3,103 Matching Annotations
  1. Mar 2018
    1. insulator

      Material or substance that prevents the loss of heat to the environment.

    2. Our approach was to use long-term trends and interannual variability across the ITEX control plots to evaluate change in plant phenology in relation to temperature.

      Plant phenology changes were measured using trends and interannual variations.

    3. photoperiod

      The period of time every day that the plant receives light.

    4. anthesis

      The period at which the plant grows and opens its flowers.

    5. threshold

      The specific temperature that needs to be reached in order for a result to occur.

    6. Senescence

      The process of aging.

    7. bud

      A type of structure that develops on the stem of the plant which later grows into another part of the plant like a flower.

    8. evergreen

      Retaining green leaves throughout the year.

    9. forb

      Herbaceous plant without grass-like features in contrast to graminoids.

    10. synthesis

      A collection and combination of data.

    11. Ground-based phenological observations of individual plant species and growth forms have the potential to improve our understanding of the mechanisms behind the vegetation response to climate warming.

      Climate change brings about higher temperature which means more snow will melt in the arctic tundras. This might impact the growth of new plants in this environment.

      Read more in Livescience https://www.livescience.com/28406-arctic-tundra-turning-green.html

      Watch a video from National Geographic. https://voices.nationalgeographic.org/2016/11/17/climate-and-the-dividing-line-between-forest-and-tundra/

    12. heterogeneous

      Being different in structure or composition.

    13. deciduous

      Characteristic of shedding leaves.

    14. green-up

      The start of the growth cycle of a plant.

    15. Plant phenological responses to these increases in season length and temperature are uncertain, but understanding changes as they occur is essential for predicting future changes in tundra vegetation processes

      Constantly observing and following the seasonal changes that occur with these plants is very important in understanding the future of the plants and their habitat.

    16. heat sum thresholds

      The accumulated daily temperature required for plants to flower or start growing or produce fruits.

    17. moisture gradients

      The difference in moisture ( Liquid such as water present as vapor) between the inside and outside of a material like wood or soil.

    18. Tundra

      Region characterized by low temperatures, freezing soil and treeless terrain composed mainly of cold-resistant plants.

    19. trace gas

      Gas that is present in very small concentrations in the Earth's atmosphere.

    20. phenology

      Key seasonal changes in plants like the timing of flowering, especially in relation to climate.

    21. alpine

      Relating to high-elevation mountains.

    1. with many reports of butterflies and hawkmoths pollinating species of this family (Haber 1984; Darrault and Schlindwein 2005; Sugiura and Yamazaki 2005; Moré et al. 2007).

      Haber found that hawkmoths are frequent pollinators of these families, but require a significant nectar reward to do so.

      Darrault and Schlindwein found these butterflies and moths do pollinate. Furthermore, in contrast to this study, they found that diameter of the mouth parts showed no correlation with pollen collected.

    2. Many studies of other plant–pollinator systems provide evidence that the morphological match between the pollination apparatus and the length of the proboscis is associated with pollination effectiveness (Inouye 1980; Waser et al. 1996; Castellanos et al. 2004; Moré et al. 2012; Miller et al. 2014).

      Inouye found that proboscis length was correlated with a bee's time spent at a flower. Waser found that many pollination systems tend towards specialization.

      This implies that flowers adapt their shape and length to accomodate one group of pollinators. Length is a great determinant in these cases.

    3. In many self-incompatible Apocynaceae, flower revisitation increases the probability that self-pollen is deposited onto the stigma, leading to ovule and fruit abortion (Lipow and Wyatt 1999, 2000; Wyatt et al. 2000; Wyatt and Lipow 2007).

      Lipow and Wyatt found in multiple studies that self pollination in this family of plants prevents fruit bearing. This can be problematic, as it can decrease seed output. As such, it could create pressure for plants to evolve to punish revisitors.

    4. South Florida


      Given that bees are being shown to be very important pollinators, it is relevant that South Florida is currently undergoing efforts to preserve bee populations.

    5. Pollination success was quantified for these same flowers by recording the fruit production of visited flowers on the potted plants, maintained in the greenhouse. We placed at least 15 plants per day, each with one to three open flowers, over 20 days of observations, using a new set of plants each day. We recorded a total of 69 visits to over 400 flowers observed in this potted plant placement experiment. Pollination efficiency of each visitor group was assessed by comparing the percentage of visited flowers that produced fruit after a single visit.

      The success rate of the pollination was determined by recording the fruit produced by visited flowers. 15 potted plants having 1-3 open flowers were studied over 20 days, and a new set of plants was used every day. 69 total visits to over 400 flowers were observed throughout the course of the experiment.

    6. To determine the most effective pollinator, we placed 15 greenhouse-grown potted plants in the field to quantify pollination success at Site 3, the site with the highest visitation frequency (B. B. Roque, personal observations). On 20 different days during the flowering period, we compared the qualitative effectiveness of the different pollinator groups by allowing a single visit to individual flowers on the potted plants. Flowers that were ready to open prior to observation periods were bagged, while in bud, to exclude visitors. At the time of observation (from 9:00 am to 12:00 pm), bags were removed and flowers exposed to foraging insects. For a specific flower, pollinator visits were restricted to a single visit by one individual from one of the four groups of pollinators. After visitation, a flower was labelled (by pollinator group) and bagged to exclude subsequent visitors.

      For this experiment, the authors wanted to determine which was the best pollinator in relation to effectiveness. They grew 15 plants in the greenhouse and then placed them at the site with the highest number of visitors. Over 20 days, a single visit by pollinators was allowed for each individual flower. Bags were placed on the flowers whenever they were not being studied so as to avoid pollinator visits.

    7. To examine a possible relationship between line thickness and pollen deposition, we hand pollinated fresh flowers using fishing line of four different diameters. Each thickness was inserted into a fresh flower to the bottom of the corolla tube to collect pollen (as above); we then stained entire length of the fishing line with methylene blue to stain the adhering pollen grains and introduced the stained portion into another new fresh flower.

      In this experiment, fresh flowers were pollinated using four fishing lines of different diameters to simulate different proboscis diameters. The fishing lines were inserted into the floral tube in order to collect pollen. Then, the length of the fishing lines were stained blue. The fishing lines were re-inserted and the pollen that attached were stained blue. The same fishing lines were then inserted into other fresh flowers.

    8. To quantify the efficiency of each visitor group, we estimated pollen on the visitor mouthparts as the average number of pollen grains per individual visitor of each group.

      The authors counted average number of pollen grains per group, as well as time spent at each flower, and the behavior of the pollinator after leaving the flower.

      All of these metrics are important to pollination efficiency.

    9. We haphazardly selected plants with open flowers for each of the intervals.

      The authors use the word 'haphazardly' to indicate randomness in the sampling of the flowers. It is important to have randomness to avoid bias.

    10. The flowers have no notable fragrance, and offer viscous nectar as a pollinator reward, with the sugar concentration of the nectar ranging from 30 to 67 %

      This species has no fragrance and uses nectar as a reward with 30-67% sugar concentration as the reward.

    11. stigma

      This part of the flower collects the pollen that has been delivered, whether by wind or pollinators.

    12. foraging

      The process in which resources are searched for and gathered.

    13. Angadenia berteroi 

      A flower species that is known as the Pineland Golden Trumpet. This plant is native to Pine Rocklands.

    14. pollinia

      A mass of pollen grains. These pollen grains are the product of each anther lobe of some flowers (especially orchids). Single or paired pollinia are attached to, and carried by pollinating insects.

    15. Proboscis

      In many insects, the proboscis is the elongated sucking mouthpart that is typically tubular and flexible. Pollinators use this to suck the nectar of flowers.

    16. conspecific

      Refers to another organism of the same species.

    17. perianth

      The outer part of the flower, which consists of sepals and pedals.

    1. Solitary invasive orchid bee outperforms co-occurring native bees to promote fruit set of an invasive Solanum

      Does There Need To Be an "I" in Team? Loner bee excels in promoting fruit set on Invasive plant species Solanum when compared to socially outgoing native bees

    1. Why can’t we tickle ourselves (2)

      This article discusses how researchers are exploring why humans can't tickle themselves.

      Read more about self-tickling in Discover: http://discovermagazine.com/2014/sept/2-tickle-yourself-elmo

    2. ultrasonic vocalizations

      Noises rats make that are outside the range of human hearing.

  2. Feb 2018
    1. This suggests that the follower-aggregate dynamics are driven by self-organization


      Explain how the results support this conclusion

    2. closure


    3. snowballing


    4. The specific criterion for inclusion in the list was that the group explicitly expressed its support for ISIS, publishing ISIS-related news or propaganda and/or calling for jihad in the name of ISIS

      Author's experiments

      why did they choose these criteria? why are they important?

    5. Chechen origin focused in the Caucasus region near ISIS’s main area of influence in the Levant

      Author's experiments

      Please give background on why this is important

    6. We chose VKontakte for our pro-ISIS analysis because

      Author's experiments

    7. language-agnostic


    8. how support for an entity like ISIS develops online

      Author's experiments

      Question they're asking

    9. Recent research has used records of attacks to help elucidate group structure in past organizations for which the Internet was not a key component (3, 6, 12), the nature of attacks by lone-wolf actors (13), and the relationship between general online buzz and real-world events (14–16)

      Previous work

    10. ad hoc


    11. extremist


    1. DEET repellency

      DEET is a ubiquitous repellent known to effectively provide protection from many biting insects, particularly mosquitoes. Its exact interaction between itself and the organisms it targets are not yet fully known. Yet, what is understood is that it possesses two primary lines of negative feedback that act as a defense to prevent feeding. These two are the olfactory and gustatory levels. This, along with other smaller contributors are what give DEET its ability to deter insects

  3. Jan 2018
    1. Original publication date 11/01/1911 Reference 11


      This is me looking at my annotation as I annotate.

    1. P. F. A. Maderson, When? Why? and How?: Some speculations on evolution of vertebrate integument. Am. Zool. 12, 159–171 (1972).

      A 1970's review discussing the formation of integuments (hard, protective layers covering the body), scales, and hair.

      The paper explores the different hypotheses of the time, including scaled animals as precursors to nonscaled animals, ossified (bony) scales as a precursor to the scales found on today's reptiles, and the evolution of hair from sensory appendages.

    2. A. M. Turing, The chemical basis of morphogenesis. Philos. Trans. R. Soc. London Ser. B 237, 37–72 (1952).

      In this landmark paper, Turing proposes the reaction diffusion theory to explain morphogenesis.

      This theory states that when two chemicals react with each other they diffuse to form chemical gradients. These gradients form patterns that direct morphogenesis.

    3. Both models assume that the development of an anatomical placode and of a dermal papilla occurred, at a minimum, twice (once in birds and once in mammals) through the independent parallel co-option of the same set of signaling pathways (WNTs, β-catenin, EDAR, BMPs, and SHH).

      Previous models have tried to explain the apparent lack of homology by suggesting that anatomical placodes and dermal papillae developed at least twice (once in birds and once in mammals).

      Further, the models suggest that, although the anatomical placodes and dermal papillae in mammals and birds would have evolved independently, they would have came about through the co-option of the same set of signaling pathways.

    4. integument

      A tough outer protective layer.

    5. generates a new splice donor site (gt) 42 bases upstream of the wild-type donor site, thus generating a 14–amino acid deletion in the corresponding transcript (Fig. 3D).

      The authors found that the scaleless mutation is caused by the deletion of 14 amino acids in the EDF protein.

      Their analysis indicates that the deletion is caused by the insertion of a 688-base-pair fragment which changes the way the gene is spliced (a process by which noncoding sequences are removed from mRNA before a protein is transcribed).

    6. cDNA

      DNA synthesized from single-stranded RNA.


    7. ectodermal dysplasia syndrome

      A genetic disease affecting the growth of hair, teeth, nails, and sweat glands.

    8. caudal, spinal, cervical, ventral, humeral, and femoral

      Caudal: pertaining to the tail

      Spinal: pertaining to the spine

      Cervical: pertaining to the neck

      Ventral: pertaining to the underside or abdominal part of the body

      Humeral: pertaining to the humerus (a bone in the arm)

      Femoral: pertaining to the femur (a bone in the leg)

    9. whole-mount in situ hybridization (WMISH) with species-specific probes, we show that crocodile, lizard, and snake placodes all exhibit spatial expression of Shh

      WMISH is a common technique for visualizing the location of expressed RNAs in embryos.

      In this study, the authors used WMISH to show that Shh was expressed in the placode.

    10. in-frame deletion

      Because an RNA sequence is read three bases at a time, if the number of bases deleted is a multiple of three, it will not change the reading frame.

    11. material cracking

      Crocodilian scales are formed through exertion of force: Scale tissues are physically cracked by living materials, leading to unique patterns on each reptile's face.

    12. These results reveal a new evolutionary scenario where hairs, feathers, and scales of extant species are homologous structures inherited, with modification, from their shared reptilian ancestor’s skin appendages already characterized by an anatomical placode and associated signaling molecules.

      The authors found that the placode and the placode's signaling molecules are highly conserved—meaning they are found across many species. This study shows that the placode is responsible for the formation of many different structures such as feathers, scales, and hair.

    13. anatomical placode

      A thick, platelike structure in the ectoderm that is a site of development in early embryos.

    14. squamates

      Members of the order squamata, or scaled reptiles. They are the largest and most recent order of reptiles and comprise all lizards and snakes.

    15. we show for the first time

      To read a popular science version of this paper, check out Motherboard's article, which includes quotes from the author.


    16. placode

      A thickening of the ectoderm marking a site of future development of hair follicles, feathers, or teeth in the early embryo.

    17. fossil intermediate

      A transitional fossil that shows a transitional form between one species and another.

    18. These results indicate that all three characteristics (epidermal thickening, expression of epidermal placode markers, and expression of dermal Bmp4), that is, the presence of an anatomical placode, are required for proper development of scales in reptiles.

      Epidermal thickening, patterning of markers, and expression of dermal Bmp4, all characteristics of an anatomical placode, are necessary for reptiles to properly develop scales.

    19. R. B. Widelitz, T.-X. Jiang, J. Lu, C.-M. Chuong, b-catenin in epithelial morphogenesis: Conversion of part of avian foot scales into feather buds with a mutated b-catenin. Dev. Biol. 219, 98–114 (2000).

      Explores the role of β-catenin, which is expressed in the placode.

      When this protein was mutated in chickens, their feet were scaleless and they had abnormal feather growth.

    20. C. Blanpain, E. Fuchs, Epidermal stem cells of the skin. Annu. Rev. Cell Dev. Biol. 22, 339–373 (2006).

      Reviews the development of skin cells that give rise to hairs.

      A hair placode forms, allowing the expression of genes that direct skin cell and hair follicle development.

    21. J. M. Musser, G. P. Wagner, R. O. Prum, Nuclear b-catenin localization supports homology of feathers, avian scutate scales, and alligator scales in early development. Evol. Dev. 17, 185–194 (2015).

      Explores the relationship between feathers and scales.

      Visualization of the location and amount of β-catenin during the development of feathers and scales revealed similar patterns between the two. The authors concluded that feathers and scales share an evolutionary ancestor.

    22. D. Dhouailly, A new scenario for the evolutionary origin of hair, feather, and avian scales. J. Anat. 214, 587–606 (2009).

      Proposed the theory that mammalian hair evolved from glandular structures, whereas reptile and bird skin evolved from a thick protective coating.

    23. P. F. A.Maderson,Mammalian skin evolution: A reevaluation. Exp. Dermatol. 12, 233–236 (2003).

      A revision to a 1972 model of how mammalian hair evolved.

      This new model proposes that the development of hair was caused by mutations in patterning genes, which resulted in hair becoming more useful insulation.

    24. M. C. Milinkovitch, L. Manukyan, A. Debry, N. Di-Poï, S. Martin, D. Singh, D. Lambert, M. Zwicker, Crocodile head scales are not developmental units but emerge from physical cracking. Science 339, 78–81 (2013).

      This paper discusses the way that crocodile head scales form. Unlike feathers, hair, and other scales, crocodile facial scales are formed when growing cells physically crack to form unique patterns.

    25. It has been previously hypothesized (47) that reptilian scales are more similar to avian reticulate scales (covering the foot pad) than to both avian scutate scales (covering the anterior metatarsal region) and feathers

      It was previously thought that reptilian scales are more similar to some types of avian scales (such as those covering the foot pad) than others. However, the current study suggests that this is not the case.

      All avian scales develop from an anatomical placode similar to reptile scales.

    26. The squamate anatomical placode, whose existence had remained undetected because of its transitory developmental dynamic, exhibits all the major features characterizing avian and mammalian placodes: local epidermal thickening with columnar cells and reduced proliferation rate, shared early spatially restricted expression of epidermal molecular markers, and localized conserved signaling in the underlying dermis

      The major finding of this paper is that reptile scales develop from an anatomical placode, similar to mammalian hair and avian feathers.

      Scientists were previously unsure if this was the case because the reptilian anatomical placode is very short-lived during development (and thus hard to detect).

    27. The data presented here put this debate to rest by demonstrating that most skin appendages in amniotes, including snake and lizard overlapping scales, not only share signaling pathways during morphogenesis but also truly develop from anatomical placodes.

      The results here support the idea that most skin appendages in reptiles, mammals, and birds are homologous because they share signaling pathways and arise from an anatomical placode.

    28. Conversely, other authors argue that the similarities in molecular signaling observed among all skin appendages suffice to support their homology (9). Note that such placodal signaling centers have been recently evidenced as underlying the development of Chelonia shell scutes

      Some other models reject the idea that the placode and the dermal papilla evolved independently, suggesting that the similarities in the molecular signaling involved in development are sufficient to show that they are homologous (meaning the pathway evolved once, in a common ancestor).

      It is also suggested that this is true for turtles, which have been found to need the placode for the development of their shell.

    29. sebocytes

      A cell that secretes sebum, an oily substance that waterproofs and lubricates skin.

    30. The fossil record lacks any evidence of intermediate forms (hence, of homology) between scales and hairs.

      One of the major challenges of tracing an organism's evolutionary history is an incomplete fossil record. Where there is no intermediate between two forms, scientists have to use the available evidence to make predictions about what this intermediate would have looked like.

    31. keratinized

      To change to a form that contains keratine, a fibrous protein found in hair, nails, and hooves.

    32. Similarly, Ctnnb1 andEdar, two other placode markers, also show marked differences in expression between wild-type and scaleless dragons. In both phenotypes, expression of these two genes is first ubiquitous across the whole epidermis before becoming restricted to the placodes in wild-type individuals only (Fig. 4B). These results indicate that expression of each of these three placode markers in reptiles is similar to the expression dynamic of the corresponding genes in mammals (27) and birds (20, 28,39). On the other hand, the absence of an anatomical placode in scaleless dragons coincides with the inability of signaling pathways to pattern the skin, similar to what is observed in mice deficient in Eda/Edar(40).

      The authors demonstrate that Shh, Ctnnb1, and Edar expression is similar in reptiles, mammals, and birds. They also conclude that the absence of an anatomical placode in scaleless lizards disrupts these pathways' ability to pattern the skin, which has also been observed in mice (a mammal) with similar mutations.

    33. breeding experiments

      Individual lizards with different physical traits were bred together in order to observe how those traits were passed on to the offspring.

    34. cryosections

      Sections of tissue that are made in a cryostat, a device that keeps samples at a very low temperature to preserve them.

    35. BMP

      A group of signaling molecules responsible for coordinating development in many different parts of the body.

    36. each of these dermoepidermal elevations that generate scales in crocodiles, lizards, and snakes occurs at the location of a transient developmental unit that exhibits the characteristics (Fig. 1B) of the mammalian and avian anatomical placode

      The authors of this study expand on the findings of previous studies by showing that the elevations that result in scales correspond to the anatomical placode in mammals and birds, which gives rise to hair and feathers.

    37. skin developmental series (Fig. 1A) in crocodiles (Crocodylus niloticus), bearded dragon lizards (P. vitticeps), and corn snakes (Pantherophis guttatus)

      The authors took successive microscopic images of different body parts in both lizards and snakes, specifically focusing on the places that scales form.

    38. indicate that early scale morphogenesis in reptiles consists of regular dermoepidermal elevations that typically further develop into oriented asymmetrical scales with various levels of overlap, depending on the species and body area

      As was found in previous studies, scale development begins with the formation of risen areas on the skin. The symmetry and degree of overlap of the final scales depends on the species and location on the body.

    39. Extant

      Exists today.

    1. knockout

      A technique that allows a gene to be shut down and made nonfunctional. Researchers knock out genes to see what happens when they aren't active.

    1. warm mixed forest

      A temperate biome that is slightly warmer than the global average, marked by distinct seasons, sometimes with dry or rainy seasons. The forests are, as the name implies, of mixed composition. In this particular biome the predominant trees are broadleaf (ex: maple or oak) and conifers (ex: pine).

    2. temperate conifer forest

      A biome found in temperate regions with warm summers, cool winters, and enough precipitation to support coniferous trees ("evergreens").

  4. Dec 2017
    1. pleurodont

      Tooth fused to the inner edge of the jaw. They are loosely attached and can regenerate if lost.

    2. autopod

      Part of the limb farthest from the body, such as the hand or foot.

    3. similar phenotypes in other vertebrates because of impairments of the EDA receptor (EDAR; a member of the TNF family) (18) or its ligand EDA, indicating a conserved role of this pathway in reptiles as well

      Similar phenotypes are observed in other vertebrates (including mammals and birds) when the same pathway is interrupted. This suggests the pathway is conserved in reptiles, too.

    4. homozygous for a codominant mutation

      The scaleless bearded dragons have two copies of the same alleles (Sca). This gene is codominant, meaning both alleles are expressed even in heterozygotes.

    5. superposed

      Placed on top of one another.

    6. The most marked and derived macropatterning of skin in reptiles is observed in snakes

      Compared to other reptiles, snakes' scale development is unique.

    7. argued homologous to those characterized in chicken

      The authors found that the patterns between patterning of the tracts that give rise to chicken feathers and those that give rise to reptile scales could be homologous.

    8. spatiotemporal development is highly similar between the two species

      In Nile crocodiles and bearded dragons, scales developed from a similar anatomical placode and patterned similarly both spatially and temporally.

    9. feathers are organized into discrete tracts associated to different body areas

      In chickens, feathers develop in 10 distinct areas (tracts) which correspond to different parts of the body. These tracts develop at different rates and have their own patterning.

    10. Bmp4 is also shown for lizard. Red double-headed arrows indicate the body region processed for sectioning.

      The expression of Bmp4 in lizards strongly suggests a developmental evolutionary link among all reptiles, as well as birds and mammals.

    11. immunohistochemistry

      The use of antibodies to detect specific proteins in a tissue (using the principle that antibodies will selectively bind to certain antigens).

    12. proliferating cell nuclear antigen (PCNA) analyses indicate a reduced proliferation rate of the placode epidermal cells

      PCNA is a protein involved in cell division, so it is used as a marker to locate cells that are actively dividing.

      This analysis showed that the cells of the placode were reproducing very slowly.

    13. nested subpopulation

      A subset of a larger population.

    14. histological analyses

      Analysis of the structure of a tissue.

    15. This set of new results coherently and conclusively indicates that most skin appendages in amniotes are homologous

      The authors' results suggest that, because the anatomical placode is crucial to the development of skin appendages in mammals, birds, and reptiles, these appendages are homologous.

    16. wild-type

      The "typical" phenotype that is seen in nature.

    17. TNF

      The tumor necrosis factor (TNF) superfamily is a group of proteins involved in programmed cell death.

    18. codominant

      A type of dominance where two alleles of a gene in a heterozygote are fully expressed.

    19. that is, they are difficult to identify on any specific embryo because they establish multiple tracts whose developmental timing and locations vary across the body

      The authors believe that previous studies have overlooked anatomical placodes in reptiles because they are difficult to see during development.

    20. transitorily in time and nonconcurrently in space

      Placodes are very short-lived during development and do not form in the same place.

    21. associated with the presence of an anatomical placode presenting all the characteristics observed in avian and mammalian placodes

      The authors of this study provide evidence for the theory that hair, feathers, and scales are homologous structures.

    22. similarities in signaling are due to independent co-option of these molecular pathways

      Although some scientists think that the similarities in development of hair, feathers, and scales are evidence that they are homologous, others believe that they evolved independently.

      They propose that these pathways served a different function in the common ancestor of mammals, reptiles, and birds, and that they were only later co-opted for the development of hair, feathers, and scales.

    23. Several studies (9, 18–23) have shown that conserved signaling pathways, evidenced by the expression of the Sonic hedgehog (Shh), β-catenin (Ctnnb1), ectodysplasin A receptor (Edar), and/or bone morphogenetic protein (Bmp) genes, are involved in skin patterning and early morphogenesis of all amniote skin appendages

      Several signaling pathways involved in skin development and patterning are conserved across species. Different authors have reached different conclusions about whether these pathways are homologous or whether they evolved independently.

    24. dermoepidermal elevations

      Bumps in the layer that joins the epidermis (outer layer of the skin) and the dermis (middle layer of the skin).

    25. follicular organs

      Small, spherical groups of cells that contain a cavity from which hair, teeth, feathers, etc. can grow.

    26. scutate

      Covered by bony or horny plates or scales.

    27. avian

      Related to birds.

    28. homology

      Similarity of structure, physiology, or development of different species that is a result of a common evolutionary ancestor.

    29. discrete developmental units through reaction-diffusion

      Morphogens (chemicals which direct the development of different structures) interact to form gradients or concentrate in different parts of an organism. This leads to patterns in the placement and arrangement of appendages.

    30. lineage

      Refers to evolutionary lineage (species linked by a common ancestor).

    31. molecular markers

      Specific molecules that, when present, indicate the presence of a structure or a particular stage of development.

    32. columnar cells

      Cells shaped like columns.

    33. ectodysplasin A

      A protein involved in cell signaling between two layers of skin (ectoderm and mesoderm). It is especially important in embryo formation and promotes the formation of hair follicles, sweat glands, and teeth.

    34. histological

      Related to the study of tissues.

    35. co-option

      The process by which a structure or pathway that evolved for one function gains additional functions.

    36. common ancestry

      The idea that two species share an ancestor somewhere in their lineage. Common ancestry is visualized in a phylogenetic tree.

    1. F. A. Ran et al., Cell 154, 1380–1389 (2013).

      This study investigated offset nicking as a means of reducing off-target modifications. The authors found that by using Cas9 mutants with sgRNAs, a targeted double-stranded break can be performed. Off-target activity was reduced 50- to 1000-fold with this technique.

    2. K. T. Flaherty et al., N. Engl. J. Med. 363, 809–819 (2010).

      This study investigates the BRAF mutation in melanoma and the BRAF protein kinase inhibitor vemurafenib (PLX). The researchers found that PLX reduced tumor growth in cells that had a mutated BRAF gene.

    3. P. Mali et al., Science 339, 823–826 (2013).

      This study demonstrated that Cas9 is effective at introducing specific loss-of-function mutations in the genome and creating specific double-stranded breaks in DNA sequences.

    4. GeCKO can identify essential genes and that enrichment analysis of depleted sgRNAs can pinpoint key functional gene categories in negative selection screens.

      The significant decrease in the diversity of sgRNAs present at the end of the 14-day screen suggested that the GeCKO library was an effective way to identify survival genes.

      Because of this, the authors concluded that they could use this method to identify genes essential for cell function.

    5. when targeted to coding regions of genes can create frame shift insertion/deletion (indel) mutations that result in a loss-of-function allele

      Using a CRISPR RNA (crRNA) that is base-paired to a trans-activating crRNA (tracrRNA) will allow the scientists to direct the Cas9 to a specified area of the DNA and cause a double-strand break at the target location.

    6. The RNA-guided CRISPR (clustered regularly interspaced short palindrome repeats)–associated nuclease Cas9 provides an effective means of introducing targeted loss-of-function mutations at specific sites in the genome

      The CRISPR-Cas9 system can be used to target and remove specific sequences from DNA. This is done by using a guide RNA that directs the CRISPR/Cas9 system to the correct location in the DNA sequence.

    7. predominant method for genome-wide loss-of-function screening

      RNAi is triggered by double stranded RNAs, which are processed into small interfering RNAs (siRNAs). siRNAs target complementary RNAs for destruction, which inhibits gene expression and allows for creation of knockouts.

      Human and Drosophila RNAi libraries have been made to map out the effectiveness of RNAi and the knockout ability in particular genes. Vector-based short hairpin RNAs are artificial molecules that can be used to selectively target genes. Libraries of these molecules can be used for genetic screens in both short-term and long-term assays.

      Although RNAi is a very effective tool, there are sometimes problems with completely turning off specific genes or targeting the correct gene.

    8. Human Genome Project

      The Human Genome Project was an effort to map and understand all of the genes that make up the human genome. Although it was announced complete in 2003, we still have much to learn about the genome.

    9. GeCKO

      Genome-scale CRISPR knockout.

  5. Nov 2017
  6. Oct 2017
    1. L. A. Gilbert et al., Cell 154, 442–451 (2013).

      This study investigated how different Cas9 mutants are more effective for different situations.

    2. S. R. Whittaker et al., Cancer Discovery 3, 350–362 (2013).

      This study investigated PLX drug resistance in A375 cells. The authors found that NF1 is the most common mutation leading to PLX resistance, a finding that is supported by the current study. The Raf inhibitor vemurafenib was used in both studies. The authors in this paper used a pooled RNAi screen that targeted 16500 genes to look at loss-of-function mutations leading to PLX resistance.

    3. A. L. Jackson et al., RNA 12, 1179–1187 (2006).

      This paper investigates some of the unintended consequences of RNAi, such as the lack of specificity. While one sequence may be the target, other sequences could also be silenced in this process. If a sequence shows some complementarity to the target sequence, it may be targeted, as well. The paper predicts that perfect specificity will be difficult to achieve with RNAi.

    4. J. E. Carette et al., Science 326, 1231–1235 (2009).

      This study is another example of a loss-of-function screen. The initial experiment found host factors that were necessary for influenza infection, such as genes important for the synthesis pathway of diphthamide and genes that are necessary for cytolethal distending toxin. The authors knocked these genes out to investigate their effects.

    5. M. Boutros et al., Heidelberg Fly Array Consortium, Science 303, 832–835 (2004).

      This study uses RNAi to screen for loss-of-function alleles. The initial experiment tested the function of 91% of the genome of Drosophila. Testing was done by using an RNAi of the known 19,470 genes involved in cell growth and viability.

    6. Whereas RNAi reduces protein expression by targeting RNA, GeCKO introduces loss-of-function mutations into genomic DNA

      For more on the differences between RNAi and CRISPR, see this article in Genetic Engineering and Biotechnology News:


    7. which may be alleviated using an offset nicking approach

      Cas9 nickase creates a break in one strand of the double-stranded helix. These nicks are repaired with a very high fidelity.

      Using Cas9 with off-set sgRNA simultaneously nicks both strands, and may lead to a reduction of off-target modifications.

    8. Interestingly, although all five sgRNAs conferred resistance to PLX, only the best shRNA achieved sufficient knockdown to increase PLX resistance

      Not only did the authors find that GeCKO more consistently identified candidate genes, they found that the genes that were identified were better at providing PLX resistance.

    9. Western blot

      A technique used to determine which proteins are present in a sample.

    10. Lower P values for the GeCKO versus shRNA screen indicate better scoring consistency among sgRNAs

      The authors compared the top 100 hits in each screen and found that the sgRNA screen using GeCKO was more effective.

    11. we used several methods to evaluate the degree of consistency among the sgRNAs or shRNAs targeting the top candidate genes

      The authors compared GeCKO screening to a similar screen performed with shRNA.

    12. Our highest-ranking genes included previously reported candidates NF1 and MED12 (18, 19) and also several genes not previously implicated in PLX resistance, including neurofibromin 2 (NF2), Cullin 3 E3 ligase (CUL3), and members of the STAGA histone acetyltransferase complex (TADA1 and TADA2B)

      The RIGER algorithm identified NF1 (neurofibromin, a tumor suppressor protein that inhibits RAS), MED12 (helps regulate transcription of RNA polymerase II-dependent genes), NF2 (gene for merlin which is used to control cell shape, movement, and communication), CUL3 (plays a key role in the polyubiquitination and degradation of proteins as a component of the E3 ubiquitin ligase), TADA1 (subunit of STAGA a chromatin modifying complex of proteins), and TADA2B (promotes transcription by organizing HAT activity). All were implicated in PLX resistance.

    13. epigenetic

      Genetic changes that do not involve a change in DNA sequence and involve external or environmental factors.

    14. neurofibromatosis

      A genetic disease in which tumors develop on nerve tissue (including the brain, spinal cord, and nerves).

    15. These candidates yield new testable hypotheses regarding PLX resistance mechanisms

      The authors were able to identify new candidate genes for PLX resistance, and suggest that further research be done on how these genes confer this resistance.

    16. RNAi Gene Enrichment Ranking (RIGER) algorithm

      The authors used an algorithm to rank the genes enriched in their screen by how likely it is these genes contribute to PLX resistance.

    17. we found enrichment of multiple sgRNAs that target each gene after 14 days of PLX treatment (Fig. 3E), suggesting that loss of these particular genes contributes to PLX resistance.

      After 14 days, the authors saw a change in the distribution of sgRNAs in drug-resistant cells. From the new distribution of sgRNAs, they were able to identify genes that may contribute to PLX resistance.

    18. enrichment of a small group of cells that were rendered drug-resistant by Cas9:sgRNA-mediated modification.

      PLX exposure stops growth in cells with a specific BRAF mutation. Treating a group of cells with PLX will halt the growth of cells without resistance, but cells that are resistant to PLX will continue to grow. This allowed the researchers to isolate drug-resistant cells.

    19. we sought to identify gene knockouts that result in resistance to the BRAF protein kinase inhibitor vemurafenib (PLX) in melanoma

      To test the GeCKO library's effectiveness for positive selection (genetic variation that is beneficial to the cell), the authors tried to use it to identify which genes result in resistance to PLX.

      PLX is a BRAF enzyme inhibitor. BRAF is involved in the uncontrolled (cancerous) cell growth in melanoma.

    20. we conducted a negative selection screen by profiling the depletion of sgRNAs targeting essential survival genes

      To determine how effective the GeCKO library is at knocking out targeted genes, the authors first used a negative selection screen (which tests for deleterious effects).

      They infected cells with the library of sgRNAs. At the end of 14 days, they observed a reduction in the diversity of sgRNAs, as those sgRNAs that targeted genes necessary for survival were lost when cells died.

    21. we designed a single lentiviral vector to deliver Cas9, a sgRNA, and a puromycin selection marker into target cells (lentiCRISPR)

      For more on how lentiviral vectors aid in the use of CRISPR, see this article in Science


    22. endogenous

      Substances that naturally occur in a cell.

    23. We designed a library of sgRNAs targeting 5′ constitutive exons (Fig. 2A) of 18,080 genes in the human genome with an average coverage of 3 to 4 sgRNAs per gene (table S1), and each target site was selected to minimize off-target modification

      The authors produced a wide variety of sgRNAs that were used to find the 5’ end of constitutive exons, sequences that are constantly turned on and being used to create proteins.

    24. we tested the feasibility of conducting genome-scale CRISPR-Cas9 knockout (GeCKO) screening with a pooled lentiCRISPR library

      See AddGene for more information about designing sgRNAs and genome-scale sgRNA libraries (including the GeCKO library):


    25. lentiCRISPRs abolished EGFP fluorescence in 93 ± 8% (mean ± SD) of cells after 11 days

      The efficacy of gene knockout by lentiCRISPR transduction was high. The sgRNAs eliminated 93+/- 8% of EGFP fluorescence in the experiment.

      Further, lentiCRISPR transduction was more effective than transduction of cells with lentiviral vectors expressing EGFP-targeting shRNA, which produced an incomplete knockdown of EGFP.

    26. transduction

      The process of genetic material being incorporated into a cell through the use of a virus.

    27. they can be easily titrated to control transgene copy number and are stably maintained as genomic integrants during subsequent cell replication

      Lentiviral vectors are commonly used for gene insertion because of their stability. It is easy to control the number of vectors, and once integrated into the gene the inserted DNA segment is likely to stay there.

    28. Lentiviral vectors

      Lentiviruses are a group of viruses that incorporate their own RNA into the DNA of the host cell they infect. They can infect both dividing and nondividing cells.

      Modified lentiviruses that carry experimental RNA molecules are called "lentiviral vectors." Researchers can use them to insert, modify, or delete genetic material in an organism.

    29. potential of Cas9 for pooled genome-scale functional screening

      As noted above, genome-wide screening has been successfully performed with RNAi. Here, the authors wanted to know if CRISPR could offer a more accurate and precise way to screen genomes.

    30. oligonucleotide

      Short DNA or RNA molecules that form a chain of approximately 20 nucleotides.

    31. single-guide RNA (sgRNA)

      A synthetic RNA that guides Cas9 to a specific spot on a DNA molecule.

    32. RNA interference (RNAi)

      A process that uses RNA molecules to inhibit genes, usually by destroying specific messenger RNA.

    33. therapeutic RAF inhibitor

      A type of drug used to treat cancers. These drugs help regulate genes that are disrupted by cancer.

    34. melanoma

      A cancer in the pigment-producing cells of the skin.

    35. library

      Compilation of DNA fragments which can be used to determine which genes in a genome to alter and knock out.

    36. the promise of genome-scale screening with Cas9

      For more on possible future uses of CRISPR-Cas9, see this article in Science Daily:


    37. interrogate


    38. CRISPR

      A technique that allows for targeted changes in the genome by cutting, replacing, and adding gene sequences.

    1. monogenic neurological disorders

      Disorders caused by a single gene.

    2. homozygous deletions

      Deletions in which the genetic information is missing on both chromosomes.

    1. Scaleless dragons show an irregular skin surface with the initiation of some dermoepidermal undulations of the skin (Fig. 3G), indicating that this phenomenon does not fully require the presence of anatomical placodes.

      Mutant dragons displayed evidence of scale patterns, despite the absence of fully formed scales. This shows that there are factors other than the anatomical placode at play in scale formation.

    2. morphogenesis

      The formation of an organism's structures and features.

    1. narrow-and-deep approach

      This refers to results of studies that go into detail on a specific area, without covering a wide range of different topics.

    2. (such as experience and expertise)

      The expertise of researchers conducting the replication attempts has been the topic of much debate.

      In a recent study, Protzko and Schooler have conducted a study on the question whether researchers' "caliber" influences their success in reproducing studies.

      Read more in PsyArXiv Preprints:


    3. Also, the replication “succeeds” when the result is near zero but not estimated with sufficiently high precision to be distinguished from the original effect size.

      Here, the authors describe a problem of judging the replication success by evaluating the replication effect against the original effect size. When the replication effects size is near zero, it could be possible that the data shows no effect, and therefore we would find an unsuccessful replication attempt.

      However, the estimation of the effect size could be imprecise. This means that there could be a lot of “noise” in the data, from random or systematic errors in the measurement. If there was a lot of noise in the data, it could distort our impression of whether the effect is really zero or not.

      We might conclude that a replication with an effect size close to zero was sufficiently different from zero and thus successful, although the effect was really just produced by noise in the data, and the true effect is zero, meaning that the replication could be falsely taken as a success.

    4. A key weakness of this method is that it treats the 0.05 threshold as a bright-line criterion between replication success and failure (28)

      Braver, Thoemmes, and Rosenthal (28) argue that judging the success of a replication only by whether it shows a significant effect (in the current study, at the 0.05 threshold) would be inappropriate.

      They argue that replication success depends a lot on the statistical power and therefore on the sample size used in the replication study. The replication study must have sufficiently many subjects so that it is probable enough that the effect in question, should it really exist in the population, can be found in this sample. If a replication study had low power, for example because the size of the original effect was overestimated and the replication sample size was consequently too small, this makes it less likely that the replication attempt will be successful and show a result that is statistically significant at the 0.05 threshold.

      For each individual replication study, the replication success therefore depends on the sample size. If you assess several replication attempts individually, the replication success rate could therefore be distorted to underestimate how reproducible an effect really is.

      To circumvent this problem, the authors suggest using a different technique than counting if individual replications were significant at the 0.05 threshold. They analysis is called “continuously cumulating meta-analysis”. The data of several replication attempts are combined, so that conclusions on whether the data of all the replication attempts supports the effect of interest.

      After a new replication attempt is conducted, its data is added to the pool of data from previous replication attempts. This data is then taken together, and on the combined data, a test is run to estimate the effect of interest.

    5. Results

      The authors used 5 measures for replication success to check to what extent the 100 original studies could be successfully replicated.

    6. The overall replication evidence is summarized in Table 1 

      The authors wanted to know if successfully replicable studies differed from studies that could not be replicated in a systematic way. As the criterion for replication success, they used their first approach (significance testing). They found that studies from social psychology and studies from social psychology journals were less likely to replicate than those stemming from cognitive psychology and cognitive psychology journals. Moreover, studies were more likely to replicate if the original study reported a lower p-value and a larger effect size, and if the original finding was subjectively judged to be less surprising. However, successfully replicated studies were not judged to be more important for the field or conducted by more experienced research teams.

    7. and 25%

      Prinz and colleagues (11) comment on their experience as employees of a pharmaceutical company, which relies on preclinical research to decide whether to invest into the exploration and development of new drugs. Because companies find many preclinical research findings unreliable, they now often conduct their own research to reproduce the original findings before they decide to move on and invest large sums of money into the actual drug development.

      Only in about 20% to 25% of the cases did the company scientists report finding results of the reproduction that were in line with the originally reported findings.

    8. in only 11

      Begley and Ellis (10) are cancer researchers, who propose ways for research methods, publication practices and incentives for researchers to change so that research would yield more reliable results, such as more effective drugs and treatments. They argue that often new drugs and treatments enter clinical trials, which test their effectiveness to treat cancer in humans, before they reach sufficient standards in preclinical testing, leading to non-reproducible findings. To achieve more reliable preclinical results, they argue that more focus should be placed on reproducing promising findings in the preclinical phase.

    9. insufficient specification of the conditions necessary or sufficient to obtain the results (12–23)

      Making an experimental setup transparent and reproducible can be quite difficult, because undetected but theoretically relevant variations to the study protocol could produce different results. However, there are some new ideas about how such transparency could be achieved.

      Read more in The New Yorker: http://www.newyorker.com/tech/elements/how-methods-videos-are-making-science-smarter

    10. psychology or other disciplines

      Reproducibility has become the focus of attention in many areas of science. So far, you have read about examples from cancer research and biology, as well as pharmaceutical research. Another scientific discipline that has recently begun addressing the topic of reproducibility is the field of economics. In their approach to evaluating the reproducibility of studies in experimental economics, Camerer and colleagues have also used a somewhat different methodology.

      Read more in Science:


    11. Moreover, correlational evidence is consistent with the conclusion that variation in the strength of initial evidence (such as original P value) was more predictive of replication success than was variation in the characteristics of the teams conducting the research (such as experience and expertise).

      From this study, we can conclude that the efforts made to reduce the influence of the researchers involved in the replication studies on replication success seemed merited. Importantly, replication success was less influenced by the characteristics of the replication team than by how strong the results of the original study were. Stronger evidence for the effect the original study investigated was related to a successful replication.

    12. The disadvantage of the descriptive comparison of effect sizes is that it does not provide information about the precision of either estimate or resolution of the cumulative evidence for the effect.

      For the fourth measure, the authors combined the original and replication effect sizes and calculated a joint estimation of the effects. They wanted to see how many of the studies that could be analyzed this way would show an effect that was significantly different from zero if the evidence from the original study and that of the replication study was combined.

      Results showed that 68% of the studies analyzed this way indicated that an effect existed. In the remaining 32% of the studies, the effect found in the original study, when combined with the data from the replication study, could no longer be detected.

    13. A complementary method for evaluating replication is to test whether the original effect size is within the 95% CI of the effect size estimate from the replication.

      A second way to evaluate the replication success was to compare the sizes of the effects of the original studies and those of the replication studies using confidence intervals (CIs). They checked if the effects size of the original study was a value that was also among the range of values revealed as good estimates of the true effect size in reality, which was calculated from the size of the effect in the replication study.

      Using this measure, they found that slightly fewer than half the replications were successful.