransmitter

    46. dopaminergic

      neurons that contain neurotransmitter, dopamine. Dopamine plays a vital role in the reward pathway

    47. integration

      to combine the similarities together

    48. convergence

      bringing together two different concepts that share similarities

    49. reward

      recognition of one’s work or effort

    50. ventral striatum

      contains the brain region, nucleus accumbens

    51. nucleus accumbens

      A brain region in the forebrain. It has two parts: core and shell

    52. addictive

      causing someone to become dependent

    53. cocaine

      Recreational drug. Referred as coke.

    54. nicotine

      primary chemical present in tobacco

    55. addiction

      dependency, craving

    56. modulated

      modify

    57. enhanced

      increased

    58. place preference

      preferred choice of one place over another

    59. conditioned

      trained or habituated

    60. sensitization

      Repeated administration of a stimulus can cause a response to the stimulus.

      Eg. If you give your cat piping hot milk the first day, the cat may not drink it as it will burn its mouth. However, if you continue to give your cat hot milk for several days in a row, the cat will eventually start drinking the milk as it is habituated to the new stimulus (hot milk) and will not complain

    61. Locomotor

      the movement of a living being from one place to another

    62. sequential

      one by one; logical order

    63. determinant

      a key factor

    64. irrelevant

      not important

    65. molecular genetic

      study of the structure and function of genes involved in the behavior

    66. electrophysiological

      observing the electrical properties of neurons in the mouse brain

    67. behavioral

      observing the behavior of the mouse

    68. exert

      influence

    69. gateway drugs

      the substances are mild and not addictive on consumption. However, the continuous consumption of these mild substances can lead to the use of other addictive drugs. They are also known as ‘habit-forming drug.’

      Eg. Alcohol, Cigarettes.

    70. epidemiological

      Deals with incidence and distribution of diseases and societal issues

    71. illicit drug

      Substances that are addictive to the central nervous system.

      These substances are illegal to be possessed, have no documented therapeutic effect, and are referred to as drugs of abuse.

      Eg. Cocaine, Heroin

    72. marijuana

      ‘weed’ or ‘pot.’

      Read more about marijuana here: https://www.drugabuse.gov/publications/research-reports/marijuana/what-marijuana

    1. discipline

      A specific branch of knowledge, such as physics or biology.

    2. 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. The higher the z-score, the more different a data point is from the average.

    3. continuous

      Continuous variables have an infinite number of possible values. This is in contrast to categorical variables, which have a discrete number of defined values (for example, in this study "man" or "woman" for gender).

    4. SD

      Standard deviation, a measure of the amount of variation in data.

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

    5. negative relation

      A condition in which when the value of one variable goes up (endorsement of the gender stereotype), the value of the other variable goes down (exam scores).

    6. as a function of

      A function defines one variable in terms of another. Here, the more strongly a woman in the control group endorsed the gender stereotype, the lower her exam scores were.

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

    7. χ2

      Chi-squared, a test which tells whether there is a statistically significant difference between the distribution of two categorical variables (for example, gender).

    8. SE

      Refers to standard error, which is a measure of how far away the mean of your data is likely to be from the true mean of the population.

    9. P

      The P value is a measure of how likely it is that your null hypothesis (that values affirmation has no effect) is true.

    10. outcome measure

      Tools used to assess a subject's performance.

    11. condition

      Assigned group, either the intervention group or the control group. In this case, the control group contained students who did not participate in the values affirmation intervention.

    12. social-psychological

      Effects that result from interactions within groups, and between both groups and individuals.

    13. randomized

      Participants are randomly assigned to different test conditions.

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

    1. trophic downgrading

      Impacts from the loss of the top-level consumers.

    2. pervasive

      Widely felt.

    3. trophic

      Feeding relationships.

    4. function

      How a system works.

    5. resilience

      How quickly a community is able to recover from a change in the environment.

    6. empirical

      Based on data.

    7. mass extinction events

      Periods of Earth's history when vast numbers of species went extinct in a short period of time.

    8. herbivory

      Eating only vegetation for food.

    9. abundance

      Number.

    10. distribution

      Location.

    11. topology

      Structure.

    12. basins of attraction

      Conditions that allow for stability in an ecosystem.

    13. flux

      Change.

    14. perturbed

      Altered.

    15. extirpated

      Removed.

    16. weakly motile

      Not able to move far.

    17. autotrophs

      Self-feeding organisms such as plants, algae, many protists, and some bacteria.

    18. regime shifts

      Changes in abundance or dominance of species within an ecosystem.

    19. “natural experiments”

      Data collected from unintended consequences seen in nature.

    20. mesopredators

      Predators found in the middle of the food web—that is, they both eat prey and are eaten as prey.

    21. megaherbivores

      Large, plant-eating organisms.

    22. aggregate

      Collective.

    23. alternative stable states

      A different persistent community structure from the original in an ecosystem, typically resulting from a disturbance.

    24. recruitment failure

      Inability of seeds to germinate.

    25. trophic cascades

      Also known as top-down controls, these refer to the effects of predators that propagate downward through food webs across multiple trophic levels—where trophic level refers to an organism's position in the food chain.

    1. zona incerta (ZI)

      A part of the brain.

      The function of this area is poorly understood but is thought to regulate behavior of an animal in response to internal (such as hunger) and external (such as pain) sensory cues.

    2. γ-aminobutyric acid (GABA)

      An inhibitory neurotransmitter. Neurons communicate with each other by releasing neurotransmitters. Neurons respond to inhibitory neurotransmitters by reducing their activity.

    3. type A GABA (GABAA) receptor antagonist bicuculline (Bic)

      A light-sensitive competitive agonist of GABA<sub>A</sub> receptors. It was originally isolated and identified over 40 years ago in the Dicentra cucullaria plant.

    1. Parkinson's disease

      A progressive degenerative disorder primarily impacting motor control that can lead to tremors or stiffness. Pathologically characterized by the loss of dopamine-secreting neurons in two parts of the brain (the substantia nigra pars compacta and basal ganglia), as well as the presence of Lewy bodies—aggregates of a protein called alpha synuclein contained within the neuron.

  2. May 2019
    1. motivational valence

      The degree to which something is perceived as pleasurable (positive valence) or unpleasant (negative valence).

    2. excited by

      Activated by.

    3. Anterograde

      Occurring along the nerve processes away from the neuron body, as opposed to retrograde.

    4. lateral hypothalamic neurons

      A region of the brain in close proximity to ZI known to promote food intake.

    5. glutamate

      An excitatory neurotransmitter, which causes neurons to become activated.

    6. parasubthalamic nucleus

      A part of the brain located below the thalamus, which functions in motor control.

    7. ghrelin

      A hormone produced in the gut in response to food deprivation.

      Also known as the "hunger hormone," ghrelin increases appetite and food intake and energy storage.

    8. excitatory

      Neurons that express excitatory neurotransmitters cause downstream neurons to become activated.

    1. germinal center

      Germinal centers are areas in the lymph nodes and spleen where B cells reside. Within these centers B cells replicate, mature and prepare to create antibodies.

    2. epitopes

      An antigen on the surface of the virus that antibodies can attach to.

    3. effector phenotypes

      The characteristics that are representative of activated T cells.

    4. T follicular helper (TFH

      This subset of T cells that aid in the production of antibodies by activating B cells.

    5. antigen

      An antigen is a part of a pathogen that stimulates an immune response. This may be a protein, lipid, or a carbohydrate.

    6. B cells

      B cells are immune cells that produce antibodies.

    7. induced

      In molecular genetics when a gene is induced, it means the amount of mRNA transcripts from that gene is increased.

    8. elucidated

      Elucidated is another way of saying explained or investigated.

    9. cytokines

      Cytokines are proteins that are released by immune cells to activate the immune response in other cells.

      Example: When a cell is infected with a virus, it can release the cytokine interferon to signal neighboring cells of an incoming viral attack. This allows the neighboring cells to increase production of anti-viral proteins.

    10. choline acetyltransferase (ChAT),

      Choline acetyltransferase is a protein that is responsible for the creation of acetylcholine.

    11. prototypic

      Prototypic means the original model in which further knowledge is based off of.

      Since acetylcholine was the first neurotransmitter discovered, its function/ behavior is what all other neurotransmitters are based off of.

    12. vasodilation

      Vasodilation in when blood vessels expand. This is an important response to viral infection because it allows immune cells to reach the site of infection.

    13. ablated

      Ablated in this context means that mice did not have vasodilation in response to viral infection.

    14. IL-21

      IL-21 is a protein released by CD4 T cells that activates cytotoxic T cells and NK cells.

    15. CD8+

      A CD8 positive T cell (referred to as a cytotoxic T cell) is responsible for killing intracellular pathogens, cancer cells and other damaged cells.

    16. CD4+

      A CD4 positive T cell (referred to as a helper T cell) is a subset of T cells responsible for activating and directing different types of immune cells.

    17. lymphocyte

      T cells, B cells and Natural Killer (NK) cells are immune cells that are referred to as lymphocytes.

    18. T cell

      A T cell is a type of immune cell responsible for directing the adaptive immune system's response to infection, allergy and cancer.

      • note: think of the T cell as a general of an army.
    19. neurotransmitter

      A neurotransmitter is a molecule released by nerves to communicate with other nerves, muscles fibers, or organ systems.

    1. catalysis

      Catalysis is the initiation and acceleration of a chemical reaction.

      In this case, the authors point to KDM6B as the catalyst for Dmrt1 expression and thus male sex development.

    2. testicular Sertoli cell

      Male sex cells that are required to form testes and sperm.

    3. primordial germ cells

      Progenitor sex cells that go on to make all the reproductive cells in an organism.

    1. will stand for no amino acid—that is, will be nonsense

      As a general rule, there are four kinds of codons: codons that initiate the reading frame, codons that stop the reading frame, codons that code for amino acids to make proteins, and codons that don't code for anything at all (called nonsense codons).

    2. rII locus

      A locus is a specific location or section of genetic material. The r<sub>II</sub> locus is one of three loci composing the genetic material of bacteriophage T4 (described below).

    3. protein synthesis

      The process of making proteins.

    4. RNA

      Ribonucleic acid, or RNA for short, is one class of genetic material. It is an example of a nucleic acid molecule.

      RNA is composed of three chemical building blocks: a sugar (called ribose), a phosphate group, and a nitrogenous base.

      RNA has many functions in a cell, and scientists are still studying RNA today. Some hope that RNA might be the key to disease prevention.

      https://cen.acs.org/pharmaceuticals/decade-RNA/97/web/2019/01

    5. enzyme

      A special class of proteins which catalyze (i.e., cause or speed up) a chemical reaction in biological systems.

      Remember, that a protein is a chain of amino acids.

    6. amino acid

      The chemical building blocks of proteins. All amino acids contain an amine group (-NH<sub>2</sub>) and a carboxylic acid group (-COOH).

      https://www.neb.com/tools-and-resources/usage-guidelines/amino-acid-structures

    7. Deductions

      Crick relies on deductive reasoning to make his argument for the nature of the genetic code.

      Deductive reasoning draws specific conclusions from general principles or premises, whereas inductive reasoning infers general principles from specific instances.

    8. 2',3' hydroxyls on the sugar.

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

      Check out this image to identify the hydroxyls found on second and third carbon.

    9. "right-hand" end

      Just as your left and right hands are distinct mirror images, certain molecules have distinct mirror images, too. When a molecule has a distinct mirror image, we say the molecule is chiral.

      All sugars in the body are "right handed." On a strand of genetic material, the sugars are linked together such that only one end of the chain is "handed."

    10. 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.

    11. polyuridylic acid

      An RNA molecule in which every base is uracil.

    12. synthetic RNA

      RNA that is made in the lab as opposed to natural RNA found in a cell.

    13. acridines

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

      Acridines were previously used in some dyes and many have antiseptic properties, but usage largely stopped since acridines are also a skin irritant.

    14. bacteriophage T4

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

    15. A and B cistrons

      A section of DNA or RNA that codes for a specific chain of amino acids, or "polypeptide chain." Cistron is synonymous with gene, meaning A and B cistrons are two different genes. The term cistron has largely fallen out of favor.

    16. 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.

    17. the amino end

      Imagine kids lined up holding hands: The line leader will have no one to hold her left hand and the caboose will have no one to hold her right hand.

      Amino acids on a protein have a similar feature. The first amino acid will have an amine group exposed and the last amino acid will have an acid group exposed. The "amino end" refers to the end of the strand where the amine group is exposed.

    18. Gamow's

      George Gamow (1904–1968) was a theoretical physicist. Curious about the natural world, he was often in contact with scientific giants outside of physics, such as 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.

    19. Watson

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

      https://www.nobelprize.org/prizes/medicine/1962/watson/biographical/

    20. Beadle

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

      https://www.nobelprize.org/prizes/medicine/1958/beadle/biographical/

    1. F

      Another measure of statistical difference between the means of different groups.

    2. Cohen’s d

      A statistical measure of effect size.

    3. t

      The t statistic is used with the T test, which determines if there is a difference between the average result of two different groups.

    4. gateway courses

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

    5. snowballing effect

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

    6. 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.

    7. residual

      Amount left unexplained by other variables.

    8. grand mean

      The mean of the mean of several sub-samples.

    9. 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.

    10. 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.

    11. nationally normed standardized test

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

    1. orthologs

      Orthologs are derived from a common ancestor gene and have some degree of sequence similarity

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

    2. 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).

    3. 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.

    4. 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.

    5. 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.

    6. 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.

    7. 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.

    8. 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.

    9. 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.

    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.