886 Matching Annotations
  1. Last 7 days
    1. 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).

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

      Kendrick and colleagues measured GABA in the mouse ZI in awake 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. 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. 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.

    9. 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.

    10. 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.

    11. 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.

    12. 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.

    13. 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. 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.

  3. 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. 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.

      This is important because 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.

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

      A comprehensive review on research into ADAR proteins.

    6. 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.

    7. 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.

    8. 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

    9. 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.

    10. 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.

    11. 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. 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.

    2. 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.

    3. 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 6 months of age but not 2-year old rats.

    4. 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.

    5. 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 this study, the authors examined that 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

    6. 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

    7. 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.

    8. 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.

    9. 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.

    10. 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.

    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)

  4. 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.

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

      The authors investigated a red-shifted cation-conducting opsin variant from 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.

    4. 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.

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

      A paper describing the first use of halorhodopsin - a chloride pump expressed in 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.

    6. 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. 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.

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

      von Ehrenstein and Lipmann demonstrate the genetic materials of rabbits (a mammal) and E Coli (a bacteria) are compatible, suggesting the genetic code is universal!

    2. 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).

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

      In this seminal Nature paper, Crick and coworkers demonstrate that 1) a group of three bases codes for one amino acid 2) the code does not overlap 3) the sequence of bases is read from a fixed starting point and 4) the code is degenerate.

    4. 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?".

    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."

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

      Karlsson and colleagues characterized the faecal 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.

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

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

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

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

    8. 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 US. 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.

    9. 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.

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

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

    1. N. E. Klepeis et al., J. Expo. Anal. Environ. Epidemiol. 11, 231–252 (2001).

      Telephone survey that monitored where people in the United States spent the majority of their time. Found that 87% of time was spent in buildings and 6% of time was spent inside of automobiles.

      Since 93% of human activities are indoors, indoor air quality is extremely important.

    2. G. J. Dollard, P. Dumitrean, S. Telling, J. Dixon, R. G. Derwent, Atmos. Environ. 41, 2559–2569 (2007).

      Study analyzed VOC emissions in the United Kingdom from 1993 to 2004. Found that VOC emissions from automobiles were decreasing at a rate of 20% per year due to more stringent automobile emissions regulations.

    3. B. C. McDonald, D. R. Gentner, A. H. Goldstein, R. A. Harley, Environ. Sci. Technol. 47, 10022–10031 (2013).

      Study looked at emissions from automobile traffic in the United States between 1990 and 2010. Found that fuel consumption increased by 10% - 40% during the time period, but emissions such as carbon monoxide and VOCs decreased by 80% - 90% due to increased fuel efficiency and regulations.

    4. Q. Di et al., N. Engl. J. Med. 376, 2513–2522 (2017).

      The United States' air quality standards sets advisable levels for different pollutants. Human health was shown to be negatively impacted even when fine particulate matter and ozone were present at levels below the current air quality standards.

    1. 8. D. Ribitsch et al., Biocatalysis Biotransform. 30, 2–9 (2012).

      Rititsch et al. report cutinases from the bacteria Thermobifida alba. While the reported cutinases don't degrade PET particularly quickly, they do produce a novel degradation product.

      The authors were able to obtain a crystal structure, a type of picture on a molecular scale, of the enzyme degrading PET. This allowed them to identify parts of the enzyme that may be responsible for PET degradation.

    2. 1. V. Sinha, M. R. Patel, J. V. Patel, J. Polym. Environ. 18, 8–25 (2010).

      In this paper, Sinha et al. discuss the current best methods of disposing of and recycling plastic. The authors focus in particular on tertiary recycling techniques. These techniques use chemicals to break down the chemical bonds inside polymers.

    1. K. J. Willis, S. A. Bhagwat, Biodiversity and climate change. Science 326, 806–807 (2009).

      This article is a review about species distribution modeling, or, the ability to predict how species ranges could change under global warming. Authors highlight the fact that models published in the past have overlooked microclimates (small places that provide species with climate different than in the overall area). For example, in a place where heat waves are felt, some species could be able to use the surrounding vegetation to remain cool, and essentially be unaffected by the heat wave. Willis et al. (2009) show how important it is to consider such areas when estimating species’ future ranges under climate change since they could halt or at least slow many species’ extinctions.

    2. J. M. Sunday, A. E. Bates, M. R. Kearney, R. K. Colwell, N. K. Dulvy, J. T. Longino, R. B. Huey, Thermal-safety margins and the necessity of thermoregulatory behavior across latitude and elevation. Proc. Natl. Acad. Sci. U.S.A. 111, 5610–5615 (2014).

      Thermal limits of ectotherms (cold-blooded species) are often much higher than the temperature of the surrounding air. When limits are exceeded however, it was previously thought that organisms internally regulated their body in order to survive. However, this study shows that most ectotherms must use their behavior by retreating to suitable habitat when the air temperature becomes unsuitable (too cold or too hot). These behaviors are costly, obligating ectotherms, like bees, to direct their energy into preserving their heat/cool, instead of directing it into reproduction, feeding, and other essential activities. Extreme temperatures are predicted to happen more often as climate change progresses, and is likely to be problematic to bees.

    3. P. Rasmont, S. Iserbyt, The bumblebee scarcity syndrome: Are heat waves leading to local extinctions of bumblebees (Hymenoptera: Apidae: Bombus)? Ann. Soc. Entomol. Fr. 48, 275–280 (2012).

      Authors discuss the effect of heat waves on bumblebee decline. Heat waves and drought occurrences in France, the United Kingdom, Scandinavia, and Turkey led to bumblebee declines. It highlights that bumblebees are sensitive to extreme temperature events.

      Different aspects of heat waves could be affecting bees, as discussed in this paper. It could be that temperatures are rising above a tolerable threshold killing the bees, the length of the heat wave, the drought that is often associated with heat waves, starvation if bees are overheating and cannot feed themselves properly, or that heat waves are occurring during winter which could interrupt the queens’ hibernation while flowers providing their food are not yet available. Climate change is estimated to increase the probabilities for the occurrence of extreme temperature events in the future, a factor that may further threaten bee decline.

    4. S. J. Leroux, M. Larrivée, V. Boucher-Lalonde, A. Hurford, J. Zuloaga, J. T. Kerr, F. Lutscher, Mechanistic models for the spatial spread of species under climate change. Ecol. Appl. 23, 815–828(2013).

      Authors described an approach to model species’ distributions under climate change which takes into consideration ecological characteristics of species like reproduction, dispersal, and adaptation. We call these “mechanistic” models because they include mechanisms into their predictions.

      Using this approach, they modeled the distribution of 12 butterfly species and found that the ability to colonize unoccupied areas that are newly suitable and maintain populations in these areas is essential for species to track their suitable conditions. Otherwise, species can fall behind the pace of climate change and loose range.

    5. P. R. Whitehorn, S. O’Connor, F. L. Wackers, D. Goulson, Neonicotinoid pesticide reduces bumble bee colony growth and queen production. Science 336, 351–352 (2012).

      Testing for the effect of pesticides was important as field experiments have their negative impacts on bumblebees in the past. Whitehorn et al. (2015) showed that Bombus terrestris colonies exposed to pesticides in a lab had a lower growth rate and produced 85% fewer queens (bees that would eventually leave the colony to start a new colony) than those that were not exposed to the chemical. While this was observed on a small scale, the effect of pesticides was not measurable when Kerr et al. (2015) asked if it affected bumblebees’ wide scale shrinking range.

    6. D. Goulson, E. Nicholls, C. Botías, E. L. Rotheray, Bee declines driven by combined stress from parasites, pesticides, and lack of flowers. Science 347, 1255957 (2015).

      This review explains the multiple threats that bees are currently facing. Pesticides and other agrochemicals, parasites spread by humans, climate change, and land use change, are threats that either act on their own or interact, to cause negative effects on bees.

      For the study design, Kerr et al. (2015) took these threats into consideration to measure what effect was responsible for the results that they obtained, and chose to look at pesticides and land-use change; effects which, surprisingly, were not responsible for bumblebee range loss in the south and the inability for them to expand their range in the north. This is not to say pesticides and land-use change cannot create population declines at a smaller scale.

    7. V. Kellermann, J. Overgaard, A. A. Hoffmann, C. Fløjgaard, J. C. Svenning, V. Loeschcke, Upper thermal limits of Drosophila are linked to species distributions and strongly constrained phylogenetically. Proc. Natl. Acad. Sci. U.S.A. 109, 16228–16233 (2012).

      This study showed that Drosophila (a type of fruit fly species) adapted to hot and dry regions were more resistant to heat. The upper thermal limits tolerated by Drosophila could influence range limits. Authors conducted trait analyses and found that heat tolerance was an ancestral trait, kept over time. Trait-based analyses for bumblebees conducted by Kerr et al. (2015) also correspond to these results.

    8. M. B. Araújo, F. Ferri-Yáñez, F. Bozinovic, P. A. Marquet, F. Valladares, S. L. Chown, Heat freezes niche evolution. Ecol. Lett. 16, 1206–1219 (2013).

      This paper answers the research question “Can species physiologically adapt to climate warming?” They analyzed data from numerous other studies that described the thermal tolerances of species worldwide. Main findings of this study are that tolerance to heat was mostly conserved within closely related species, whereas tolerance to the cold was a trait that could vary.

      Trait-based analyses conducted by Kerr et al. (2015) correspond to these results. The upper thermal limits of bumblebees were found to be an ancestral trait, since it was conserved across closely related species.

    9. I. C. Chen, J. K. Hill, R. Ohlemüller, D. B. Roy, C. D. Thomas, Rapid range shifts of species associated with high levels of climate warming. Science 333, 1024–1026 (2011).

      Authors conducted a meta-analysis, a type of analysis that looks at a group of studies on the subject. They demonstrate that many terrestrial species shifted their range higher in altitude as well as further north. Chen et al. (2011) found that the rate at which species can shift varies strongly between species. Thus, it is likely for individual species traits to play an important role in their ability to shift.

      Findings by Chen et al. (2011) were important to frame the research question in Kerr et al. (2015). Since species from many different taxa have shifted, it was reasonable to ask if bumblebees are shifting as well.

    10. M. Pacifici, W. B. Foden, P. Visconti, J. E. M. Watson, S. H. M. Butchart, K. M. Kovacs, B. R. Scheffers, D. G. Hole, T. G. Martin, H. R. Akçakaya, R. T. Corlett, B. Huntley, D. Bickford, J. A. Carr, A. A. Hoffmann, G. F. Midgley, P. Pearce-Kelly, R. G. Pearson, S. E. Williams, S. G. Willis, B. Young, C. Rondinini, Assessing species vulnerability to climate change. Nat. Clim. Change 5, 215–224 (2015).

      This paper is a review of the different ways to measure how much species are threatened by climate change, and how they might respond. For instance, you can do this by estimating how a species range could change in the future. Understanding how climate change is affecting specific species is the first step to develop conservation strategies. Kerr et al. (2015) accomplished a first step toward this goal by demonstrating that climate change is linked to widespread losses and an overall shrink in distribution.

    11. C. D. Thomas, A. Cameron, R. E. Green, M. Bakkenes, L. J. Beaumont, Y. C. Collingham, B. F. Erasmus,M. F. De Siqueira, A. Grainger, L. Hannah, L. Hughes, B. Huntley, A. S. Van Jaarsveld, G. F. Midgley, L.Miles, M. A. Ortega-Huerta, A. T. Peterson, O. L. Phillips, S. E. Williams, Extinction risk from climate change. Nature 427, 145–148 (2004).

      It is now clear that climate change has affected species, as shown by endless amounts of papers in the primary literature. This paper estimates sizeable species extinctions by 2050 linked to climate change. They do this with species distribution modeling. This technique uses known species distributions and climatic conditions, and estimates how the distribution could change in the future according to models of future climate. Authors used optimistic and pessimistic estimates of future climate data (since, we do not know how much humans will cut down on activities that aggravate climate change), and even took into account the capacity for some species to move to and colonize other places. They estimated extinctions of 15% to 37% of the species included in their study. Studies that look at future impacts of climate change yield uncertain results since these cannot be verified.

      The IPCC (Intergovernmental Panel on Climate Change) put together a report summarizing climate literature. Refer to the PDF of the synthesis of this report here if you are interested in finding out more information on climate change: https://www.ipcc.ch/pdf/assessment-report/ar4/wg1/ar4-wg1-spm.pdf

    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 author use the same metallic cluster as a base and demonstrate how the small molecule linkers can be functionnalized to tune its properties.

    2. S. H. Schneider, Encyclopedia of Climate and Weather (Oxford Univ. Press, 1996

      A comprehensive description of the phenomena responsible for the world's climate and weather events, as well as the history of atmospheric science.

    3. S. Narayanan, S. Yang, H. Kim, E. N. Wang, Int. J. Heat Mass Transfer 77, 288–300 (2014).

      A computational modeling study of adsorption dynamics evaluating how multiple parameters such as vapor pressure and porosity affect the adsorption performance. The simulation results were confirmed experimentally with an adsorbing zeolite.

    4. J. H. Cavka et al., J. Am. Chem. Soc. 130, 13850–13851 (2008).

      The design and characterization of a zirconium-based MOF displaying very high thermal and chemical stability.

    5. H. Furukawa, K. E. Cordova, M. O’Keeffe, O. M. Yaghi, Science 341, 1230444 (2013).

      A review on the preparation of MOFs and their structural properties as well as their applications.

    6. J. Lee et al., Chem. Soc. Rev. 38, 1450–1459 (2009).

      An overview of the usage of the use of MOFs as selective catalyst to perform chemical reactions between substrates.

    7. H. Furukawa et al., J. Am. Chem. Soc. 136, 4369–4381 (2014).

      The same group previously described how to prepare MOF-801 and characterized its water adsorption properties.

    8. R. V. Wahlgren, Water Res. 35, 1–22 (2001).

      A review on existing systems to extract water from the atmosphere.

    9. M. M. Mekonnen, A. Y. Hoekstra, Sci. Adv. 2, e1500323 (2016).

      A study showing that about 4 billion people do not have access to fresh water for at least a month per year, half of them in China and India.

    1. K. D. Ersche et al., Science 335, 601–604 (2012).

      Ersche et al. studied the brain structure and behavior control capacities of 50 sibling pairs where one of the siblings was considered drug dependent, and compared them with 50 volunteer controls. The authors found that both siblings had deficits in regulating behavior with brain structure. They saw a reduction of white matter in drug dependent individuals and their biological siblings, which may predispose to drug use and indicate a genetic component to drug dependency..

    2. F. J. Miles, B. J. Everitt, A. Dickinson, Behav. Neurosci. 117, 927–938 (2003).

      In this study, Miles et al. were interested in looking at how chronic cocaine use in rats affects response to outcome devaluation. His group noted that chronic cocaine users were not responsive to changes.

    3. R. J. Beninger, S. T. Mason, A. G. Phillips, H. C. Fibiger, J. Pharmacol. Exp. Ther. 213, 623–627 (1980).

      Beninger et al. studied the effect of pimozide treatment, a dopamine receptor blocker, to determine if treated rats would avoid the negative outcomes that were previously associated with a particular stimulus.

      They found that treated animals could not avoid the negative outcomes due to their inability to initiate a response to the stimulus.

  7. Sep 2018
    1. C. S. Velden, T. L. Olander, R. M. Zehr, Weather and Forecasting 13, 172 (1998)

      Velden and co-authors came up with an algorithm based technique for examining satellite imagery and cataloging storm systems. Their "Objective Dvorak Technique" is a modified version of the original Dvorak scheme which uses patterns in winds and moisture content to rate a storm on its intensity and characteristics.

      Instead of humans eye-balling characteristics, now computers do the calculations for us to determine storm behavior.

    2. G. J. Holland, Aust. Meteorol. Mag. 29, 169 (1981)

      Greg Holland studied a subset of global data in order to see how enhanced observational technology has improved the detection of intense tropical storms.

      He found that prior to the use of satellite imagery to recognize storms, records tend to underestimate the true number of events. This may be due to the amount of storms which form and remain far offshore which did not make it into historical records. Thus in the 1960's when satellites really started getting widespread usage for tracking weather, scientists "saw" more hurricanes than previously reported.

    1. White TD. 1980. Evolutionary implications of pliocene hominid footprints. Science 208:175–176. doi: 10.1126/science.208.4440.175, PMID: 17745537

      At the time this article was written, the author stated that the 3.6-million-year-old Laetoli footprints were the earliest evidence of bipedalism in human evolution.

    2. Reno PL, Meindl RS, McCollum MA, Lovejoy CO. 2003. Sexual dimorphism in Australopithecus Afarensis was similar to that of modern humans. PNAS 100:9404–9409. doi: 10.1073/pnas.1133180100, PMID: 12878734

      The authors estimated the degree of sexual dimorphism present in Australopithecus afarensis through a systematic, random sampling of skeletal fossils. Simulations using the same sampling strategy with modern humans, chimpanzees, and gorillas confirmed the accuracy of the technique. It was determined that A. afarensis exhibited moderate sexual dimorphism similar to that of modern humans. This, coupled with the presence of a reduced male canine, is consistent with monogamy.

    3. Johanson DC, White TD, Coppens Y. 1978. A new species of the genus Australopithecus (Primates: Hominidae) from the Pliocene of eastern Africa. Kirtlandia 28:1–14.

      A large assortment bones was unearthed in Laetoli, Tanzania and Hadar, Ethiopa. The authors attribute them to a new species of Australopithecus. The soil types and depth of each bone is described and mapped.

    4. Harcourt-Smith WEH. 2005. Did Australopithecus Afarensis make the Laetoli footprint trail? New insights into an old problem. American Journal of Physical Anthropology S40:116. doi: 10.1002/ajpa.20217

      The authors investigated the hotly debated question: "Did early bipeds walk more like humans or more like apes?" Modern humans walk with extended hind limbs whereas apes walk with flexed hind limbs. By comparing the Laetoli trackway prints with those made by modern humans walking along a sand pathway, the authors conclude that A. afarensis walked in an energetically economical way—more like modern humans.

    5. Haile-Selassie Y, Latimer BM, Alene M, Deino AL, Gibert L, Melillo SM, Saylor BZ, Scott GR, Lovejoy CO. 2010. An early Australopithecus afarensis postcranium from Woranso-Mille, Ethiopia. PNAS 107:12121–12126. doi: 10.1073/pnas.1004527107

      The partial skeleton of A. afarensis specimen KSD-VP-1 was studied to learn more about stature, body mass, and bipedality in the species. KSD-VP-1/1 antedates Lucy (A.L.288-1) by about 0.4 million years. Based on measurements of bones it was determined KSD-VP-1/1 is a larger-bodied specimen than Lucy and likely a male. There is evidence of a high degree of sexual dimorphism and a well-developed thorax different from present-day apes.

    6. Gordon AD, Green DJ, Richmond BG. 2008. Strong postcranial size dimorphism in Australopithecus afarensis: results from two new resampling methods for multivariate data sets with missing data.

      There has been much debate over the degree of sexual dimorphism and implied social behavior in Australopithecus afarensis. Previous studies have suffered from limited sample size. The authors present two new resampling techniques that do not rely on template specimen and its associated assumptions. Postcranial size dimorphism is determined measuring the femur, tibia, humerus, and radius in samples of A. afarensis, modern humans, chimpanzees, gorillas, and orangutans. Based on their findings, the authors concluded that postcranial dimorphism in A. afarensis is similar to that of gorillas and orangutans, and significantly greater than in modern humans and chimpanzees. Though not conclusive, the authors feel that there is a strong evidence of behavioral and mating strategies employed by A. afarensis.

    7. Bennett MR, Reynolds SC, Morse SA, Budka M. 2016. Laetoli’s lost tracks: 3D generated mean shape and missing footprints. Scientific Reports 6:21916. doi: 10.1038/srep21916

      The authors employed a new technique, color-rendered optical laser scanning, to decouple the G2/3 Laetoli hominin footprints. Scientists had speculated that the G2/3 print was made by a smaller individual walking in the footsteps of a larger individual. Some had argued that the G2/3 trackway was made by only one individual and not a composite. Until this study, the G2/3 trackway had not been well studied. This article describes how the use of color-rendered optical laser scanning allowed the authors to decouple the G2 and G3 tracks, end the argument, and render the footprints usable for data analyses.

    8. Anton SC, Potts R, Aiello LC. 2014. Human evolution. Evolution of early Homo: an integrated biological perspective. Science 345:1236828. doi: 10.1126/science.1236828, PMID: 24994657

      Three lineages of early Homo evolved between 2.5 and 1.5 million years ago. Evidence collected over the past few decades has resulted in a revision in the thinking about how and when adaptations such as our large, linear bodies, long legs, large brains, and reduced sexual dimorphism first appeared. Originally, it was thought these adaptations occurred as a package. Fossil analysis and environmental data indicate that many of the traits associated with Homo sapiens appeared at different times. Some arose earlier and others later. Environmental changes gave a selective advantage to different traits.

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

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

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

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

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

      The paper by N. G. Hairston, F. .E. Smith, and L. B. Slobodkin, "Community structure, Population Control, and Competition," observed what and how organisms are limited by their respective resources. Producers may be limited by an array of variables: light, water, and nutrients. These limiting resources can cause a change in competition throughout the trophic levels. In this paper, the limiting resources are the nutrients from guano. As the foxes prey and decrease the number of seabirds visiting the island, the dispersal of guano also decreases on the island.

    1. 15. S. Dasgupta, A. Gupta, Random Structures Algorithms 22, 60–65 (2003).

      Dasgupta and Gupta prove one result of the Johnson-Lindenstrauss theorem. This proof shows that a set of points in high-dimensional space can be mapped into a smaller dimensional space such that the distance between any two points changes only by a very small amount (1 ± ε).

      This result forms the foundation of many LSH algorithms.

    2. 10. A. Andoni, P. Indyk, Commun. ACM 51, 117 (2008).

      Andoni and Indyk provide an overview of efficient algorithms for nearest neighbor search problems.

      They focus specifically on locality-sensitive hashing algorithms, highlighting one specific option within the LSH family that provides near-optimal performance on nearest neighbor search problems.

    3. 8. S. R. Olsen, V. Bhandawat, R. I. Wilson, Neuron 66, 287–299 (2010).

      Olsen, Bhandawat, and Wilson describe one specific type of computation that occurs in olfactory processing in flies.

      They show that this computation, known as divisive normalization, helps to equalize responses to different input stimuli. This same computation is also known to serve a similar purpose in many parts of the visual system.

    4. 2. D. Owald, S. Waddell, Curr. Opin. Neurobiol. 35, 178–184 (2015).

      Owald and Waddell explore how memories of odors manifest in the fly's olfactory circuit and drive fly behavior

      Specifically, they discover that dopamine plays a key role in this process. During learning, dopaminergic neurons reactivate Kenyon cells associated with specific odor tags. In this way, the fly recalls previously-learned odors.

    5. 1. C. F. Stevens, Proc. Natl. Acad. Sci. U.S.A. 112, 9460–9465 (2015).

      Stevens outlines the three-layer architecture that makes up the fly's olfactory circuit.

      He also presents the idea of a unique odor label, or "tag" that is comprised of a small set of neurons and helps the fly identify distinct odors.

    1. V. Devictor, C. van Swaay, T. Brereton, L. Brotons, D. Chamberlain, J. Heliölä, S. Herrando, R. Julliard,M. Kuussaari, Å. Lindström, J. Reif, D. B. Roy, O. Schweiger, J. Settele, C. Stefanescu, A. Van Strien, C.Van Turnhout, Z. Vermouzek, M. WallisDeVries, I. Wynhoff, F. Jiguet, Differences in the climatic debts of birds and butterflies at a continental scale. Nat. Clim. Change 2, 121–124 (2012).

      This paper demonstrates how bird and butterfly communities have changed over time, and while they shifted through time, they failed to keep up with climate change. They show that northward shifts for bird communities shifted by 37 km, and butterfly communities shifted by 114 km. The climate shifted much faster than this, leaving lags of 212 km for birds, and 135 km for butterflies. These are the distances that birds and butterflies would need to travel to reach temperatures similar to that of their historical range shifts.

  8. Aug 2018
    1. T.C. LaJeunesse, Marine Biology 141, 387–400 (2002).

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

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

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

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

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

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

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