929 Matching Annotations
  1. Jun 2019
    1. 20. T. Schmader, M. Johns, M. Barquissau, Sex Roles 50, 835 (2004).

      Schmader, Johns, and Barquissau found that the level of endorsement of the stereotype that men are better than women at math was a moderating variable for gender performance.

      Women who more strongly endorsed the stereotype performed worse.

    2. 31. G. L. Cohen, J. Garcia, V. Purdie-Vaughns, N. Apfel, P. Brzustoski, Science 324, 400 (2009).

      Cohen et al. found that an initial values affirmation intervention could have long-lasting positive effects.

    3. 30. A. Martens, M. Johns, J. Greenberg, J. Schimel, J. Exp. Soc. Psychol. 42, 236 (2006).

      Martens et al. showed that values affirmation was effective under laboratory conditions.

    4. 29. J. D. Creswell et al., Psychol. Sci. 16, 846 (2005).

      Creswell et al. identified a physical reaction to stereotype threat, and found that values affirmation reduces this reaction.

    5. 23. G. L. Cohen, J. Garcia, N. Apfel, A. Master, Science 313, 1307 (2006).

      Cohen et al. performed a large scale examination of the efficacy of values affirmation in an authentic classroom environment. They tested whether a simple intervention could reduce the effects of stereotype threat for African American students. 

      They found that having students complete a short writing exercise, in which they wrote about a value they found important (values affirmation), reduced the gap in performance between African American students and other students.

    6. 22. C. Good, J. Aronson, M. Inzlicht, Appl. Dev. Psychol. 24, 645 (2003).

      Good, Aronson, and Inzlicht assessed whether specific kinds of mentoring could reduce the effects of stereotype threat in female, minority or low-income seventh-graders.

      They found that students paired with a college-student mentor who either 1) encouraged them to view intelligence as malleable, or 2) told them to attribute academic difficulties to the novelty of the educational setting, performed much better than students who did not get this framing.

    7. 13. M. Lorenzo, C. Crouch, E. Mazur, Am. J. Phys. 74, 118 (2006).

      Using more interactive teaching methods has been shown to improve conceptual understanding for students in college-level physics compared to traditional lecture-based teaching.

      Interactive teaching has also been shown to reduce the gap in performance between women and men.

    8. 6. S. J. Pollock, N. D. Finkelstein, L. E. Kost, Phys. Rev. Spec. Top. Phys. Ed. Res. 3, 010107 (2007).

      Kost, Pollock, and Finkelstein performed the initial assessment of the gender achievement gap in college students taking introductory physics at the University of Colorado at Boulder.

      They found that most (but not all) of the gender achievement gap, could be attributed to previous preparation in the field.

    9. 21. T. Schmader, M. Johns, C. Forbes, Psychol. Rev. 115, 336 (2008).

      Schmader, Johns, and Forbes suggest that stereotype threat might affect women's performance through three interconnected mechanisms:

      1) It causes a physical stress response that can impair some aspects of brain function, reducing the baseline level of mental resources.

      2) It causes women to actively monitor their performance, taking valuable mental resources away from the assigned task.

      3) It causes women to actively repress negative feelings and thoughts, which also consumes mental resources.

    10. 18. S. J. Spencer, C. M. Steele, D. M. Quinn, J. Exp. Soc. Psychol. 35, 4 (1999).

      Spencer, Steele, and Quinn performed some of the original experiments showing that the stereotype that men are better at math than women affected women's performance on math tests.

    1. J. A. Kessler, J. E. Adler, M. C. Bohn, I. B. Black, Science 214, 335 (1981); J. A. Kessler, J. E. Adler, W. O. Bell, I. B. Black, Neuroscience 9, 309 (1983)

      In these studies, the authors examined the role of the neurotransmitter substance P in nerve ganglia. The authors confirmed that the activity of substance P is dependent on sodium currents, changes within the cell, and impulsive activity.

    2. J. E. Adler and I. B. Black, Science, in press

      Given that the plasticity occurs during development, the authors tested whether the plasticity can be observed in mature neurons as well. The authors performed these experiments in ganglia of young and old rats and assessed the changes in neurotransmitter, substance P.

      The substance P had a significant increase in expression at young age and at six months of age but not two-year old rats.

    1. D. B. Kandel, Stages and Pathways of Drug Involvement: Examining the Gateway Hypothesis (Cambridge Univ. Press, Cambridge, UK, 2002), pp. 3–15

      The book chapter introduces the concept of gateway hypothesis – a model to inform how teenagers initiate and progress in the usage of illicit drugs. The chapter addresses these crucial questions from various fronts – neurobiology, animal studies, and epidemiological studies.

    2. F. E. Pontieri, G. Tanda, F. Orzi, G. Di Chiara, Effects of nicotine on the nucleus accumbens and similarity to those of addictive drugs. Nature 382, 255–257 (1996).

      The article addresses a fundamental question: is nicotine a habit-forming drug or an addictive drug? The authors performed experiments in mice and concluded that nicotine shares several biological aspects with the drugs of abuse.

    3. J. A. Kauer, R. C. Malenka, Synaptic plasticity and addiction. Nat. Rev. Neurosci. 8, 844–858 (2007)

      The review presents the available evidence that the drugs of abuse can alter the synaptic plasticity mechanisms in the dopaminergic circuit, the key pathway to processing reward in the brain.

    4. A. Kumar, K. H. Choi, W. Renthal, N. M. Tsankova, D. E. Theobald, H. T. Truong, S. J. Russo, Q. Laplant, T. S. Sasaki, K. N. Whistler, R. L. Neve, D. W. Self, E. J. Nestler, Chromatin remodeling is a key mechanism underlying cocaine-induced plasticity in striatum. Neuron 48, 303–314 (2005)

      The authors show that the cocaine, a drug of abuse, can activate genes at core histones, which can lead to a restructuring of chromatin. This restructuring could have an effect on long-lasting changes in the animal, for instance, modulating the body movements

    5. A. A. Levine, Z. Guan, A. Barco, S. Xu, E. R. Kandel, J. H. Schwartz, CREB-binding protein controls response to cocaine by acetylating histones at the fosB promoter in the mouse striatum. Proc. Natl. Acad. Sci. U.S.A. 102, 19186–19191 (2005).

      The authors show that the cAMP response element binding protein (CREB)-binding protein (CBP) acetylate histones at the FosB promoter in the mouse striatum, thereby regulating the responses to cocaine.

      The authors confirmed this finding by repeating this experiment in mice lacking a copy of the CBP gene. These mice exhibited a decrease response to cocaine than the animals that had an intact copy of the CBP gene.

    1. R. T. Paine, Am. Nat. 103, 91 (1969)

      In this letter, Paine notes the importance of predators to community stability not only to the system that he studied (the intertidal of the Pacific Northwest) but also that of other simple or complex systems worldwide.

    2. J. A. Estes, D. O. Duggins, Ecol. Monogr. 65, 75 (1995).

      In this observational study of 153 sites, over the course of 3-15 years, the importance of sea otters to the community structure of the kelp forests of the Aleutian Islands and Alaska. Without sea otters, the kelp forests collapsed due to overgrazing by urchins and other herbivores, leading to implications for numerous other organisms in the system. With sea otter predation on urchins, the kelp system was stable and supported a much higher diversity of organisms at all trophic levels (Fig 3).

    3. R. T. Paine, J. Anim. Ecol. 49, 667 (1980)

      A discussion of food webs, trophic relationships, species connectedness, and whether community structure and stability could be modeled based on these ideas.

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

      In this natural experiment, a result of a hydroelectric dam flooding a rainforest in Venezuela, researchers were able to measure the results of predator removal in isolated communities. Top-down regulation of these communities were discovered with drastic trophic cascades observed.

    5. N. G. Hairston, F. E. Smith, L. B. Slobodkin, Am. Nat. 94, 421 (1960)

      The authors highlight 5 lines of reasoning to underscore the importance of predators as top-down controls:

      1) the rate of planetary fossil fuel accumulation over time has not been minuscule as compared to the rate of photosynthesis in the same systems;

      2) given this, decomposers must be food-limited otherwise fossil fuels would build up at higher rates;

      3) in terrestrial systems, plants are typically not herbivore-controlled nor are they regularly destroyed by weather but are controlled by bottom-up factors such as light, water, and nutrients;

      4) terrestrial herbivores are therefore typically not limited by their food supply, even in areas where the primary consumers are overabundant;

      5) herbivore populations are therefore controlled by predators.

    6. M. E. Power, W. J. Matthews, A. J. Stewart, Ecology 66, 1448 (1985)

      This seminal paper on the indirect effects of predation in freshwater rivers demonstrated that the trophic cascades previously seen in marine and terrestrial systems also held true for river ecosystems.

  2. May 2019
    1. K. M. Kendrick, M. R. Hinton, B. A. Baldwin, Brain Res. 550, 165–168 (1991).

      Kendrick and colleagues measured GABA in the ZI in live sheep. They found that in food-deprived animals, GABA was increased in the ZI upon the sight and ingestion of food. This response did not occur when a non-food object was presented.

    2. 13. J. S. Lee, E. Y. Lee, H. S. Lee, Brain Res. 1598, 97–113 (2015).

      The authors performed retrograde mapping from the PVT and showed that neurons in the ZI directly project to the PVT. These cells were shown to express the protein cocaine- and amphetamine-related transcript (CART).

    3. 18. B. A. Stamoutsos, R. G. Carpenter, L. Grossman, S. P. Grossman, Physiol. Behav. 23, 771–776 (1979).

      The authors show that rats administered with 2-deoxy-D-glucose (2-DG) increase their food intake while this is abolished in animals with ZI lesions. 2-DG is a modified glucose molecule that inhibits the breakdown of glucose, leading to low levels of blood glucose. This increases food intake in order to restore blood glucose levels. The reduced food intake in 2-DG treated rats with ZI lesions suggests that the ZI is necessary for food intake in response to low blood glucose.

    4. 19. Y. Aponte, D. Atasoy, S. M. Sternson, Nat. Neurosci. 14, 351–355 (2011)

      This paper was one of the first to show that two populations of neurons in the arcuate nucleus of the hypothalamus have opposing effects on food intake. They demonstrated that opotogenetic activation of AgRP-expressing neurons increases food intake while activation of POMC-expressing neurons decreases food intake.

    1. F. H. C. Crick, L. Barnett, S. Brenner, R. J. Watts-Tobin, Nature 192, 1227 (1961)

      In this seminal Nature paper, Crick and co-workers demonstrate that a group of three bases codes for one amino acid; the code does not overlap; the sequence of bases is read from a fixed starting point; and the code is degenerate.

    2. F. H. C. Crick, in Progress in Nucleic Acid Research, J. N. Davidson and Waldo E. Cohn, Eds. (Academic Press, New York, in press).

      This review paper is an extended version of the paper you've read here with sections dedicated to similar questions such as: "Is the code universal?" and "Is the code overlapping?"

    3. G. von Ehrenstein and F. Lipmann, ibid. 47, 941 (1961)

      Von Ehrenstein and Lipmann demonstrate the genetic materials of a rabbit (a mammal) and E. coli (a bacterium) are compatible, suggesting the genetic code is universal!

    1. 18. M. N. Weedon et al., Nat. Genet. 40, 575–583 (2008).

      Weedon et al. concluded that the HMGA2 was one of several that has a role in influencing height in adult humans.

    2. 23. P. R. Grant, B. R. Grant, Biol. J. Linn. Soc. London 117, 812–822 (2016).

      Introgression, the movement of a gene from one species into the gene pool of another, has been known to speed up a population's response to an evolutionary selective pressure. It does this by increasing genetic diversity.

      Grant and Grant documented recurring introgressive hybridization between medium ground finches and small ground finches.

    3. 19. G. Fatemifar et al., Hum. Mol. Genet. 22, 3807–3817 (2013).

      Fatemifar et al. (2013) showed that HMGA2 is associated with craniofacial features, such as the width of the eye region, the width of the lower part of the nose, and the height of the mid-brow prominence.

    4. 17. X. Zhou, K. F. Benson, H. R. Ashar, K. Chada, Nature 376, 771–774 (1995).

      Zhou (1995) found that, in mice, mutant alleles sometimes arise from deleted DNA or from chromosomal inversions.

      When these mutations cause the protein Hmgi-c to inactivate and not be expressed in mice, the result in dwarfism. This protein is associated with the HMGA2 gene.

    5. 16. K. Pfannkuche, H. Summer, O. Li, J. Hescheler, P. Dröge, Stem Cell Rev. Rep. 5, 224–230 (2009).

      Pfannkuche and colleagues (2009) found that HMGA2 is an important factor in embryonic stem cells and seems to magnify other factors, such as the regulation of body height in humans, the repression of certain genes, and several other functions.

    6. 3. W. L. Brown Jr., E. O. Wilson, Syst. Zool. 5, 49–64 (1956).

      Brown and Wilson (1956) argued that character displacement was a common part of geographical speciation. They explained that displacement happened most often as a product of genetic and ecological interaction when species first met.

    7. 11. P. R. Grant, B. R. Grant, Science 313, 224–226 (2006).

      Grant and Grant (2006) reported that the finch species Geospiza fortis diverged in beak size from one of its competitors, G. maguirostris. This divergence happened on an isolated Galapagos island 22 years after G. maguirostris arrived to share a habitat with G. fortis.

    8. 13. P. R. Grant, B. R. Grant, Evolution 48, 297–316 (1994).

      Grant and Grant (1994) explored hybridization among finch species over 17 years. They concluded that hybrid traits were morphologically intermediate, which indicated the parent genes contributed to the offspring phenotype equally. Hybrids also varied more phenotypically.

    9. 14. A. Abzhanov, M. Protas, B. R. Grant, P. R. Grant, C. J. Tabin, Science 305, 1462–1465 (2004).

      Abzhanov and colleagues (2004) analyzed various growth factors that were known to be expressed during craniofacial development of birds. When looking at Darwin's finch species, some factors showed simply showed no correlation while other factors showed a correlation with beak size, but not beak shape.

      However, researchers did find that the expression of the Bmp4 molecule had strong association with both beak size and shape.

    10. 15. S. Lamichhaney et al., Nature 518, 371–375 (2015).

      The previous tree from Lamichhaney and colleagues in 2015 showed that the initial split between warbler finches and other finches happened 900,000 years ago. Rapid divergence of ground and tree finches occurred 100,000 - 300,000 years ago.

    1. 20. Y. Zheng, C. Lorenzo, P. A. Beal, Nucleic Acids Res. 45, 3369–3377 (2017)

      The authors showed that ADAR proteins were able to deaminate adenosines not only in RNA duplexes but also in RNA-DNA heteroduplexes.

      While this work was done in vitro, it may help understand the functions of ADAR in the cell, specifically the link between ADAR impairment and the autoimmune disease Aicardi-Goutieres Syndrome (AGS). Also it may be used as a new tool for DNA editing techniques.

    2. 10. O. O. Abudayyeh et al., Science 353, aaf5573 (2016).

      A large group of scientists from several labs conducted an extensive study on the protein C2c2 (now known as Cas13a). They demonstrated that C2c2 was an RNA-guided RNA nuclease and predicted that it would be an important tool for RNA targeting.

      Moreover, they showed that in vitro C2c2 once activated by the target binding could cleave not only the target but also the surrounding mRNA molecules. The authors termed this effect "the collateral cleavage."

      https://youtu.be/RtYEiyoMOlM

    1. A. Z. Szeri, Tribology: Friction, Lubrication, and Wear (Hemisphere, Panama City, Panama, 1980)

      This book provides an overview of theory and practice of tribology, that is, the science of interacting surfaces in motion.

    2. C. Lee et al., Science 328, 76–80 (2010).

      This study compares the nanotribological properties of atomically thin sheets of 2D materials such as graphene, molybdenum disulfide, boron nitride, and Niobium diselenide using friction force microscopy. The dependence of friction on the number of atomic sheets and substrate effect are also reported.

    3. A. Erdemir, C. Donnet, J. Phys. D Appl. Phys. 39, R311–R327 (2006).

      This review outlines the synthesis, characterization, and applications of DLC films. The mechanism of friction and wear behaviors of DLC films and the conditions to achieve superlubricity are reported.

  3. Apr 2019
    1. M. Eddaoudi et al., Science 295, 469–472 (2002)

      A systematic study on the influence of the organic linkers on the pore properties of a metal-organic framework. In this work, the authors use the same metallic cluster as a base and demonstrate how the small molecule linkers can be functionnalized to tune its properties.

    1. M. P. Baldwin et al., Geophys. Res. Lett. 21, 1141 (1994).

      Baldwin et al. described the relationship between the stratosphere and the troposphere. Changes to stratospheric circulation can, in turn, affect tropospheric weather patterns. This study notes that the North Atlantic Oscillation (NAO) was the pattern most strongly related to wintertime changes in stratospheric temperatures and circulation.

    2. D. T. Shindell et al., Nature 399, 452 (1999).

      Shindell et al. described the importance of modeling stratospheric atmosphere dynamics to improve predictions of global climate conditions. They also determined that it was possible to program climate models to simulate climate patterns like the Arctic Oscillation when including greenhouse gas concentrations. This suggested that greenhouse gases can influence regional climates.

    3. R. W. Reynolds and T. S. Smith, J. Clim. 7, 929 (1994)

      This was a pivotal paper in helping to develop a method of correcting satellite temperature data. By using satellite measurements over the early 1990s during the time of the Mount Pinatubo eruption, Reynolds and Smith were able to factor out the volcanic aerosols for a more accurate measurement of global temperatures.

    4. R. Dickson, J. Lazier, J. Meincke, P. Rhines, J. Swift, Prog. Oceanogr. 38, 241 (1996).

      This paper reviews the recent history of North Atlantic changes in convection and deep water formation. Waters are mixed downwards in the Greenland and Labrador Seas, but this study found that these locations are currently at opposite convective extremes.

      The authors proposed that atmospheric forcings (such as the North Atlantic Oscillation) are influencing the location and quantity of water sinking into the deep ocean.

    5. J. R. N. Lazier, in Natural Climate Variability on Decade-to-Century Time Scales, D. G. Martinson et al., Eds. (National Academy Press, Washington, DC, 1995), chap. 3, pp. 295–302

      "Approaches to studying the ocean's role in climate can be divided into two types: understanding and modeling the ocean as part of the fully coupled climate system, and observing, quantifying, and modeling the dynamics of the ocean itself."

      This comes from Lazier's chapter "The Oceans" in the book Natural Climate Variability on Decade-to-Century Time Scales, available online: https://www.nap.edu/read/5142/chapter/5#234

    6. K. Hasselmann, R. Sausen, E. Maier-Reimer, R. Voss , Clim. Dyn. 9, 53 (1993)

      One of the elements of a global climate model is a simulation of CO<sub>2</sub> circulation.  However, models that begin in pre-industrial times include so much data that computers take a long time to complete the simulation. To decrease processing time, scientists sometimes set the start date of the simulation later, but this introduces error into the model. The authors of this paper found a way to account for this error (called the "cold-start" error) and discussed the implications for the climate models used by the IPCC. 

    7. S. Levitus , J. Geophys. Res. Oceans 94, 6091 (1989)

      Levitus had previously performed a very similar study that focused on the temperature and salinity of the North Atlantic. More measurements have been collected since this study in 1989, making it possible to examine more of the world's oceans and to update the scientific understanding of what was going on in the North Atlantic.

    8. T. Nitta, S. Yamada, J. Meteorol. Soc. Jpn. 67, 375 (1989)

      Nitta and Yamada used global ocean temperature data to discover that, since the late 1970s, surface temperatures were rising in the tropics, particularly in the eastern Pacific and the Indian Ocean. Their research suggests the changes in ocean temperature may have contributed to a change in climate patterns, affecting the Pacific-North American in particular.

    9. J. I. Antonov , J. Clim. 6, 1928 (1993)

      Antonov investigated temperature changes in the North Atlantic and North Pacific oceans within the depth range of 300 to 3000 meters over the years 1957–1981.

      He found that, while the North Pacific did not change temperature in deeper areas, it cooled between 300 and 500m. On the other hand, over the same period, North Atlantic ocean temperatures increased in the 800 to 2500 meter layer.

    1. M. Hirano, K. Shinjo, R. Kaneko, Y. Murata, Phys. Rev. Lett. 78, 1448–1451 (1997).

      This study reports measurements of friction as a function of commensurability of the contacting surfaces using ultra high vacuum scanning tunneling microscopy. Authors have used atomically clean surfaces to experimentally check the superlubric conditions. They found a match between experimental results and theoretical predictions.

    2. Y. Guo, W. Guo, C. Chen, Phys. Rev. B 76, 155429 (2007)

      This study investigates theoretically, the dependence of superlubricity on interlayer distance between graphene sheets and atomic defects on graphene for both commensurate and incommensurate configurations.

    3. D. Berman, A. Erdemir, A. V. Sumant, Carbon 54, 454–459 (2013)

      This earlier study by the current authors identifies and reports the potential of graphene layers in reducing friction and wear at the tribological interface of steel in air.

    4. Y. Mo, K. T. Turner, I. Szlufarska, Nature 457, 1116–1119 (2009)

      The authors report bridging the gap between macroscale and nanoscale laws of friction. A linear relationship found to exists between friction force and contact area at both regimes. In the present study, authors also observed a similar phenomenon.

    5. J. Cumings, A. Zettl, Science 289, 602–604 (2000)

      The authors demonstrate an experimental set up for finding friction between multiwalled nanotube layers using a nanomanipulator and insitu TEM imaging. Ultra low friction is observed between the core and outer nanotube layers in a dry environment, which is similar to the superlubricity conditions in the present study.

    6. Z. Liu et al., Phys. Rev. Lett. 108, 205503 (2012)

      This study details the first experimental evidence of reproducible superlubricity at the microscale under ambient conditions. The self retraction of graphite mesas upon shearing is described as a direct evidence of ultra low friction between the incommensurate surfaces. The variation in superlubric conditions with contact area is also described. A similar observation is made in the current study as well.

    7. D. Berman, A. Erdemir, A. V. Sumant, Carbon 59, 167–175 (2013)

      This study reports the tribological properties of graphene lubricated 440C steel. At medium loads and under dry nitrogen environment, graphene is found to maximize its performance as a solid lubricant.

    1. I. Martínez et al., Cell Rep. 11, 527–538 (2015).

      Martinez and colleagues compared the gut microbiome of individuals from Papua New Guinea and the United States. Individuals from Papua New Guinea had greater bacterial diversity and abundances, suggesting that industrialization may have an impact on the gut microbiome and, consequently, human health.

    2. J. K. Goodrich et al., Cell 159, 789–799 (2014).

      Goodrich and colleagues compared the gut microbiomes from individuals in the TwinsUK population and found that there is a correlation between the host genetics, metabolism, and gut microbiome.

    3. T. Yatsunenko et al., Nature 486, 222–227 (2012).

      Yatsunenko and colleagues sequenced the gut microbiome of three vastly different populations and found that there were pronounced differences between individuals from the United States than from Venezuela or Malawi. They suggest that the gut microbiome may be impacted by human development and Westernization.

    4. F. H. Karlsson et al., Nature 498, 99–103 (2013).

      Karlsson and colleagues characterized the fecal microbiota of European women and found that predictive tools for type-2 diabetes-associated markers could be useful if the age and location of the individual is accounted for.

  4. Mar 2019
    1. M. Schumer, G. G. Rosenthal, P. Andolfatto, Evolution 68, 1553-1560 (2014)

      In the article "How Common is Homoploid Hybrid Speciation?" Schumer et al. indicate that in the study of this topic future research needs to clarify the mechanisms of this type of event. They also propose criteria by which to judge the strength of evidence for this event, arguing that evidence for its hybridization's role in speciation is somewhat limited.

    2. R. J. Abbott, N. H. Barton, J. M. Good, Mol. Ecol. 25, 2325-2332 (2016).

      Abbott et al. summarize why studying hybridization is important to evolutionary biologists, and how the genomic data now available can help scientists better understand the mechanisms of speciation and the particular genes responsible for maintaining hybrids as separate populations.

      The authors indicate that homoploid hybrid speciation, while theoretically possible, has few strongly supported examples and there is little detail known about how it works. This helps us understand why this research paper is so important and interesting.

    1. F. Zhang et al., Nat. Neurosci. 11, 631 (2008)

      The authors investigated a red-shifted cation-conducting opsin variant from the algae species, Volvox carteri, that could be stimulated at a wavelength of 595nm. VChR1 can be stimulated by yellow light and offered a third class of microbial opsins.

    2. V. Gradinaru, K. R. Thompson, K. Deisseroth, Brain Cell Biol. 36, 129 (2008)

      The authors engineered the NpHR from F.Zhang et al., paper in 2007 to be better expressed at the cell membrane by inserting a membrane insertion signal and an endoplasmic reticulum export signal. Both interventions created eNpHR (enhanced NpHR) that improved protein trafficking and membrane expression. This was a necessary modification for the current paper published by the same first author. Temporal precision is a key parameter when dealing with neural firing which can occur at millisecond resolution.

    3. F. Zhang et al., Nature 446, 633 (2007).

      A paper describing the first use of halorhodopsin—a chloride pump expressed in an archaeon named Natronomonas pharaonis, that expressed temporal optical inhibition of neural activity. The investigators were then able to co-express both NpHR and ChR2 in the same cell and optically control its activity.

    4. E. S. Boyden, F. Zhang, E. Bamberg, G. Nagel, K. Deisseroth, Nat. Neurosci. 8, 1263 (2005).

      The first paper describing the algal protein, Channelrhodopsin-2, which was successfully cloned and expressed into mammalian neurons. The authors performed electrophysiological recordings of neurons expressing an opsin and measured the spiking activity.

    1. C. F. Dreyfus, K. A. Markey, M. Goldstein, I. B. Black, Dev. Biol. 97, 48 (1983)

      Dreyfus et al. used locus coeruleus, a region in the brain, to study the neurotransmitter expression in brain. His group was able to show that the catecholamines can be expressed both in culture and in animal making the locus coeruleus an excellent system to study the plasticity in brain.

    2. G. M. Jonakait, J. Wolf, P. Cochard, M. Goldstein, I. B. Black, ibid. 76, 4683 (1979)

      Jonakait et al. used the embryonic neural cells in the rat gut to understand the expression of noradrenergic cells.

      It was shown that these neural cells exhibit several characteristics of noradrenergic cells at embryonic stages. The authors wanted to know if there is a change in expression levels of noradrenergic during the development. For a certain time period during the development, the expression of noradrenergic is lost, however, the uptake system of norepinephrine is present and functional.

    3. G. M. Jonakait, K. A. Markey, M. Goldstein, I. B. Black, Dev. Biol. 101, 51 (1984)

      Jonakait et al. show that the loss of expression is not confined to rat gut, but it is also observed in cranial sensory and dorsal root ganglia of the embryonic rats. Here the authors have shown that the expression of catecholamine is lost for a certain time period during the development.

      These studies suggest that, irrespective of embryonic origin, the loss in expression of neurotransmitters, catecholamine and noradrenergic occur during development

    4. E. J. Furshpan, P. R. MacLeish, P. H. O'Lague, D. D. Potter, Proc. Natl. Acad. Sci. U.S.A. 73, 4225 (1976)

      In this study, Furshpan et al. were interested in identifying the neurotransmitter that is being released in response to different liquids or drugs. His group noted that neurons release acetylcholine, catecholamine or both in response to the drugs.

    5. T. Hokfelt, O. Johansson, A. Ljungdahl, J. M. Lundberg, M. Schultzberg, Nature (London) 238, 515 (1980)

      This review by Hökfelt T et al. discusses about the identification of new neurotransmitters that are peptidergic in nature. Peptidergic refers to the neurons that release small peptides as their neurotransmitters.

      The article provides a snapshot of peptidergic neurons identified in the nervous system, namely, brain, spinal cord and peripheral nervous system.

  5. Feb 2019
    1. N. Gold, A. M. Colman, B. D. Pulford, Judgm. Decis. Mak. 9, 65–76 (2014).

      This study asked Chinese and U.K. citizens if an individual should be sacrificed to save many.

      Chinese participants were less willing to sacrifice the lone individual, and were less likely to think that it was the more moral choice.

    2. J. A. C. Everett, D. A. Pizarro, M. J. Crockett, J. Exp. Psychol. Gen. 145, 772–787 (2016).

      This paper found a general pattern across all its different studies—that people who decide that something is moral based on rules are considered more trustworthy.

      This paper thus supports the idea that the methods used in "The social dilemma of autonomous vehicles" provide a representative view of the U.S. population, even though the respondents themselves might not entirely represent people in the U.S.

    1. D. L. Lack, Darwin's Finches (Cambridge Univ. Press, 1947)

      Lack's book recounts what he learned about Darwin's finches from a visit to the Galapagos in the late 1938-9, one of the first visits to the island focused on the finches since Darwin's time. The work includes the classification of the finches as well as notes on speciation, adaptive radiation, and evolution.

    2. H. S. Swarth, Occas. Pap. Calif. Acad. Sci. 18, 1-299 (1931)

      Swarth's paper reorganized the classification of Darwin's finches slightly, particularly with regard to the Geospiza genus.

    3. S. Lamichhaney, J. Berglund, M. S. Almen, K. Maqbool, M. Grabherr, A. Martinez-Barrio, M. Promerova, C. -J. Rubin, C. Wang, N. Zamani, B. R. Grant, P. R. Grant, M. T. Webster, L. Andersson, Nature 518, 371-375 (2015).

      This paper presents the results of a whole genome study of 120 of Darwin's finches, and identifies the ALX1 gene as important in determining beak shape. The study also helps revise the phylogenetic tree of the finches and provides evidence for hybridization as the finches evolved.

    4. S. Lamichhaney, F. Han, J. Berglund, C. Wang, M. S. Almen, M. T. Webster, B. R. Grant, P. R. Grant, L. Andersson, Science 352, 470-474 (2016).

      This paper reports the identification of the importance of the HMGA2 gene in affecting beak shape in Darwin's finches, especially during natural selection that occurred during a drought in 2004-5.

    5. P. R. Grant, B. R. Grant, Proc. Natl. Acad. Sci. U.S.A. 106, 20131-20148 (2009)

      In this paper, Grant and Grant report the establishment of the Big Bird lineage and discuss the mechanisms of reproductive isolation that exist for its population.

    6. P. R. Grant, B. R. Grant, How and Why Species Multiply (Princeton Univ. Press, 2008)

      This book gives a complete evolutionary history of Darwin's finches. Grant and Grant explain the speciation that occured and the mechanisms that underpin the formation of different species of finches in the Galapagos Islands.

    7. B. R. Grant, P. R. Grant, 40 Years of Evolution: Darwin's Finches on Daphne Major Island (Princeton Univ. Press, 2014)

      This book summarizes the evidence for evolution gathered over the entire research project on Daphne Major that the Grants led. It concludes that natural selection occurred repeatedly during that time, and that competition for food in times of drought drove that evolution.

    8. L. H. Rieseberg, M. A. Archer, R. K Wayne, Heredity 83, 363-372 (1999)

      In this discussion of transgressive segregation, Riesenberg et al review many studies and conclude that the genetic basis of transgressive segregation is through complementary alleles: new combinations of alleles that provide novel combinations of genotypes.

      They find that transgressive segregation occurs most frequently in crosses between closely related species, and that niche separation is the most important factor in favoring the establishments of hybrids.

    9. P. R. Grant, B. R. Grant, Philos. Trans. R. Soc. Lond. B Biol Sci. 365, 1065-1076 (2010)

      Grant and Grant use genetic information to quantify the effect of the exchange of genes between populations of birds. They explore two situations: genes that enter a population through mating with a bird of the same species (conspecific) but from a different population on another island; and genes that enter a population from a member of a different species (heterospecific). They conclude that while both types of gene flow are rare, they do occur and have measurable effects on the populations that are complex and change through time, rather than being steady.

    10. A. W. Nolte, D. Tautz, Trends Genet. 26, 54-58 (2010).

      Nolte and Tautz discuss homoploid hybrid speciation and indicate that there is a need to understand the mechanisms involved in this type of speciation. They argue that the best way to examine these mechanisms is through observing hybrid populations that may or may not be on their way to forming new species, either in natural situations or in experiments.

    11. P. R. Grant, B. R. Grant, Evolution 48, 297-316 (1994).

      In this summary of genes and traits of hybridizing finches on Daphne Major, the authors established general patterns found in hybridization of the finches on this island: that hybrids are generally intermediate between parental species, and often go on to mate with members of the parental species.

      They discuss hybridization as a source of genetic variation within existing species, and suggest that it can happen through new combinations of genes (additive genetic variance) as well as new patterns of dominance or co-dominance among known genes, or even the establishment of new combinations of genes on chromosomes.

      They also note how rare it would be to see hybridization produce birds much larger than parent species, and how unusual occurrences might be necessary to provide the conditions for this to happen.

    1. From our annotated research papers to our trainings and workshops, we're dedicated to bridging the communication gap between scientists and everyone else.

      Beth, Shelby, and I will be in the AAAS Lounge starting at 10am on Friday.

  6. Jan 2019
    1. 28. K. A. Lehmann, B. L. Bass, Biochemistry 39, 12875–12884 (2000)

      The authors of this work investigated and described the activity of the human ADAR1 and ADAR2 deaminases.

      They showed that ADAR proteins had certain sequence preferences, including the nucleotides around the target and the position of the target relative to the RNA duplex ends. Additionally, they determined that ADARs did not edit all accessible adenosines. That implied these proteins possessed some specificity with unknown mechanism.

    2. 22. S. K. Wong, S. Sato, D. W. Lazinski, RNA 7, 846–858 (2001).

      This paper demonstrated that ADAR deaminases preferentially edit adenosine bases that are mismatched with a cytidine.

    3. 21. A. Kuttan, B. L. Bass, Proc. Natl. Acad. Sci. U.S.A. 109, E3295–E3304 (2012).

      The authors of the paper mutated the ADAR2 protein and, by screening of multiple mutants, identified the E488Q variant that could edit adenosine in all possible triplet targets.

    4. 16. K. Nishikura, Annu. Rev. Biochem. 79, 321–349 (2010).

      A comprehensive review on research into ADAR proteins.

    5. 15. O. O. Abudayyeh et al., Nature 550, 280–284 (2017).

      The authors of this study showed that the Cas13a protein was comparable to RNAi in its efficiency at knocking down RNA, but has superior specificity.

      They also generated a catalytically dead Cas13a and demonstrated that it retained RNA-binding properties. This dCas13a was successfully used for RNA tracking.

      Finally, the authors did not observe cleavage at sites surrounding the target (collateral cleavage) with Cas13a in mammalian cells. This was extremely important as it suggests the nuclease can be safely used to target specific sites without major adverse effects.

    6. 14. J. S. Gootenberg et al., Science 356, 438–442 (2017).

      The authors of the paper presented a new application of the CRISPR-based tools as diagnostic devices. They created a technique called SHERLOCK (Specific High-Sensitivity Enzymatic Reporter UnLOCKing) which was able to detect very small amounts of disease-causing viruses and bacteria, as well as mutations in human DNA.

    7. 9. Y. B. Kim et al., Nat. Biotechnol. 35, 371–376 (2017).

      The same group of researchers that developed the first DNA base editor (7) improved the complex's specificity and expanded its ability to target.

      They improved specificity by making the targeting window smaller, and expanded its ability to target different sequences by fusing the complex to Cas9 proteins that use different PAM sequences.

    8. 7. A. C. Komor, Y. B. Kim, M. S. Packer, J. A. Zuris, D. R. Liu, Nature 533, 420–424 (2016)

      The authors of the study suggested an alternative strategy to genome editing that doesn't use DNA breaks and donor templates. They created a DNA base-editor complex composed of a mutant Cas9 and a cytidine deaminase APOBEC1. This complex was able to convert all C-G pairs into T-A within a narrow targeting window. However, it required additional modules to control the editing.

    9. 8. K. Nishida et al., Science 353, aaf8729 (2016).

      This group of scientists created a DNA base editor consisting of Cas9 and the cytidine deaminase PmCDA1. Similar to other work (7), this editor modified all cytidines in a target window and required an additional protein module for the control of editing.

    1. 17. A. G. Davies, J. C. Bettinger, T. R. Thiele, M. E. Judy, S. L. McIntire, Neuron 42, 731 (2004).

      First paper to establish the relationship between NPF in C. elegans and sensitivity to the effects of ethanol.

    2. 16. T. Wen, C. A. Parrish, D. Xu, Q. Wu, P. Shen, Proc. Natl. Acad. Sci. U.S.A. 102, 2141 (2005).

      First paper to establish the relationship between NPF in fruit flies and sensitivity to the effects of ethanol.

    3. 14. R. S. Hewes, P. H. Taghert, Genome Res. 11, 1126 (2001).

      A comprehensive analysis of the various genes in the Drosophila that pertain to the vast majority of—if not all—neuropeptides and their receptors.

    4. 8. S. M. McBride et al., Neuron 24, 967 (1999).

      This was one of the first studies to establish the courtship conditioning paradigm for controlling the sexual experience of male flies that is now commonly used in Drosophila research.

    1. J. A. Kessler and I. B. Black, Brain Res. 234, 182 (1982)

      In this study, the authors identified factors that regulate the substance P in nerve ganglia. The authors reported that impulse activity and decentralization of neurons (or denervation) can affect positively or negatively the expression of substance P in the nerve ganglia.

    2. S. C. Landis, Fed. Proc. Fed. Am. Soc. Exp. Biol. 42, 1633 (1983)

      This article discusses the evidence of neurotransmitter plasticity in sweat glands of rats. The authors show that the neurons change from a norepinephrine to acetylcholine during development. Though the change of neurotransmitter occurs in the system, it does not alter the uptake and storage of norepinephrine in these neurons.

    3. P. H. Patterson, Annu. Rev. Neurosci. 1, 1 (1978)

      In this review, Patterson discusses that we can manipulate the neurons’ decision to produce certain chemicals by altering the environmental factors. This manipulation can be performed during development by changing the fluid or culture conditions in which the neurons are growing.

    1. 18. G. D. Wang et al., Nat. Commun. 4, 1860 (2013).

      In 2013, scientists traced the ancestry of Chinese native dogs using whole genome sequencing. They compared the DNA of four gray wolves (three from different parts of Russia, one Chinese), three native Chinese dogs (dogs present in China for a very long time), and three dogs considered very diverse from each other—a German Shepard, Belgian Malinois, and Tibetan Mastiff.

      They suggest a Southeastern Asia origin for dogs, and domestication of Chinese indigenous dogs occurred 32,000 years ago.

    2. 16. M. Pilot et al., Proc. R. Soc. B Biol. Sci. 282, 20152189 (2015).

      Scientists studied the evolutionary history of free breeding dogs—that is, dogs without restricted, human-controlled breeding. They compared the genetic information of 200 free-breeding dogs from across Eurasia, with 51 ancient and modern breeds. They concluded that the origin for these dogs was East Asia and that they gradually moved West.

    3. 11. W. Haak et al., Nature 522, 207–211 (2015).

      A large team of scientists from around the world sought to trace the origins of one of the world's primary language families, Indo-European languages. Through tracing language, in a way the scientists also trace the origins of European people. They studied DNA from 94 Europeans who lived 8000-3000 years ago. They found that many modern day Europeans can be traced back to the Yamnaya population, nomadic herders from Steppe, a region now know as Ukraine and Russia.

    4. 9. G.-D. Wang et al., Cell Res. 26, 21–33 (2016).

      The authors suggest that dogs were domesticated 33,000 years ago in Southeast Asia.

    5. 4. T. Dayan, J. Archaeol. Sci. 21, 633–640 (1994).

      Studying teeth and facial bones from wolf/doglike animals found buried in Israel (alongside human skeletons), it was estimated that these animals were 12,000-year-old dogs that had recently been domesticated.

      A shorter face and smaller teeth are some of the most recognizable features of domestication. The author, Tamar Dayan, remains open to the possibility that there were several geographic origins of domestication and that small and large-sized wolves—from different populations—were domesticated separately, explaining why there were both large and small early dogs.

    6. 3. M. Pionnier-Capitan et al., J. Archaeol. Sci. 38, 2123–2140 (2011).

      Scientists carried out detailed archaeological studies on bones from 49 small doglike animals from three separate sites in France. The fossils were, in fact, from dogs 11,500-15,00 years old, the same time-frame that much larger dogs existed in Russia, suggesting that there may have been two origins of domestication.

    7. 2. M. Germonpré, M. Lázničková-Galetová, M. V. Sablin, J. Archaeol. Sci. 39, 184–202 (2012).

      Archaeologists discovered seven dog/wolflike skulls at a site in the Czech Republic. By measuring and comparing the skulls and skulls fragments to those of wolves and recent dogs, scientists estimated that wolves were domesticated in the early upper Paleolithic era (~30,000 years ago)

  7. Dec 2018
    1. V. Gradinaru et al., J. Neurosci. 27, 14231 (2007)

      This paper discusses targeting strategies to selectively express opsins to certain regions or cell types as well methods to readout expression and activity. Methods include electrophysiology, imaging and behavior analysis.

    2. A. R. Adamantidis, F. Zhang, A. M. Aravanis, K. Deisseroth, L. de Lecea, Nature 450, 420 (2007).

      The authors used Channelrhodopsin-2 to selectively photostimulate hypocretin producing neurons in the lateral hypothalamus and showed a frequency dependent effect on sleep-to-wakefulness transition. This paper supported optogenetics ability to stimulate cells and elicit a physiological effect.

    1. Ehrlich, P. R., and P. H. Raven. 1964. Evolution 18: 586-608.

      This reference played an important role in this paper since it also focuses on different insect types (specifically butterflies) and their relationships with a variety of plants. It also serves as a source that elaborated on plant defense mechanisms and how it correlates to herbivores. Although this paper's main focus revolved around evolution, it still brought up many important observations that were relevant to this paper.

    2. Endara, M. J., and P. D. Coley. 2011. Functional Ecology 25: 389-398.

      This reference is very important in understanding how biodiversity and the ecosystem, particularly the fauna, relate to each-other. It sets the base to understanding how it is possible that species of insects and animals can prefer to live or even need to live in a certain fauna/ecosystem.

    3. Kursar, T. A., K. G. Dexter, J. Lokvam, R. T. Pennington, J. E. Richardson, M. G. Weber, E. T. Murakami, C. Drake, R. McGregor, and P. D. Coley. 2009. Proceedings of the National Academy of Sciences USA 106: 18073-18078.

      This paper is a different version of the same type of research. This study provided backup information to further prove what was being stated and identified in this research.

    1. Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, Yang P, Zhang L, Wang X, Qi H, et al. 2012. Nature. 490:49–54.

      This paper focuses on the member of the Mollusca phyla, Crassostrea gigas. It goes into depth on how the genome of the oyster reveals how it has been able heat chock protein 70 and apoptosis inhibitors contribute to the organisms ability to survive in very stressful environmental conditions. this contributes to the GIGA project because the genome had to have been coded and that can go towards the GIGA coalition.

    2. Vinson JP, Jaffe DB, O’Neill K, Karlsson EK, Stange-Thomann N, Anderson S, Mesirov JP, Satoh N, Satou Y, Nusbaum C, et al. 2005. Genome Res. 15:1127–1135.

      "Whole-genome assembly is now used routinely to obtain high-quality draft sequence." This supports the main idea of which GIGA stands for. A database for easy access to high- quality sequences of a certain organism.

    3. Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sanchez-Flores A, Brooks KL, Tracey A, Bobes RJ, Fragoso G, Sciutto E, et al..; Taenia solium Genome Consortium. 2013. Nature. 496:57–63.

      This paper speaks of how parasitisms has developed in worms. Scientist have been able to figure this information out using the genome of 3 different tapeworms. They also identify treatments to ride humans of these parasites. This aids with the GIGA project because uses the genetic code of invertebrates, which can be a part of the GIGA database.

    4. Struck TH, Paul C, Hill N, Hartmann S, Hösel C, Kube M, Lieb B, Meyer A, Tiedemann R, Purschke G, et al. 2011. Nature. 471:95–9

      This paper is on ring phylum Annelid. With the information in this study Animal body plan evolution can be more defined which can help researchers better understand the evolution of metazoans. It mentions on how other organisms who were classified under different phyla should actually fall under Annelid. Showing how this paper can help researchers narrow down the evolution of these creatures consisting of invertebrates.

    5. Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A, Carpenter ML, et al. 2008. Nature. 454:955–960.

      This study focuses on the Placozoan Trichoplax genome in order to understand the organisms that fall under this category. It focuses in where they stand in categories of animals as one of the first emerging animals. It can be used to study how the first animals ever looked on this earth and their DNA can present a lot more information that can still be found out.

    6. Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW, Cunningham CW. 2010. Nature. 463:1079–1083.

      This has to do with how arthropods are more closely related to aquatic invertebrates than other terrestrial invertebrates. This shows how evolution of invertebrates were different then originally thought and with the help of data from this study other scientist can know this and use it for themselves.

    7. Philippe H, Brinkmann H, Copley RR, Moroz LL, Nakano H, Poustka AJ, Wallberg A, Peterson KJ, Telford MJ. 2011. Nature. 470:255

      This paper focuses on how to two taxa are actually very similar to one another. This all contributes to the database for flatworms and the taxa they pertain to.

    8. Mardis ER. 2011. Nature. 470:198–203

      This study focuses on how the Human Genome Project has lead humanity to leap into the future and gain a ton of knowledge. This is more of an example of how the GIGA project can be of use. It goes into detail of what we have learned since the HGP was completed. This is more of a reflection of the possibilities the GIGA project can have for marine invertebrate genome.

    9. Lewin HA, Larkin DM, Pontius J, O’Brien SJ. 2009. Genome Res. 19:1925–1928

      This is an article that is justifying the reasons for mapping a genome and how it can be useful in advancing knowledge, research, and technology.

    10. Jeffery NW, Jardine CB, Gregory TR. 2013. Genome. 56:451–456.

      Focuses on the genome size of an early branching phylum. This is all scarce information so this study is important into better understanding the entire phylum which is pretty wide spread. This is perfect example of what GIGA is trying to prevent. They want to create a global database of information of marine invertebrates especially due to the lack of information on these creatures.

    11. Human Microbiome Project. 2012. Nature. 486:207–214.

      This project is essentially a genomic mapping project of the the microbes that live within humans. Another example of how databases are useful, which supports the reasoning for creating the GIGA project.

    12. Hill CA, Wikel SK. 2005. Trends Parasitol. 21:151–153.

      This is a perfect example of how creating a database of a genome can enhance the spread of information and the use of certain standards and information in order go further into research of the tick genome. Shows how the GIGA initiative can be of use.

    13. Funch P, Kristensen RM. 1995. Nature. 378:711–714

      This is an older paper, published establishing a new phylum Cycliophora. This contributes to database on new discoveries on marine invertebrates. it foes into depth on the larva of the organism and what makes it different form other invertebrates.

    14. Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E. 2012. Nature. 489:52–55

      This article focuses on the ENCODE project and goes to explain its functions and what it can lead to. It focuses on learning and understanding the functional regions of the human DNA, but it makes you think that if this can work for humans why can it not work for any other species? This shows incentive to the GIGA coalition and what it can mean for researchers in the marine invertebrate field.

    15. Delsuc F, Brinkmann H, Chourrout D, Philippe H. 2006. Nature. 439:965–968.

      This paper focuses on how Tunicates are the closest living relatives to vertebrates. This study can assist from en evolutionary standpoint to picture a transition from an invertebrate to vertebrate creatures. This pertains to paper at hand because it will contribute to the database for GIGA.

    16. Davidson EH, Erwin DH. 2006. Science. 311:796–800.

      This article focuses on the evolution of body plans of invertebrates. So due to the nature of the paper it refers to a lot of invertebrates and focuses on their development. The GIGA project focuses on invertebrates

    17. Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC. 1994. Science. 263:802–805.

      The name of this paper is called "Green Fluorescent Protein as a Marker for Gene Expression." The marine invertebrate mentioned is the Aequorea victoria. This will contribute to the papers database. Can help with focusing on proteins of jelly fish.

    18. C. elegans Sequencing Consortium. 1998. Science. 282:2012–2018.

      This article contains the genome of the nematode C. elegans. The main purpose of GIGA is to obtain and database the genomes and infomration of the genome for others to use so this paper is a perfect candidate that reach this criteria.

    19. Birney E. 2012. Nature. 489:49–51

      This article speaks on the ENCODE project. ENCODE is a mass collection of functional parts of DNA. It focuses on the do's and do not's of database creation. This can serve as a source of how the creators of GIGA can go about creating their database, and steps they should take to ensure its success.

    20. Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, et al. 2009. Nature. 460:352–358.

      "Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries." It contains the genome for this species and goes into depth the characteristics of the genetic code. for instance it says that it contains a large amount of introns. Also shows how the information gathered has led researchers to begin new ideas of possible treatments and regulations of the disease.

    21. REFERENCES

      This paper proposes a project so it isn't necessarily a topic that many people have researched. Due to the nature of the paper, the resources and past works will consist of published works that describe the pros of creating a database and examples of the types of works that will contribute to the GIGA project.

    1. Vandegehuchte, M.B., Lemiere, F., Janssen, C.R., 2009. Quantitative DNA-methylation in Daphnia magna and effects of multigeneration Zn exposure. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 150, 343–348.

      A paper published in 2009, concluding that different exposure histories results in different levels of methylation.

    2. Valdiglesias, V., Fernandez-Tajes, J., Mendez, J., Pasaro, E., Laffon, B., 2013. The marine toxin okadaic acid induces alterations in the expression level of cancer-related genes in human neuronal cells. Ecotoxicol. Environ. Saf. 92,303–311

      A study in which the effect of the marine toxin Okadaic acid (OA) on certain genes that are related to cancer. In the study it was seen that there are alterations to the genes that could explain the relationship of OA to cancer.

    3. Sunda, W.G., Burleson, C., Hardison, D.R., Morey, J.S., Wang, Z., Wolny, J., Corcoran, A.A., Flewelling, L.J., Van Dolah, F.M., 2013. Osmotic stress does not trigger brevetoxin production in the dinoflagellate Karenia brevis. Proc. Natl. Acad. Sci.U. S. A. 110, 10223–10228.

      Sunda has previously concluded that exposure to brevetoxins limit growth

    4. Murrell, R.N., Gibson, J.E., 2009. Brevetoxins 2, 3, 6, and 9 show variability in potency and cause significant induction of DNA damage and apoptosis in Jurkat E6-1 cells. Arch. Toxicol. 83, 1009–1019.

      Murell and Gibsons reviewed the effect of Red Tides on human health, particularly on the effect it has with DNA strands. It further supported their reasoning into investigate on Histone 2 dynamics during the toxic experiment.

    5. Flewelling, L.J., Naar, J.P., Abbott, J.P., Baden, D.G., Barros, N.B., Bossart, G.D., Bottein,M.Y., Hammond, D.G., Haubold, E.M., Heil, C.A., Henry, M.S., Jacocks, H.M.,Leighfield, T.A., Pierce, R.H., Pitchford, T.D., Rommel, S.A., Scott, P.S., Steidinger, K.A., Truby, E.W., Van Dolah, F.M., Landsberg, J.H., 2005. Brevetoxicosis: red tides and marine mammal mortalities. Nature 435, 755–756

      Flewelling published a paper pinpointing areas in which saxitoxin (HABs) were found in food around the world. The Southeastern U.S was one of these areas in which saxitoxins were found. (DZ)

      Also the paper talks about the effect of Karenia brevis's brevetoxins on food webs and the effects.

    6. Dame, R.F., 1972. The ecological energies of growth, respiration, and assimilation in the intertidal American oyster Crassostrea virginica. Mar. Biol. 17, 243–250

      Dame's paper studies the interactions between the grazing of bivalves and their role in their respective environments (specifically, carrying capacity).

    7. Cardozo, K.H., Guaratini, T., Barros, M.P., Falcao, V.R., Tonon, A.P., Lopes, N.P.,Campos, S., Torres, M.A., Souza, A.O., Colepicolo, P., Pinto, E., 2007. Metabolites from algae with economical impact. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 146, 60–78.

      Cardozo focuses on the effects of the biotoxins released by the algae. From these effects the experiment is conducted upon what the toxins do on marine life organism in which the toxic effect is a natural defense mechanism.

    8. Brand, L.E., Campbell, L., Bresnan, E., 2012. Karenia: the biology and ecology of atoxic genus. Harmful Algae 14, 156–178.

      A paper describing the dinoflagellate, karenia brevis. The paper explains the biotoxins released by it, how the biotoxins build up in shellfish, and what damage it does to other marine organisms.

    1. Garwood, N.C., 1983. Ecology 53, 159–181

      Garwood focused on seed germination in tropical environments in Panama. He was looking to help determine primary selective factors that controlled the timing of germination, the significance of seed dormancy, and to identify any major seed germination syndromes. These are all related to the success of a plant population and help scientists better understand and map out conservation efforts for species diversity.

    2. Galetti, M., Dirzo, R., 2013. Biol. Conserv. 163, 1–6.

      Galetti and Dirzo reviewed the anthropogenic drivers of defaunation. They determined that direct drivers include hunting, poaching, and the presence of invasive species. Indirect drivers of defaunation include deforestation and fragmentation as a result of human activities. Some of the many consequences of defaunation are reduced ecosystem services and evolutionary changes in populations.

    3. Bond, W.J., Keeley, J.E., 2005. Trends Ecol. Evol. 20, 387–394. Borchert, R., 1998. Clim. Chang. 39, 381–393.

      Bond and his colleagues reviewed previous research in order to draw parallels between the effects of fire and herbivory on ecosystems. They concluded that, like herbivores, fires select for particular plant traits. For example, small herbaceous plants that require a lot of light for growth and seed establishment are more likely to be wiped out by fires. They also suggested that species that thrive under conditions of repeated defoliation would dominate communities where fires are likely to occur.

    4. Alvarado, S.T., Buisson, E., Rabarison, H., Rajeriarison, C., Birkinshaw, C., Lowry Ii, P.P., Morellato, L.P.C., 2014. S. Afr. J. Bot. 94, 79–87.

      Alvarado and colleagues analyzed the reproductive success of Madagascar sclerophyllous tapia woodlands in relation to fire frequency. They determined that more frequent fires resulted in increased latency of reproductive phenological events (flowering and fruit production in particular). Additionally, frequent fires reduced the overall number of individuals producing flower and fruits. It should be noted that the fires mentioned in this study were related to human activities.

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

      Ali and his colleagues focused their studies on the species diversity and conservation of various bird communities in Pakistan. This is important in understanding the relationship between the animal organisms within an ecosystem and their neighboring plants in order to obtain an optimal amount of species diversity within the ecosystem. This helps answer the question: what are the influences of climate change on phenology and what are the implications of those influences within a tropical environment?

    6. Alberton, B., Almeida, J., Helm, R., da Torres, S.R., Menzel, A., Morellato, L.P.C., 2014. Ecol. Inform. 19, 62–70.

      Alberton and colleagues tested whether or not digital cameras (used as a near-surface monitoring system) can be used effectively for measuring phenological changes in plants (specifically leaf color change). They determined that digital cameras are a reliable tool to monitor change in regional leafing patterns. This means that on-the-ground phenological observations of individual plants may no longer need to be used. However, the authors suggest that both methods, on-ground and near-surface monitoring through photographs, should be used to collect the most accurate picture of phenological change.

    7. increases in temperature and drought frequency may lead to premature leaf senescence in deciduous forests, affecting the efficiency of nutrient resorption and the length of growing seasons, impacting carbon uptake and ecosystem nutrient cycling (Estiarte & Peñuelas 2015), and therefore management practices (e.g. Eriksson et al., 2015)

      This study looks at how climate change alters the rate of leaf senescence in which drought advances it and warming decreases it. This change affects the flow of nutrients within an ecosystem. This information helps us to understand how shifts in climate activity influences plant phenology, such as losing leaves sooner and disrupting the nutrient cycle.

    1. D. Anglesea, C. Veltkamp, G. H. Greenhalgh, The upper cortex of Parmelia saxatilis and other lichen thalli. Lichenologist 14, 29–38 (1982).

      An important paper that shows the role of glue-like polysaccharides in filling the spaces between fungal cells and holding the lichen together. The yeasts described in this paper live in this filler zone.

    2. I. A. Aschenbrenner, T. Cernava, G. Berg, M. Grube, Understanding microbial multi-species symbioses. Front. Microbiol. 7, 180 (2016).

      This paper highlights the possible role bacterial symbionts might play in lichen formation and maintenance.

    3. R. Honegger, Developmental biology of lichens. New Phytol. 125, 659–677 (1993).

      This review discusses how lichens develop, their structure and function, their growth patterns, and how thalli are differentiated.

    4. V. Ahmadjian, The Lichen Symbiosis (John Wiley & Sons, 1993).

      This paper describes the cortex deficiencies of lichens grown from only the two previously known symbiotic partners.

  8. Nov 2018
    1. 19. Y. Lin, R. Jin, D. Cai, S. Yan, X. Li, in 2013 IEEE Conference on Computer Vision and Pattern Recognition (IEEE Computer Society, 2013), pp. 446–451.

      Lin et al. address a known issue in hashing methods, which is that they often require a large number of hash tables to be effective.

      To solve this problem, the authors propose a novel approach called compressed hashing. This approach uses sparse coding and is shown to be more effective than previously known hashing algorithms.

    2. 6. E. A. Hallem, J. R. Carlson, Cell 125, 143–160 (2006).

      Hallem and Carlson analyze how the fly olfactory circuit encodes information about the specific qualities—such as quality, quantity, and duration–of an individual odor.

      They test over 100 different odors and create an "odor space" that shows how the responses of olfactory receptors depend on an odor's chemical class, concentration, and molecular complexity.

    3. 4. A. C. Lin, A. M. Bygrave, A. de Calignon, T. Lee, G. Miesenböck, Nat. Neurosci. 17, 559–568 (2014).

      Lin et al. consider the role of sparse coding in helping organisms remember specific odors.

      They discover that sparsity in the olfactory circuit is controlled by a "negative feedback circuit" involving Kenyon cells and anterior paired lateral neurons. From their results, they suggest that sparse coding is important for helping flies store a large number of odor-specific memories without confusing or overlapping information.

    1. M. S. Bretscher and M. Grunberg-Manago, Nature 195, 283 (1962).

      Bretscher and Grunberg-Manago debunk the hypothesis that all codons must contain uracil by analyzing the coded proteins from poly(C, A).

    1. P. Kersey et al., Nucleic Acids Res. 33, D297–D302 (2005).

      This paper presents intrgr8. Intrgr8 is a database that helps researchers find information about the many different genomes that have been sequenced. Specifically, it links the sequenced genomes to information about that organism's proteins and any papers published about the genome.

    2. 12. C. M. Silva et al., J. Polym. Sci. A Polym. Chem. 43, 2448–2450 (2005).

      Describes the use of a cutinase from Fusarium solani pisi to degrade the surfaces of fibers to make them more hydrophilic and appropriate for use in the clothing industry. They found that the cutinase degraded the surface of a variety of fibers, including PET, to varying extents.

    3. 2. R. J. Müller, I. Kleeberg, W. D. Deckwer, J. Biotechnol. 86, 87–95 (2001).

      In this review, the authors discuss the work to create polymers that are both biodegradable and useful. Historically, most aliphatic polymers did not have the correct properties to be useful and most aromatic polymers were difficult to biodegrade. The review article details different techniques for making copolymers which have portions that are aromatic and portions that are aliphatic, allowing them to be both biodegradable and useful.

    1. 14. S. Schiffels, R. Durbin, Nat. Genet. 46, 919–925 (2014)

      A new technique—multiple sequentially Markovian coalescent (MSMC)—was developed. Eight haplotypes from four individuals can be analysed at the same time to trace lineages until the most recent common ancestor is identified. It is a powerful technique that provides information about population sizes, population splits, and migration patterns. In this study, they analyzed the genomes of nine different human populations and discovered that humans began to migrate out of Africa over 50,000 years ago.

    2. 6. A. H. Freedman et al., PLOS Genet. 10, e1004016 (2014).

      Dogs and wolves diverged 11,000-16,000 years ago, the authors conclude. A severe reduction in the population (a bottleneck) of wolves occurred shorly thereafter. They traced the ancestry of the amylase gene, a gene that allows dogs to eat starchy foods. Their data showed that dogs were mostly carnivores when they were first domesticated, which supports the theory that dogs were domesticated by hunter-gatherers, rather than starch-loving farmers.

    3. 19. P. Savolainen, Y. P. Zhang, J. Luo, J. Lundeberg, T. Leitner, Science 298, 1610–1613 (2002).

      The authors investigate the specific time and place of domestication by using the mitochondrial DNA of over 600 dogs and 38 wolves to trace the maternal lineage.They determine that dogs were domesticated about 15,000 years ago in East Asia, and that dogs were isolated to East Asia for a long time thereafter.

    4. 5. M. Ollivier et al., PLOS One 8, e75110 (2013)

      Scientists traced the ancestry of two genes associated with coat color. They examined DNA from teeth and bones from 28 different sites across Europe and Asia and determined that coat color was lost when dogs were domesticated. Variants in one coat color gene was detected in the early "ancient" breeds, which suggested that a pool of early dogs may have been geographically isolated 14,000-12,000 years ago, maybe as a result of rising sea levels.

    1. V. F. Dvorak, Mon. Weather Rev. 103, 420 (1975)

      The Dvorak scheme is a method of determining storm intensity based off satellite images and certain characteristics. Tropical cyclone patterns used to estimate intensity come from 1) the “shear” pattern, which examines how tilted a hurricane may be from the upper to lower atmosphere, 2) the “curved band” pattern of how the clouds swirl around a cyclone, 3) the “central dense overcast” pattern as in how thick the cloud cover appears, and 4) the “eye” pattern that examines the shape of the storm's center.

      Here is an image presents some of the common patterns seen during tropical cyclone formation along with their Dvorak-assigned intensities: Description

      A Dvorak T-Number of 1.0-2.0 is considered a tropical depression, 2.5-3.5 is a tropical storm, 4.0-4.5 represents a category 1 hurricane, 4.5-5.0 is a category 2, 5.5 is considered a category 3, with 6.0-6.5 representing category 4, and T numbers of 7.0-8.5 correspond to category 5 hurricanes.

    2. W. M. Gray, Mon. Weather Rev. 112, 1649 (1984)

      In this study, William Gray discusses the seasonal variability in Atlantic hurricane frequency.

      He found that during years with strong El Nino conditions in the Pacific, there were fewer hurricanes, hurricane days and tropical storms in the Atlantic. He also discovered that when stratospheric winds (at 30 mb in the atmosphere) were from an easterly direction, there tended to be fewer storms.

      In contrast, more tropical storms and hurricanes occurred during non-El Nino years as well as when stratospheric winds blew from a westerly direction.

      Thus global and regional climate oscillations in addition to upper atmosphere weather dynamics influence hurricane frequency.

    3. T. R. Knutson, R. E. Tuleya, J. Clim. 17, 3477 (2004)

      Knutson and Tuleya explored how the choice of climate model and convective wind parameters simulating hurricanes can impact the model results. By running experiments examining higher carbon dioxide futures using different climate models and different wind and atmospheric assumptions, the authors looked at whether different models produced the same results.

      They found that "nearly all combinations of climate model boundary conditions and hurricane model convection schemes show a CO2-induced increase in both storm intensity and near-storm precipitation rates." They also found a "gradually increasing risk in the occurrence of highly destructive category-5 storms" if global climate continued to warm.

      Based on this study, it appears that most climate models tend to produce similar results regardless of differences in certain background parameters and assumptions.

    4. W. M. Gray, Mon. Weather Rev. 96, 669 (1968)

      For this study, William Gray examined measurements of upper atmospheric conditions which had only recently become available from over the tropical oceans. Using about a decade's worth of airplane and sensor readings, Gray noticed that cyclone storms develop under certain conditions with regard to temperatures and atmospheric moisture content.

      Development of storms appears to be due to the combination of surface winds converging due to frictional forces in addition to conditions inhibiting atmospheric vertical mixing (such as specific wind shear and cloud conditions). Under certain atmospheric conditions, warm oceans and evaporation-condensation reactions of water can concentrate energy into a cyclonic system and cause a hurricane to form.

    5. K. A. Emanuel, Nature 326, 483 (1987).

      Using a simple model that takes the thermodynamic attributes of the atmosphere into account, Emanuel determined that if carbon dioxide concentrations doubled there would be a "40–50% increase in the destructive potential of hurricanes".

      This is due to the well-studied heat-trapping potential of carbon dioxide which contributes to a warming climate and increasing sea surface temperatures. Warmer waters in turn alter atmospheric pressures and wind speeds. Thus on a theoretical basis using knowledge of atmospheric gases and their relationship to temperature, a warmer world is likely to produce more destructive hurricane events.

    6. C. W. Landsea, R. A. Pielke Jr., A. M. Maestas-Nunez, J. A. Knaff, Clim. Change 42, 89 (1999)

      Landsea and coauthors compared the record of hurricane activity in the Atlantic with other climate records of sea level pressures, wind, climate oscillations (like the El Niño-Southern Oscillation), African West Sahel rainfall, and Atlantic sea surface temperatures.

      They found that variability in the background climate state of the region affects the frequency, intensity and duration of Atlantic hurricanes.

      With improved understanding of the large-scale climate conditions of the Atlantic and how regional climate changes over multi-decadal timescales should improve our ability to predict hurricane activity.

    7. K. E. Trenberth et al., Bull. Am. Meteorol. Soc. 84, 1205 (2003)

      Trenberth and coauthors wrote this paper in order to summarize the environmental controls on precipitation events and to point out how climate models were not yet considering all the variables influencing precipitation.

      Since "climate change is certainly very likely to locally change the intensity, frequency, duration, and amounts of precipitation" we need to be developing models which can accurately reproduce these types of changes if we want to accurately predict how the water cycle may vary as climate changes.

    8. K. E. Trenberth, Science 308, 1753 (2005)

      In this perspective piece "Uncertainty in Hurricanes and Global Warming" Trenberth notes that while the effects of human-driven climate change have already begun altering the environment in hurricane formation regions, it is not yet possible to connect changes in climate to the number of storms forming.

      Trenberth suggests that instead of focusing on just the number of storms and the tracks they move along, the bigger scientific question is how hurricane attributes such as intensity and rainfall are changing in today's world.

    9. S. B. Goldenberg, C. W. Landsea, A. M. Maestas-Nunez, W. M. Gray, Science 293, 474 (2001)

      Goldenberg and coauthors studied "The recent increase in Atlantic hurricane activity: causes and implications."

      After examining hurricane data from 1944 to 2000, these authors also found that there has been an increase in cyclone activity and the number of major hurricanes since 1995. They attribute the greater storm activity on increases in North Atlantic sea-surface temperatures and decreases in vertical wind shear.

      These changes in storm activity appear to coincide with changes in the climatic state of the Atlantic, specifically in how the Atlantic responds with regard to El Nino and La Nina conditions that vary on the timescales of a few decades. Due to the current climate of the North Atlantic, Goldenberg and coauthors predict "the present high level of hurricane activity is likely to persist for an additional ∼10 to 40 years."

  9. Oct 2018
    1. 4. K. R. Kaun, R. Azanchi, Z. Maung, J. Hirsh, U. Heberlein, Nat. Neurosci. 14, 612 (2011).

      This paper established the odor-ethanol pairing method for probing motivation and rewarding properties that is used in the current study. It is by the same authors.

    2. 15. T. E. Thiele, D. J. Marsh, L. Ste. Marie, I. L. Bernstein, R. D. Palmiter, Nature 396, 366 (1998).

      First paper to establish the relationship between NPY in mice and ethanol consumption/sensitivity.

    3. 10. W. W. Ja et al., Proc. Natl. Acad. Sci. U.S.A. 104, 8253 (2007).

      The first paper to establish the two-choice preference assay for flies using food, including a method to precisely measure how much food was being consumed at any given time.

    4. 6. G. E. Robinson, R. D. Fernald, D. F. Clayton, Science 322, 896 (2008).

      A review paper highlighting various past studies that have shown that it is possible to establish direct causal links between genetics and behavior.

    5. 1. A. E. Kelley, K. C. Berridge, J. Neurosci. 22, 3306 (2002).

      A landmark review paper outlining how and why addiction occurs. This paper has been cited over 750 times.

    1. 9. S. J. Caron, V. Ruta, L. F. Abbott, R. Axel, Nature 497, 113–117 (2013).

      Caron et al. investigate the specific process by which Kenyon cells integrate information sent to them from glomeruli.

      Their results suggest that the input to KCs is random; that is, there is no discernible organization in how the glomeruli project information to individual KCs.

    2. 17. Z. Allen-Zhu, R. Gelashvili, S. Micali, N. Shavit, Proc. Natl. Acad. Sci. U.S.A. 111, 16872–16876 (2014).

      Zhu et al. consider whether the physical properties of neural tissue are actually conducive to performing Johnson-Lindenstrauss (JL) calculations in the brain. For example, the fact that neurons are either inhibitory or excitatory has certain implications for the signs (+ or -) in a JL matrix.

      They determine that it is indeed possible to construct JL matrices that accurately reflect the physical properties of the brain.

    1. J. C. Clemente, L. K. Ursell, L. W. Parfrey, R. Knight, Cell 148, 1258–1270 (2012).

      Clemente and colleagues review the interactions between microbes in the human gut and their effect on the host's immune system.

    2. J. F. Cryan, T. G. Dinan, Nat. Rev. Neurosci. 13, 701–712 (2012).

      Dinan and Cyran suggest that the gut microbiome may have a role in regulating and influencing brain function and behavior.

    3. E. Le Chatelier et al., Nature 500, 541–546 (2013).

      Le Chatelier and colleagues conduct a similar study on non-obese and obese Danish individuals. They find that they are able to classify subsets of individuals that may be at risk of obesity or associated comorbidities based on variation in the gut microbiota.

    4. J. Qin et al., Nature 490, 55–60 (2012).

      Qin and colleagues conducted a metagenome-wide association study in Chinese individuals. They identified type-2 diabetes-associated markers based on sequencing of the gut microbiome.

    5. M. Rajilić-Stojanović et al., Am. J. Gastroenterol. 110, 278–287 (2015).

      Rajilić-Stojanović and colleagues provide a review of current research on and suggest mechanisms regarding the impact of diet and the intestinal microbiome on irritable bowel syndrome symptoms.

    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.