5,190 Matching Annotations
  1. Mar 2016
    1. chimeric

      A chimeric fly has two distinct cell populations. In this case, a mutagenic event occurred early in the development of the female chimera, causing it to have one genotype on one half of its body, and a different genotype on the other half.

    2. wild-type

      Refers to the phenotype of an organism as it was found in nature. In contrast to a mutant allele, the wildtype phenotype is the product of the "normal" allele for a particular gene.

    3. homology arms

      Homology arms are DNA sequences in a plasmid that are identical to a specific genomic DNA sequence. The homology arms are used to direct homologous recombination of a plasmid into the genome.

    1. wavelength

      Light travels from place to place in the form of a wave. All types of light have a characteristic wavelength. In the visible spectrum, red light has the longest wavelengths and purple has the shortest. UV light has shorter wavelengths than visible light.

    2. bacterial respiration

      Bacterial respiration is when microbes “eat” organic carbon, causing it to break down into smaller molecules. In most cases, bacteria require oxygen to break down organic carbon.

    3. mineralization

      Mineralization refers to the break down of organic molecules to inorganic molecules. For the purposes of this paper, it means conversion of organic carbon to carbon dioxide.

    4. quantum yields

      Quantum yield is a measurement of how much of a chemical reacts when exposed to light. For example, in this study it would be the amount of carbon dioxide produced divided by the amount of UV sunlight absorbed by dissolved organic carbon.

    5. Areal rates

      Areal rate refers to the amount of something that happens over an amount of surface area. For example the rate of bacterial respiration is measured as the amount of oxygen released per day, but the areal rate would be measured as the amount of oxygen released per square meter per day.

    1. About 20% had been arrested at baseline, and just over 20% had been victimized

      Baseline measurements are measurements that report on the sample population prior to the experiment. In this case, prior to the start of the jobs summer jobs program, 20% of the youth in the study had been arrested and 20% had been victims of violent activity.

    2. operative mechanism

      By operative mechanism, the author is referring to the thing or factor that helps us understand why this summer jobs program helps reduce violent crime.

    3. The empirical literature

      Empirical literature refers to articles that are based on data that has been collected in a field (real-world) or laboratory setting. Because science is a process that builds upon itself, scientists are always looking to see what the existing empirical literature establishes so that a study that presents something new can be designed.

    4. outcome measures

      In this experimental study, outcome measures refer to violent activity as well as other types of crime and schooling outcomes. This paper reports specifically on whether summer jobs have any affect on violent activity.

    1. disturbance

      What is a disturbance, in this context? In ecology, a disturbance is anything that changes the ecosystem. For example, a forest fire, tornado, human activity (building more houses in an area that used to be a grassland), etc.

    2. slower regrowth dynamics

      Why do boreal forests grow slower than other forest types? For starters, boreal forests have shorter growing seasons. Also, boreal forests have only conifer tree species that do not grow as quickly as deciduous trees.

    3. carbon storage

      Why is carbon storage important? Find out by following this link to explore carbon "sequestration" (just a fancy term for "storage") and how this process can help curb global warming.

    4. importance of forest ecosystem services

      What are important ecosystem services that forests provide?

      First, let's break this down into what an ecosystem service is. These services include any benefit that an ecosystem can provide to people.

      So, what can forests provide that benefit people? Here are some examples: Forests provide timber, store carbon, purify air and water, and provide space for recreation (e.g., hiking in the woods!).

    5. biodiversity richness

      Richness is simply the number of different species.

      Biodiversity refers to the diversity of biology (a.k.a. the number of different species).

      Putting this all together, we can determine that forests, compared with other types of ecosystems (e.g., deserts), have a lot of different species of plants, animals, bacteria, etc. (this is especially the case in tropical forests).

    6. spatially explicit

      Describes where things are in relation to each other. In this case, the satellite images of Earth provide a clear picture of where forests are located and distributed.

      Imagine having spatially explicit data of Earth's surface, all collected at the same time. This is what satellite-based imaging systems do. By examining these pictures over time, we are able to map forest loss and gain. Imagine trying to do this task from the ground. It would be very hard indeed.

    7. tropical, subtropical, temperate, and boreal

      Tropical: Areas near Earth's equator that are warm/hot year-round with consistent or seasonal rainfall.

      Subtropical: Areas with hot and humid summers and mild winters.

      Temperate: Areas with four seasons (summer, fall/autumn, winter, and spring) divided mainly by differences in temperature.

      Boreal: Subarctic areas with long, cold winters and short, cool summers.

      Check out where these climate domains/zones are around the world on this map.

    8. deforestation dynamics

      "Deforestation dynamics" refers to changes (i.e., dynamics) in forests due to cutting down trees and replacing them with nonforest land uses, such as agriculture or development (houses, buildings, etc.).

    9. statistically significant trend

      This wording implies that Hansen and colleagues ran a statistical model to determine whether the loss or gain in forest cover over time was more or less than what you would expect if forest cover did not change.

      The tropics experienced a clear increasing rate of forest loss, expressed in units of forest area loss per year, whereas other climate domains (e.g., temperate, boreal, subtropical) all lost and gained forest cover

      However, when you add all of the subtropical regions of Earth together, for instance, there isn't a clear net loss or gain in forest cover. This is because of the fact that most forest change in the subtropics is due to forestry land uses where trees are grown as a crop. In forestry land uses, trees are continuously grown and cut down to make products such as lumber and paper.

    10. short-cycle tree planting and harvesting

      This statement refers to "short rotation forestry," which is a type of forestry that densely plants fast-growing tree species (e.g., poplar trees).

      Once these trees reach a certain size (e.g., stems that are 10–20 cm in diameter at breast height), they are then cut down and harvested for lumber, pulp, and paper products, or energy.

      The trees then regrow from the stumps, sending up new trunks. This process of cutting down a tree to stimulate regrowth is called "coppice."

    11. systematic global image acquisitions

      In this context, the authors are describing the satellite images—these images are widespread (e.g., systemic) in that they photograph the entire surface of Earth.

    12. Google cloud

      The authors used Google Earth Engine to process the Landsat images.

      The Google Earth Engine is a cloud platform, meaning that a network of thousands of computers works together to perform a task that a single computer would take years to do.

      Similarly, Google Cloud provides the same features. Google Cloud allows you to store, manage, and process information on computer servers that are accessed through the Google Cloud website.

      Cloud computing is especially helpful for processing large amounts of data/information.

      Hansen and colleagues processed 700,000 images of Earth. Processing this information through the Google Earth Engine with 10,000 computers took approximately 15 days. If the authors only had one computer to work with, these calculations would have taken a few years!

  2. Nov 2015
    1. SWS × REM sleep duration

      A measure that reflects the amount of time participants spent in slow-wave sleep and rapid-eye-movement sleep.

      It is calculated by multiplying the number of minutes of SWS by the number of minutes of REM sleep.

  3. Oct 2015
    1. NHEJ events

      In non-homologous end joining splices in DNA are repaired by splicing rather than by referring to an intact complementary strand of DNA. This method of repair is less accurate than homologous recombination.

    2. PGP1 human induced pluripotent stem (iPS) cells

      Induced pluripotent stem cells come from adult cells which have been artificially changed to exhibit stem cell properties. These properties are immortality and the ability to develop into various different cell types. These cells are thus unspecialized. https://www.thermofisher.com/us/en/home/references/protocols/cell-culture/stem-cell-protocols/ipsc-protocols/generation-human-induced-pluripotent-stem-cells-fibroblasts.html

    3. integrated reporter

      The integrated reporter was the green fluorescent DNA sequence which was integrated into the target DNA. The green fluorescent sequence could then be manipulated, and the results could be measured.

    4. 68-bp

      Since DNA consists of a double strand, the bases form into pairs such that cytosine always pairs with guanine and adenine always pairs with thymine. A 68 bp sequence would contain 68 of these pairs.

    5. PAM (protospacer-adjacent motif)

      The PAM is a short DNA sequence close to the targeted DNA sequence of the invading organism. The PAM is crucial for the system to recognize whether or not the DNA sequence is self or not self. If the PAM is missing the system will not be activated

    6. RNA

      In contrast to DNA, which is a double strand of linked amino acids, RNA is a single strand. The four "letters" in the DNA alphabet are adenine, thymine, cytosine, and guanine. RNA is made up of adenine, thymine, and cytosine, but in place of guanine it has uracil.

    7. DNA

      Deoxyribonucleic acid (DNA) is a double stranded helix (coiled in a spiral) of proteins which form a sort of "alphabet" to encode genetic information. The "letters" of this alphabet consist of adenine, thymine, cytosine, and guanine.

      Adenine always pairs with thymine, and cytosine always pairs with guanine, thus, when the two strands are divided the complete DNA molecule can be exactly reproduced. http://ghr.nlm.nih.gov/handbook/basics/dna

    8. viral

      Viruses are submicroscopic parasites with a simple structure. Their main parts are a strand of nucleic acid (DNA or RNA) and an surrounding protein shell called a capsid. Some viruses also have an outer viral envelope surrounding their capsid. Viruses are not capable of reproducing on their own, but rather must invade a cell and commandeer that cell's resources to reproduce themselves http://www.ncbi.nlm.nih.gov/books/NBK21523/

    9. clustered regularly interspaced short palindromic repeats

      Clustered regularly interspaced short palindromic repeats (CRISPRs) are strands of DNA with repeating sequences (repeats) interspersed with other sequences which don't repeat (spacers).

    1. memory consolidation

      The process by which memories become more stable (less likely to be forgotten). The authors' work is based on previous findings that sleep is particularly important for memory consolidation.

  4. Aug 2015
    1. epitaxial

      The growth of one crystalline material on the surface of another crystalline.

      In this case, the crystalline surface upon which epitaxial growth occurs is the exposed crystalline core of the cylindrical micelle. The exposed core can continue to elongate as more block copolymers are added to the solution.

    2. colloidal dispersions

      A solution that has evenly dispersed particles that are 1 nm to 1000 nm. The particles are in solution and do not settle out. An example of a colloidal dispersion is milk.

    3. non-centrosymmetric

      Glossary: Molecules have different degrees of molecular symmetry. A molecule that is noncentrosymmetric will not contain an inversion center or a center of symmetry. An example of a molecule that is centrosymmetric is a benzene ring (C6H6) where the inversion center is the center of the ring.

    4. micelle corona

      A micelle is an aggregate comprised of amphiphilic molecules. A micelle will have a core (inside-lipophilic) and a corona (outside-hydrophilic).

      The individual components that make up this aggregate are referred to as unimers.

      Although most micelles are have hydrophobic cores and hydrophilic corona, these micelles don't fit this classification. The corona is PI (hydrophobic) and the core is PFS (also hydrophobic). Self-assembly is induced because hexane/decane are poor solvents for PFS but good for PI .

    5. block copolymers

      A block copolymer is a polymer chain comprised of homopolymer subunits linked by a covalent bond.

      For example:

      Homopolymer (where A is the monomer unit) : A-A-A-A-A-A-A-A

      Block copolymer (where A and B are monomer units): A-A-A-A-B-B-B-B

    6. Abstract

      As the field of nanotechnology continues to grow, the ability to carefully control nanoparticle size, shape, and composition still remains a challenge. Most nanoparticles exhibit a great deal of symmetry. The authors of this paper focused on developing a method to create block copolymer micelles that had very little symmetry (i.e., noncentrosymmetric). They were able to achieve their goal through unidirectional micelle growth. The authors later used this same strategy to synthesize a "supermicelle."

  5. Jul 2015
    1. coimmunoprecipitated

      Coimmunoprecipitation (Co-IP) is the immunoprecipitation of intact protein complexes. Co-IP works by selecting an antibody that targets a known protein that is believed to be a member of a larger complex of proteins. By targeting this known member with an antibody it may become possible to pull the entire protein complex out of solution and thereby identify unknown members of the complex.

      Immunoprecipitation (IP) is the technique of precipitating a protein antigen out of solution using an antibody that specifically binds to that particular protein. This process can be used to isolate and concentrate a particular protein from a sample containing many thousands of different proteins.

    2. point mutations

      Point mutation is a technique in which a single base nucleotide is replaced with another nucleotide. As a result, the mutant protein has a different primary sequence with respect to the wild-type protein.

    3. RNA interference (RNAi)

      RNAi is a biological process in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecules. The final result is the depletion of specific target proteins.

    4. helical viral ribonucleoproteins (vRNPs)

      The genome of influenza A viruses consists of eight segments of single-stranded, negative-sense RNA that are encapsidated as individual rod-shaped ribonucleoprotein complexes (RNPs). Each RNP contains a viral RNA, a viral polymerase and multiple copies of the viral nucleoprotein (NP).

    5. supramacromolecular

      A supramolecular complex is a well-defined assembly of molecules held together by noncovalent bonds. While a supramolecular assembly can be simply composed of two molecules (e.g., a DNA double helix), it is more often used to denote larger complexes of molecules that form sphere-, rod-, or sheetlike species.

    6. single-stranded, negative-sense RNA genome

      Viral RNA with a base sequence complementary to that of mRNA; during replication it serves as a template for the transcription of viral complementary RNA. Negative-sense (3' to 5') viral RNA cannot be translated into protein directly. Instead, it must first be transcribed into a positive-sense RNA (5' to 3') which acts as an mRNA. Some viruses (influenza, for example) have negative-sense genomes and so must carry an RNA polymerase inside the virion.

    1. coalescence

      Coalescence is a merging of two units. For example, here the authors consider that Middle East or China are unlikely centers of dog origin because such a scenario would require that ancient wolves and dogs from these areas are united by a common ancestor.

    2. two-phase bottleneck

      A population bottleneck is the reduction of the population size, followed by an expansion, e.g. a small group leaves the first population and immigrates elsewhere.

      This reduction often leads to the loss of genetic diversity in the population; it is called the founder effect.

    3. tochastic effects

      Stochasticity is randomness; in this context, the fact that several lineages mixed resulted in different offspring but each did not recapitulate all the characteristics of its ancestors.

    4. phylogenetically

      A phylogeny is the method to resolve the evolutionary history of a group of species. The relationship between these species can be inferred from various statistical analyses that estimate the genetic relatedness of each species to one another, depending on their differences either in DNA or protein material.

    5. mitochondrialgenomes

      DNA located in the mitochondria. All animal mitochondrial genomes, with a few exceptions, contain the same 37 genes, making them useful as a model for genome evolution.

      Specifically, the comparison of mitochondrial gene arrangements in animals has been critical to inferring ancient evolutionary relationships.

    1. tochastic effects

      Stochasticity is randomness; in this context, the fact that several lineages mixed resulted in different offspring but each did not recapitulate all the characteristics of its ancestors.

    2. Molecular dating

      Molecular dating is a technique that allows biologists to determine the divergence time for two genes or for two species. It is based on the theory of the molecular clock stating that mutations accumulate in organisms at a stable speed.

      Thus, if you compare genes or protein sequences in different species, you can, assuming you know the speed of variation for these sequences, estimate the age of the last common ancestor.

    3. phylogenetically

      A phylogeny is the method to resolve the evolutionary history of a group of species. The relationship between these species can be inferred from various statistical analyses that estimate the genetic relatedness of each species to one another, depending on their differences either in DNA or protein material.

    4. mitochondrial genomes

      DNA located in the mitochondria. All animal mitochondrial genomes, with a few exceptions, contain the same 37 genes, making them useful as a model for genome evolution.

      Specifically, the comparison of mitochondrial gene arrangements in animals has been critical to inferring ancient evolutionary relationships.

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  6. Feb 2014