1,157 Matching Annotations
  1. May 2019
    1. As part of an online survey typically given in the course (week 2), students also indicated their endorsement of the stereotype that men perform better than women in physics.

      Level of endorsement of the stereotype that men perform better than women in physics is a moderating variable. Its value influences how much the values affirmation intervention affects course performance.

    2. attempts to reduce identity threat in authentic classroom contexts have been limited

      One of the key features of this study is that it takes places in an authentic college classroom, rather than being an artificial, one-time laboratory experiment.

    1. We performed a genome-wide screen for loci affecting overall body size in six species of Darwin’s finches that primarily differ in size and size-related traits: the small, medium, and large ground finches, and the small, medium, and large tree finches (Fig. 1, A and B, and table S1)

      The investigators initially had to decide that they were going to use samples from six species of finches. Then, they screened the entire genome of these species to look for genetic variants in different individuals. The objective was to see if any variation at any given location was associated with size and/or size-related traits.

    2. We constructed a maximum-likelihood phylogenetic tree on the basis of this ~525-kb region

      The genome-wide fixation index scan found that a region around 525 kb in size showed the most striking differences.

      Lamichhaney and colleagues constructed another phylogenetic tree based on the alignment of this region in all of the samples.

    3. We constructed a maximum-likelihood phylogenetic tree on the basis of all 180 genome sequences (Fig. 1C)

      The nucleotide alignment of the variable positions from all 180 samples (60 birds plus 120 from previous study) allowed the scientists to generate a phylogeny using software FastTree.

      See here to learn more about FastTree and its maximum-likelihood method.

    4. We sequenced 10 birds from each of the six species (total 60 birds) to ~10× coverage per individual, using 2 × 125–base pair paired-end reads. The sequences were aligned to the reference genome from a female medium ground finch (12).

      Lamichhaney and colleagues sequenced a total of 60 birds. Sequencing is a technique used to actually read the DNA.

      For a history of DNA sequencing and assembly, this resource from HHMI BioInteractive is a great tool.

      This video shows specifically how Illumina Sequencing Technology works.

      If a finch genome is 1 Gbp (one trillion base pairs), sequencing "to ~10x coverage per individual" would mean that you obtain 10 Gbp of sequencing data.

      "Using 2 x 125-base pair paired-end reads" refers to the fact that the fragments sequenced were sequenced from both ends and not just one. Refer to the videos above for more information.

    5. We then genotyped individuals of the Daphne population of medium ground finches that succumbed or survived during the drought of 2004–2005.

      Genotyping establishes a genetic code for each individual finch. With birds, this can typically be done using plucked feathers, blood, or eggshell membranes.

      The researchers here used blood samples that were collected on FTA paper and then stored at -80°C. FTA paper is treated to bind and protect nucleic acids from degrading.

      This type of scanning is used to identify specific gene markers that are highly variable. Researchers wanted to identify a locus that showed beak size variation.

    1. Compared with REPAIRv1, REPAIRv2 exhibited increased specificity, with a reduction from 18,385 to 20 transcriptome-wide off-targets with high-coverage sequencing (125x coverage, 10 ng of REPAIR vector transfected)

      To more rigorously compare the off-target activity of two systems, the authors performed sequencing with higher coverage.

      Recall that earlier they used 12.5x coverage. Here, they used 125x coverage.

      Why is this important? Cellular genes are expressed at different levels which leads to a different number of individual mRNA molecules. The more abundant a particular molecule is, the easier it is to detect it at a given coverage. When you increase the coverage, you have a chance to catch molecules that are less abundant in the cell.

      This is exactly what happened in the experiment with the REPAIRv1. At 125x coverage, the authors detected off-targets in the majority of transcripts (18385 of around 20000 protein-coding genes in our genome). By contrast, the REPAIRv2 system was astonishingly more specific and produced off-targets 1000 times less frequently.

    2. We further explored motifs surrounding off-targets for the various specificity mutants

      Inspired by other explorations into 3' and 5' motifs, the authors looked at transcripts with off-target effects—specifically at two nucleotides surrounding the edited adenosine.

    3. A majority of mutants either significantly improved the luciferase activity for the targeting guide or increased the ratio of targeting to nontargeting guide activity, which we termed the specificity score

      The authors looked at two characteristics of the modified protein variants.

      First, they tested whether the mutant had changed its editing activity. This was calculated by looking at the restoration of the Cluc luciferase signal. While the authors didn't necessarily want increased editing activity, they wanted to avoid a loss of editing activity. 

      However, catalytic activity sometimes leads to more off-target effects. Therefore, they authors calculated the ratio between the Cluc signal in targeting and non-targeting conditions, i.e. the specificity score. The higher the score, the more specific a mutant variant was.

    4. we generated an RNA-editing reporter on Cluc by introducing a nonsense mutation [W85X (UGG→UAG)],

      To create the reporter, the researchers "broke" the gene for the Cluc luciferase by introducing a mutation in the UGG codon, changing it to UAG (a nonsense mutation, which signals the ribosome to stop translation). Since this codon was positioned in the beginning of the Cluc transcript, no luciferase was synthesized in the cell.

      The A (adenosine) in the UAG codon was the target for RNA editing. Both Cas13b-mediated RNA recognition and ADAR-mediated editing were required to remove the stop codon at the beginning of the Cluc transcript, which would restore Cluc expression.

      This means that Cluc luminescence would only be seen where editing (both targeting and cleavage) was successful.

    5. We next characterized the interference specificity of PspCas13b and LwaCas13a across the mRNA fraction of the transcriptome.

      The next question was to understand the specificity of Cas13 in the whole cellular transcriptome (the portion of the genome that's transcribed). In the previous experiments, the researchers looked at the expression of only one target (unmodified or modified). Here, they narrowed their focus from the entire genome to just the transcriptome.

      To do that, the authors transfected the cells with Cas13, LwaCas13a or PspCas13b, a gRNA to target Gluc, and a plasmid containing the gene for Gluc.

      The control cells got an irrelevant gRNA instead of the gRNA targeting Gluc. As an additional control for comparison, the authors used shRNA-mediated knockdown of Gluc in a parallel cell culture.

      After 48 hours the researchers collected the cells, extracted mRNA, and determined the sequences and the number of copies for each transcript.

    6. We transfected HEK293FT cells with either LwaCas13a or PspCas13b, a fixed guide RNA targeting the unmodified target sequence, and the mismatched target library corresponding to the appropriate system.

      The cells were transfected with a nuclease, a gRNA for the non-mutated target site and a whole library with all possible plasmid variants. After 48 hours the researchers collected the cells, extracted RNA, and determined which mutated sequences from the library were left uncleaved.

      The transcript with the unmodified sequence was depleted most efficiently so that its level was the lowest after the cleavage. The levels of all other sequences with substitutions decreased to a lesser extent or did not decrease at all. The better Cas13 cut the sequence, the higher the depletion of this sequence was.

      The authors then compared the sequences by their "depletion scores."

    7. Sequencing showed that almost all PFS combinations allowed robust knockdown

      Substitutions in the PFS motifs did not affect how well Cas13a and Cas13b found and cut the target sequences. As a result, sequences with such substitutions were depleted as successfully as the control sequence, which was unmodified.

    8. To more rigorously define the activity of PspCas13b and LwaCas13a, we designed position-matched guides tiling along both Gluc and Cluc transcripts and assayed their activity using our luciferase reporter assay.

      To figure out which parts of the Gluc or Cluc RNA molecules were the best targets for Cas13, the authors generated a series of gRNA guides where each guide was shifted one to several nucleotides relative to the previous one. This is called tiling.

      In this way, the guides together could cover the whole sequence or a part of a sequence that a researcher was interested in. See figure 4A and 4C or figure 5A for a visual of how the guides were "tiled."

    9. Therefore, we tested the interference activity of the seven selected Cas13 orthologs C-terminally fused to one of six different localization tags without msfGFP.

      The authors took six of the best-performing orthologs from the previous part of the study and replaced the msfGFP domain at the C-terminus of each ortholog with different localization sequences. They then tested Gluc knockdown in the same way they previously tested LwaCas13a.

    10. We transfected human embryonic kidney (HEK) 293FT cells with Cas13-expression, guide RNA, and reporter plasmids and then quantified levels of Cas13 expression and the targeted Gluc 48 hours later

      To directly compare the effectiveness of Cas13a, b, and c orthologs, the authors transfected cells with two luciferases, Cas13 and two different gRNAs targeting Gluc luciferase.

      They measured Gluc luciferase activity. Reduced Gluc luciferase activity indicated interference from the Cas13 ortholog and successful targeting by the gRNA.

      They determined the expression of Cas13 to see whether Gluc knockdown was dependent on the quantity of Cas13 rather than the specific orthology.

    11. Here, we describe the development of a precise and flexible RNA base editing technology using the type VI CRISPR-associated RNA-guided ribonuclease (RNase) Cas13

      In this article, the authors describe how they created a system that can edit RNA molecules. They used a Cas13 protein fused to an adenine deaminase. The Cas13 protein recognized specific sequences on an RNA molecule, and the adenine deaminase edited bases, which can convert A to I (which is functionally read as a G).

      The authors improved the targeting specificity (accuracy) and editing rate (precision) by Cas13 and deaminase mutagenesis, and determined the sequences for which this system is most effective. They showed one application of this technology by correcting a series of disease-causing mutations at the cellular level.

    1. We evaluated the collective scrolling and tribological behavior of many individual graphene patches and created a density distribution of their tribological state in order to assess their contribution to the observed friction

      Authors have conducted theoretical simulation to investigate the sliding behavior of an ensemble of graphene sheets to elucidate the macroscale scrolling phenomena. To explore the mesoscopic friction behavior, number density (number of particles per unit volume) of the patches as a function of the coefficient of friction and time is calculated by grouping the friction coefficients collected over the ensemble of graphene patches.

    2. we performed a large-scale MD simulation for an ensemble of graphene-plus-nanodiamonds present between DLC and the underlying multilayered graphene substrate (fig. S8).

      To understand the transition of friction from the nanoscale to the macroscopic superlubric condition observed in experiments, authors have simulated a mesoscopic scenario. They have created and analyzed an ensemble (assembly of systems) of graphene patches and nanodiamonds between the DLC and graphene substrate subjected to sliding friction.

    3. We have simulated the effects of surface chemistry and considered the role of defects

      To understand the role of defects in superlubricity, the authors performed computer simulations by introducing double vacancies and Stone-Wales defects on graphene sheets. Studies were conducted in both dry and humid environments.

    4. DLC-nanodiamond-graphene system in a humid environment

      Upon observing experimentally the effect of humidity on friction conditions, authors have extended their studies. They have performed computer simulations to further analyze the interaction between water molecules and graphene in the DLC-nanodiamond-graphene system in a humid environment.

  2. Apr 2019
    1. This prototype includes a MOF-801 layer (packing porosity of ~0.85, 5 by 5 by 0.31 cm, containing 1.34 g of activated MOF), an acrylic enclosure, and a condenser

      Since this paper was published, the authors refined and optimized the devise and tested it under desert conditions with record high efficiency.

      See "Related Content" tab for: Kim, Hyunho, et al. "Adsorption-based atmospheric water harvesting device for arid climates." Nature communications 9.1 (2018): 1191.

    2. Experiments were performed in a RH-controlled environmental chamber interfaced with a solar simulator.

      To test the material in a laboratory setup, the authors use an enclosed chamber in which conditions such as humidity, temperature, and solar illumination can be regulated. This guarantees control over the experimental conditions and reproducibility.

    3. activated (solvent removal from the pores) by heating at 150°C under vacuum for 24 hours

      Heating under reduced pressure lowers the boiling point of liquids. This allows all the solvent and water molecules trapped in the MOF to evaporate easily, emptying all the cavities before starting the experiment.

    1. We carried out more detailed analysis of the wear track that

      In order to understand the wear properties of the graphene-nanodiamond compound after the sliding experiments, the authors performed electron microscopy studies which can reveal the structure of the material in the wear debris.

    2. Raman analysis

      Raman spectroscopy is a chemical analysis technique capable of probing the chemical structure, crystallinity, and molecular interactions of materials.

    3. The contact area normalized with respect to the initial value at t = 0 is ~1 (22), as shown in Fig. 4C

      The authors defined contact area as the area of graphene atoms which are in the range of chemical interactions from the DLC tip atoms. The normalized contact area is defined as the contact area at any time (t) with respect to the initial contact area at time t=0 (when the graphene patches are fully expanded).

    4. To further explore the superlubricity mechanism, we performed molecular dynamics (MD) simulations (table S1)

      In order to elucidate the mechanism of graphene nanoscroll formation and the origin of superlubric state, the authors have conducted computer simulation studies.

    5. Our experiments suggest that the humid environment

      To investigate the effect of environmental conditions on nanoscale friction and superlubricity, the authors have conducted experiments in humid air in place of dry nitrogen.

    1. computed by subtracting the climatological temperature value (17) for the month in which the profile was measured

      For example, if a temperature profile was taken on Feb. 19th, for each depth in that profile the authors subtracted out the average value for all Februaries over the last 50 years for each depth point. This removes the seasonal temperature changes from the data-set, allowing the authors to focus on the long term variability instead.

    2. computed the contribution to the vertically integrated field shown in Fig. 3B from each 500-m layer

      By examining the ocean in distinct depth increments of 500m each, the authors aimed to determine where most of the cooling and heating of the North Atlantic is occurring.

    3. computed as the time derivative of heat content

      The authors calculated how much heat is being stored in the deep sea by looking at the cumulative temperature change from 1955-59 to 1970-74, as well as from 1970-74 to 1988-92.

      By integrating, or combining, the temperature data for all depths between 0 and 300m and between 0 and 3000 m, the authors aimed to examine where the heat is going - into the surface ocean or the deep ocean.

    4. running 5-year composites

      The authors combine 5 years of data into one value, typically by averaging all values. A running composite (sometimes known as a moving or running average) is calculated by creating a series of averages of different subsets of the full data set in order to compare to the original data set.

      Calculating a running composite is a common technique used with time series data in order to smooth out short-term fluctuations and highlight longer-term trends or cycles.

      For more information on how to calculate a moving average: http://www.statisticshowto.com/moving-average/

    5. Computation of the anomaly fields was similar to our earlier work (7), but some procedures were changed

      The authors calculated temperature anomalies by subtracting the seasonal temperature cycle from monthly data values.

      Every now and then a shipboard temperature measurement can malfunction or be used incorrectly, recording temperatures far higher or far lower than what is realistic. These values need to be excluded to accurately study the oceans. To make sure these errors do not affect the study, the authors considered a particular range of data points with cutoffs at the higher and lower end of the range.

      Unlike their previous work, the authors used a less strict cutoff for when data values were considered good enough to use in their analysis. This is because they found that some large-scale temperature features were mistakenly being flagged as "bad" data under the stricter cutoff, despite those features being real and measurable events in the ocean.

    6. yearly and year-season objectively analyzed temperature

      Using data available in the World Ocean Database, Levitus et al. looked at both annual temperature data and average season temperatures within each year (for winter, spring, summer, fall).

      However, because temperature changes over the course of a year due to the changing of the seasons (summers are warm, winters are cold), this seasonality must be taken into account when studying the overall change in ocean temperatures. To "objectively analyze" the data, the natural seasonal temperature cycle was subtracted from each data point in order to focus on the trends over time.

      For each monthly temperature data point, the average temperature for that month the sample was measured was subtracted. The difference between the data point and the monthly average is called an anomaly.

    7. Using these data, yearly, objectively analyzed, gridded analyses of the existing data were prepared and distributed (7) for individual years for the period 1960 to 1990.

      The authors averaged monthly oceanographic data acquired by ship-of-opportunity and research vessels into annual temperature measurements for every year from 1960 to 1990.

      Scientists measure locations on Earth using longitude (180° E ↔ 180° W) and latitude (90° N ↔ 90° S).  Lines of longitude and latitude cross to create a grid across the planet.

      For this study, Levitus et al. combined temperature data for every 1° longitude by 1° latitude area of the ocean. Where multiple ships frequented the same location, those multiple data points were averaged into one value for each matching depth.

    1. unconstrained canonical correspondence analysis

      Refers to a statistical method that searches for multivariate relationships between two data sets.

      This method is most often used in genetics and ecological sciences. Learn more about why, how, and when to use it here.

    1. To investigate PFS constraints on REPAIRv1, we designed a plasmid library that carryies a series of four randomized nucleotides at the 5′ end of a target site on the Cluc transcript

      Though the authors had already characterized PFS preferences for Cas13b, they needed to check that the fusion of Cas13b with ADAR did not change its targeting efficiency and specificity. The researchers also wanted to confirm that PFS would work when generating RNA edits. This is important as DNA base editors are limited by the PAM of Cas9 and Cpf1 making RNA more powerful since you can target anywhere in the transcriptome. Therefore, it was important to check PFS constraints again.

    2. We mutated residues in ADAR2DD(E488Q) previously determined to contact the duplex region of the target RNA (Fig. 6A) (19).

      The researchers mutated amino acids in ADAR involved with binding to the RNA target or catalytic deamination to test whether they affected deamination.

  3. Mar 2019
    1. A gradual increase in homozygosity was then observed over the next five generations (Fig. 2D), as expected from the small number of breeding pairs

      The authors measured genetic diversity through the inbreeding coefficient and average nucleotide diversity, finding that the pattern of decreasing genetic diversity was as expected for an inbreeding population.

    2. the allele frequency

      The authors measure allele frequencies to see if they are changing, which is an indication of continuing natural selection.

    3. more detailed morphological analysis

      The authors analyzed body size and several components of bill size to give a more complete comparison of the Big Bird lineage to both of its parental species. Results of these analyses are found in Figure 3.

    1. To probe the functional connectivity between these layer V projection neurons and STN in the PD animals, we conducted a separated-optrode experiment in anesthetized animals in which the fiber-optic and recording electrodes were placed in two different brain regions in Thy1::ChR2 animals

      Based upon previous findings that the cortex and STN are connected, the investigators wanted to know if driving M1 layer V neurons had an effect on STN neuronal firing and subsequent behavioral output. So they placed an optrode over M1 and a recording electrode in the STN.

    2. we used Thy1::ChR2 transgenic mice (22, 23) in which ChR2 is expressed in projection neurons, and we verified that in Thy1::ChR2 line 18, ChR2-YFP is excluded from cell bodies in the STN but is abundant in afferent fibers

      Thy1 (thymocyte differentiation antigen 1) is expressed in the axonal projections of mature neurons. When its promoter is placed in control over ChR2 expression, the protein would be expressed in the projection neurons as opposed to the somata of local neurons.

    3. The STN is a predominantly excitatory structure (30) embedded within an inhibitory network. This anatomical arrangement enables a targeting strategy for selective STN inhibition (Fig. 1B), in which enhanced NpHR (eNpHR) (21) is expressed under control of the calcium/calmodulin-dependent protein kinase IIα (CaMKIIα) promoter, which is selective for excitatory glutamatergic neurons and not inhibitory cells, fibers of passage, glia, or neighboring structures

      Since the subthalamic nucleus is excitatory, meaning the neurons within release the neurotransmitter glutamate, selectively targeting this region can be accomplished via the promoter calcium/calmodulin-dependent protein kinase II alpha (CaMKIIα). Placing a gene downstream of the CaMKIIα promoter will cause the gene to be selectively expressed only in excitatory neurons.

      The authors placed the gene sequence for halorhodopsin under the control of the CaMKIIα promoter and were able to selectively inhibit the firing of excitatory glutamatergic neurons in the subthalamic nucleus.

    1. Dot blot analysis

      A quantitative method to detect mRNA levels in the explants. Here, mRNA levels of proenkephalin is measured using this method.

      Learn more with this video from Abnova.

    2. Denervation

      A technique used to separate or eliminate a particular nerve supply to specific area(s) in the nervous system.

    1. We performed a parametric study, including varying the packing porosity (0.5, 0.7, and 0.9) and layer thickness (1, 3, 5, and 10 mm), and determined the time and amount of harvestable water for a solar flux of 1 sun

      The authors examined different parameters to optimize the water harvesting properties of the material. The porosity and thickness of the material are assumed to be the parameters having the largest effect because they determine the amount of water that can be adsorbed for a chosen compacted adsorbent layer.

    1. Dirichlet multinomial mixtures

      Refers to a computational technique to model the probability of microbial metagenomics data by representing the data as a frequency matrix of the number of times each taxa is observed in a sample.

    2. To achieve a balance between number of phenotypes of interest and rates of false discovery, a stepwise approach was applied.

      The researchers wanted to ensure that the phenotypes of interest were not falsely correlated with microbiota genera. To avoid overfitting, they reduced the phenotypic data in different stages. By approaching the problem in a series of distinct stages, the researchers could determine the most important variables that affect the abundance and diversity of gut microbiota.

  4. Feb 2019
    1. Participants indicated whether it was the duty of the government to enforce regulations that would minimize the casualties in such circumstances, whether they would consider the purchase of an AV under such regulations, and whether they would consider purchasing an AV under no such regulations

      n the final experiment, the researchers presented participants with a scenario in which an AV would have to sacrifice passengers to minimize overall casualties. They were then asked whether governments should regulate autonomous vehicles, so that they are programmed to minimize casualties; whether they would buy a vehicle that was subject to those regulations; and whether they would buy a vehicle that was not regulated in that way.

    2. Study four (n = 267 participants) offers another demonstration of this phenomenon. Participants were given 100 points to allocate between different types of algorithms, to indicate (i) how moral the algorithms were, (ii) how comfortable participants were for other AVs to be programmed in a given manner, and (iii) how likely participants would be to buy an AV programmed in a given manner.

      In Study 4, participants were given a "budget" of 100 points to assign to different algorithms, which was a way for researchers to look at their priorities.

      For example, if there were three algorithms, a participant could choose to allocate 20 points to the first one, 30 points to the second, and 50 to the third. This allowed the authors to directly compare how participants felt about the different algorithms presented in Study 4.

      There were three algorithms, and participants had a separate budget for each in which they answered the questions:

      1. How moral is this algorithm relative to the others?
      2. If self-driving cars were programmed with this particular algorithm over the others, how comfortable would you be with it?
      3. How likely would you buy a self-driving car programmed with this algorithm?
    3. In study two (n = 451 participants), participants were presented with dilemmas that varied the number of pedestrians’ lives that could be saved, from 1 to 100.

      Participants read scenarios in which the self-driving vehicle would sacrifice its single passenger to save pedestrians, with the number of pedestrians ranging from one to 100.

      The participants were asked which situation (saving the passenger versus some number of pedestrians) would be the most moral choice.

    4. The last item in every study was an easy question (e.g., how many pedestrians were on the road) relative to the traffic situation that participants had just considered. Participants who failed this attention check (typically 10% of the sample) were discarded from subsequent analyses.

      With the last question in each study, the authors were checking if the participant was still paying attention. If the participant got the question wrong, their answers were discarded because the authors assumed that the participant was not actively engaged.

      Attention checks can help make sure that the data you are collecting is higher quality. For example, participants could start speeding through the survey without thinking through their answers, which results in data that is not informative or useful.

    5. Amazon Mechanical Turk (MTurk) platform

      Amazon Mechanical Turk (MTurk) is a website that lets users earn money for doing small tasks. It has become increasingly popular for researchers, who use it to reach a wide audience online.

      With MTurk, a large and diverse set of data can be collected in a short period of time.

    6. our scenarios did not feature any uncertainty about decision outcomes

      The scenarios presented in the study always assumed that someone would be killed by the autonomous vehicle. The authors did not look into situations where the outcome was uncertain, like if the passenger had a greater chance of survival than a pedestrian.

    7. But would people approve of government regulations imposing utilitarian algorithms in AVs, and would they be more likely to buy AVs under such regulations?

      In the final two studies, the authors wanted to discover if people approve of governments legally enforcing utilitarian algorithms in AVs, and whether people would want to buy AVs if these regulations existed.

    8. Regression analyses (see supplementary materials) showed that enthusiasm for self-driving cars was consistently greater for younger, male participants. Accordingly, all subsequent analyses included age and sex as covariates.

      Regression analyses allow you to understand how different things may or may not be related. For example, how does the number of views for a YouTube video change based on the video's content?

      In this study, the authors used regression to investigate how factors like gender, age, and religion might be related to someone's enthusiasm about self-driving cars.

      This is important for finding potential covariates in the experiment. Covariates are characteristics of the people in an experiment, like age, gender, and income. These variables cannot be controlled like experimental ones, but they can affect the outcome of an experiment and bias your results in an unexpected way. They can also reveal interesting trends in society.

      By determining the covariates that could sway the experiment, scientists can make the model more accurate. Here, the authors determined that the experiments should account for age and gender.

    9. broad public exposure and a disproportionate weight in individual and public decisions about AVs

      Even though the situations where AVs would sacrifice their passengers are rare, these are emotional events that would have a large influence on the public despite their infrequency.

    10. Consider, for example, the case displayed in Fig. 1A, and assume that the most common moral attitude is that the AV should swerve. This would fit a utilitarian moral doctrine (11), according to which the moral course of action is to minimize casualties. But consider then the case displayed in Fig. 1C. The utilitarian course of action, in that situation, would be for the AV to swerve and kill its passenger, but AVs programmed to follow this course of action might discourage buyers who believe their own safety should trump other considerations.

      In Fig. 1C, the car must decide between killing its own passenger or several pedestrians. A utilitarian viewpoint, which calls for the choice resulting in the "most good," would be to sacrifice one (the passenger) to save many.

      However, people who prioritize their own safety will not want to buy a car that's programmed this way because the result could be that their car would sacrifice them.

    1. morphological measurements and whole genome sequencing

      The authors used bill size and body mass (morphological measurements) and genetic data.

      The genetic data used was the entire DNA sequence for each bird (whole genome sequencing) for sections to analyze, not just particular sections of DNA, as had been done in the past.

    2. analysis

      The phylogenetic tree analysis consists of scanning the genomes of all 46 members of the Big Bird lineage and comparing them to the genomes of 180 other finches from Daphne Major for which there are genome data.

      A computer program is used to generate many phylogenetic trees, and mathematical parameters are used to ensure that the data are properly interpreted in the program. Then, a statistical test is used to evaluate the reliability of each split in the tree.

    1. Relationships between temperature and insect population growth rates drive logistic population increases of insects during each crop’s growing season, and they also scale the fractional survival rate of insects over the rest of the year (14), termed the diapause survival, ϕo.

      This sentence is saying that the higher number of insects you see during the growing season and the lower numbers seen throughout the rest of the year is because of the relationships between insects and temperature, where warmer temperatures result in greater insect populations. This pattern, fewer insects during colder months and more insects during warmer months, is called diapause and means that insects, and also some other animals, go into a dormancy until environmental conditions are more favorable for survival.

  5. Jan 2019
    1. If the NPF-NPFR system were to function generally to signal the state of the Drosophila reward system, NPF levels should be increased by rewarding experiences other than mating, such as exposure to intoxicating levels of ethanol. To test this hypothesis, we exposed virgin males to ethanol vapor using an exposure paradigm previously shown to be rewarding (three 10-min exposures spaced by 1 hour) (4).

      Throughout this paper, the researchers have been making the claim that activity of the NPF system signals the fly's "reward state." According to this theory, when the fly experiences something rewarding (such as mating), the amount of NPF in the brain and the activity of associated neurons increases, which in turn leads to a reduced urge to seek additional rewards (such as alcohol). To this end, they have shown that there is an increased amount of NPF in the flies' brains following mating. However, if their theory were true, then the opposite should also be observed. That is, the consumption of alcohol should also increase NPF levels in the brain, since alcohol is also a source of reward (just like mating).

      To test this hypothesis, the researchers decided to measure NPF levels after exposure to both air and an alcohol vapor (the former being neutral/not rewarding, and the latter being rewarding). If their theory about NPF generally signalling reward were true, one would expect to see increased levels of NPF in the brain following exposure to alcohol (just like was observed following mating in Figure 2A).

    2. development of a preference for the odor associated with these experiences would imply that flies found the events rewarding

      You might be wondering why this step is necessary, especially for alcohol, since the researchers have already shown that flies consume more alcohol-laden food. However, in the alcohol/food consumption paradigm, it is impossible to completely dissociate the contribution of the hunger and the caloric contribution of alcohol from the objective enjoyment of the experience. Here, what is being tested for is the preference for odor (which is otherwise neutral) that has been paired in memory with the experience of alcohol consumption, independent of any confounding factors. Further, the actual test phase occurs 24 hours after the alcohol exposure, when the flies are fully sober. For these reasons, this type of odor-paired conditioning assay is a much better indicator of whether an experience of substance is objectively rewarding for a fly.

    3. We propose that the activity of the NPF-NPFR system may be a neural representation of the state of the Drosophila reward system. If so, experiences that change NPF-NPFR activity should promote behaviors that restore the system to its normal state. In this model, sexual deprivation would create an NPF deficit that increases reward-seeking behavior such as ethanol consumption. Conversely, successful copulation would create a NPF surfeit that reduces reward seeking.

      Here, the researchers put forth their theory for the mechanism driving all of the effects they have observed so far. This mechanism is based on the concept of homeostasis, which basically states that there is an "ideal state" for one's internal physiological make-up. Any time the body deviates from the ideal state, it will attempt to correct itself and return to this state. The researchers thus theorize that the amount of NPF in the brain is a marker for the "reward state."

      If the fly mates repeatedly, it experiences something highly rewarding, leading to an increase in NPF beyond "normal" levels. The fly's body thus wants to return to a normal level of NPF. To do this, it must forgo alternate rewards such as alcohol. This would explain why mated flies do not have a preference for alcohol. Sexually deprived flies, on the other hand, experience a lack of reward, which leads to a decrease in NPF beyond normal levels. To compensate for this, when these flies are exposed to a second possible reward in the form of alcohol, they consume it excessively. This would explain why sexually deprived, virgin flies show an alcohol preference.

    4. heads of males subjected to different sexual experiences: rejected-isolated, virgin-grouped, and mated-grouped

      Since past work in Drosophila, mice, and C. elegans has shown that altering NPF/NPY can affect how organisms react to alcohol, the researchers in this study hypothesized that sexual deprivation might lead to changes in levels of NPF in the flies' brains, which in turn caused them to consume more alcohol. To test this, they extracted the brains from male flies with three distinct sexual histories (mated, virgin, and sexually rejected), and measured their NPF levels.

    5. Second, we tested the effect of artificial activation of NPF neurons by expressing the heat-activated cation channel dTRPA1 (21) under NPF-GAL4 control (22).

      In order to further confirm this causal relationship, the authors used the protein dTRPA1 (which activates specific neurons at a high temperature). Specifically, they inserted dTRPA1 into all of the same neurons that also contained NPF. Therefore, at a low temperature there would be no effect, but at a high temperature all of the neurons related to NPF would be activated. If the relationship between NPF and alcohol preference were indeed causal, then artificially increasing the activity of NPF-related neurons should reduce preference for alcohol.

    6. Finally, we sought to establish whether there was a role for the repellant chemosensory cue

      Since cis-vaccenyl acetate (cVA) is used by females to turn away unwanted mating attempts by males, it is only released by females who have already mated. Virgin females, who may still be looking to mate, do not release this chemical cue. This difference raises the possibility that the increased preference for alcohol amongst the rejected males could be because they smelled this chemical cue (which the mated male flies would not have smelled).

    7. males were exposed individually to decapitated virgin females on the same schedule as the rejected-isolated cohort, using a protocol that results in courtship suppression

      To test this possibility, they exposed the virgin male flies to dead female flies. These virgin males were still exposed to the visual cue of a female fly (especially the rear half of the body where mating occurs). However, they were neither able to mate, nor were they exposed to active rejection by a female.

    8. we compared males that differed in sexual experience but not in housing conditions—that is, mated and virgin males that were both group-housed.

      For the first follow-up experiment, the researchers ensured that both the mated male flies and the virgin male flies were housed in large groups (consisting exclusively of other male flies). This was done to see if social isolation (as the virgin male flies in the initial experiment might have experienced) might have been the cause for the alcohol preference.

    9. We compared males trained with either mated females (rejected-isolated) or decapitated virgin females (11). Both groups endured sexual deprivation (lack of copulation), but only the former was exposed to cVA.

      To test the possibility that cis-vaccenyl acetate (cVA) was the driving factor behind the alcohol preference amongst rejected males, the researchers conducted a follow up experiment in which one group of males was exposed to mated females, and the other was exposed to dead virgin females. Both of these groups thus experienced sexual rejection. However, the group exposed to the dead virgin females would not be exposed to the cVA cue, whereas the group exposed to mated females would. If there were a difference in alcohol preference between these two cohorts of male flies, then one could conclude that the preference for alcohol was not caused by sexual deprivation specifically, but instead due to exposure to cVA.

    10. We used two distinct sexual experiences to generate two cohorts of male flies.

      To test the effect of sexual experience on alcohol consumption, the researchers first had to create two groups of male flies, each with a different sexual history. They did this by allowing one group to mate freely with multiple different females for four days. This became the "mated-grouped cohort." The second group was only exposed to female flies who had already mated. Female flies who have already mated once will not mate a second time until they have laid their eggs. For this reason, the second group of males experienced repeated sexual rejection by the mated females for four days. This became the "rejected-isolated cohort." These two cohorts, (one mated and the other sexually rejected) could then be tested for the differences between them.

    11. ethanol preference index

      A calculated score, from –1 to 1, that indicates how much the flies preferred the alcohol-spiked food relative to the regular food. A number above zero means the flies ate more food with alcohol in it, and a number below zero means they ate more regular, nonalcoholic food.

    12. food with or without 15% ethanol supplementation

      Drosophila are typically fed a jellylike substance in the lab consisting largely of sugar. In this experiment, the flies were given a choice between just a regular tube of food or a tube that contained the food mixed with alcohol.

    13. two-choice preference assay

      A behavioral model in which an organism is offered a choice between two alternatives. Typically, the organism is allowed to freely choose amongst these alternatives, and its choices are used to define whether or not the organism has a preference for one alternative over another.

    1. Furthermore, we speculated that different transcriptome states could also potentially alter the number of off-targeting events.

      Different cell types specialized to performing particular functions require different proteins for their work. Therefore, they have distinct transcriptomes.

      Moreover, a cell's transcriptome changes depending on where it is in the cell cycle and the conditions and needs of the surrounding environment.

      As a result, off-targets of the REPAIR system may vary from one cell type to another, reflecting changes in the presence and abundance of individual transcripts.

    2. REPAIRv1 off-target edits were predicted to result in numerous variants, including 1000 missense base changes (fig. S13C), with 93 events in genes related to cancer processes

      Earlier the authors only counted off-targets and did not look at the effect of adenosine modification on the transcript function. Here, they determined the position of the modification and the possible impact on the amino acid choice if the edit was in the protein coding region.

    3. We selected a subset of these mutants (Fig. 6B) for transcriptome-wide specificity profiling by next-generation sequencing.

      The recovery of the Cluc signal is an easy way to get the first look at the activity of the mutants. However, a single transcript cannot reflect changes in the whole transcriptome.

    4. we tested 17 single mutants with both targeting and nontargeting guides, under the assumption that background luciferase restoration in the nontargeting condition would be indicative of broader off-target activity.

      It would be too expensive to test all the mutants by RNA sequencing to find whole-transcriptome off-targets. Instead, the authors looked at a single transcript for Cluc luciferase.

      The authors assumed that if luciferase activity was restored even non-targeting guide RNAs, it would mean that ADAR2 increased off-target activity.

    5. To reduce the size, we tested a variety of N-terminal and C-terminal truncations of dCas13

      AAVs can accommodate up to 4.7kb, meaning dCas13b and the extra regulatory sequences are too big to fit in one virus. To solve this problem, the authors truncated (shortened) dCas13b by removing sections of the protein with unnecessary functions.

      The dCas13b nuclease is composed of different domains (parts), some of which are used for RNA binding and some which are used for cleavage. The RNA cleavage is mediated by two well-defined HEPN domains which are located close to the N- and C-terminus of the protein. We are still unsure which domains mediate binding.

      However, the REPAIRv1 system needs only the RNA binding ability of dCas13b. Therefore, the researchers were able to remove sections of dCas13b containing HEPN while retaining its binding function.

    6. AAV vectors have a packaging limit of 4.7 kb

      Almost the entire AAV genome can be replaced with a desired construct of max length of 4.7kb. This limits how much genetic material the virus can carry, so some essential viral genes are carried in an additional construct or constructs (the "helper plasmid" in the picture below).

      Learn more about AAV at Addgene.

    7. We then tested the ability of REPAIRv1 to correct 34 different disease-relevant G→A mutations

      The researchers chose 34 disease causing mutations to test. Each mutation was a G to A substitution that changed the amino acid sequence of the protein and disrupted normal function.

    8. Using guide RNAs containing 50-nt spacers

      The authors chose three 50-nt spacers to target two genes carrying disease-relevant mutations. As was determined at the previous step, the spacers of 50-nt length showed higher rates of editing but more off-target effects than 30-nt spacers.

    9. To demonstrate the broad applicability of the REPAIRv1 system for RNA editing in mammalian cells, we designed REPAIRv1 guides against two disease-relevant mutations

      After the authors had generated successful REPAIRv1-mediated editing of mRNA for an exogenous gene (i.e., a gene introduced from outside the organism), they chose two endogenous genes (i.e., native to the organism) to further explore the power of REPAIRv1.

      They tested Cas13b nuclease activity in the same way as they did with the exogenous gene.

    10. we modified the linker between dCas13b and ADAR2DD(E488Q)

      The dCas13b and ADAR2 protein parts are joined together via a stretch of amino acids called a linker. There are more than a thousand linker variants in different multi-domain proteins. The sequence of a linker can influence protein folding and stability, as well as functional properties of individual domains. Therefore, the choice of linker is an important step in protein design.

      The authors tested linkers of different length and flexibility and found that shorter and more flexible variants produced the best results.

    11. To validate that restoration of luciferase activity was due to bona fide editing events, we directly measured REPAIRv1-mediated editing of Cluc transcripts via reverse transcription and targeted next-generation sequencing.

      The ADAR deaminase can introduce changes not only into the target adenosine but also in the surrounding adenosine bases. To check how specific the dCas13-ADAR2 protein was in targeting the correct adenosine base, the researchers sequenced edited Cluc transcripts and determined all positions with A to I substitutions.

      Further, they used tiling gRNA molecules in order to determine the influence of the spacer (PFS) length and the mismatch distance on the off-target editing.

    12. position-matched guides

      The authors directly compared the RNA knockdown efficiency of two technologies, Cas13 cleavage and RNA interference (RNAi). Both technologies require guide RNA (gRNA) molecules for targeted recognition. Cas13 is directed by a gRNA, while RNAi complex uses a molecule termed shRNA.

      Different parts of an RNA molecule can be more or less accessible to gRNAs. Therefore, gRNA and shRNA target sequences have to be selected such that they are close to each other, i.e. position-matched, so that a more fair comparison between Cas13 and RNAi can be made.

    13. Cas13b from Prevotella sp. P5-125 (PspCas13b) and Cas13b from Porphyromonas gulae (PguCas13b) C-terminally fused to the HIV Rev nuclear export sequence (NES), and Cas13b from Riemerella anatipestifer (RanCas13b) C-terminally fused to the mitogen-activated protein kinase NES

      Why did the authors test several NESs from different proteins?

      Over 200 NESs from different proteins have been described. Each NES is around 10 amino acids long and has a unique structure. The variation between NESs means that they have different effects on export efficiency and protein stability in different environments.

    14. To engineer a PspCas13b lacking nuclease activity (dPspCas13b, referred to as dCas13b hereafter), we mutated conserved catalytic residues in the HEPN domains and observed loss of luciferase RNA knockdown

      The authors hypothesized that even without nuclease activity, Cas13b would still be able to recognize target molecules directed by a gRNA.

      Mutations of the key part of the protein responsible for RNA cleavage eliminated Cas13b's catalytic ability. The next step was to test whether the mutated Cas13b was still able to find the target sequences, even if it couldn't cleave them.

    15. We found that LwaCas13a and PspCas13b had a central region that was relatively intolerant to single mismatches

      The sequences with substitutions in the middle part (between 12 and 26 nucleotides) had the lowest depletion scores. A lower depletion score means that the nuclease was not as successful at cleaving the RNA sequence (i.e. depleting expression).

    16. To characterize the interference specificities of PspCas13b and LwaCas13a, we designed a plasmid library of luciferase targets containing single mismatches and double mismatches throughout the target sequence and the three flanking 5′ and 3′ base pairs

      To figure out how specifically the Cas13 orthologs would target RNA, they created a "library" (collection) of sequences with one or two mutations in the gRNA target site for the Gluc gene. The idea was to see how different a sequence could be and still be recognized by the nuclease.

      Remember that the goal is to find a highly specific nuclease. This means that ideally the nuclease would not recognize sequences with mutations.

    17. without msfGFP

      The authors ran the assay without msfGFP to determine if any of the orthologs do not require stabilization domains. This is important because orthologs that do not require these domains could be used when an experimental construct needs to be small.

    18. For each Cas13 ortholog, we designed PFS-compatible guide RNAs, using the Cas13b PFS motifs derived from an ampicillin interference assay

      Cas13a prefers to recognize target sequences when a spacer (target sequence) is surrounded by specific PFS motifs.

      To determine which PFS sequences Cas13b orthologs prefer, the researchers used an ampicillin interference assay. They transformed bacterial cells with two plasmids: One contained a Cas13b ortholog while the second plasmid included an ampicillin resistance gene and a gRNA against this gene with randomly generated 5' and 3' PFS around the target sequence. If the PFS led to the Cas13b ortholog targeting the correct gene, bacterial cells would die because they would lose ampicillin resistance when the gene was cleaved.

      The authors collected and analyzed cells that survived to determine which PFS sequences were irrelevant for targeting. They then subtracted these PFSs from the starting pool to determine which PFSs are preferred by Cas13b orthologs.

    19. To assay interference in mammalian cells, we designed a dual-reporter construct expressing the independent Gaussia (Gluc) and Cypridina (Cluc) luciferases under separate promoters, allowing one luciferase to function as a measure of Cas13 interference activity and the other to serve as an internal control.

      To monitor the effect of Cas13 nuclease activity, the researchers constructed a vector that contained genes for two different luciferases. These luciferases use different substrates (source materials) to generate light.

      One luciferase was used to measure Cas13 interference, and the other was used as a control. In cells where Cas13 did not interfere, both luciferases would emit light. In cells with interference, however, activity from one of the luciferases would decrease.

    1. A genome-wide PCA analysis

      Analyzing multiple whole genomes at the same time is so complex that scientists needed to simplify the data to make it easier to see patterns and differences between the genomes. The mathematical tool that they used was PCA analysis, which reduces the complexity of the data and retains its variance.

      PCA analysis works by setting principal components (e.g. PC1, PC2, PC3), which are essentially directions in which the data has the largest spread.

      In this case, PC1 and PC2 are studied.

    2. sequenced and analyzed 59 hypervariable mtDNA fragments from ancient dogs spread across Europe, and we combined those with 167 modern sequences

      The d-loop sequences of mitochondrial DNA are considered to be mutational hotspots (places where mutations appear to happen more frequently than others), and therefore looking at this region can provide important information about how evolution occurred.

      Modern dog sequences and seven of the 59 ancient d-loop sequences were already available on a public database. The rest of the sequences were generated from ancient DNA samples by polymerase chain reaction (PCR). The sequences were then compared to each other using DomeTree, a program that creates haplogroup phylogenetic trees based on mitochondrial DNA.

    3. we used the radiocarbon age of the Newgrange dog to calibrate the mutation rate for dogs

      The team of scientists used radiocarbon dating techniques to calculate the dog as 4700-4900 years old.

      Since they knew how old the Newgrange dog was, they were able to estimate the time at which the Newgrange dog and the Portuguese village dogs last had a common ancestor, and figure out when they diverged from each other.

      Based on the assumption that a new generation of dogs were born every 3 years, the scientists were able to calculate the mutation rate.

    4. we defined Western Eurasian and East Asian “core” groups (Fig. 1A), supported by the strength of the node leading to each cluster (12).

      The information represented in Figure 1A was used to define the two core groups. The dogs needed to have very high bootstrap values (>90)—high-quality genetic data—to support their placement in the groups.

      The Western Eurasian core group consisted of all modern breeds and Portugal village dogs. The East Asian core group consisted of Sharpei, Village dogs from China, Tibet, and Vietnam, and Tibetan Mastiffs.

    5. We used principal components analysis (PCA), D statistics, and the program TreeMix (12) to further test this pattern.

      Three tools for mining the data for ancestry information.

      Principal components analysis (PCA) simplifies the data. The number of variables is reduced but the trends and patterns are retained.

      D-statistics detects admixture events; it is used to detect gene flow between closely-related species.

      TreeMix is a genetics computer program used to estimate ancestral relationships. It can detect population splits and migration events.

    6. radiocarbon dated

      This technique allows scientists to estimate the age of a plant or animal based on the amount of carbon-14 that is present at the time of measurement. Carbon-14, also known as radiocarbon, is a weakly radioactive type of carbon molecule that decays over time. The age of samples up to 60,000 years old can be estimated.

      To learn more about radiocarbon dating, check out this video from Scientific American.

    7. CanineHD 170,000 (170 K)

      A type of genetic test that covers 170,000 single-position variations in the genome of a dog. It is essentially a chip, upon which the genetic material of the dog of interest is placed. It contains thousands (170,000 in this case) of probes—short DNA sequences that can stick to the complementary sequence in the sample, if that matching DNA variant is present. Each interaction can be recorded to easily measure the presence of a large number of genes at the same time.

    8. (28x) of an ancient dog dated to ~4800 calendar years before the present (12) from the Neolithic passage grave complex of Newgrange (Sí an Bhrú) in Ireland.

      The scientists isolated DNA from a portion of the temporal bone in the dog's skull.

      They made a library of single-stranded DNA sequences; smaller pieces of DNA that together represent the entire genome of the dog. The DNA library is sequenced on a machine that can read the order of the bases (As, Ts, Gs, and Cs) that make up the genome of the particular dog being studied.

      Check out this video from TED-Ed on how to sequence the human genome (it also applies to the dog genome).

    9. sequences from European dogs (from 14,000 to 3000 years ago)

      They sequenced the d-loop of mitochondrial DNA, an area where mutations happen more often than other parts of mitochondrial DNA.

      Seven of the d-loop sequences were already available on a public database, and the others were generated from DNA in bone samples. A very small amount of bone was ground to a fine powder. The scientists were very careful to make sure contamination of the samples did not occur. Once the cells in the bone sample were broken open, and the DNA was isolated from other parts of the cell, the DNA could be sequenced by polymerase chain reaction (PCR).

      Check out this video from Khan Academy to learn how DNA is sequenced by PCR.

    10. ancient

      In this case, the DNA specimens are ~14,000 to 3000 years old.

  6. Dec 2018
    1. Ecdysozoa (molting animals) is a major protostome clade (Figure 1) proposed by Aguinaldo et al. (1997) that includes the large phyla Arthropoda (Figure 3) and Nematoda (both of tremendous ecological, economic, and biomedical importance) and their close relatives (Tardigrada [water bears, 1150 species], Nematomorpha [351 species], Onychophora [velvet worms; 182 species], Kinorhyncha [179 species], Loricifera [30 species], and Priapulida [19 species]). Ecdysozoans are characterized by their ability to molt the cuticle during their life cycle, and for having reduced epithelial ciliation, which requires locomotion via muscular action. They include segmented or unsegmented, acoelomate, pseudocoelomate, or coelomate animals; many have annulated cuticles and a mouth located at the end of a protrusible or telescopic proboscis, and some lack circular musculature (i.e., Nematoda, Nematomorpha, Tardigrada). Here we restrict the proposed sampling to the noninsect and nonnematode ecdysozoans. The clade includes the only animals (loriciferans) thought to complete their life cycles in anoxic environments (Danovaro et al. 2010). This group is also relevant for studies of extreme cell size reduction. Other than the mentioned arthropod and nematode genomes, no genome is available for any member of the Ecdysozoa.

      This is one of the limitations that will be placed on researchers that plan on conducting research to contribute to this database. They restrict a certain proposed sampling to the non-insect and non-nematode ecdysozoans.

    2. Many of the roughly 70 invertebrate species whose genomes have been sequenced belong to the Arthropoda or Nematoda, although the number of other invertebrate genomes continues to grow (e.g., Olson et al. 2012; Takeuchi et al. 2012; Zhang et al. 2012; Simakov et al. 2013; Tsai et al. 2013; Flot et al. 2013). We propose to focus on noninsect/nonnematode phyla, and specifically on an important group of currently neglected arthropods, the crustaceans.

      They propose a certain focus for researchers that wish to dedicate time to contributing to the database by stating that they should focus more on neglected groups of arthropods, specifically crustaceans.

    3. GIGA has adopted a set of standards and best practices to help ensure that genomic resources, data, and associated metadata are acquired, documented, disseminated, and stored in ways that are directly comparable among projects and laboratories. These data should be easily and equitably shared among GIGA members and the broader scientific community, and GIGA will obey appropriate laws and regulations governing the protection of natural biodiversity. Briefly, all genome projects will report on a set of parameters that will allow assessment of genome assembly, annotation, and completeness (e.g., NG50, N50 of contigs and scaffolds, number of genes, assembled vs. estimated genome size) (Jeffery et al. 2013). Detailed descriptions of these standards and compliant protocols will be posted on the GIGA Web site. These will be revised periodically to facilitate the establishment and maintenance of current best practices common to many invertebrate genome and transcriptome sequencing projects and to help guide the researcher in selecting and assessing genomes for further analyses. The following recommendations summarize minimal project-wide standards designed to accommodate the large diversity of invertebrates, including extremely small and rare organisms, as well as those that live in close association with other organisms. Permissions: GIGA participants must comply with treaties, laws, and regulations regarding acquisition of specimens or samples, publication of sequence data, and distribution or commercialization of data or materials derived from biological resources. Participants must acquire all necessary permits required for collection and transport of biological materials prior to the onset of the work. The CBD recognizes the sovereignty of each nation over its biological resources, and under the auspices of the CBD, many nations and jurisdictions rigorously regulate the use and distribution of bioIogical materials and data. GIGA participants must be aware of these regulations and respect the established rights of potential stakeholders, including nations, states, municipalities, commercial concerns, indigenous populations, and individual citizens, with respect to any materials being collected, to all derivatives and progeny of those materials, and to all intellectual property derived from them. GIGA participants must also familiarize themselves with the conservation status of organisms to be sampled and any special permits that may be required (e.g., CITES). Moreover, GIGA participants should collect in ways that minimize impacts to the sampled species and their associated environments. Field collection and shipping: Methods for field collection and preservation of specimens and tissues should be compatible with recovery of high-quality (e.g., high molecular weight, minimally degraded) genomic DNA and RNA (Dawson et al. 1998; Riesgo et al. 2012; Wong et al. 2012). Many reagents commonly used for tissue and nucleic acid preservation (e.g., ethanol, dry ice) are regulated as hazardous and/or flammable materials. These reagents may be restricted from checked and carry-on luggage and may require special precautions for shipping or transport. GIGA participants should contact the appropriate airline carriers or shippers for information regarding safe and legal shipment of preserved biological materials. When possible, multiple samples will be collected so that extractions can be optimized and samples resequenced as technologies improve. Specimens of known origin (i.e., field-collected material) will be favored over specimens of unknown origin (e.g., material purchased from the aquarium trade). Collection data will include location (ideally, with GPS coordinates) and date, and also other data such as site photographs and environmental measurements (e.g., salinity) when relevant. Selection and preparation of tissues: It is often advisable to avoid tissues that may contain high concentration of nucleases, foreign nucleic acids, large amounts of mucus, lipid, fat, wax, or glycogen or that are insoluble, chitinous, or mineralized. To obtain the highest quality material for sequencing or library construction, it may be preferable to extract nucleic acids from living or rapidly preserved tissue from freshly sacrificed animals, from gametes or embryos, or from cell lines cultivated from the target organism (Ryder 2005; Rinkevich 2011; Pomponi et al. 2013). When appropriate, select tissues or life history stages that will avoid contamination by symbionts, parasites, commensal organisms, gut contents, and incidentally associated biological and nonbiological material. Whenever possible, DNA or RNA will be sequenced from a single individual because many taxa display sufficient polymorphism among individuals to complicate assembly. Similarly, heterozygosity can also hinder assembly: inbreeding may be used to reduced heterozygosity (Zhang et al. 2012) or, when crossings are impossible (for instance in asexual species), haplotypes may have to be assembled separately (Flot et al. 2013). Quantity and Quality: The quantity of DNA or RNA required for sequencing varies widely depending on the sequencing platform and library construction methods to be used and should be carefully considered. Recent consensus from the G10KCOS group of scientists suggests that at least 200 – 800 µg of high-quality genomic DNA is required to begin any project because of the requirement for large insert mate-pair libraries (Wong et al. 2012). However, these minimum quantities are expected to decline with improving technology. DNA quality can be assessed by size visualizatons and 260/280nm ratios. Quality of RNA will be checked using RNA integrity number (RIN > 7 is preferred); however, these values have been shown to appear degraded in arthropods due to artifacts during quantification (Schroeder et al. 2006; Winnebeck et al. 2010). Taxonomic identity: The taxonomic identity of source organisms must be verified. Whenever possible, consensus should be sought from expert systematists, supportive literature, and sequence analysis of diagnostic genes (see next section). Voucher specimens: As a prerequisite for inclusion as a GIGA sample, both morphological and nucleic acid voucher specimens must be preserved and deposited in public collections, and the associated accession numbers must be supplied to the GIGA database. Photographs should be taken of each specimen and cataloged along with other metadata. The GIGA Web site lists cooperating institutions willing to house voucher specimens for GIGA projects, such as the Smithsonian Institution or the Ocean Genome Legacy (http://www.oglf.org). Documentation of projects, specimens, and samples: Unique alphanumeric identification numbers (GIGA accession numbers) will be assigned to each GIGA project and to each associated specimen or sample used as a source of genome or transcriptome material for analysis. A single database with a web interface will be established to accommodate metadata for all specimens and samples. Metadata recording will also aim to coordinate and comply with previously established standards in the community, such as those recommended by Genomics Standards Consortium (http://gensc.org/; Field et al. 2011). Sequencing Standards: Standards for sequencing are platform and taxon specific, and sensitive to the requirements of individual sequencing facilities. For these reasons, best practices and standards will be established for individual applications. Coverage with high-quality raw sequence data is a minimal requirement to obtain reliable assemblies. An initial sequencing run and assembly will be used to estimate repeat structure and heterozygosity. These preliminary analyses will make it possible to evaluate the need for supplemental sequencing, with alternative technologies aimed at addressing specific challenges (e.g., mate-pair sequencing to resolve contig linkage). Moreover, all raw sequence reads generated as part of a GIGA project will be submitted to the NCBI Sequence Read Archive. Sequence Assembly, Annotation, and Analyses: Because assemblies vary widely in quality and completeness, each assembly should be described using a minimum set of common metrics that may include: (1) N50 (or NG50) length of scaffolds and contigs (see explanation of N50 in Bradnam et al. 2013), (2) percent gaps, (3) percent detection of conserved eukaryotic genes (e.g., Core Eukaryotic Genes Mapping Approach (Parra et al. 2007), (4) statistical assessment of assembly (Howison et al, 2013), (5) alignment to any available syntenic or physical maps (Lewin et al. 2009), and (6) mapping statistics of any available transcript data (Ryan 2013). The current paucity of whole invertebrate genome sequence projects can pose problems for gene calling, gene annotation, and identification of orthologous genes. In cases where the genome is difficult to assemble, we recommend that genome maps be developed for selected taxa via traditional methods or new methods (e.g., optical mapping of restriction sites) to aid and improve the quality of genome assembly (Lewin et al. 2009) and that GIGA genome projects be accompanied by transcriptome sequencing and analysis when possible. Such transcriptome data will assist open reading frame and gene annotation and are valuable in their own right.

      GIGA aims to set standards for data acquisition and the processing of that data as well as the input of that data into their system. These standards will be progressively revised as better methods are discovered. These standards are to be used for a large variety of invertebrates. This standardization will allow for a more easily accessible and usable bank of information.

    4. We also recognize the existence and formation of other recent genome science initiatives and coordination networks and will synchronize efforts with such groups through future projects. Because GIGA is an international consortium of scientists, agencies, and institutions, we will also abide by the rules of global funding agencies for data release (e.g., those proposed by the Global Research Council; http://www.globalresearchcouncil.org). We are aware that different nations have different constraints and regulations on the use of biological samples. Given the international nature of GIGA, we will work to ensure that national genomic legacies are protected and will consult with the pertinent governmental agencies in the countries from which samples originate. We will deposit sequence data in public databases (e.g., GenBank), as well as deposit DNA vouchers in publically accessible repositories (e.g. Global Genome Biodiversity Network, Smithsonian). GIGA is an inclusive enterprise that invites all interested parties to join the effort of invertebrate genomics. We will attempt to capture the impact of the effort in the wider scientific and public arenas by following relevant publications and other products that result from GIGA initiatives.

      The project coordinators will also join with other networks to work together on future projects of common interest. They also understand that different countries have limits on the use of biological samples and thus their governments will be consulted with so that the international program is protected from any government agencies in the countries where the samples come from.

    5. GIGA embraces a transparent process of project coordination, collaboration, and data sharing that is designed to be fair to all involved parties. The ENCODE project may be emulated in this regard (Birney 2012). We are committed to the rapid release of genomic data, minimizing the period of knowledge latency prior to public release while protecting the rights of data product developers (Contreras 2010). The data accepted as part of GIGA resources will undergo quality control steps that will follow preestablished and evolving standards (see Standards section) prior to data release. Efforts such as those of Albertin et al. (2012) have addressed data sharing issues relevant to GIGA and other large-scale genomics consortia.

      Once the data has been submitted by researchers, it will go through a quality control process to make sure that it reaches the quality and accuracy which the project requires. As well as to avoid duplicate data being published.

    6. but there are currently no published genomes for the other 21 invertebrate phyla. We examined current phylogenetic hypotheses and selected key invertebrate species that span the phylogenetic diversity and morphological disparity on the animal tree of life (see Supplementary Material). New invertebrate genome data can reveal novel sequences with sufficient phylogenetic signal to resolve longstanding questions.

      The currently available genome sequences at the time were reviewed and the missing phyla were taken note of. These missing areas in the so called "tree of life" were added to the list of species to be researched so that the data could be used to further other research.

    7. Therefore, the geographic scope of the project in terms of participation, taxa collected, stored, and sequenced, data analysis and sharing, and derived benefits, requires global partnerships beyond the individuals and institutions represented at the inaugural workshop. Because international and interinstitutional cooperation is essential for long-term success, the new GIGA Web site will be used to foster cooperative research projects. For now, the GIGA Web site can serve as a community nexus to link projects and collaborators, but it could also eventually expand to host multiple shared data sets or interactive genome browsers. The broad scope of GIGA also necessitates growth in the genomics-enabled community overall. Sequencing and analyzing the large amount of resulting data pose significant bioinformatic and computational challenges and will require the identification and creation of shared bioinformatics infrastructure resources.

      The information gathered from experimentation will be unified by being submitted to the GIGA website, thus allowing researchers from all over the world to have access to the information at a moments notice. The website will also be used to host cooperative research projects that scientists from around the world could participate in and contribute data towards.

    8. Selection and prioritization of taxa to be sequenced will occur through future discussion and coordination within GIGA. Thus, the target number is a somewhat arbitrary compromise between the desire to encompass as much phylogenetic, morphological, and ecological diversity as possible and the practical limitations of the initiative. Given the large population sizes of many invertebrate species, collection of a sufficient number of individuals may be relatively easy for the first set of targets. Collection of invertebrates usually involves fewer difficulties with regard to permits than collection of vertebrate tissues. However, some invertebrate taxa pose various logistic and technological challenges for whole-genome sequencing: many species live in relatively inaccessible habitats (e.g., as parasites, in the deep sea, or geographically remote) or are too small to yield sufficient amounts of DNA from single individuals. These challenges will be considered with other criteria as sequencing projects are developed and prioritized.

      Selecting which organisms genetic information is to be gathered and recorded first will be determined at a meeting among researchers in the field. The priority of these organisms will also be determined by their accessibility to researchers as well as their ease of retrieving genetic information.

    9. We propose to sequence, assemble, and annotate whole genomes and/or transcriptomes of 7000 invertebrate species, complementing ongoing efforts to sequence vertebrates, insects, and nematodes (Genome 10K Community of Scientists [G10KCOS], 2009; Robinson et al. 2011; Kumar et al. 2012) (Table 1).

      The purpose of the experiment is to create a genetic database of 7000 invertebrate species.

    10. A main goal of GIGA is to build an international multidisciplinary community to pursue comparative invertebrate genomic studies. We seek to develop tools to enable and facilitate genomic research and encourage collaboration. We will develop standards that ensure data quality, comparability, and integration. By coordinating sample collecting and sequencing efforts among invertebrate biologists, we aim to avoid duplication of effort and leverage resources more efficiently. We envision a scientific commons where shared resources, data, data standards, and innovations move the generation and analysis of invertebrate genomic data to a level that likely could not be achieved with the traditional piecemeal single-investigator–driven approach.

      The main goal of the project is to build an international community whose goal is to perform invertebrate research. This community will be used to avoid duplicate research and wasting time on studies that have already been conducted. They will also set in place standards by which the data must be gathered and presented so that is can be universally understood by everyone around the world and so that the data is accurate enough.

    1. Datta, A., Rane, A., 2013. Trop. Conserv. Sci. 6, 674–689.

      Referencing Box 1, this study was reviewed by the author classified this study as looking at population/species and as qualitative or quantitative estimate of flower or fruit production. The big conclusion of this study is that a rare species is seed-limited while dispersal limitation may play a secondary role in determining its abundance.

    2. Peres, C.A., 1994a. Biotropica 285-294.

      Referencing Box 1; The author of this paper looks at how plant phenology changes across succession in a community. Peres is studying keystone resources over many different seasons and how phenology changes over time. This aids in answering this papers research question of how phenology can be used in conservation to help keystone species.

    3. Schmidt, I.B., Figueiredo, I.B., Scariot, A., 2007. Econ. Bot. 61, 73–85.

      Referencing Box 1; Schmidt and his colleagues focused on sustainability in harvesting non-timber forest products. They did this by analyzing flowering and fruiting time, as well as, the abundance and size of the fruits produced. This conservation effort was done using a large scale population control effort.

    4. Rossi, S., Morin, H., Deslauriers, A., 2012. J. Exp. Bot. 63, 2117–2126.

      Referencing Box 1; Rossi and his colleagues focused their studies and conservations efforts on estimating carbon stocks and developing growth models in order to track and plan for future phenological changes and their effects on different tree species. Their models were developed by looking at tree growth rings within the trunks of various trees in order to look at the relative amounts of carbon dioxide intake and atmospheric carbon stocks at the time of the ring growth.

    5. Ali, N.S., Trivedi, C., 2011. Biodivers. Conserv. 20, 295–307.

      Referencing Box 1; Ali and his colleagues established a calendar for the collection of seeds and other plant resources in order to properly manage the conservation of genetic resources in natural plant populations. This was done throughout population and species scale conservation. They made direct ground observations of plant phenophases (leafing, flowering, fruiting) and the environmental factors that effected these actions. Advancements in this conservation can be seen in efforts such as seed banks.

    6. We focus on shifts in plant phenology induced by global change, their impacts on species diversity and plant–animal interactions in the tropics, and how conservation efforts could be enhanced in relation to plant resource organization

      Research question:

      How can phenology be used to further our knowledge and success in conservation biology? What are the influences of climate change on phenology and what are the implications of those influences within a tropical environment?

    1. Treatments applied to caterpillars were: (1) no barriers (no tanglefoot/no cage), (2) tanglefoot present/no cage, (3) no tanglefoot/cage with holes present, (4) tanglefoot present/cage with holes present, (5) no tanglefoot/cage present, and (6) tanglefoot present/cage present.

      These are the parameters made to make sure that the experiment itself is not biased and there are different variables being tested.

    1. The role of histone variants was further investigated by studying H2A.X, H2A.Z and macroH2A protein expression levels (Fig. 3)

      The scientists further studied the relationship between histone proteins and stress levels after acknowledging that a possible cause and effect exists.

      By discovering that antibodies connected to the histones were valid, it also proved the oyster to be the best model to test on.

    2. Genomic DNA was purified from gill tissue as described elsewhere (Fernandez-Tajes et al., 2007)

      The authors recorded and purified DNA from the gill tissue of the oysters in order to measure DNA methylation.

      Later, the DNA sequences were amplified.

      By using PCR methods, the samples were digested in order to asses the patterns of methylation and used to identify loci using Gowers Coefficient of Similarity.

    3. Histone protein isolation was performed as described elsewhere (Ausio and Moore, 1998), adapting the protocol to oyster gill tissues in the present work

      The purpose in the experiment was conducted in the extraction of histone proteins. By using classic centrifuging and electrophoresis techniques, the histone proteins were separated in order to retrieve the different types of anti-proteins. The antibodies were then analyzed with the Western Blot using the antibodies.

    4. Dosage was adjusted to maintain homogeneous microalgae concentrations across replicates (Fig. 1B). Specimens (n = 2 oysters per biological replicate) were collected at 4 different time points: T0, before exposure begins; T1, after 3 h exposure; T2, after 5 h exposure; T3, after 24 h exposure.

      The collection of the the oysters were at different time intervals in order to monitor and view different relationships between the algae concentrations and oyster infection number.The gills were the main focus of the time intervals to indicate how much of the algae was found in the oysters system.

    5. Experimental HAB simulation

      A 24h simulation using a culture of K. brevis and the eastern oyster specimens.

      They were fed less prior so that during the simulation they would actively feed.

      There were 4 time points where data was collected: 0hr, 3hr, 5hr, and 24hr.

      The oysters were opened and the gills were flash frozen for later examination. This is because the brevetoxins contact the gills first and thus would experience DNA damage first.

    6. Specimen collection and laboratory acclimatization

      Explains how oysters were collected and kept.

      Collected: Rookery Bay National Estuarine Research Reserve, Naples FL

      Kept: In lab tanks with controlled conditions. Fed twice a day.

    7. The study of the epigenetic mechanisms mediating exposure-response relationships constitutes the basis for environmental epigenetic analyses (Baccarelli and Bollati, 2009; Bollati and Baccarelli, 2010), providing information about how different environmental factors influence phenotypic variation (Cortessis et al., 2012; Suarez-Ulloa et al., 2015; Etchegaray and Mostoslavsky, 2016)

      In one experiment, one of the authors (Suarez-Ulloa) had previously studied the cause-effect relationship between environmental factors and subsequent epigenetic modifications triggering adaptive responses in marine invertebrates.

    8. Consequently, bivalve molluscs are generally used as sentinel organisms to study HAB pollution

      In previous experiments conducted on Eastern Oysters, the author has successfully used bivalve mollusks as sentinel organisms.

    1. We compared absolute and qualitative differences in leaf defense. First, we compared the dry mass of leaf defense chemicals in a linear model with soil type and study region as independent variables. Second, we tested whether habitat type, sampling site, or the interaction of the two, was a significant determinant of the relative allocation among flavan, flavone, quinic acid derivatives, and oxidized terpenes in each plant using a factorial analysis of variance.

      When doing comparison, it helps to create a table to have a better understanding on the differences in leaf defense.

    2. Second, we used a factorial analysis of variance (McArdle and Anderson 2001) to assess whether habitat type, sampling site, or the interaction of the two was a significant determinant of herbivore species composition.

      This was done to determine the different variables that affect insect populations and which ones were more important than others. With this information they set the parameters to create an observable experiment with a limited amount of discrepancies.

    3. But little is known about the mechanisms underlying the evolution of habitat specialization and the extent to which herbivores contribute to phenotypic divergence during the speciation process,

      The authors have a clear goal in their experiment. Through this observation that is lacking a response they build an experiment to identify natures processes.

    1. We therefore developed protocols for fluorescent in situ hybridization (FISH) targeting specific ascomycete and cystobasidiomycete rRNA sequences.

      A molecular probe is created against a specific DNA sequence, in this case rRNA from either ascomycetes or basidiomycetes. The probe is designed with a recognizable tag on the end. Then a second probe is used to match the first probe, and finally a third probe to match the second one with a fluorescent tag on it. By using multiple probes we can amplify even the smallest signals to our first probe. These probes are then mixed with a biological sample that is fixed in place. If fluorescence is observed the probe has found a target.

      In some experiments, as in this example, researchers use multiple probes in a single experiment. This provides information about how close two organisms of interest are in a given sample.

    2. incorporated into a broader sample of published cystobasidiomycete rDNA sequence data

      Often researchers only publish a single gene for a newly described taxon, as it is sometimes too expensive to generate sequence information for the entire genome. When research first began working with DNA sequence data to determine evolutionary relationships it was decided that the ribosomal DNA (rDNA), shared by every living thing, was the best single gene to determine evolutionary relationships between taxa. Currently this is hotly debated, however, the use of rDNA is still very common in eukaryotic taxonomy.

    3. using gene sequences inferred from our transcriptome data set and other available genomes (table S1).

      Phylogenies are often used to determine the taxonomy of a lineage, that is the evolutionary context of an organism within the greater tree of life. The researchers could recognize that the new symbiont was a basidiomycete from the sequence information, but only by comparing the sequence information of the new organism to the previously known organisms can we determine when and from which ancestor the new species evolved. To account for the millions of years that have passed after all the basidiomycetes diverged from one another, the researchers incorporate as much sequence data as possible. Here, they use 349 loci to determine the placement of the new lineage.

    4. amplicon sequencing

      Refers to sequencing of target genes obtained by a procedure called polymerase chain reaction (PCR) using gene-specific primers. Amplicon sequencing provides a snapshot of the microbial populations in an environment.

    5. attempts to culture the basidiomycete from fresh thalli were unsuccessful

      Researchers attempted to grow and isolate basidiomycete cells independent from their lichen partners, the algae and the ascomycete fungus. Often times it is very difficult to culture new organisms because we do not know enough about the growth requirements. This is frequently the case with organisms that form symbiotic relationships, as they often lose the ability to grow independent of their symbiotic partners.

    6. we designed specific primers for ribosomal DNA [rDNA; 18S, internal transcribed spacer (ITS), and D1D2 domains of 28S) to screen lichens growing physically adjacent to Bryoria in Montana forests.

      Primers are small oligonucleotide sequences that are used as probes to determine if something is present in an unknown mixed sample. In this case, the primer is designed to match a piece of ribosomal DNA specifically in basidiomycete genomes found in the previous experiments. If the primer finds a target in a biological sample it is highly likely that a basidiomycete is present in the sample. In these experiments, the biological samples are other wild lichens found next to Bryoria lichens in Montana forests. Primers operate on the molecular level, and so very little biological material is needed to determine if basidiomycetes are present.

    7. expanding the taxonomic range to consider all Fungi, we found 506 contigs with significantly higher abundances in vulpinic acid–rich B. tortuosa thalli

      The author initially looked only at the expressed gene copies (contiguous sections of messenger RNA, or contigs) that corresponded either to known ascomycete or known algal DNA. They limited their search to these two because until then, a lichen was thought to only consist of those two partners. When they could not find any difference that would explain the phenotype differences between the two lichens, they expanded their search to see what other kinds of DNA was found in every single lichen, and perhaps had not been accounted for yet. They found 506 contiguous snippets of DNA that were found in every lichen that appeared to come from a second fungus, a basidiomycete, that wasn’t supposed to occur in lichens.

    8. transcriptome-wide analysis

      A transcriptome is a way for researchers to count the number of messenger RNA copies that has been produced from each gene in an organism, which is a measure of how much this gene is expressed. By comparing the level of gene expression between two different species, researchers can get an idea of which genes might be involved in producing different phenotypes in those species.

    1. the complexity of the evolutionary history of dogs

      For a recent study on the history of dogs in the Americas (published by some of the same authors of this paper), check out the 2018 research article in the "Related content" tab.

    1. To test if mating is rewarding, males were exposed sequentially for 30 min to two odorants [ethyl acetate (EA) or isoamyl alcohol (IAA)], one in the absence and the other in the presence of virgin females, and tested for odor preference 24 hours later in the absence of females

      This sentence describes how the researchers used the conditioning assay to test whether mating is rewarding. The two odors they used came from the chemicals ethyl acetate (EA) and isoamyl alcohol (IAA). The specifics of these two chemicals are not important—any two clearly distinct smelling chemicals could have been used. Male flies were exposed to one of the two odors in the presence of sexually receptive females (who the males presumably mated with), and were exposed to the remaining odor in the absence of females. They then tested to see whether males preferred the females/mating-associated odor over the other neutral odor.

    2. To test these predictions, we used a series of conditioning assays in which male flies were trained to associate the proposed rewarding experiences (mating, ethanol exposure, or NPF circuit activation) with one of two neutral odor cues.

      Here, the researchers are aiming to verify their theory about how mating, ethanol, and activity of the NPF circuit are connected (for more on this, check out the previous paragraph) by proving that each of these three things are inherently rewarding.

      An example of how they could do this would be to repeatedly expose the flies to alcohol while simultaneously also exposing them to a particular odor cue—let's call it odor A. After repeated exposure to alcohol and odor A in conjunction, the flies will learn that if they smell odor A, alcohol must be near.

      Once this association has formed, the researchers could put the flies in a Y maze, with one prong containing odor A, and the other prong containing a random odor—say odor B. Since odor A predicts alcohol, if the flies spend the majority of their time in the prong containing odor A, it would indicate that they are seeking out alcohol, presumably because it is rewarding.

      This type of manipulation is exactly what the researchers did here, except that they also investigated mating and manual activation of the NPF circuit (in addition to alcohol) as possible rewarding elements.

    3. Several experiments were designed to determine which of these was the predominant contributor to the enhanced ethanol preference seen in rejected-isolated males

      Since the initial experiment does not allow us to clearly conclude why the virgin males preferred the alcohol (the list of possible reasons is given in the prior sentence), the researchers designed a series of follow-up experiments, each designed to examine a slightly different possibility.

    4. rejected-isolated

      The group of male flies that were exposed only to females who had already mated and were thus no longer sexually receptive. These male flies experience sexual rejection.

    5. mated-grouped

      The group of male flies that experienced repeated, lengthy mating sessions with multiple virgin female flies.

  7. Nov 2018
    1. D statistics

      Can detect admixture events; it is used to detect gene flow between closely related species.

    2. Mitochondrial sequences as well as genotype files (in plink format) were deposited on Dryad (doi:10.5061/dryad. 8gp06).

      Genetic sequences of the modern and ancient dogs used in this study are publicly available. Check out their data on Dryad!

    3. cross coalescence rate (CCR)

      A method of estimating the time at which populations had a common ancestor, based on their genetic differences and similarities.

    4. multiple sequentially Markovian coalescent (MSMC)

      A technique that looks at the pattern of DNA sequence changes (mutations) in multiple individuals, focusing on the most recent common ancestor of any two sequences. It can provide information about the timing of shared ancestry, population sizes, population splits, and migration rates.

    5. complete (28x) genome

      Certain bases that are always present in dogs were covered by sequencing 28 times, so the whole genome is said to have been covered 28 times.

    1. To perform a fair comparison, we fixed the computational complexity of both algorithms to be the same

      The fly algorithm is so much more efficient that it can perform more computations for the same cost as the LSH algorithm. This is the because the cost per projection is so different—for each projection in LSH, it requires 2d operations. For each projection in the fly algorithm, it only requires 0.1d operations. To even it out so that the total operational cost is the same means that the fly algorithm is able to generate 20 times the number of projections as the LSH algorithm.

    2. mean average precision

      The mean average precision (MAP) is a way of measuring how well an algorithm is doing at a task.

      Here, the authors took each algorithm (fly and LSH) and ran it against each data set (SIFT, GLOVE, and MNIST) for 1,000 different query inputs. This produced a list—also called a rank—of all the images or words that were similar to the query. Each item in the rank comes with a certain precision value that represents its accuracy.

      Next, the authors added up all the precision values in the ranking (with the top-ranked values carrying the most weight) and divided the sum by the total number of items in the ranking to get the average precision (AP). They then took the average of all 1,000 APs (one for each query) to get the MAP.

      Calculating a MAP for each algorithm and data set allowed the authors to compare the effectiveness of the algorithms.

    3. We compared the two algorithms for finding nearest neighbors in three benchmark data sets: SIFT (d = 128), GLOVE (d = 300), and MNIST (d = 784)

      SIFT, GLOVE, and MNIST are three well-known data sets that researchers and computer scientists often use to test similarity search algorithms.

      MNIST is the Modified National Standards of Instruments and Technology data set. It consists of handwritten digits, and each row of the matrix corresponds to an image.

      SIFT stands for Scale-Invariant Feature Transform. It consists of reference images and can be used to extract specific features of those images (e.g. the corners of a door frame).

      GLOVE, or Global Vectors for Word Representation, consists of word vectors. It is useful for measuring the linguistic or semantic similarity between two words.

    4. provides a conceptually new algorithm for solving a fundamental computational problem

      This "fundamental computing problem" is the problem of being able to quickly and efficiently pick out objects that are similar to one another from very large data sets.

      For example, Google needs to be able to pick out search results that are similar to what you typed—and it needs to do this very quickly. Likewise, Netflix needs to compare your watch history to that of all its other users so that it can make recommendations for what else you might like.

      These and other similar problems pop up all over the place in your everyday life. The process of solving them is called a "similarity search" and is of intense interest to computer scientists who want to make these searches faster, more efficient, and better quality.

    1. We injected Yob mRNA into nonsexed preblastoderm embryos of A. gambiaeand its sibling species A. arabiensis to assess whether ectopic Yob transcripts affect mosquito sex ratios. To control for successful injection, we coinjected a plasmid with a green fluorescent protein (GFP) expression cassette (embryos that receive sufficient nucleic acids develop into larvae transiently expressing GFP; fig. S9). Surviving individuals were sorted at the larval stage into a GFP-positive and a GFP-negative group (Fig. 3A), and at the pupal stage mosquitoes were sexed.

      In this experiment, the authors injected normal Yob transcripts into normal embryos, along with a fluorescent marker to let them know that injection was successful, and allowed the embryos to grow. Once at the larval stage, they could see the fluorescent injection marker and sorted the larvae based on expression of the marker. At the pupal state, the authors were able to sex the mosquitoes.

    2. We transfected the Sua5.1 cells with two modified Yobtranscripts containing putative nonsynonymous point mutations r.1A>C and [r.5U>A; 6U>G] and investigated the effects of the deduced amino acid changes Met1→Leu and Phe2→Stop, respectively, on dsx splicing.

      Based on what the authors found by analyzing other species, they hypothesize that Yob actually codes for a protein. They made new lab-generated transcripts of Yob with sequence changes that would result in no protein product (either removing the start codon, or adding in a premature stop codon) and transfected those transcripts in to cells to monitor dsx splicing.

    3. we evaluated the protein-coding potential of Yob by comparing its sequence to PCR-isolated orthologous sequences from Anopheles arabiensis and Anopheles quadriannulatus, two members of the Anopheles gambiae complex.

      The authors isolated sequences from closely related mosquito species and compared similarities and differences in those sequences computationally.

    4. We investigated the effect of in vitro–synthesized mRNA corresponding to the shortest, presumably mature A. gambiae Yob transcript isoform on dsxsplicing

      The authors made mRNA in the lab. The mRNA has the same sequence of what they think is the shortest, but functional Yob transcript. They are testing whether Yob has a direct effect on dsx.

    5. ectopic embryonic delivery of Yob transcripts

      The scientists artificially inserted the gene-reading Yob into the embryos of Anopheles gambiae.

    6. transcription of Yob is limited to males. Transcription begins in embryos between 2 and 2.5 hours after oviposition,

      As seen in Figure 1, they are analyzing Yob mRNA through use of a gel, not sequencing, in this experiment. The authors find that transcription of this male factor begins very early after fertilization, at the same time as other genetic markers of zygotic expression.

    7. we analyzed transcriptomes of male and female embryos (18), whose sexual identity was determined by polymerase chain reaction (PCR) (fig. S1). Separate pools of mRNA were sequenced, yielding ~500,000 Roche 454 reads from each sex.

      Because mosquito embryos look identical whether male or female, the authors had to use molecular techniques to find out the sex of each embryo. The embryos were separated based on their sexual identity (male or female) and mRNA was extracted and sequenced from the collective male or female embryos.

    1. We are sometimes asked what the result would be if we put four +'s in one gene. To answer this my colleagues have recently put together not merely four but six +'s. Such a combination is active, as expected on the basis of our theory, although sets of four or five of them are not.

      This experiment is an extension of the frameshift experiment. If the bases are read in triplets, then you'd expect that four or five extra bases would ruin the code. However, six extra bases would still encode the amino acids for the native protein (with two extra amino acid residues).

    1. FGFP data set provided a unique opportunity to perform an informed power analysis

      The authors performed a power analysis study, which allows researchers to determine the sample size required to detect an effect, due to the large number of samples with broad characteristics. They first calculated the number of samples needed to determine a difference in microbiota diversity when the cause is unknown. To do so, they need to determine the effect size (the minimum deviation that is considered significant), the significance level (the probability of determining that a condition is true given that it is false), and the power (the probability of determining that a condition is false given that it is true).

      Read more: http://www.biostathandbook.com/power.html

    1. SEM

      Acronym for standard error of the mean, a measure that represents how far the mean of a sample is from the estimated true population mean. It is a good estimate of how accurately your mean reflects the true population.

      To learn more about SEM: https://www.khanacademy.org/math/ap-statistics/sampling-distribution-ap/sampling-distribution-mean/v/standard-error-of-the-mean

    2. Analysis of covariance

      An analysis of covariance is used to see how two independent variables change together.

      Here, the authors used it to determine whether the response to a reward or devaluated stimuli was due to habitual learning, rather than external factors such as outcome-action knowledge, working-memory/inhibition, or the ability to learn how to discriminate during the training phase of the test.

      To learn more about analysis of covariance: http://www.lehigh.edu/~wh02/ancova.html

  8. Oct 2018
    1. To test whether activation of the NPF-NPFR pathway is rewarding per se, we trained virgin males to associate artificial activation of NPF neurons with either EA or IAA. Males expressing dTRPA1 in NPF neurons (NPF-GAL4 + UAS-dTRPA1) and the genetic controls each carrying only one of the two transgenes were trained for three 1-hour sessions at 29°C, with dTRPA1 active, interspersed with three 1-hour rest periods at 18°C, with dTRPA1 inactive (Fig. 4B).

      The final thing the researchers wanted to test was whether artificial activation of the NPF circuit was inherently rewarding. To do this, they once again relied on the dTRPA1 proteins, which can activate neurons at high temperatures. The researchers inserted this protein into neurons that were part of the NPF circuit. They then exposed the flies to one smell while keeping a high temperature (thus activating the NPF neurons). This smell became associated with a state of high NPF circuit activity. Conversely, they exposed the flies to the second smell while keeping a low temperature. This smell became associated with a state of normal/low NPF circuit activity. Finally, they placed the flies in a Y maze (as before) and checked to see if the flies would prefer the prong containing the NPF-activity paired odor, or the unpaired odor.

    2. A conditioned odor preference index (CPI) for mating was calculated by averaging preference indices for reciprocally trained groups of flies. Positive CPI values indicate conditioned preference, negative values indicate aversion.

      The researchers used time spent in the two prongs of the Y maze to develop a preference score. Per this score, a positive value would indicate that the flies preferred the odor that was associated with one of the three activities (mating, alcohol exposure, or activation of the NPF circuit). Conversely, a negative score would indicate that the flies preferred the odor that was not associated with these activities. A score of zero would indicate no obvious preference between the two.

    3. To determine whether the inverse correlation between NPF levels and ethanol preference reflects a cause-and-effect relationship, we manipulated the NPF-NPFR system genetically.

      So far, the researchers have shown that changes in NPF levels correlate with both sexual experience and alcohol preference. Specifically, a more active sexual history is correlated with an increase in NPF levels, which is correlated with a decrease in preference for alcohol (and vice versa). However, one of the most important rules to remember in science is that correlation does not equal causation. The researchers thus decided to follow up with a direct genetic manipulation of NPF in order to establish a causal relationship.

    4. To further test the strength of this conclusion, we divided a cohort of rejected-isolated males into two subgroups, one of which was left undisturbed, and the other of which was allowed to mate with virgin females for 2.5 hours immediately before testing.

      As a final follow-up experiment, the researchers took a group of sexually rejected males and split them up into two. One subgroup was left alone, and then tested for alcohol preference. The other subgroup was exposed to virgin females just before testing. As such, these males did in fact get an opportunity to mate before undergoing the alcohol preference test. If the first subgroup continued to prefer alcohol, but this preference were to disappear for the second group (who initially experienced rejection, but then were able to mate just before testing), it would indicate that the main cause for the alcohol preference was indeed sexual deprivation.

    5. We next investigated ethanol preference in males that were sexually deprived (blocked from copulating) but not exposed to the social experience of rejection.

      For the second follow-up experiment, the researchers wanted to investigate the possibility that it was not actually the lack of sex, but rather the experience of rejection by a female that was driving the virgin males to prefer alcohol.

    1. To identify nonredundant covariates of microbiome variations from our shortlist of 69 correlating factors

      A redundant covariate is a factor that either has the same value for every sample or multiple factors that are highly correlated and can be used as substitutes for one another. The researchers removed redundant covariates from their study because they can hamper interpretability of the results.

    2. forward stepwise redundancy analysis (RDA)

      This is a statistical technique used to describe linear relationships between components of dependent variables that can be explained by a set of independent variables. Here, the independent variables were the 69 covariates and the dependent variable was the microbiota variation in each sample.

    3. PCoA

      Stands for Principal Coordinate Analysis, a statistical technique used to visualize similarities between variables by representing the variance in as few axes/dimensions as possible. The arrows show the direction of the original variables and the angle between arrows gives a rough estimate of the correlation between features.

    4. 16S ribosomal RNA (rRNA) gene amplicon sequencing

      Almost all bacteria have a copy of the 16S rRNA gene. Comparing their sequences is a common tool to identify and differentiate bacteria at the species level.

      Learn more about how bacteria are identified with this resource from iBiology: https://www.ibiology.org/microbiology/genome-sequencing/

    1. We then found the top 2% of predicted nearest neighbors in m-dimensional hash space

      For the fly, the data is organized into a higher dimensional space. For LSH, it is organized in a lower dimensional space. But if the algorithms work effectively, the data should still be arranged so that similar features are near one another.

      Instead of feature vectors, the algorithms arrange items in hashes or "tags" (just like the fly brain uses a tag to represent an odor, the algorithms use a tag to represent a specific image or word). Finding the hashes that are closest to each other in this new m-dimensional space should reveal the images/words that are most similar to each other (again, if the algorithm works correctly).

      These nearby hashes are called "predicted nearest neighbors" because they predict which items in the data set are the most similar.

    2. we show analytically that sparse, binary random projections of the type in the fly olfactory circuit generate tags that preserve the neighborhood structure of input points.

      In a mathematical proof, the authors took a matrix of input odors and multiplied it by a vector of projection values to create a new matrix of Kenyon Cell values. In this new matrix, the relative positions of the input odors were approximately the same as they were in the original matrix.

      This shows that the fly algorithm preserves the distance between input points when sending information from PNs to KCs.

    1. scanning electron microscopy

      In bright field microscopy, an image is produced by bouncing light off of an object and the image is magnified by lenses. In scanning electron microscopy, an image is produced by bouncing electrons off of an object and the image is interpreted and produced by a computer. By using electrons instead of light, researchers can observe incredibly fine detail in the image created.

    2. initial microscopic imaging

      Researchers look at a sample through a bright field microscope to look for evidence of cell morphology that could be basidiomycetes.

    3. When assaying for the basidiomycete

      To take a measurement of a sample, usually meaning a biochemical or chemical measurement of a biological sample; in this case, basidiomycete yeasts.

    4. we estimated transcript abundances by mapping raw reads back to a single, pooled metatranscriptome assembly and binning

      In a biological sample that contains more than one organism, before gene expression can be evaluated, the researchers must identify which genes belong to which organism. To do this, gene expression data is mapped onto the genomes of the organisms that are known in the mixture, and genes are sorted, or binned, into groups by the genomes they match. This way the gene expression data for each known organism can be determined.

    5. We hypothesized that differential gene expression might account for the increased production of vulpinic acid in B. tortuosa.

      The authors knew that the difference between these two lichen species was poorly understood. One species produces vulpinic acid, and the other does not. Phylogenetic analysis could not identify differences in the symbionts of the two species. The authors decided to test if differential gene expression of a gene shared between the species might be the cause of the phenotypic difference.

    1. We purified the corresponding recombinant I. sakaiensis proteins (fig. S5) and incubated them with PET film at 30°C for 18 hours.

      Using genetic engineering, the authors isolated the protein strand the two organisms had in common and exposed it to a PET film without any microbes present.

    2. We collected 250 PET debris–contaminated environmental samples including sediment, soil, wastewater, and activated sludge from a PET bottle recycling site (7). Using these samples, we screened for microorganisms that could use low-crystallinity (1.9%)

      The authors collected samples from different environments where PET plastic waste was likely to be found. In this case they chose to sample near a PET recycling plant. The plant specifically recycled high-crystallinity PET. They took some dirt, water, and sludge and put the samples in an environment including low-crystallinity PET. Low crystallinity PET is more disorganized and easier to break down than polymers with higher crystallinity.

      It was ultimately one of the samples of sediment that grew bacteria. When looking at the bacteria under a microscope, the researchers were able to see that it was growing on a thin layer of PET plastic.

    3. We compared the activity of the ISF6_4831 protein with that of three evolutionarily divergent PET-hydrolytic enzymes identified from a phylogenetic tree that we constructed using published enzymes (Fig. 2C and table S2). We purified TfH from a thermophilic actinomycete (10), cutinase homolog from leaf-branch compost metagenome (LC cutinase, or LCC) (11), and F. solanicutinase (FsC) from a fungus (fig. S5) (12), and we measured their activities

      The authors used published data of proteins having similar activity as the ISF6_4831 enzyme and analyzed it using statistical tests to select three enzymes that divergently evolved—meaning that the enzymes evolved from a common ancestor and accumulated enough differences to result in the formation of a new species.

    1. Monte Carlo analysis

      This technique is used in calculations for complicated systems where changes in one variable influences many parts of the calculation. In this technique many calculations are run with each calculation having different beginning conditions. The end results are then analyzed to look at the range of possible outcomes. The error bars in parentheses in Figure 4 are determined by a Monte Carlo simulation.

      See more about Monte Carlo simulations from the Massachusetts Institute of Technology: http://news.mit.edu/2010/exp-monte-carlo-0517

    2. R2

      R-squared (\(R^2\)) values represent how close the data points are to the predictions from a model. An \(R^2\) value of 1 means that all of the data points lie on the prediction from the model. In this case, the researchers are using the solid line that represents perfect agreement between the box model calculation and the experimental data. An \(R^2\) value of 1 in this case would mean that the box model calculations and the experimental data are in perfect agreement. In general, the closer the \(R^2\) value is to 1, the closer the model and data match.

      Without the inclusion of VCPs in the model calculation the \(R^2\) value was 0.59 (Panel A of Figure 3). With the inclusion of VCPs into the model the \(R^2\) value improved to 0.94 (Panel B of Figure 3).

    3. Here, we assess the importance of VCP emissions to ambient air pollution, again using Los Angeles as a test case (Fig. 4). Los Angeles currently violates the U.S. 8-hour O3 standard,

      The air in Los Angeles, California has ozone (\(O_3\)) levels that are higher than those recommended by the Environmental Protection Agency. The amounts and types of VOCs present influences ozone levels.

    4. We therefore conclude that large underpredictions are due to missing emission sources.

      Comparisons are made between experimental data and model calculations. The model calculations are influenced by what molecules are emitted, how those emissions chemically react, and how wind and other variables cause emissions to move from one place to another. The calculations use techniques from other researchers (including this paper's co-authors Joost de Gouw and Si-Wan Kim) to take into account chemical reactions and movement of the emissions from one place to another.

      The authors then make different predictions with their model assuming different types of chemical emissions (fossil fuels and/or VCPs).

    5. we found that fossil fuel VOCs [from mobile sources and from local oil and natural gas production and distribution (36)] can only account for 61% of the mass of freshly emitted VOCs measured, and 59% of their variability

      Box model calculations were carried out under various conditions. The authors can make various assumptions about what sources are emitting VOCs into the air (mobile sources or VCPs). The results of the calculations under these various conditions are then compared to experimental data. This allows the researchers to examine what sources are important contributors to VOCs in air.

    1. boundary conditions and idealizations in the simulation

      The authors define a series of constraints for their simulation. The scientific model assumes facts about the phenomenon that make the problem easier to solve. In this case, the authors assume among others that the pore structure is homogeneous, that the vapor pressure is the same for the MOF and the condenser, and that the diffusivity of the crystal does not vary.

    2. For visualization purposes, we used a condenser with a temperature controller to maintain the temperature slightly below ambient levels but above the dew point, in order to prevent vapor condensation on the inner walls of the enclosure.

      To simplify the experiments, the author maintain the condenser at a temperature cooler than the surrounding temperature. This results in the condenser being cooler than the walls of the box, so that all the water condenses on the condenser and can be easily collected. In practice, ambient temperature is enough to harvest water without the need for additional cooling of the condenser.

    3. A solar flux (1 kW m–2, air mass 1.5 spectrum) was introduced to the graphite-coated substrate layer

      The authors simulate natural sunlight in the laboratory. The air mass is the ratio of the path length that sunlight has to travel through the atmosphere to the vertical path length (when sun is at the highest point in the sky, which corresponds to the shortest path length). An air mass of 1.5 is the condition most commonly use to quantify the efficiency of solar devices.

    4. The environmental temperature above standard ambient temperature was necessary to perform the experiments at >1 kPa

      In order to efficiently harvest water, a large difference of temperature between the MOF and the condenser is needed. In their experiment, the authors set the temperature at 35°C in order to be able to condense the vapor with a condenser at 10°C.

    5. In this simulation, MOF-801 was initially equilibrated at 20% RH, and the vapor content in the air-vapor mixture that surrounds the layer during desorption increased rapidly from 20 to 100% RH at 25°C

      The authors performed a simulation in conditions reflecting an accurate, real-life use of the MOF. The results show an increase in RH upon water desorption, followed by return to the initial 20% value upon water adsorption.

    1. Ordinary least squares (OLS) regression summary statistics (adjusted R2)

      Like PGLS, this method examines the relationship between two or more variables. However, this method does not account for phylogeny. OLS regression was used to compare with PGLS results to see if it would produce similar results.

    2. We measured differences in species’ northern and southern range limits, the warmest or coolest temperatures occupied, and their mean elevations in three periods (1975 to 1986, 1987 to 1998, and 1999 to 2010) (figs. S2 to S4) relative to a baseline period (1901 to 1974)

      To test whether climate change has impacted species ranges, the authors had to measure, for each species, the latitudes of the northern and southern range limits (and the distance between these), the warmest and coolest temperature the species were observed, and the mean elevation of the species.

      These measurements are based on the average of the five most relevant species observations in each case. For example, to find the northern range limit, the authors took the average of the five northernmost observations of the species, while to find the coolest temperatures within the species' range, they took the average of the five coolest points that the species was observed at. This helps avoid skewed results from a signal sighting.

      Check out the Supplemental Materials for more information on how the authors took all their measurements.