3,078 Matching Annotations
  1. Nov 2018
    1. default female development in the absence of the Y-linked factor, whereas in males the M may be preventing establishment of trafunction by an unknown mechanism

      In other flies, there is a female "default" mode of sex determination. Only a maleness signal on the Y chromosome can initiate the male pathway.

    2. cofactor

      A compound that is required for the activity of a protein; in this case, TRA2 is needed to help tra cut dsx.

    1. Fecal

      Describes waste excreted after the digestion of food from the bowels or intestines.

    2. 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. executive impairments in the control task

      Executive impairments refers to reduced function of processes such as memory, controlled response to stimuli, capacity to shift between different topics and tasks, and focus—which regulate and control cognitive functions.

    2. instrumental learning task

      Training that is done to reinforce a particular response.

    1. monomers

      A building block molecule, can combine to create polymers.

    2. p-nitrophenol–linked aliphatic esters (pNP-aliphatic esters)

      Aliphatic means that there is no aromatic group on the ester part of this molecule. A p-nitrophenol group is an aromatic ring with an oxygen linked to one carbon and a nitrogen attached to two oxygens linked to the opposite carbon.

    3. In the course of subculturing no. 46, we found a subconsortium that lost its PET degradation capability. This subconsortium lacked I. sakaiensis (fig. S3), indicating that I. sakaiensis is functionally involved in PET degradation.

      When the authors removed l. sakaiensis from sample no. 46, the plastic was not degraded. The authors therefore concluded that I. sakaiensis is responsible and necessary for the PET degradation activity in the sample.

    4. we successfully isolated a bacterium capable of degrading and assimilating PET.

      There have been a variety of recent scientific reports focusing on degrading PET. While they are scientifically exciting, Chemical and Engineering News (C&EN News) wrote an article detailing work that needs to be done before such methods could be viable on a large scale.

      Read more at C&EN News: https://cen.acs.org/environment/sustainability/Plastics-recycling-microbes-worms-further/96/i25

    5. accumulation of PET in ecosystems

      In 2015, the Ocean Conservancy and McKinsey Center for Business and Environment showed that there will be 1 pound of plastic for every 3 pounds of fish by 2025.

      Here is the report in full: https://oceanconservancy.org/wp-content/uploads/2017/04/full-report-stemming-the.pdf

    1. 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!

    2. 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.

    3. temporal origins

      Referring to the point in time when dogs first appeared.

  2. Oct 2018
    1. in vitro and in vivo

      In vitro: takes place outside the organism (in a test tube, culture dish, etc.)

      In vivo: takes place inside the organism

    2. perturbation

      Changing the function of an enzyme.

    3. Cas13 enzymes have two higher eukaryotes and prokaryotes nucleotide-binding (HEPN) endoRNase domains

      A domain is a section of a protein that has a specific function.

    4. adenosine-to-inosine deaminase activity

      A common method of RNA editing in which the nucleoside adenosine is converted to inosine by the removal of an amino group.

    5. knockdown

      A process when expression of a particular protein is suppressed at the level of RNA.

      This is similar to knockout, where the expression of a protein is blocked at the DNA level. Unlike knockout, knockdown can be reversed.

      The most widely used method for knockdown is RNA interference.

    6. post-mitotic

      Cells that are no longer capable of dividing (undergoing mitosis).

    7. cleavage


    8. prokaryotic

      Prokaryotes are a class of single-celled organisms with no membrane-bound nucleus, mitochondria, or other membrane-bound organelles.

      Examples include bacteria and archaea.

    9. ribonuclease

      A nuclease is a special enzyme that catalyzes reactions that break down nucleic acids.

      A ribonuclease specifically works on RNA molecules.

    10. Nucleic acid

      A type of organic molecule that is made of chains of compounds called nucleotides.

      Common examples are DNA and RNA.

    1. antihistamine

      Drugs that inhibit the effects of histamines, compounds released by cells in response to inflammatory reactions. These are commonly used to treat allergies.

    2. 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.

    3. biotic

      Describes systems consisting of living organisms. Here, the authors believe that interactions between different microbiota communities may contribute to some variation in genera abundance they could not account for.

    4. Of those covariates, 26 had an analog in the LLDeep record

      26 of the 69 (37.6%) covariates found in the FGFP data had a comparable factor in the LLDeep cohort.

    5. collinear variables

      Two variables are collinear if they can be predicted from each other accurately, suggesting that they are highly correlated. It is often redundant to have both variables if they are collinear because they can be used as proxies for each other and may hamper interpretation of results.

    6. female hormones

      These drugs might include birth control.

    7. hydrogenotrophic

      Refers to organisms that convert hydrogen into an energy source.

    8. genera

      Plural form of the taxonomic rank, genus.

    1. C. L. Schoch, K. A. Seifert, S. Huhndorf, V. Robert, J. L. Spouge, C. A. Levesque, W. Chen, E. Bolchacova, K. Voigt, P. W. Crous, A. N. Miller, M. J. Wingfield, M. C. Aime, K.-D. An, F.-Y. Bai, R. W. Barreto, D. Begerow, M.-J. Bergeron, M. Blackwell, T. Boekhout, M. Bogale, N. Boonyuen, A. R. Burgaz, B.Buyck, L. Cai, Q. Cai, G. Cardinali, P. Chaverri, B. J. Coppins, A. Crespo, P. Cubas, C. Cummings, U. Damm, Z. W. de Beer, G. S. de Hoog, R. Del-Prado, B. Dentinger, J. Dieguez-Uribeondo, P. K. Divakar, B.Douglas, M. Duenas, T. A. Duong, U. Eberhardt, J. E. Edwards, M. S. Elshahed, K. Fliegerova, M. Furtado,M. A. Garcia, Z.-W. Ge, G. W. Griffith, K. Griffiths, J. Z. Groenewald, M. Groenewald, M. Grube, M.Gryzenhout, L.-D. Guo, F. Hagen, S. Hambleton, R. C. Hamelin, K. Hansen, P. Harrold, G. Heller, C.Herrera, K. Hirayama, Y. Hirooka, H.-M. Ho, K. Hoffmann, V. Hofstetter, F. Hognabba, P. M. Hollingsworth,S.-B. Hong, K. Hosaka, J. Houbraken, K. Hughes, S. Huhtinen, K. D. Hyde, T. James, E. M. Johnson, J. E.Johnson, P. R. Johnston, E. B. G. Jones, L. J. Kelly, P. M. Kirk, D. G. Knapp, U. Koljalg, G. M. Kovacs, C. P.Kurtzman, S. Landvik, S. D. Leavitt, A. S. Liggenstoffer, K. Liimatainen, L. Lombard, J. J. Luangsa-ard, H. T. Lumbsch, H. Maganti, S. S. N. Maharachchikumbura, M. P. Martin, T. W. May, A. R. McTaggart, A. S.Methven, W. Meyer, J.-M. Moncalvo, S. Mongkolsamrit, L. G. Nagy, R. H. Nilsson, T. Niskanen, I. Nyilasi, G.Okada, I. Okane, I. Olariaga, J. Otte, T. Papp, D. Park, T. Petkovits, R. Pino-Bodas, W. Quaedvlieg, H. A.Raja, D. Redecker, T. L. Rintoul, C. Ruibal, J. M. Sarmiento-Ramirez, I. Schmitt, A. Schussler, C. Shearer,K. Sotome, F. O. P. Stefani, S. Stenroos, B. Stielow, H. Stockinger, S. Suetrong, S.-O. Suh, G.-H. Sung, M.Suzuki, K. Tanaka, L. Tedersoo, M. T. Telleria, E. Tretter, W. A. Untereiner, H. Urbina, C. Vagvolgyi, A.Vialle, T. D. Vu, G. Walther, Q.-M. Wang, Y. Wang, B. S. Weir, M. Weiss, M. M. White, J. Xu, R. Yahr, Z. L.Yang, A. Yurkov, J.-C. Zamora, N. Zhang, W.-Y. Zhuang, D. Schindel, Fungal Barcoding Consortium,Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. U.S.A. 109, 6241–6246 (2012).

      This paper describes the use of the phylogenetic marker that is used to barcode fungal species. One of the reasons that the yeast symbiotic partner was missed is because this barcode doesn't work for that species.

    2. A. M. Millanes, P. Diederich, M. Wedin, Cyphobasidium gen. nov., a new lichen-inhabiting lineage in the Cystobasidiomycetes (Pucciniomycotina, Basidiomycota, Fungi). Fungal Biol., 10.1016/j.funbio.2015.12.003 (2015).

      This paper describes the discovery of the genus Cyphobasidium.

    3. H. Lindgren, S. Velmala, F. Högnabba, T. Goward, H. Holien, L. Myllys, High fungal selectivity for algal symbionts in the genus Bryoria. Lichenologist 46, 681–695 (2014).

      This paper examines the specificity of fungal and algal partners in the lichen symbosis.

    4. S. Velmala, L. Myllys, P. Halonen, T. Goward, T. Ahti, Molecular data show that Bryoria fremontii and B. tortuosa (Parmeliaceae) are conspecific. Lichenologist 41, 231–242 (2009).

      Genomic data is used to show that the two main species of Bryoria fungi examined in this work are conspecific, that is they are genomically identical to one another.

    5. S. T. Bates, D. Berg-Lyons, C. L. Lauber, W. A. Walters, R. Knight, N. Fierer, A preliminary survey of lichen associated eukaryotes using pyrosequencing. Lichenologist 44, 137–146 (2012).

      This paper used pyrosequencing to look for additional eukaryotic symbiotic partners in lichens, like the one discovered in this paper.

    6. D. L. Hawksworth, The variety of fungal-algal symbioses, their evolutionary significance, and the nature of lichens. Bot. J. Linn. Soc. 96, 3–20 (1988).

      Lichens evolved independently many times as a symbiosis between fungi and algae.

    7. A. Gargas, P. T. DePriest, M. Grube, A. Tehler, Multiple origins of lichen symbioses in fungi suggested by SSU rDNA phylogeny. Science 268, 1492–1495 (1995).

      This is a foundational paper that describes how lichen symbiosis arose multiple times through evolutionary history.

    8. This definition has brought order to the field, but may also have constrained it by forcing untested assumptions about the true nature of the symbiosis. We suggest that the discovery of Cyphobasidium yeasts should change expectations about the potential diversity and ubiquity of organisms involved in one of the oldest known and most recognizable symbioses in science.

      The old definition of one fungus with one photobiont was helpful in guiding science's understanding of lichens. Yet, sometimes strict definitions can prevent us from asking good questions. This paper concludes that researchers should always push their investigations further. There might still be interactions we haven't identified in symbiotic relationships.

    9. secondary metabolites

      Any organic substance that is not directly involved in the growth, development, or reproduction of an organism. Vulpinic acid is an example of a secondary metabolite.

    10. intron

      A segment of DNA that does not code for proteins and interrupts the sequence of genes.

    11. multi-template polymerase chain reaction bias

      Multi-template polymerase chain reaction (PCR) is a technique to amplify multiple targets in a single PCR experiment. However, this technique sometimes produces bias and overamplifications in specific templates.

      To learn more, check out this seminal paper by Polz and Cavanaugh (1998).

    12. anamorphic

      This is the asexual life stage of fungi, where reproduction is achieved by budding of mononucleated cells.

    13. 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.

    14. morphology

      The shape or form of an organism.

    15. failed to reveal

      NGSS Nature of Science: Scientific Investigations Use a Variety of Methods and Scientific Knowledge is Open to Revision in Light of New Evidence

    16. initial microscopic imaging

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

    17. fossil calibrations

      The molecular clock can be adjusted (i.e. calibrated) using fossil data from any taxa represented in a rooted phylogeny, in order to put an approximate date on the nodes of a phylogeny.

      Recently, new lichen fossils were found, giving us more insight into the co-evolution of lichen symbionts.


    18. monophyletic clade

      A group of organisms that clusters together on a phylogenetic tree to the exclusion of all other groups.

    19. galls

      In this case, meaning an abnormal outgrowth on the Parmeliaceae thalli.

    20. genera

      Plural form of the taxonomic rank, genus.

    21. 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.

    22. ribosomal RNA (rRNA)

      This is a gene that helps stabilize the ribosome. It is found in all living organisms, so this gene is often used in phylogenetic comparisons of different species.

    23. We next sought to determine whether this uncharacterized basidiomycete was specific to the studied Bryoria species or could be found in other lichens.

      How do scientists learn to ask the right questions about novel data?

      Read about the life and academic path of the first author in The Atlantic at: https://www.theatlantic.com/science/archive/2016/07/how-a-guy-from-a-montana-trailer-park-upturned-150-years-of-biology/491702/

    24. These data suggested that a previously unrecognized basidiomycete was present in thalli of both species but was more abundant whenever vulpinic acid was present in large amounts

      After concluding that gene expression in the two symbionts could not account for lichen differences, the authors continued to investigate what might account for vulpinic acid production. The results of the transcriptome analysis indicated that gene expression from a basidiomycete was correlated with the presence of vulpinic acid.

    25. these analyses confirm previous conclusions

      Researchers have compared the genomes of these two lichen species and found that, for the most part, these two organisms have the same sets of genes.

    26. taxon

      A taxonomic group of any rank, such as species, family, or class.

    27. 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.

    28. phenotype

      The traits that an organism displays. Phenotype results from the interaction of a genotype with the environment.

    29. genotype

      The gene sequence that an organism carries.

    30. showed no correlation

      Next Generation Standards LS3.B Cross cut: Cause and Effect

    31. 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.

    32. mycobiont

      The fungal partner in the lichen symbiosis.

    33. metatranscriptomics

      A transcriptome sample that is taken from a collection of organisms. mRNAs must be mapped onto each of the genomes from the organisms in the sample in order to figure out which gene came from which organism. In some cases, there is not a genome available for mapping and instead mRNA is mapped against a large database in order to find a close relative and guess where the mRNA could have come from.

    34. in vitro

      In a laboratory setting; that is, outside of their normal biological context.

    35. recalcitrance

      Resistance, in this case.

    36. axenic

      Denotes a laboratory culture that is free from living organisms other than the species required. In this case, lichens could not be formed in a laboratory using only the two known species.

    37. Attempts to synthesize lichen thalli from the accepted two components

      Researchers have tried to create a lichen in the laboratory by only mixing an algae and a fungus known to produce lichens in the wild. These attempts were not successful as the cortex layer did not develop.

    38. these organisms form stratified, often leafy or shrubby body plans (thalli) that resemble none of the symbionts in isolation, a feature thought to be unique among symbioses

      Next Generation Standards LS1.A: Structure and Function LS2.A: Interdependent Relationships in Ecosystems

      AP Biology Standards EK2.D.1: All biological systems are affected by complex biotic and abiotic interactions.

    39. mutualism

      A type of symbiosis in that the relationship is beneficial to both organisms involved.

    40. The structurally important lichen cortex, long treated as a zone of differentiated ascomycete cells, appears to consistently contain two unrelated fungi.

      A 60-second podcast on the findings of this paper from Scientific American at: https://www.scientificamerican.com/podcast/episode/for-lichens-3-s-not-a-crowd/

    41. cortex

      The outermost layer of the lichen's thallus, where the lichen comes into contact with the environment.

    42. Here we show that many common lichens are composed of the known ascomycete, the photosynthesizing partner, and, unexpectedly, specific basidiomycete yeasts.

      Two's Company, Three's a Lichen?

      Read more about the results of this study in The New York Times Science column at: https://www.nytimes.com/2016/07/22/science/lichen-symbiotic-relationship.html

    43. endophytes

      Organisms, often fungi or bacteria, that live within a plant.

    1. Baggerly’s test

      A specific statistical method that compares the proportions in a group of samples against those of another group of samples.

    2. The catalytic preference of the ISF6_4831 protein for PET film over pNP-aliphatic esters was also substantially higher than that of TfH, LCC, and FsC (380, 48, and 400 times as high on average, respectively) (Fig. 2D). Thus, the ISF6_4831 protein prefers PET to aliphatic esters, compared with the other enzymes, leading to its designation as a PET hydrolase (termed PETase).

      The authors found that the enzyme (ISF6_4831 protein) they determined was responsible for degrading PET in l. sakaiensis was better at degrading PET than its ability to degrade other molecules, in this case paranitrophenol linked aliphatic esters also called pNP-aliphatic esters, that don't look like PET.

      Furthermore, the authors saw that other enzymes that are known to sometimes degrade PET degraded more pNP-aliphatic esters relative to PET than this new enzyme ISF6_4831. This led them to include that ISF6_4831 was specifically specialized at degrading PET.

      Thus, the authors begin referring to the ISF6_4831 protein as PETase.

    3. 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.

    4. putative

      Commonly accepted. In this case, the hydrolase from Thermobifida fusca is already known to break down PET.

    5. environmentally benign

      Plastics are wreaking havoc to ecosystems all over the planet. An ecologically harmless solution for plastic recycling is desperately needed.

      Learn more from this 2012 case study created by Montana State University: https://serc.carleton.edu/NAGTWorkshops/health/case_studies/plastics.html

    6. The activity ratios of PETase relative to the other enzymes decreased as the enzyme concentrations increased, indicating that PETase efficiently hydrolyzed PET with less enzyme diffusion into the aqueous phase and/or plastic vessels used for the reaction. PETase lacks apparent substrate-binding motifs such as the carbohydrate-binding modules generally observed in glycoside hydrolases.

      The authors added more protein to a sample of PET. The three previously discovered enzymes produced more product as the enzyme concentration increased. The new enzyme, PETase, did not increase the amount of product as more enzyme was added. The authors concluded that this was because PETase was attached to the film. So adding more enzyme once the film was already covered would not increase the rate.

    7. For pNP-aliphatic esters, which are preferred by lipases and cutinases, the activity of the ISF6_4831 protein was lower than that of TfH, LCC, and FsC (Fig. 2D). The activity of the ISF6_4831 protein against the PET film, however, was 120, 5.5, and 88 times as high as that of TfH, LCC, and FsC, respectively.

      The authors exposed all of the enzymes to the different oligomers and measured the activity of each enzyme. The other enzymes did a better job of degrading substrates without aromatic groups, but ISF6_4831 did the best job degrading PET. From these results the authors concluded that ISF6_4831 had high specificity towards PET.

    8. a hydrolase from Thermobifida fusca (TfH) (fig. S4 and table S2) that exhibits PET-hydrolytic activity

      The authors found a part of I. sakaiensis's DNA that had 51% of the same patterns found in another protein known to degrade PET. They concluded that this stretch of DNA also made the protein that allowed l. sakaiensis to degrade PET.

    9. across the globe (4).

      In 2015, J. R. Jambeck et al. calculated that about 8 million tons of plastic make it into the ocean each year.

    1. made in Pasadena during 2010

      A previous study measured the amounts of VOCs present in outdoor air in Pasadena, California from 15 May to 15 June in 2010. The research included both measurements on the ground and measurements via aircraft.

      This study is using those measurements to test their model.

    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).

    1. Assemblages showing pronounced northward range expansions and limited southern-range losses, like butterflies, originated and diversified in tropical climates and retain ancestral tolerances to warmer conditions (21). Those species’ warming-related extinction risks in temperate environments are low (8) but increase toward warmer areas where climatic conditions resemble those under which they evolved

      One possible explanation of why some temperate species' ranges would expand with climate change is that these species evolved in the tropics, and have not lost a high tolerance for heat, even as they moved further north. Therefore, even as temperatures heat up in the southern regions of their current ranges, these temperature still do not approach their ancestral tolerances, and species can continue to live there. This could explain why species in the tropics are currently suffering under warming climates; the increase in temperature is surpassing their ancestral heat tolerance.

    2. Neonicotinoid effects on bumblebees have been demonstrated experimentally using field-realistic treatments

      Whitehorn and colleagues took laboratory colonies of a common European bumblebee species (Bombus terrestris), and exposed them to levels of neonicotinoids similar to what they might be exposed to near a farm field. They found that colonies exposed to these levels had slower growth rates and produced less queens than "control" colonies that were not exposed.

    3. Such responses depend on species’ traits, such as heat or cold tolerance, that reflect shared evolutionary history and climatic origins (e.g., tropical or temperate) of taxa

      Every living organism has certain traits. For example, reptiles have scaly skin, birds have feathers, mammals produce milk, and so on. These traits are inherited from the organisms' parents, of course, but ultimately, those traits tend to remain similar across very large periods of time.

      We can trace how traits change over evolutionary time scales, and show that some traits tend to remain quite similar, even though a huge amount of time might have passed. Traits like a species' tolerance to heat are like this: This trait tends to remain similar across evolutionary time, despite the fact that a species might evolve and change in many other ways, even splitting into two or more different species. In other words, it's hard to evolve tolerance to hotter temperatures—at least for many species.

    4. In addition to shifts in the timing of species’ life cycles, warming has caused range expansion toward the poles and higher elevations

      In one study, Chen and colleagues put together a huge analysis of 1367 species from the United Kingdom and some other places around the world. Those authors looked at whether the places those species were found had changed over time. On average, those species were shifting toward cooler areas at about 17 kilometers every 10 years. They were also shifting upward in elevation by about 11 meters every ten years, reflecting the fact that it is generally cooler at higher elevations than at lower elevations.

      The Chen study is called a meta-analysis, where they take results from many other studies and put them all together into one big analysis. That work focused especially on butterflies, which are very sensitive to climate change, but it did not include critical pollinator species, like bumblebees.

    5. full extents of their latitudinal and thermal limits

      Latitudinal range limits are the northernmost and southernmost edges of where a species can be found.

      Thermal range limits are the hottest and coldest places of where a species live.

    1. has not been developed. We report the design and demonstration of a device

      A Framework for K-12 Science Education: Disciplinary Core Ideas, Practice ETS1.A: Defining and Delimiting an Engineering Problem.

  3. Sep 2018
    1. MinHash

      In 1997, Andrei Broder invented MinHash, which is a type of LSH that allows a user to quickly estimate how similar two data sets are. In his seminal paper on this topic, Broder discussed the math behind this idea and applied it specifically to the process of comparing two documents on the internet.

    2. «

      This symbol means "much less than."

    3. d-dimensional

      When a vector is d-dimensional, d refers to a placeholder value that could stand for any integer, depending on how many feature values are associated with each image.

    4. hash function

      Hashing is used in computer science to reorganize large data sets (regardless of their size) into tables of fixed size. During this process, multiple data points will typically be stored in the same bin (or hash) based on how similar they are. The hash is then represented with a shortened name, or key, that takes up less storage space in the computer.

      In other words, this process helps compress the data so that a computer can use it more efficiently. It also makes it easier and faster to look up data in the table.

      ![] (https://upload.wikimedia.org/wikipedia/commons/5/58/Hash_table_4_1_1_0_0_1_0_LL.svg)

    5. Illustrative odor responses.

      Here, the authors use chemicals (ethanol, methanol, and dimethyl sulfide) to demonstrate similarity tagging/hashing.

    6. for image search, the tag of an elephant image will be more similar to the tag of another elephant image than to the tag of a skyscraper image.

      Common Core State Standards English Language Arts-Literacy, RST 11-12.6: Students should be able to explain why the authors provided this example in the paper, specifically addressing how it adds to the reader's understanding of the research.


    7. Schematic

      A simplified and symbolic representation of elements in a system. Here, the authors use a schematic to represent cell types in the fly olfactory circuit.

    8. neural circuits

      A grouping of neurons organized to process specific kinds of information.

    1. Colonization of previously unoccupied areas and maintenance of new populations strongly affect whether species track shifting climatic conditions

      Two factors that help determine how well a species will track climate change are dispersal (how well the species can move to new areas and start new populations) and persistence (how well the species can maintain and grow these new populations).

    2. Over recent decades, alpine tree lines have advanced upslope in response to human activities, geomorphological factors, and warming

      From analysis of aerial surveys, Gehrig-Fasel and colleagues found that about 4% of upward shifts in tree line (i.e. trees growing further uphill than previously) from 1985 to 1997 could be attributed directly to climate change. The rest were attributed to changes in land-use.

    3. constructed from nuclear and mitochondrial markers

      Cameron, Hines, and Williams used DNA sequence data on 218 of the 250 currently known bumblebee species to create a phylogeny (phylogenetic tree).

    4. many of which are declining

      Using museum records, Bartomeus and colleagues found that bumblebee species richness in northeastern North America has decreased significantly since 1877.

      More recently, a 2017 study found that one third of bumblebee species are in decline.

    5. Such global changes can alter or erode ecological services provided by the affected species

      Goulson and colleagues review the various global change drivers that are causing declines in bees, and by extension their pollination services.

      This infographic from their study shows some of the main drivers and how they may interact together. (c) Goulson et al. 2015

    6. Climate impacts could cause losses from parts of species’ trailing range margins

      By modelling the probability of extinction for lizards in Mexico, Sinervo and colleagues found that unabated climate change would result in the extinction of 58% of species in the Schleporus genus. They determined that increasing temperatures forced Schleporus lizards to spend more time in cool refuges avoiding the heat, therefore limiting time for foraging and reproduction, and reducing population growth rates. They also found that high-elevation species were particularly at risk from increased competition as low-elevation species moved higher.

    7. Regional analyses suggest that latitudinal range shifts toward the poles are accelerating in most species groups (3), while their trailing range margins remain relatively stable

      Most species that have been studied so far are expanding further north as climate warming makes these areas habitable for them, but are still able to tolerate to increasing temperatures in the equator-ward regions of their ranges. In other words, it appears that climate change has helped many species increase their total range sizes! (Although it likely still affects their ability to live within these expanded ranges.)

    8. Neither total pesticide nor neonicotinoid applications there relate to observed shifts in bumblebee species’ historical ranges or thermal limits (table S1).

      As we can see in Table S3, the land-use and pesticide variables were not useful in predicting range shifts.

      See the Supplementary Materials for more information.

    1. ambient VOC measurements

      The VOC measurements were part of a large community-wide effort by atmospheric scientists to better understand issues posed by air pollution and climate change in California. A link to the field study (including a white paper and policy-relevant findings) can be found at: https://www.esrl.noaa.gov/csd/projects/calnex/.

    1. avoidance behavior

      Behaviors that can help someone escape uncomfortable feelings and unpleasant situations (such as electric shock).

    2. maladaptive behavior

      Behaviors that someone develops as a way to respond to their environment, but that end up causing them harm instead of good.

    1. subangular

      Not smoothly rounded. The particles would have blunt, not sharp angles.

    2. loam

      Soil composed of clay and sand that contains decomposed organic matter (leaves, grasses, etc.).

    3. 3D photogrammetric elevation model

      Photogrammetry is a 3D measuring system that uses photographs. In this study, the Laetoli footprints were measured and photographed from two different locations. Lines of sight were developed from each camera to points on the footprint. The lines of sight were then used to mathematically produce 3D coordinates of the points of interest.

    4. faults/fractures

      Faults are cracks in Earth's crust due to movement. Fractures are cracks in Earth's crust along which there is no movement. A fracture is called a fault when stresses cause the rock surfaces along the fracture to move in opposite directions.

    5. other remains of Au. afarensis (Leakey et al., 1976; Johanson et al., 1978) and remarkable evidence of the earliest bipedal hominin tracks (Leakey and Hay, 1979; Leakey and Harris, 1987) dated to 3.66 million years ago (Ma) (Deino, 2011).

      The discovery of the first Laetoli trail during an expedition led by Dr. Mary Leakey helped to settle one of the great paleoanthropological debates. Some argued that upright posture and bipedalism had to evolve before the hands would be free to make tools. Stone toolmaking was thought to be the critical factor in the evolution of hominins. The analysis of hominid bones could not provide the answer. The discovery of the Laetoli footprints provided evidence that dated bipedalism to 3.6 million years ago. The earliest stone tools are known to be around 2.6 million years old. The feet came first.

    6. Australopithecus afarensis

      An extinct hominin species that lived between 3.9 and 2.9 million years ago. It is one of the longest lived and best known early human species.

    7. Our results

      Hear one of the authors of this paper, Marco Cherin, discuss the findings of this research in the eLife Podcast.

    8. femoral head

      Referring to the highest point of the thigh bone, called the femur.

    9. palaeontological locality

      An area where fossils of prehistoric organisms can be studied.

    1. wetland ecosystems

      An area of land that is saturated with water, either permanently or seasonally.

    2. CO2

      Carbon Dioxide gas.

    3. freshwater marsh

      A wetland that is dominated by leafy rather than woody plant species and is predominately freshwater.

    4. DAYCENT model

      A daily time series model used in ecosystems to simulate influxes of carbon and nitrogen between the atmosphere, vegetation, and soil.

    5. ppm

      Parts per million.

    6. C


    7. inundation


    8. hydric

      Very moist or containing large amounts of water.

    9. terrestrial


    10. will maintain current soil C pools

      Will not lose carbon (which is actually bad).

    11. NEE

      NEE stands for net ecosystem exchange, referring to the ecosystem's carbon cycle.

    12. GEE

      GEE stands for gross ecosystem exchange, referring to the ecosystem's carbon cycle.

    13. dry season

      The dry season in the Everglades is typically November through March.

    14. We explored a low, moderate, and high scenario for atmospheric CO2 concentration (550, 850, and 950 ppm, respectively: EPA and IPCC 2007) and each climate driver: mean annual air temperature (+1, +2.5, and +4.2°C; IPCC 2013) and precipitation (−2, +7, and +14%; IPCC 2013) (Fig. 4).

      Here, the authors explains how they ran different scenarios in the simulation system with the data they had collected in the field, making for more realistic results.

    15. maximum

      The highest temperature which will allow for production.

    16. optimum

      The temperature which is best for production.

    17. Fig. 2. Long-term daily weather data from the NCDC Royal Palm Ranger Station from 1963 to 2012. In climate change simulations weather data variability during 2000 to 2100 was based on variability at the Royal Palm weather station during 1963 to 2011 and weather data from TS and SRS in 2012.

      These data collected from 1963-2012 wereinputted into the DAYCENT system to simulate conditions during the next 100 years (from 2000-2100).

    18. Table 1. DAYCENT site characteristics for Taylor Slough (TS) and Shark River Slough (SRS). Site data was obtained from the Florida coastal Everglades Long-term Ecological Research (FCE LTER sites TS-1 and SRS-2), AmeriFlux and the literature.

      This table shows the two different sites, Taylor Slough (TS) and Shark River Slough (SRS) along with their exact location using the coordinate system, characteristics of each site, such as root:shoot ratio, soil composition, depth of roots, Nitrogen deposition along with the amount of Carbon found at each site.

    19. Periphyton

      A freshwater organism that is attached to plants above the bottom of sediments.

    20. C4 grass

      A C4 plant has light dependent reactions in its mesophyll cells and the Calvin Cycle in the specialized cells around the leaf veins. The 4-carbon organic acid, oxaloacetate is fixed from CO2. This is carried out by PEP carboxylase.

    21. C3

      Most types of plants are C3, meaning that it does not have photosynthetic adaptations to reduce photorespiration. It utilizes the Calvin cycle.

    22. hydroperiods

      The seasonal pattern of water levels in a specific wetland. Typically a wetland's hydroperiod is unique "signature" of that specific wetland.

    23. photorespiration

      A process where plants take up oxygen and give out some carbon dioxide.

    24. soil-plant-atmosphere continuum

      SPAC for short, is the pathway for water moving from soil through plants to the atmosphere.

    25. anthropogenic

      Environmental pollution usually caused by human activity.

    26. m

      Meter, measure of distance.

    27. g

      Gram, measure of weight.

    28. °C

      Degrees Celsius, measure of temperature.

    29. hydroperiod

      Seasonal pattern of the water level of a wetland.

    30. IPCC

      Intergovernmental Panel on Climate Change, a scientific and international body of experts under the United Nations.

    31. Hydrology

      The scientific study of the movement, distribution, and quality of water.

    32. watershed

      An area or ridge of land that separates waters flowing to different rivers, basins, or seas.

    1. morphospecies

      A species distinguished from others by its morphology —that is, its form/structure.

    2. recruited

      In ecology, refers to when new individuals join the population.

    3. (d.b.h.)

      Stands for diameter at breast height, which is the standard method of measuring tree trunks at the height of an adult's breast. It is now standardized to 1.3m above the ground.

    4. a priori

      Phrase that describes deductive reasoning made without reference to facts or experience, presumptive.

    5. ecosystem processes and services

      Also known as ecosystem functions, these are the biological, geochemical, and physical factors that take place in every ecosystem (including water, nutrient, and energy cycles).

      Services are the benefits that people gain from nature.

    1. There are several reasons why the Aleutian archipelago provides an ideal large-scale experimental system to study the effects of introduced predators: (i) Most islands are small; (ii) high-latitude floral diversity is relatively low; (iii) there are no native vertebrate herbivores; (iv) the islands are geologically and climatologically homogeneous with similar overall soil properties; (v) the large number of islands in the archipelago provides the opportunity for meaningful replication; (vi) the islands are isolated from anthropogenic nutrient inputs; and (vii) fox introductions were not targeted for particular island types, and the history of introductions is reasonably well known.

      The Aleutian Islands were chosen to be the place of study for many reasons, the main one being the similarity between the individual islands in the chain. The islands are of fair size, with similar soil makeup and weather. There are also numerous islands making the sample size large enough to be used for replication and to ensure the results were not due to chance. There was also the curious distribution of fox introductions that directly lead to a split in islands by type: fox-free vs. fox-infested.

    2. J. Terborgh et al., Science 294, 1923 (2001).

      In the paper by Terborgh et al., the different views on trophic cascades are investigated: top-down where predators limit herbivores and therefore prevent large destruction to vegetation, whereas bottom-up looks at the effects of plant defense in keeping predators at bay. This study touched upon the idea of top down interactions with the predation of seabirds by foxes having effects on plant communities, but in a more indirect way.

    3. terrestrial

      Relating to Earth or an organism residing on land. In this experiment, the foxes and plants are terrestrial organisms.

    4. avifaunas

      The birds of a particular geographic region, in this case seabirds such as; the lapland longspur and song sparrows that are being reduced by fox populations.

    1. Physics had to be modified

      It would be more accurate to say that the models used to describe physics had to be modified.

      As physics progressed, physicists revised their theories in light of new evidence and knowledge (and they continue to do so today). Here, Einstein describes how the special theory of relativity came about, in part, to solve the problem of classical mechanics' compatibility with electromagnetic theory.

      Modern physicists consider classical mechanics an approximate theory that is useful for the study of non-quantum mechanical, low-energy particles in weak gravitational fields. It is usually the starting point for students learning physics.

  4. Aug 2018
    1. archipelago

      A group of scattered islands within a larger body of water. In this case, the Aleutian archipelago is a grouping of volcanic islands located in the Pacific ocean that are under the possession of both the United States and Russia.

    2. biomass

      The total mass of an organism or multiple for any given area or plot. Usually refers to dried mass of plant matter from above or below ground.

    3. trophic levels

      Categorical feeding positions of groups of organisms in a food chain or web. Some common trophic levels would be primary producers (grasses), primary consumers (birds), and secondary consumers, (birds or foxes).

    1. T.C. LaJeunesse, Marine Biology 141, 387–400 (2002).

      Following LaJeunesse and Trench's 2000 publication on DGGE, this work expands on the applications, effectiveness, and usefulness of DGGE -a technique that separates DNA fragments.

    2. T.C. LaJeunesse, Journal of Phycology 37, 866–880 (2001).

      This work was used in this research since it is based on a characteristic molecular region in the Symbiodinium species.

    3. corals

      Dr. Rachel Levin and her team of researchers may have found a solution to minimize coral bleaching, which is caused by ocean warming and is a huge threat to coral reefs. She proposed a way to genetically modify Symbiodinum (a group of microalgae in corals) such that they may increase their stress tolerance to changes in ocean temperature and inherently save coral reefs.

      Read more in the Science Daily: https://www.sciencedaily.com/releases/2017/07/170720095111.htm

    4. T.C. LaJeunesse, R.K. Trench, Biological Bulletin 199, 126–134 (2000).

      Reviews the technique denaturing gradient gel electrophoresis (DGGE) and how it is used for molecular identification.

    5. R. Rowan, D.A. Powers, Marine Ecology Progress Series 71, 65–73 (1991).

      Gives background information on different types of amplification techniques used to determine molecular identification.

    6. D.L. Taylor, In: Symbiosis in the Sea (ed. Vernberg WB), pp. 245–262. (University of South Carolina Press, South Carolina, 1974).

      Prior to the introduction of molecular techniques, early work such as this reference discusses dinoflagellates and how they were thought to belong to one pandemic species.

    7. X. Pochon, R.D. Gates, Molecular Phylogenetics and Evolution 56, 492–497 (2010).

      Gives background information on the Symbiodinium genus for the reader to understand the main interest of the research in this paper.

    8. M.A. Coffroth, S.R. Santos, Protist 156, 19–34 (2005).

      Gives background information on the Symbiodinium genus for the reader to understand the main interest of the research in this paper.

    9. H.D. Freudenthal, Journal of Protozoology 9, 45–52 (1962).

      This reference explains why there are so many types of Symbiodinium.

    10. J.H. Connell, Science 199, 1302–1310 (1978).

      This information is used in order to introduce what species this research is going to focus on. Although the focus is on Symbiodinium, this information highlights the importance of this genus.

    1. Using a similar approach, Darrault and Schlindwein (2005) observed that proboscis width played an important role in pollen transfer efficiency in Hancornia speciosa (Apocynaceae).

      The two experiments are similar because they take proboscis dimensions into account. The previous experiment that the author is talking about, measured out the thickness of the proboscis and how they can be efficient in transferring pollen.

      In the experiment above, the author took into account on how the length and width of the proboscis can play a role in pollination. Since both the width and length of the proboscis were measured, more information was able to be attained. With these two different approaches, some differences can be taken into account and can be compared.

    2. Fig. 3.

      Figure 3 shows the number of pollen grains adhering on the y axis and on the x axis is the fishing line difference. There showed to be no significant difference between the line thickness as you can see from the lines on the graph the largest size fishing line showed the greatest amount of pollen grains.

    3. stigmatic

      Relating to the stigma.

    4. proboscides

      An elongated sucking mouthpart that is typically tubular and flexible, plural of proboscis.

    5. Kruskal–Wallis test

      Used to determine if samples come from the same distribution.

    6. We were unable to accurately calculate pollinator importance confidence intervals as we only estimated the relative frequency data (see above).

      Since much of the calculations were done using estimations, the authors could not provide a range of values that's likely to encompass the true value. For example, when scientists say this value falls within the 95% confidence interval it means that the intervals contain the true value 95 percent of the time and fail to contain the true value the other 5 percent of the time.

    7. Foraging behaviour was categorized by following visitor movements after they visited A. berteroi flowers. Visitation frequency of the floral visitors was estimated by counting the number of visits of each of the visitor groups to A. berteroi flowers during the observation periods where at least one visitor was seen, and calculating the corresponding percentage of the total visits observed in those periods.

      In order to determine the pollination efficiency of the insects, the authors tracked how often a specific visitor groups arrived and how long each individual stayed. Then the authors calculated an “efficiency” by estimating pollen on the visitors’ mouthparts. This was calculated as the average number of pollen grains per individual visitor of each group.

    8. Pollen grains were collected from the insect bodies to see whether visitors carried A. berteroi and/or other pollen.

      The reason behind this technique is to determine what species the carriers favored.

    9. We conducted pollinator watches weekly, for 3 h per week per site (12 intervals of 15 min per day), from 9:00 am to 12:00 pm (the hours with the highest visitation rates, B. B. Roque, personal observations) during the flowering period (April–June)

      The author monitored when the pollinators came around and interacted with the plants. Reason behind this is to determine how frequently the flower will have visitors. Another reason why the author monitored the plants, was to determine the period of time when the flower had the most visitors. With both of these factors being monitored, the author can determine more or less how frequently these plants can have their pollen spread throughout an area.

    10. anthers

      A structure in the flower which contains pollen.

    11. perennial

      A type of plant that persists for many growing seasons. Generally, perennial plants keep their leaves year round.

    12. Proboscis length is an important determinant of pollination efficiency

      It is well known that insects use their proboscides or mouthparts to sip nectar and collect pollen. However, according to new research, the proboscis actually works more like a paper towel than a straw.

    13. communities

      A gathering of species, excluding non-living factors.

    14. selective pressures

      Agents that condition organisms to have either a survival benefit or a disadvantage. Selective pressures drive natural selection. They can include environmental conditions, availability of food and energy sources, predators, diseases, and direct human influence among others.

    15. phylogenetic position

      Location on evolutionary tree based on physical or genetic characteristics.

    16. morphology,

      The study of the form and structure of organisms and their specific structural features. Floral morphology relates the to structural features of the flower.

    17. pollinator

      Any animal that, intentionally or not, takes pollen from one flower to another.

    1. The two known populations of C. jimenezii have a small number of individuals; however, it seems that stochastic events associated with drift and inbreeding have not been fully operating in these populations despite their very small size.

      Given how closely related and interbred they were, there was more genetic diversity in the Coccothrinax palms than expected.

    2. Linkage disequilibrium (LD)

      Refers to the non-random association of alleles at different loci in a given population. This experiment included a test for linkage disequilibrium (LD). To achieve this the researcher used ARLEQUIN v. which is an integrated software for population genetics data analysis. From this program they used the likelihood ratio test which tested for LD.

    3. loci

      The location or position in a chromosome of a particular gene. Plural of locus.

    4. SSR microsatellite

      Microsatellites, also known simple sequence repeats (SSRs) in plant genetics, are identified through sequencing. This research helps to identify the biological functions of the genes and how they affect the plant in terms of its genomic makeup.

    5. The Caribbean Island Biodiversity Hotspot has a high priority for conservation

      The Caribbean Island Biodiversity Hotspot has a great need to practice conservation since it has been subject to many events that are threatening of native species.

    6. endemic species

      Plants or animals that exist in one geographical location.

    7. hypersaline Lago Enriquillo

      A land-locked lake in Hispaniola that contains a high concentration of salt.