1,136 Matching Annotations
  1. Jun 2016
    1. It remains unclear which molecules are responsible for the activity of the nerve and wound epidermis

      This is really the main question the authors are trying to answer. Which molecule, if any, is producing the effect seen in the previous experiments?

    1. Southern blotting (DNA) analysis re- vealed that several resultant clones had undergone the desired recombination event

      Southern blotting is a technique that uses radioactive probes to detect DNA sequences. The probes will only stick to complementary DNA, enabling researchers to look for very specific sequences.

      Here, the authors are using it to confirm that cells have incorporated a foreign DNA sequence.

    2. Transfection was done with LipofectAmine (Life Technologies) and subconfluent monolayers of cells

      Lipofectamine is a lipid-based compound that helps cells take up foreign DNA, a process called transfection. Researchers can generate a DNA sequence, combine the DNA with lipofectamine, and add this mix to the cell culture. The foreign DNA will be able to enter the cell and code for a protein of interest.

    3. Time lapse experiments

      These types of experiments can monitor the level or location of a protein over the course of minutes, hours, or even days.

      Here, the authors tracked a fluorescently labeled histone protein for 36 hours, taking pictures at specific intervals (see Figure 5). This allowed them to detect defects in mitosis when p53 or p21 was removed.

    4. histone H2B–green fluorescent protein fusion vector

      Here, the authors used a combination of two proteins fused together: (1) a histone protein (H2B), which is found only in the nucleus of a cell and helps organize the DNA, and (2) a green fluorescent protein (GFP), originally found in jellyfish, which glows green in response to a particular wavelength of light.

      This combination enables scientists to watch the nucleus of a cell, because only H2B will glow green.

    5. we disrupted the p53 gene by homologous recombination

      The authors introduced a piece of DNA that is similar in sequence to the p53 gene and the surrounding area. But instead of p53, this DNA encodes a resistance gene that allows a cell to tolerate a toxic drug. The cell recognizes the "p53-like" DNA, triggering a repair response.

      Homologous recombination replaces the normal p53 gene with the antibiotic resistance gene. But only a small number of cells will undergo this replacement. After treatment with the drug, though, only cells that have incorporated the resistance gene will survive. This allows scientists to isolate only the cells that incorporated the resistance gene (and are therefore lacking the p53 gene). They now have a line of cells without p53, and they can use this line to study the role of the gene.

    6. This may be because some p53-independent p21 synthesis occurred after irradiation of p53−/−cells

      The authors ran a western blot (a technique to separate and identify specific proteins) to analyze the levels of p53 and p21 protein (see Figure 4A).

      They authors found that in cells lacking p53 (the last two lanes on the right), there is a small amount of p21 in cells that were subjected to radiation. This tells them that something other than p53 must be turning on expression of p21 in response to DNA damage.

    7. Smad4 gene

      As a control, the authors disrupted a gene that is involved in a different pathway than p53 (the Smad4 gene) to make sure that gene disruption itself did not affect their results.

    8. The HCT116 cell line was chosen because it has apparently intact DNA damage–dependent and spindle-dependent checkpoints, and it is suitable for targeted homologous recombination (4, 9, 15)

      Recall that cancer cell lines can carry lots of mutations and other changes in important regulatory genes (see above).

      The researchers had to be careful when choosing a cell line to study because there could be additional factors other than p53 status (so-called "confounding variables") that would affect their results. So they started with a cell line that had p53 genes and various other checkpoint genes intact, and then disrupted only the p53 gene by homologous recombination.

    9. three with intact p53 genes and three with mutant genes

      Here, the authors wanted to compare cells with normal p53 with cells with mutant p53. They treated each of the six lines with radiation to induce DNA damage, and then looked at what happened to the different cells. In this way, they could investigate the role of p53 in the DNA damage response.

    1. To address whether the development of functional blood vessels was required for the recruitment of myeloid precursors into the brain rudiment

      Using a mouse model knock-out for a sodium calcium exchanger 1 gene (Ncx-1), the authors were able to show that established and functional vasculature is necessary for the migration of yolk sac macrophages into the brain.

    2. To determine at which stage Runx1+ precursors or their progeny seed the brain during development, we injected Runx1Cre/wt:Rosa26R26R-LacZ pregnant females with a single dose of 4′OHT at E7.25 to E7.5 and traced the apparition of labeled cells into the brain rudiment at different time points after injection

      In this experiment the authors again crossed two knock-in mice strains.

      The first one had CRE fused to an estrogen receptor and expressed under the Runx1 promoter as described previously.

      The second knock-in strain was similar to the strain expressing eYFP downstream of the ROSA26 transcription start site described above, but instead of using eYFP, the authors used another reporter gene called LacZ. LacZ encodes the protein β-galactosidase (β-gal), which can be easily detected by immunohistochemistry.

      In the ROSA26 lacZ reporter (ROSA26R) mouse, a transcriptional stop cassette flanked by loxP sites was inserted just downstream of a transcription start site at ROSA26 locus. When intact, this cassette prevents expression of β-gal from the downstream lacZ coding sequence. The stop cassette is excised upon exposure to CRE recombinase, which mediates recombination between the loxP sites, thus permitting expression from the lacZ reporter.

      The activity of galactosidase can easily be detected with single-cell resolution by staining tissues with X-Gal. Thereby, CRE activity eventually results in a blue dye precipitate.

    3. We crossed the Runx1-MER-Cre-MER mice (Runx1Cre/wt) with the Cre-reporter mouse strain Rosa26R26R-eYFP/R26R-eYFP and induced recombination by a single injection of 4-hydroxytamoxifen (4′OHT) into pregnant females at different days of gestation

      The authors used two transgenic mouse strains.

      The first strain expressed a CRE recombinase protein fused to two murine estrogen-receptor ligand-binding domains (MERs) downstream of the promoter of the Runx1 gene. That ensured that CRE would only be expressed in Runx1-positive cells and will be functional only following its activation with the estrogen receptor antagonist tamoxifen.

      The second strain of mice had enhanced yellow fluorescent protein (eYFP) cDNA knocked-in (inserted) downstream of a transcription start site at the ubiquitously expressed ROSA26 locus. A transcriptional stop cassette flanked by loxP sites was inserted between the transcription start site and the eYFP cDNA. When intact, this cassette prevents expression of eYFP. The stop cassette is excised upon exposure to CRE recombinase activated by tamoxifen, permitting expression of the eYFP reporter gene.

      After crossing these two strains of mice, the authors injected pregnant dams with 4-hydroxytamoxifen, which is an active metabolite of tamoxifen and selective estrogen receptor antagonist. It bound to the estrogen receptor in the MER-CRE-MER fusion protein construct, which then entered the nucleus allowing CRE to act on the floxed genes.

      This recombination resulted in progeny that expressed eYFP in Runx1-expressing cells.

    4. we used Cx3cr1gfp/+ knockin mice (17) because the fractalkine receptor (CX3CR1) is a marker of early myeloid progenitors (18) and microglia

      To be able to detect myeloid cells expressing the CX3CR1 receptor (aka fractalkine receptor) in the brain, the authors used a reporter mouse with an inserted, or knocked in, gene that codes for a green fluorescent protein in the locus of CX3CR1 gene. This way, every time the CX3CR1 gene is expressed, the cell fluoresces in green color.

      Read more here about how specific genes are targeted:


    5. we reconstituted sublethally irradiated C57BL/6 CD45.2+ newborns with hematopoietic cells isolated from CD45.1+ congenic mice

      The authors exposed recipient C57BL/6 newborn mice to a slightly less than lethal dose of irradiation to obliterate their developing bone marrow and any blood cell progenitors present outside the bone marrow such as in the fetal liver or spleen. They then restored their bone marrow and hematopoietic system by injecting bone marrow cells or fetal liver cells that contained hematopoietic progenitors from the donor mice.

      The donor mice were genetically identical to the recipient mice with the exception of the CD45 allele (CD45.1), which codes for a transmembrane protein expressed on all white blood cells.

      Using flow cytometry the authors were able to distinguish resident CD45.2+ (positive, or expressing) cells from donor CD45.1+ cells stained with an allele-specific antibody.


    1. Second, a 6-day treatment of primary brain capillary endothelial cells with rGDF11 (40 ng/ml) increased their proliferation by 22.9% as compared with that of controls (fig. S11), but not in the presence of a TGF-β inhibitor (fig. S12), confirming that GDF11 has a direct biological effect on these cells through the p-SMAD pathway

      The authors conducted an in vitro experiment to test the specific downstream effects of GDF11. They treated brain capillary endothelial cells with GDF11, as well as a TGF-beta inhibitor, for 6 days.

      GDF11-treated cells did not increase cell proliferation in the presence of the inhibitor.

      This indicates that GDF11 acts directly on the TGF-beta SMAD pathway, in order to have an effect on blood vessels.

    2. Given the interconnection between the vasculature and neural stem cells, we asked whether young blood factors can also rejuvenate blood vessel architecture and function. To test this, we created “angiograms,” 3D reconstructions of the blood vessels

      To measure the volume of blood vessels, and to create an "angiogram," the authors imaged mouse blood vessels on a confocal microscope and captured z-plane stacks over the total thickness of the section. The z-stacks were added to create 3D angiograms for calculation of total blood vessel volume.

    3. To test the functional implication of these findings, we performed an olfaction assay

      The goal of this experiment is to test any difference in sensitivity of smell between heterochornic old, isochronic old, and young mice. If there is a change in smell sensitivity, this is due to increased neurogenesis.

    4. We pulsed parabiotic pairs with BrdU to label newborn neurons, and after 3 weeks, the mice were analyzed for BrdU+/NeuN+ cells to quantify newborn neurons (Fig. 2A). As expected from our in vitro studies, we observed increased olfactory neurogenesis in vivo.

      Bromodeoxyuridine (BrdU) is a synthetic nucleoside that is incorporated into DNA of replicating cells.

      NeuN+ denotes neuronal nuclei.

      The authors use BrdU and NeuN double-positive staining to identify and track newborn neurons in hetero-chronic old mice.

      This is an in vivo study to complement the results of increased neurogenesis observed in their in vitro study (Fig. 1). The in vitro study is in the supplemental data.

    5. we generated heterochronic parabiotic pairs between 15-month-old (Het-O) and 2-month-old (Het-Y) male mice, as well as control groups of age-matched pairs, namely isochronic young (Iso-Y) and isochronic old (Iso-O) pairs

      The authors report a novel finding of the possibility of reversing and remodeling the neural stem niche of old mice, by exposing them to systemic factors present in young mice.

    6. Thus, we have observed that age-dependent remodeling of this niche is reversible by means of systemic intervention.

      The authors report a novel finding of the possibility of reversing and remodeling the neural stem niche of old mice, by exposing them to systemic factors present in young mice.

  2. May 2016
    1. Solid Al2O3ceramic lattices were prepared in the microlithography system by using photosensitive PEGDA liquid prepolymer loaded with ~150-nm alumina nanoparticles (Baikowski Inc., ~12.5% alumina by volume)

      Instead of coating the base polymer lattice after microstereolithography, nanoparticles can be added to the resin bath and thus create ceramic lattices.

      The authors created solid alumina ceramic lattices by using a resin bath containing alumina nanoparticles.

    2. Uniaxial compression of these structures is shown in movies S1 to S3

      These movies can be accessed on this page:


    3. The microstructured mechanical metamaterials were tested to determine

      The samples were mechanically tested to obtain their properties.

    4. The densities of all samples were calculated by measuring the weight and fabricated dimensions of the completed microlattices

      The authors estimated the densities of the created samples by measuring their weights and volumes (dimensions).

    5. These hybrid lattices are converted to pure Al2O3 octet-truss microlattices

      The stereolithography process applied using a resin bath with nanoparticles results in an hybrid microlattice (made of a mixture of solid polymer and nanoparticles).

      An additional step is needed to obtain a microlattice made of pure alumina.

    6. A similar templating approach is used to generate hollow-tube aluminum oxide (amorphous Al2O3, alumina) microlattices; however, the coating is produced by

      A different coating process was applied to generate hollow-tube lattices with a different material (alumina). This process is called atomic layer deposition.

    7. The polymer template is subsequently removed by thermal decomposition, leaving behind the hollow-tube nickel-phosphorus (Ni-P) stretch-dominated microlattice

      After covering the initial polymer microlattice with a nickel alloy, the polymer base was destroyed by heating the lattice. A hollow-tube nickel microlattice was thus obtained.

    8. to convert the structures to metallic and ceramic microlattices. Metallic lattices were generated

      The base polymer lattice obtained through the microstereolithography was transformed in a metallic lattice by first covering the formed polymer with a nickel alloy.

    9. Although projection microstereolithography requires a photopolymer, other constituent materials such as metals and ceramics can be incorporated with additional processing

      The projection microstereolithography technique was used to generate a base polymer lattice.

      This template is then converted into the desired metallic or ceramic microlattices using nanoscale coating techniques.

    10. By combining projection microstereolithography with nanoscale coating methods, 3D lattices with ultralow relative densities below 0.1% can be created

      The different samples were created using two combined techniques.

      First, a base polymer lattice was generated with projection microstereolithography.

      This template was then converted into metallic and ceramic microlattices using nanoscale coating methods.

    11. as a point of comparison, a bend-dominated tetrakaidecahedron unit cell (40, 41) of the same size scale was generated and the corresponding cubic-symmetric foams (known as Kelvin foams) were fabricated with a variety of densities

      The structure proposed by the authors is based on a stretch-dominated lattice. A series of foams based on the other type of lattice, bend-dominated lattice, was fabricated to compare with the new proposed structure.

    12. we analyzed, fabricated, and tested them in a variety of orientations

      The behavior of a material can depend on the direction of the applied load. It also depends on the orientation of its architecture.

      To investigate the relationship between the elastic response and the orientation and load direction, different samples with varying orientations were created and they were tested with different loading directions.

    13. The densities of samples produced in this work ranged from 0.87 kg/m3 to 468 kg/m3, corresponding to 0.025% to 20% relative density

      The authors created samples with a wide range of densities to investigate the evolution of the elastic properties when the density changes.

    14. We report a group of ultralight mechanical metamaterials that maintain a nearly linear scaling between stiffness and density spanning three orders of magnitude in density, over a variety of constituent materials

      Authors designed and realized samples of ultralight mechanical metamaterials with a specific set of properties (namely, the coupling between stiffness and weight density is reduced to the theoretical limit).

    1. use of computed tomography to track pulmonary edema over time revealed partial protection from ALI in mice deficient in Mac-1 and almost complete protection when PSGL-1 interactions were blocked

      Using CT, the authors observed that in mice deficient for PSGL-1, the accumulation of fluid in the lungs (pulmonary edema) during ALI was reduced.

    2. deficiency in PSGL-1 or Mac-1, or inhibition of PSGL-1, resulted in moderate protection from ALI-induced death

      The authors extended the observation of neutrophil-platelet interaction via PSGL-1 during ALI. By inhibiting PSGL-1, they observed that mice were protected from ALI-induced death as the interaction between neutrophils and platelets was inhibited.

    3. hematopoietic-specific deletion of the gene encoding Cdc42

      Mx-1Cre-Transgenic mice are used to create inducible Cdc42 knockout mice. These mice have hematopoietic cells that are deficient in Cdc42.

      Read more on the transgenic mice used:


      Read more on inducible gene targeting:


      Ref: A Guide to Methods in the Biomedical Sciences. By Ronald B. Corley. Page 113: Description on bone marrow chimeras

    4. To test this hypothesis, we first induced transient depletion of platelets

      Besides using a gene knockout, the authors also used a model where depleting platelets was in their control. This was done by treating the mice with antiplatelet serum.

      It is important to support data from gene knockout experiments with blocking experiments to be able to translate one's findings to humans (we will not find gene knockouts in humans).

    5. blocking antibody injected after neutrophils had adhered

      Just prior to imaging the mice, the authors injected through IV an antibody that blocks PSGL-1.

    6. In vivo labeling for P-selectin

      In order to visualize some of the molecules, the authors inject dyes/antibodies with a fluorescent color tagged. These will specifically target the molecule of interest. (In vivo means inside the animal.)

    7. IVM, we could obtain three-dimensional (3D) reconstructions of polarized neutrophils within inflamed venules of Dock2-GFP mice

      Spinning disk microscopy rapidly captures multiple images in real time, up to 10,000 frames per second. The authors utilize this technique of IVM to capture multiple images to construct a 3D image of cells.


    8. revealed colocalization of Dock2 with PSGL-1 clusters on crawling neutrophils

      In this case, the authors tagged Dock-2 protein with GFP that allows them to view the molecule through the fluorescence emitted.

      They observed Dock-2 fluorescence on sites where PSGL-1 formed clusters.

    9. In vivo labeling of Mac-1 and PSGL-1

      Fluorescently labeled antibodies to Mac-1 and PSGL-1 were injected into the mice so as to trace these molecules by IVM based on the fluorescence they emit.

    10. deficiency in the β2 integrin Mac-1 (Itgam–/–) resulted in reductions at both the uropod and leading edge

      As a positive control, the authors use mice that lack another cell adhesion molecule, Mac-1. This molecule is required for neutrophils to interact with other cell types at both the leading edge and the uropod.

    11. revealed marked reductions in platelet interactions with the uropod, whereas those at the leading edge remained unaffected

      To confirm whether PSGL-1 on neutrophils is what is mediating these interactions, the authors see what happens in the absence of PSGL-1.

    12. mice deficient in PSGL-1

      To test the requirement of a molecule, researchers generally question what happens in the absence of the molecule. Thus, they generate knockouts.


      This is done by completely removing the gene that encodes the molecule.

    13. blockade of this domain protected mice against thromboinflammatory injury

      Blocking the interaction of neutrophils and platelets that lead to neutrophil migration and inflammation protected mice from excessive injury in the blood vessels (thrombo-inflammatory injury).

    1. For our linguistic analysis, we recorded word-use frequencies for members of the 113th U.S. Congress using relevant terms from one of the most frequently used emotion scales

      This means that the researchers looked at how often, within the 2013 U.S. Congressional Record, individuals used words taken from the Positive and Negative Affect Schedule, a common scale for measuring mood.

      In this study, the researchers were particularly interested in how often the congressmen and congresswomen used "positive affect" words: alert, determined, enthusiastic, excited, proud, etc.

      In addition to positive affect, the researchers also looked at individuals' usage of "negative affect" words (e.g., nervous, irritable, upset, scared), "joviality" words (e.g., joyful, delighted, energetic, lively), and "sadness" words (e.g., sad, alone, lonely, downhearted).

    2. A FACS-certified coder assessed the intensity of two action units (AUs) associated with genuine smiling behavior

      For this part of the study, the researchers used official photographs of the members of Congress and had someone trained in the Facial Action Coding System code how intensely both of these muscles were used in the photos.

      The key point is that both "sincere" (Duchenne) and "insincere" smiles use the zygomatic major muscle, but only "sincere" smiles tend to also involve the orbicularis oculi muscle.

    1. DOC processing was measured for streams and lakes

      The authors provide a map of their sampling sites in figure S1 (in the supplemental information). It is included here in the annotation tabs for Figure 1. Lakes are shown as open circles (135 different sites) and streams or rivers are shown as closed triangles (73 different sites).

      According to the supplemental information, water samples were collected biweekly to monthly during 2011-13.

      This video featuring primary author Rose Cory and her coworkers shows some of the sampling sites and overviews the background of this research.

      This video explains what the researchers do with the water samples they collect.

    2. were calculated by integrating apparent quantum yields with incoming UV radiation and light absorption by DOC over mean water column depth

      In order to make their results from the water samples relevant to actual streams, lakes, and rivers, the authors had to account for how much light is available over the range of depths in each water body.

      They measured the amount of incoming sunlight at the field sites and also made field measurements of how much light is available as you go from the water surface to the bottom.

      By using the bacterial respiration and photo degradation rates obtained from the water samples and the information about incoming light, the authors are able to approximate the total amount of degradation that takes place within a measured area of surface water each day.

      Some of the results of these calculations are shown in Table 1. The results are discussed further in the next paragraph.

    3. Areal rates were then scaled to the entire Kuparuk basin

      The authors used their calculated daily areal degradation rates (Table 1) to sum up the total amount of degradation that would happen in each water body over the course of a year. These calculations were based on daily measurements of sunlight during the ice-free season.

      The authors made additional measurements of light availability in the water column at sampling sites beyond those in Figure S1 in order to increase the accuracy of their calculations for the entire river basin.

      The results for degradation per year are shown in Table 2.

    4. As expected, measured light attenuation coefficients Kd,λ were strongly related to underwater light absorption by CDOM (aCDOM,λ) (R2 = 0.94, N = 100), and we used our measured aCDOM,λ (N = 2153) to predict Kd,λ when it was not measured directly (fig. S2)

      Kd,λ values in this paper are based on measurements made in the field whereas aCDOM,λ values are based on measurements on water samples taken back to the lab. The authors were able to find a mathematical correlation between the two parameters and use aCDOM,λ to calculate Kd,λ, which they used in their calculations in the information in Table 2.

      The details are provided in supplemental information.

    1. movie S1


      In the condition to the far right with a real rat trapped in the restrainer, the free rat is seen to poke its head close to the restrainer and contact the trapped rat several times.

      The black dot on the rat's head was used to track the movement depicted in Figure 1B.

    2. To examine whether individual differences in boldness influenced door-opening, we tested the latency for approach to the ledge of a half-opened cage before the experiment

      The author's wanted to determine whether the rats opened the door because they felt empathy for their cagemate or because of some inherent boldness.

      Taking this measurement allowed the authors to determine whether helping is preferentially done by bold rats.

    1. The nAG protein was detected in the medium after immunoblotting under both reducing and nonreducing conditions as a band at 18 kD

      The authors demonstrate that they can indeed detect nAG secreted into the medium by Cos 7 cells.

      They use reducing and non-reducing conditions as well. In reducing conditions disulfide bridges in the protein are broken, but in non-reducing conditions disulfide bridges are intact.

      For a picture showing disulfide bridges and other bonds found in proteins see here

    2. the axons may subsequently regenerate from the level of the star to the amputation plane, but denervated adult newt blastemas undergo fibrosis and other tissue changes that stop them from making a delayed regenerative response

      In other words, the axons in some animals are able to regrow even after being cut. However, nerves that do this are thought have no effect on regeneration.

    3. The expression of nAG protein was analyzed by reacting sections of the newt limb with the two antibodies, and these gave comparable results

      For these experiments the authors performed immunohistochemistry on sections of newt limbs to determine the location of nAG. This method is further described in the annotation for figure 2.

      Why would the authors use 2 different antibodies for nAG and what is the significance of getting the same results from both?

      Consider the "scientific process" when answering this question.

    4. The right animal has also regenerated on the control left side, but the expression of nAG has rescued the denervated blastema

      This animal had both limbs amputated, but only the right limb was denervated. In addition, the right limb was electroporated with nAG. This causes some number of those cells to express nAG when they normally would not.

      This group of animals acts as the experimental group.

    5. To deliver the protein to the adult newt limb, we electroporated plasmid DNA into the distal stump at day 5 pa

      Using focal point electroporation (previously described), the authors were able to introduce exogenous DNA into the amputated limb.

      The authors chose to use a plasmid (circular DNA) to introduce their gene into the limb.

    6. and then electroporated the nAG plasmid or empty vector on the denervated side

      The authors use an empty vector as the negative control for this experiment. The vector is essentially the exact same as nAG plasmid, but lacks the DNA sequence coding for nAG.

    1. In contrast, we examined learning-induced changes in long-standing social biases

      In contrast to previous work, the authors expand on the existing research by attempting to reduce people's biases. Unlike memories for facts, biases are acquired over a long period of time and are constantly reinforced by people's friends, family, and interpretations of their daily experiences.

    2. electroencephalographic signals

      Data obtained from EEG (electroencephalogram).

      EEG is a non-invasive method that detects electrical activity (from communicating brain cells) in the brain. Participants wear sensors on their head that detect this activity through the scalp.

      Click here for a picture of an EEG cap

      The authors used this device to detect when participants were asleep and to measure different sleep characteristics.

    3. Results were quantified by using a conventional scoring procedure

      This procedure involved calculating the reaction time (how fast participants pressed the button) for trials where the button participants used to classify trials was stereotype consistent (e.g. same button art words and female faces) and subtracting it from the reaction time for trials where the button participants used to classify trials was inconsistent with the stereotype.

      Participants who showed slower reactions when the button was inconsistent with the stereotype demonstrated more implicit bias.

      See the supplemental materials for more information.

    4. recruited as two subsamples that allowed for a direct replication

      The authors divided the 40 participants into two groups to test whether their results were found in both groups. Finding the effect in both groups makes their results more believable.

    1. We hypothesized that caffeine could affect the learning and memory of foraging pollinators.

      Caffeine blocks adenosine receptors, thus enhancing the activity of the neurons involved in learning smells and remembering them.

      Caffeine is also found in the nectar of some plants.

      Therefore, the authors of the study predict that caffeine in the nectar will in some way affect the learning of pollinating insects. They are going to test this hypothesis using behavior tests on bees in the presence of different amounts of caffeine.

    2. nectar concentrations did not exceed 0.3 mM

      See figure 1 for these data.

    3. If bees can detect caffeine, they might learn to avoid flowers offering nectar containing it

      The idea here is actually the opposite of what the authors hypothesized, but is a reasonable concern and thus important to consider.

      The authors hypothesized that caffeine could enhance a honeybee's memory of a plant, causing them to return to that plant. This is because of the memory-enhancing effect of the chemical's interaction with the bee's mushroom body neurons.

      However, the chemical is also very bitter. A bee is as unlikely to want to drink something that is very bitter as a human is. Therefore, if the honeybee can taste the bitter caffeine, it is unlikely to want to return to that plant.

      So how do we figure out which of these two opposite effects caffeine actually has on the bees?

      The authors of the study offered honeybees sugar solutions containing increasing amounts of caffeine, and observed at what concentration the bees found the solution to be repellent.

      If the concentration of caffeine in the nectar of these plants is at that repellent level or higher, it is unlikely that caffeine is attracting bees to those plants.

      However, if the amount of caffeine in the nectar is below that concentration, it is unlikely that the bees would detect its bitterness, and so would not be repelled by it.

    4. fig. S3

      Supplementary figure 3 showed proof that the honeybees have sensilla (sensory organs) that are able to detect caffeine.

      This is what is called a "proof-of-concept" experiment; it shows that the hypothesis is at least possible. Whether or not it is actually the way things are remains to be seen.

      In this case, it needed to be shown that honeybees are capable of detecting caffeine. If not, it doesn't matter that there is caffeine in the nectar of the plants - if the honeybees can't sense it and don't react to it, then caffeine in the nectar won't affect their behavior regardless of its concentration.

    5. adenosine receptor antagonist DPCPX

      The authors used DPCPX to identify whether or not the increase in nicotinic acetylcholine receptor activation they saw in response to caffeine was the result of caffeine interacting with adenosine receptors.

      DPCPX binds to adenosine receptors, preventing any other molecule, including caffeine, from binding to and interacting with the receptor. This is similar to the antagonistic action of caffeine on adenosine receptors, which blocks its activation by adenosine.

      As DPCPX was applied before caffeine, caffeine was unable to bind to adenosine receptors during this experiment. As a result, the authors could be sure that any effects seen after adding caffeine happened independently of caffeine's ability to bind adenosine receptors.

      This tells the researchers something about about how caffeine behaves in the absence of this antagonist, too - if it's able to act even when the adenosine receptors are inhibited, that means that those receptors are not necessary for this effect to occur. Conversely, if they saw that caffeine-mediated nicotinic acetylcholine receptor activation disappeared when they blocked caffeine from binding to the adenosine receptors, they would know that the adenosine receptors play an important role in inducing this effect.

    6. whole-KC recordings

      The authors took these recordings using a technique called "whole-cell patch-clamp electrophysiology."

      Patch-clamp electrophysiology allows researchers to measure the current flowing through an individual channel in a cell membrane. These currents result from the passage of ions through these channels, and act to send signals from neuron to neuron.

      Researchers isolate a tiny patch of the cell membrane using a glass micropipette. The surface of the cell membrane is suctioned into the tiny opening at the end of the pipette and forms a tight seal. This tight seal allows the current across that portion of the membrane to be measured very precisely, without any distortion of the data by surrounding factors.

      Whole-cell patch-clamp electrophysiology is a specific kind of patch-clamp in which multiple channels are individually measured at the same time. The same seal is made over a patch of the membrane using a glass pipette, but in the case of whole-cell recording, the suction is strong enough that the membrane is ruptured, allowing access to the interior of the cell.

      To see patch-clamp electrophysiology in action, see here, here, here and here.

    7. we trained bees for six trials with 30 s between each pairing of odor with reward

      In order to train the bees to associate the floral odor with receiving sucrose, the authors exposed a honeybee to the odor they wanted it to learn, then immediately fed it sucrose solution. This process was repeated 6 times per bee, with a 30 second interval between each trial.

      In order to test the effect of caffeine on the development of olfactory memory, the bees were split into eight groups. One group was fed either sucrose alone, while the other seven were fed solutions containing seven different concentrations of caffeine.

      The authors tested the bees memory of the smell twice - once 10 minutes after the last conditioning trial and once 24 hours later. The bees were tested with both the floral odor they had been taught to associate with sucrose and with another, unrelated odor to see if their memory to the floral scent was specific.

    8. This intertrial interval approximated the rate of floral visitation exhibited by honeybees foraging from multiple flowers on a single Citrus tree

      In the field, the authors had observed that bees will spend an average of 3.77 seconds at each flower they visit, and then will spend an average of 20.3 seconds traveling from one flower to the next, about 24 seconds total.

      As a result, the authors decided to use a 30 second interval between trials in this study in order to use a time frame between "flowers" (exposure to floral scent) that is similar to that seen in bees feeding in nature.

    1. In fig. S1, countries that have lost forests without gain are high on the y axis (Paraguay, Mongolia, and Zambia). Countries with a large fraction of forest area disturbed and/or reforested/afforested are high on the x axis (Swaziland, South Africa, and Uruguay).

      On page 7 of the supplemental material s Figure S2. On the x-axis are the countries with forestry programs, whereas countries on the y-axis have deforestation caused by factors other than forestry.

    2. tree canopy densities

      Tree canopy density is an important concept in this study, because it determines whether an area of land is a "forest" or not a "forest."

      To explain, Hansen and colleagues could analyze the satellite images of Earth at a resolution of 30 m by 30 m. For each of these 30 m by 30 m sections, they then calculated the proportion of that section that was covered in a tree canopy.

      Using this map, forests can be defined as a user prefers by applying a threshold of tree cover density; for example, tree cover greater than 50% can be labeled as forest.

    3. Landsat data

      Landsat is a a joint program between the U.S. Geological Service (USGS) and the National Aeronautics and Space Administration (NASA).

      In this program, satellites orbit around Earth and take photos of Earth's surface.

      The photos taken from the satellites are not the type of photos you would take with a typical smartphone. Instead, these images can show the energy that is both reflected and emitted from Earth in many different wavelengths, including blue, green, red, near-infrared, midinfrared, and thermal-infrared light.

      For a look at energy wavelengths click here.

      To distinguish forests from other land types (e.g., grasslands, water, etc.), one can look at a combination of different wavelengths in the Landsat data. For instance, looking at a combination of the red, near-infrared, and shortwave infrared wavelengths helps identify forests. Our eyes are similar to a satellite sensor, except we only see in the visible wavelengths, namely red, green, and blue. Forests, to our eyes, appear dark green, meaning low blue and red reflectance and brighter green reflectance. By using remote sensing technology, we can improve our identification of forest extent and change by adding other wavelengths of reflected and emitted energy not visible to the naked eye.

      Find out more about how the different wavelengths can help identify different features, here.

      You can view some Landsat photos here. Be sure to check out the photos of deforestation in Bolivia, which is particularly relevant to this study!

      Also check out this Landsat image video.

      Landsat images are online and available to the public. You can find data here.

    4. preprocessing of geometric and radiometric corrections of satellite imagery

      Before Hansen and colleagues could analyze the Landsat images, they had to preprocess them. This preprocessing included making corrections for clouds and shadows, assessing the quality of the images, and normalizing the images so that they can all be directly compared.

    1. sample sizes

      The total number of samples taken from a sample population.

    2. SEM

      Standard error of the mean = standard deviation/number of samples (Reference)

    3. fig. S5

      Figure 5 in Supplementary Materials shows differences in the cost of treatment in two cases: Average HRT and T=20C, Long HRT and T=25C (As mentioned before HRT describes the time necessary for particles to travel the system from the entrance till the outlet.)

      Figure S5 shows the cost of treatment per m3 of water treated in the y-axis. The x-axis presents the two different scenarios: baseline (average HRT and T=20C) and long HRT and T=25C.

      They looked at the effect of these two scenarios in two samples:

      Source water sulfate with 15 mgS/L and Source water with no sulfate. In both scenarios, source water with sulfate had higher expenses compared with the condition with no sulfate in source water.

      The long HRT condition is investigated to account for the conditions that could favor sulfide formation and corrosion in the sewer, in other words it is a representation of the worst-case scenario.

  3. Apr 2016
    1. Fourth, the estimated duration should be consistent both with the available evidence of increased risk of mortality after MV, compared with uninfected children, and with the time required to build a protective immune repertoire in early life (Fig. 1D, fig. S2, and SM 5 and 6).

      Author's Hypothesis: 4

      The estimated duration of immune suppression in hypothesis 3 must be biologically relevant. We have years of data from other scientists who have measured the amount of mortality following measles infections. Thus, to strengthen the reliability of this paper's findings, then the duration of immune-amnesia that this paper determines should agree with the time frame during which previous studies have found children to be at increased risk of mortality following measles.

      Additionally, a basic hypothesis underlying this paper is that children recover from immune-amnesia by rebuilding their immune response through re-exposure to pathogens. This process is similar to how children first build up their immune response after birth - through exposure to pathogens. Thus, if the hypothesis put forth in this paper is correct, then the time it takes to recover from measles induced immune-amnesia (i.e. the duration of immune-amnesia) should be similar to the amount of time it takes children to build an immune response in the first place.

    2. As a further test of the immunosuppressive impact of measles, we carried out a similar analysis on pertussis.

      This is a control experiment preformed by the authors.

      To test that their analysis doesn't result in falsely positive results another childhood disease, Pertussis, which is preventable by vaccination but does not cause immunomodulation was also analyzed. It was found that data did not demonstrate immunomodulation like measles disease.

    1. These y– F1♂ were considered candidates for carrying the y-MCR construct and were crossed to y+ females

      The authors also crossed the yellow F1 males to wildtype females to generate F2 offspring. A diagram of this cross is shown in Figure 2A.

    2. Six such yMCR F1♀ were crossed individually to y+♂

      After they had determined which of the F1 progeny expressed the mutagenic chain reaction allele (yMCR), they crossed the yMCR F1 females back to wildtype males to obtain the F2 progeny.

    3. Wild-type (y+) embryos were injected with the y-MCR element (see supplementary materials), and emerging F0 flies were crossed to a y+ stock

      The authors injected their construct into fly embryos so that the germline cells in the embryo would incorporate the construct into their nuclei. Once these flies (called the F0 generation) were adults, they crossed them back to wildtype flies to obtain the F1 progeny.

    1. This study tests whether summer jobs, which shift focus from remediation to prevention, can reduce crime.

      This paper uses a new approach to look at an old problem--the problem of youth violence. The new approach involves testing whether summer jobs programs result in reduced youth violence.

    1. intravital microscopy (IVM)

      Intravital microscopy is a technique used to image live animals. It is a live video of processes occurring in the animal while it is still alive. It gives information on different cellular interactions and activities in real time.

      In this experiment, the authors inject tumor necrosis factor-α, an inflammatory cytokine within the scrotum of mice, and, via IVM, study local inflammatory response in the cremaster (that covers the testis and speramtic cord) muscles.

    2. we searched for the receptor(s) mediating these contacts

      They next determined the receptor on the cell surface that allows these cells to interact with each other during these collisions.

  4. Mar 2016
    1. However, the theory on summer jobs is not entirely clear-cut

      There are also reasons why summer jobs might not have any effect or have the opposite effect by actually increasing violent activity. This is why this study is important to do.

    1. The left and right y-MCR PCR junction fragments were sequenced from y– F1 progeny from five independent F0 parents.

      In addition to the PCR genotyping, the authors performed DNA sequencing using DNA from F1 flies that were yellow (y-). DNA sequencing is a tool that allows you to determine the exact nucleotide sequence of a region of DNA. The goal of the sequencing was to confirm that the expected MCR construct had been inserted into the y locus.

    1. mean biodegradation rates and mean apparent quantum yields for photoreactions

      This is information from Table 1.

    2. measured and modeled UV radiation in the atmosphere

      In other words, measured or calculated sunlight intensities.

    3. 135 different lakes and 73 rivers

      These are the sites marked on the map in figure S1 (see Figure 1 annotations).

    4. We scaled these measures of DOC processing to the open-water period in three water types—small streams, larger rivers, and lakes

      As briefly discussed earlier in the paper, the authors used their calculated daily areal rated of dissolved organic carbon (DOC) processing to calculate the total amount of each type of DOC processing that occurs in their entire study area.

      They calculated separate rates for three different types of water bodies.

    5. Carbon processing at the scale of the Kuparuk River basin (~8000 km2) was estimated by summing areal rates over time (Fig. 2) for the period 2011–2013 and multiplying by the surface area of each water type (Table 2).

      The authors were able to use their dissolved organic carbon (DOC) degradation rates for the different types of water bodies to calculate the relative importance of sunlight- and microbial-driven DOC degradation in the whole study area (row labeled "sum" in Table 2).

    6. We quantified the importance of photodegradation in DOC processing by directly measuring dark bacterial respiration and each of the DOC photoproducts listed above.

      The authors determined how important sunlight is for breaking down organic carbon by comparing how much microbes can degrade in the dark and how much all the sunlight-driven processes can degrade.

    7. photostimulated bacterial respiration

      Measurement methods are summarized here and provided in detail in Reference 11.

      Photostimulated bacterial respiration was measured by exposing some sterile water samples to sunlight and keeping some in the dark, then adding bacteria and measuring the difference in how much carbon dioxide was produced in the bacteria in the sunlight-exposed samples versus the bacteria in samples that were kept in the dark.

    1. We mapped global tree cover extent, loss, and gain for the period from 2000 to 2012 at a spatial resolution of 30 m, with loss allocated annually.

      Hansen and colleagues looked at satellite images of Earth (see "Landsat data") for every year from 2000 to 2012 and determined how much of Earth is covered in forest, and whether forests increased or decreased in size from year to year.

      This method involves a lot of computer processing, because the raw satellite images need to be screened and assessed before they can be used.

      Hansen and colleagues performed the computational processing in Google's Earth Engine.

    2. being derived through an internally consistent approach that is exempt from the vagaries of different definitions, methods, and data inputs

      This sentence is referring to how Hansen and colleagues used Landsat data (e.g., the satellite images of Earth), which is all collected in exactly the same way each time. Thus, there are no inconsistencies between one sampling event (e.g., photo) and another sampling event.

    3. The proportion of total aggregate forest change emphasizes countries with likely forestry practices by including both loss and gain in its calculation, whereas the proportion of loss to gain measure differentiates countries experiencing deforestation or another loss dynamic without a corresponding forest recovery signal.

      By looking at the forest loss with or without subsequent forest gain, Hansen and colleagues can determine whether a country may have forestry programs or some other type of deforestation.

      To explain, forestry programs treat forests as a crop in that the trees are harvested and subsequently replanted/regrown until the next harvest, and so on. Thus, countries that experience forest loss and subsequent gain likely have forestry programs.

      Countries that have forest loss without much forest gain probably do not have forestry programs, and thus the deforestation is caused by some other factor. What could be some other causes of deforestation?

    4. efficiently process and characterize global-scale time-series data sets in quantifying land change

      Hansen and colleagues are illustrating how the work they conducted in this study can be applied and used by governments around the globe to monitor changes in land cover over time.

      Also, to clarify, "time-series data sets" refers to how their data (forest cover measurements) were collected, i.e., in this case in a series of collections through time (one collection of satellite images of Earth for each year from 2000 to 2012).

    1. Logistic regressions predicting the presence or absence of emotion words/emoticons at the tweet level were conducted, with political party followed as the independent variable

      The researchers examined whether or not an individual's usage of positive/negative words and emoticons in tweets could be statistically predicted based on that individual's assumed political party affiliation (either Democrat or Republican).

    2. In study 4, we analyzed 457 publicly available photographs of individuals from LinkedIn, a business-oriented social networking Web site.

      This study is essentially the same as the one that examined photographs of members of Congress (Study 2), but this one uses photographs from a business setting, rather than a political one.

    3. whether conservatives’ reports of greater subjective well-being, relative to liberals, could be attributed to self-enhancing tendencies

      This is the main hypothesis for Study 1. The authors predict that the reason why conservatives report higher levels of well-being is that, compared with liberals, conservatives are more likely to self-enhance.

  5. Nov 2015
    1. Stimulation was discontinued at any sign of arousal from sleep

      This procedure is necessary in order to ensure that any effect the authors find is specific to sleep (as opposed to hearing the sound consciously while awake).

    2. we administered another task wherein the same two sounds prompted participants to form a corresponding face-word pairing

      The purpose of this task is to make the association between the sound and the training stronger.

      On each trial participants were presented with a female face, a Black face, a science word and a good word.

      If they they heard the gender-associated sound they had to match the female face with the science word. If they heard the race-associated sound they had to match the Black face with the good word.

    3. Two unusual frequency-modulated sounds were presented during training

      The sounds were played immediately after a correct response. One sound was played for counter-gender bias responses, the other for counter-race bias responses.

      For some participants Sound A was played with the gender items and Sound B with the race items, and for other participants Sound B was played with the gender items and Sound A with the race items.

      Click to hear Sound A

      Click to hear Sound B

    4. Participants viewed several types of face-word pairing but were required to attend and respond only to pairings that countered the typical bias

      Participants were asked to press the spacebar as quickly as possible after seeing a face-word pair that countered the typical bias (e.g. a female face with the word 'science').

      Half the pairs countered the typical bias and half were filler trials that participants were not supposed to respond to (female + art, male + science, male + art).

  6. Oct 2015
    1. could be expanded through the use of homologs with different PAM requirements (9) or by directed evolution

      This is another area for potential future research

    2. directed evolution of these nucleases toward higher specificity

      This is another area for potential future research.

    3. off-target nuclease activity

      This is a problem that will definitely need to be resolved before these technologies can be deployed in human beings

    4. it is likely that the target locus's underlying chromatin structure and epigenetic state will also affect the efficiency of genome editing in eukaryotic cells (13), although we suspect that Cas9's helicase activity may render it more robust to these factors, but this remains to be evaluated

      This is another area for possible future research.

    5. 8 to 12 bases is less well understood and may depend on the binding strength of the matching gRNAs or on the inherent tolerance of Cas9 itself

      This could be an area of future research

    6. puromycin selection

      Puromycin is an antibiotic that can be used to select cells which have developed resistance to it by killing off all the cells which have not. It is used here to purify a cell strain by eliminating all the cells which did not develop resistance. http://agscientific.com/blog/index.php/2012/10/10/puromycin-faqs/

    7. endogenous locus

      That is, the AAVS1 locus in the PPP1R12C gene of chromosome 19 as mentioned above.

    8. next-generation sequencing of the targeted locus

      The authors checked the DNA sequence of daughter cells after they did the editing

    9. which demonstrates that CRISPR-mediated genome editing is sequence-specific

      This supports the authors' interpretation of what is happening.

    10. HR but lower nonhomologous end joining (NHEJ) rates

      By increasing the proportion of homologous recombination the researchers have better control over the process. Nonhomologous end joining is a less exact process and leads to more spontaneous errors.

    11. GFP+ cells appearing ~20 hours post transfection compared with ~40 hours for the AAVS1 TALENs.

      The results of the editing process appeared sooner in the case of the authors' engineered guide RNAs as compared with the earlier method using TALENs

    12. gene correction rates using the T1 and T2 gRNAs approaching 3% and 8%

      In other words, 3-8% of the cells returned to being fluorescent.

    13. two gRNAs

      The authors constructed two different guide RNAs

    14. the intervening AAVS1 fragment

      This is the 68-bp fragment mentioned toward the end of the last paragraph. When it is expressed, it makes the protein non-fluorescent.

    15. flow-activated cell sorting (FACS)

      This method uses a laser to identify which cells are of interest and thus sort them out. http://www.bio.davidson.edu/courses/genomics/method/facs.html

    16. renders the expressed protein fragment nonfluorescent

      By introducing the green fluorescent protein sequence and then disrupting it the authors were able to measure how well their genetic editing worked. They could measure this by determining how many of the daughter cells were fluorescent.

    17. guide RNAs

      In the natural CRISPR system guide RNAs take fragments of the viral or plasmid DNA and guide them to specific locations in the CRISPR locus. The idea here is that these artificial guide RNAs can similarly guide a short strand of nucleic acids into a specific place in the target genome.

    18. crRNA-tracrRNA fusion transcripts

      The authors combined two proteins which are needed for correct functioning of the CRISPR type II system.

    19. a mammalian expression system

      Genes code for proteins, but characteristics of the cells that the genes are in may either help or hinder the genes from actually producing the desired protein.

      For example, there are differences between insect protein and the protein of mammals. Cells can be engineered to produce the desired type of protein. For more about expression systems, see this link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848218/

    20. C-terminal SV40 nuclear localization signal

      Nuclear localization signals are amino acid sequences that mark a protein to be transported to a specific place in the nucleus.

    21. human codon–optimized version

      A codon is a sequence of DNA "letters" that corresponds to a specific amino acid. By using a sequence of codons, specific proteins can be constructed.

    1. Taking into consideration the role of sleep in memory consolidation, we adapted procedures for (i) reducing implicit social biases and (ii) reactivating this training during sleep.

      To design their study, the authors combined counterbias training (discussed in the previous paragraph) with memory reactivation during sleep (discussed in this paragraph) in order to reduce racial and gender biases.

    2. We reactivated counterbias information during sleep using subtle auditory cues that had been associated with counterbias training

      While participants were asleep, the experimenters played one of two sounds - either the sound associated with the gender counterbias training or the sound associated with the racial counterbias training. The sounds were played softly so that the participants did not wake up.

    3. implicit association test (IAT)

      The IAT is a test that measures your implicit (unconscious) biases. You initially practice classifying items based on one set of two categories (e.g. good words respond with the left hand and bad words respond with your right hand). After a number of trials you then classify another set of two categories (e.g. White faces with the left hand and Black faces with the right hand). Then the categories are paired together (e.g. if you see a good word or a White face respond with the left hand and if you see a bad word or a Black face respond with your right hand). Finally the pairings are switched (e.g. if you see a good word or a Black face respond with the left hand and if you see a bad word or a White face respond with your right hand).

      Your score is calculated based on your reaction times for responding to White faces when the same key is used to classify good words than your reaction time for responding to Black faces when the same key is used to classify good words.

      Try the IAT for yourself here!