text:
@article{Adami2014,
abstract = {Research investigating the origins of life usually focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches. Little work has been done exploring fundamental issues concerning the spontaneous emergence of life using only concepts (such as information and evolution) that are divorced from any particular chemistry. Here, I advocate studying the probability of spontaneous molecular self-replication as a function of the information contained in the replicator, and the environmental conditions that might enable this emergence. I show that (under certain simplifying assumptions) the probability to discover a self-replicator by chance depends exponentially on the rate of formation of the monomers. If the rate at which monomers are formed is somewhat similar to the rate at which they would occur in a self-replicating polymer, the likelihood to discover such a replicator by chance is increased by many orders of magnitude. I document such an increase in searches for a self-replicator within the digital life system avida},
archivePrefix = {arXiv},
arxivId = {1409.0590},
author = {Adami, Christoph},
eprint = {1409.0590},
file = {:Users/damascus/Documents/Mendeley\_papers/Adami - 2014 - Unknown.pdf:pdf},
month = sep,
pages = {9},
title = {{Information-theoretic considerations concerning the origin of life}},
url = {http://arxiv.org/abs/1409.0590},
year = {2014}
}
@article{Benner2010,
abstract = {Organic chemistry on a planetary scale is likely to have transformed carbon dioxide and reduced carbon species delivered to an accreting Earth. According to various models for the origin of life on Earth, biological molecules that jump-started Darwinian evolution arose via this planetary chemistry. The grandest of these models assumes that ribonucleic acid (RNA) arose prebiotically, together with components for compartments that held it and a primitive metabolism that nourished it. Unfortunately, it has been challenging to identify possible prebiotic chemistry that might have created RNA. Organic molecules, given energy, have a well-known propensity to form multiple products, sometimes referred to collectively as "tar" or "tholin." These mixtures appear to be unsuited to support Darwinian processes, and certainly have never been observed to spontaneously yield a homochiral genetic polymer. To date, proposed solutions to this challenge either involve too much direct human intervention to satisfy many in the community, or generate molecules that are unreactive "dead ends" under standard conditions of temperature and pressure. Carbohydrates, organic species having carbon, hydrogen, and oxygen atoms in a ratio of 1:2:1 and an aldehyde or ketone group, conspicuously embody this challenge. They are components of RNA and their reactivity can support both interesting spontaneous chemistry as part of a "carbohydrate world," but they also easily form mixtures, polymers and tars. We describe here the latest thoughts on how on this challenge, focusing on how it might be resolved using minerals containing borate, silicate, and molybdate, inter alia.},
author = {Benner, Steven a and Kim, Hyo-Joong and Kim, Myung-Jung and Ricardo, Alonso},
doi = {10.1101/cshperspect.a003467},
file = {:Users/damascus/Documents/Mendeley\_papers/Benner et al. - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Carbohydrates,Carbohydrates: chemistry,Chemistry, Organic,Polymers},
month = jul,
number = {7},
pages = {a003467},
pmid = {20504964},
title = {{Planetary organic chemistry and the origins of biomolecules.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2890202\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Blackmond2010,
abstract = {The single-handedness of biological molecules has fascinated scientists and laymen alike since Pasteur's first painstaking separation of the enantiomorphic crystals of a tartrate salt more than 150 yr ago. More recently, a number of theoretical and experimental investigations have helped to delineate models for how one enantiomer might have come to dominate over the other from what presumably was a racemic prebiotic world. This article highlights mechanisms for enantioenrichment that include either chemical or physical processes, or a combination of both. The scientific driving force for this work arises from an interest in understanding the origin of life, because the homochirality of biological molecules is a signature of life.},
author = {Blackmond, Donna G},
doi = {10.1101/cshperspect.a002147},
file = {:Users/damascus/Documents/Mendeley\_papers/Blackmond - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Amino Acids,Amino Acids: chemistry,Carbohydrates,Carbohydrates: chemistry,Stereoisomerism},
month = may,
number = {5},
pages = {a002147},
pmid = {20452962},
title = {{The origin of biological homochirality.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2857173\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Bowler2013,
abstract = {The recent synthesis of pyrimidine ribonucleoside-2',3'-cyclic phosphates under prebiotically plausible conditions has strengthened the case for the involvement of ribonucleic acid (RNA) at an early stage in the origin of life. However, a prebiotic conversion of these weakly activated monomers, and their purine counterparts, to the 3',5'-linked RNA polymers of extant biochemistry has been lacking (previous attempts led only to short oligomers with mixed linkages). Here we show that the 2'-hydroxyl group of oligoribonucleotide-3'-phosphates can be chemoselectively acetylated in water under prebiotically credible conditions, which allows rapid and efficient template-directed ligation. The 2'-O-acetyl group at the ligation junction of the product RNA strand can be removed under conditions that leave the internucleotide bonds intact. Remarkably, acetylation of mixed oligomers that possess either 2'- or 3'-terminal phosphates is selective for the 2'-hydroxyl group of the latter. This newly discovered chemistry thus suggests a prebiotic route from ribonucleoside-2',3'-cyclic phosphates to predominantly 3',5'-linked RNA via partially 2'-O-acetylated RNA.},
author = {Bowler, Frank R and Chan, Christopher K W and Duffy, Colm D and Gerland, B\'{e}atrice and Islam, Saidul and Powner, Matthew W and Sutherland, John D and Xu, Jianfeng},
doi = {10.1038/nchem.1626},
file = {:Users/damascus/Documents/Mendeley\_papers/Bowler et al. - 2013 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
keywords = {Acetylation,Biomolecular,Biopolymers,Biopolymers: chemistry,Nuclear Magnetic Resonance,Prebiotics,RNA,RNA: chemistry},
month = may,
number = {5},
pages = {383--9},
pmid = {23609088},
title = {{Prebiotically plausible oligoribonucleotide ligation facilitated by chemoselective acetylation.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4074891\&tool=pmcentrez\&rendertype=abstract},
volume = {5},
year = {2013}
}
@article{Brewer2014,
abstract = {The route by which the complex and specific molecules of life arose from the 'prebiotic soup' remains an unsolved problem. Evolution provides a large part of the answer, but this requires molecules that can carry information (that is, exist in many variants) and can replicate themselves. The process is commonplace in living organisms, but not so easy to achieve with simple chemical systems. It is especially difficult to contemplate in the chemical chaos of the prebiotic world. Although popular in many quarters, the notion that RNA was the first self-replicator carries many difficulties. Here, we present an alternative view, suggesting that there may be undiscovered self-replication mechanisms possible in much simpler systems. In particular, we highlight the possibility of information coding through stereochemical configurations of substituents in organic polymers. We also show that this coding system leads naturally to enantiopurity, solving the apparent problem of biological homochirality.},
author = {Brewer, Ashley and Davis, Anthony P},
doi = {10.1038/nchem.1981},
file = {:Users/damascus/Documents/Mendeley\_papers/Brewer, Davis - 2014 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
month = jul,
number = {7},
pages = {569--74},
pmid = {24950314},
title = {{Chiral encoding may provide a simple solution to the origin of life.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24950314},
volume = {6},
year = {2014}
}
@article{Chen2010a,
abstract = {Self-assembled vesicles are essential components of primitive cells. We review the importance of vesicles during the origins of life, fundamental thermodynamics and kinetics of self-assembly, and experimental models of simple vesicles, focusing on prebiotically plausible fatty acids and their derivatives. We review recent work on interactions of simple vesicles with RNA and other studies of the transition from vesicles to protocells. Finally we discuss current challenges in understanding the biophysics of protocells, as well as conceptual questions in information transmission and self-replication.},
author = {Chen, Irene a and Walde, Peter},
doi = {10.1101/cshperspect.a002170},
file = {:Users/damascus/Documents/Mendeley\_papers/Chen, Walde - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Cell Membrane,Cell Membrane: metabolism,Cells,Kinetics,Nucleic Acids,Nucleic Acids: metabolism,Thermodynamics},
month = jul,
number = {7},
pages = {a002170},
pmid = {20519344},
title = {{From self-assembled vesicles to protocells.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2890201\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Cheng2010,
abstract = {How life emerged on this planet is one of the most important and fundamental questions of science. Although nearly all details concerning our origins have been lost in the depths of time, there is compelling evidence to suggest that the earliest life might have exploited the catalytic and self-recognition properties of RNA to survive. If an RNA based replicating system could be constructed in the laboratory, it would be much easier to understand the challenges associated with the very earliest steps in evolution and provide important insight into the establishment of the complex metabolic systems that now dominate this planet. Recent progress into the selection and characterization of ribozymes that promote nucleotide synthesis and RNA polymerization are discussed and outstanding problems in the field of RNA-mediated RNA replication are summarized.},
author = {Cheng, Leslie K L and Unrau, Peter J},
doi = {10.1101/cshperspect.a002204},
file = {:Users/damascus/Documents/Mendeley\_papers/Cheng, Unrau - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Biogenesis,DNA-Directed RNA Polymerases,DNA-Directed RNA Polymerases: genetics,DNA-Directed RNA Polymerases: metabolism,Evolution, Molecular,Polynucleotide Ligases,Polynucleotide Ligases: genetics,Polynucleotide Ligases: metabolism,RNA,RNA, Catalytic,RNA, Catalytic: genetics,RNA, Catalytic: metabolism,RNA: biosynthesis,RNA: genetics},
month = oct,
number = {10},
pages = {a002204},
pmid = {20554706},
title = {{Closing the circle: replicating RNA with RNA.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2944364\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Damasceno,
author = {Damasceno, Pablo F and Glotzer, Sharon C.},
journal = {in prep. (2015)},
title = {{Self-Assembly of Complex Crystals via Isotropic Potentials Derived from Shape}}
}
@article{Damascenoa,
author = {Damasceno, Pablo F. and Engel, Michael and Glotzer, Sharon C.},
file = {:Users/damascus/Library/Application Support/Mendeley Desktop/Downloaded/Damasceno, Engel, Glotzer - Unknown - Self-Assembly of Homochiral Colloidal Crystals.pdf:pdf},
journal = {in prep. (2014)},
title = {{Self-Assembly of Homochiral Colloidal Crystals}}
}
@article{Damascenob,
author = {Damasceno, Pablo F. and Phillips, Carolyn L. and Engel, Michael and Glotzer, Sharon C.},
file = {:Users/damascus/Library/Application Support/Mendeley Desktop/Downloaded/Damasceno, Engel, Glotzer - Unknown - Self-Assembly of Homochiral Colloidal Crystals.pdf:pdf},
journal = {in prep. (2014)},
title = {{Self-Assembly of Complex Crystals from Simple Pair-Potentials}}
}
@article{Deamer2010,
abstract = {Bioenergetics is central to our understanding of living systems, yet has attracted relatively little attention in origins of life research. This article focuses on energy resources available to drive primitive metabolism and the synthesis of polymers that could be incorporated into molecular systems having properties associated with the living state. The compartmented systems are referred to as protocells, each different from all the rest and representing a kind of natural experiment. The origin of life was marked when a rare few protocells happened to have the ability to capture energy from the environment to initiate catalyzed heterotrophic growth directed by heritable genetic information in the polymers. This article examines potential sources of energy available to protocells, and mechanisms by which the energy could be used to drive polymer synthesis.},
author = {Deamer, David and Weber, Arthur L},
doi = {10.1101/cshperspect.a004929},
file = {:Users/damascus/Documents/Mendeley\_papers/Deamer, Weber - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Animals,Biogenesis,Catalysis,Diphosphates,Diphosphates: chemistry,Energy Metabolism,Humans,Kinetics,Life,Models, Biological,Polymers,Polymers: chemistry,Sunlight,Thermodynamics},
month = feb,
number = {2},
pages = {a004929},
pmid = {20182625},
title = {{Bioenergetics and life's origins.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2828274\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Deck2011,
abstract = {The transition from inanimate materials to the earliest forms of life must have involved multiplication of a catalytically active polymer that is able to replicate. The semiconservative replication that is characteristic of genetic information transfer requires strands that contain more than one type of nucleobase. Short strands of RNA can act as catalysts, but attempts to induce efficient self-copying of mixed sequences (containing four different nucleobases) have been unsuccessful with ribonucleotides. Here we show that inhibition by spent monomers, formed by the hydrolysis of the activated nucleotides, is the cause for incomplete extension of growing daughter strands on RNA templates. Immobilization of strands and periodic displacement of the solution containing the activated monomers overcome this inhibition. Any of the four nucleobases (A/C/G/U) is successfully copied in the absence of enzymes. We conclude therefore that in a prebiotic world, oligoribonucleotides may have formed and undergone self-copying on surfaces.},
author = {Deck, Christopher and Jauker, Mario and Richert, Clemens},
doi = {10.1038/nchem.1086},
file = {:Users/damascus/Documents/Mendeley\_papers/Deck, Jauker, Richert - 2011 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
keywords = {Base Sequence,RNA,RNA: chemistry,Ribonucleotides,Ribonucleotides: chemistry},
month = aug,
number = {8},
pages = {603--8},
pmid = {21778979},
publisher = {Nature Publishing Group},
title = {{Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21778979},
volume = {3},
year = {2011}
}
@article{Engela,
author = {Engel, Michael and Damasceno, Pablo F. and Phillips, Carolyn L. and Glotzer, Sharon C.},
file = {:Users/damascus/Documents/Mendeley\_papers//Engel et al. - Unknown - Nature materials.pdf:pdf},
journal = {Nature materials},
title = {{Computational discovery of a one-component icosahedral quasicrystal via self-assembly}}
}
@article{Engelhart2010,
abstract = {Since the structure of DNA was elucidated more than 50 years ago, Watson-Crick base pairing has been widely speculated to be the likely mode of both information storage and transfer in the earliest genetic polymers. The discovery of catalytic RNA molecules subsequently provided support for the hypothesis that RNA was perhaps even the first polymer of life. However, the de novo synthesis of RNA using only plausible prebiotic chemistry has proven difficult, to say the least. Experimental investigations, made possible by the application of synthetic and physical organic chemistry, have now provided evidence that the nucleobases (A, G, C, and T/U), the trifunctional moiety ([deoxy]ribose), and the linkage chemistry (phosphate esters) of contemporary nucleic acids may be optimally suited for their present roles-a situation that suggests refinement by evolution. Here, we consider studies of variations in these three distinct components of nucleic acids with regard to the question: Is RNA, as is generally acknowledged of DNA, the product of evolution? If so, what chemical and structural features might have been more likely and advantageous for a proto-RNA?},
author = {Engelhart, Aaron E and Hud, Nicholas V},
doi = {10.1101/cshperspect.a002196},
file = {:Users/damascus/Documents/Mendeley\_papers/Engelhart, Hud - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Biogenesis,Evolution, Chemical,Molecular Structure,Nucleic Acids,Nucleic Acids: chemistry,Polymerization,RNA,RNA: chemistry},
month = dec,
number = {12},
pages = {a002196},
pmid = {20462999},
title = {{Primitive genetic polymers.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2982173\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Engelhart2013,
abstract = {A plausible process for non-enzymatic RNA replication would greatly simplify models of the transition from prebiotic chemistry to simple biology. However, all known conditions for the chemical copying of an RNA template result in the synthesis of a complementary strand that contains a mixture of 2'-5' and 3'-5' linkages, rather than the selective synthesis of only 3'-5' linkages as found in contemporary RNA. Here we show that such backbone heterogeneity is compatible with RNA folding into defined three-dimensional structures that retain molecular recognition and catalytic properties and, therefore, would not prevent the evolution of functional RNAs such as ribozymes. Moreover, the same backbone heterogeneity lowers the melting temperature of RNA duplexes that would otherwise be too stable for thermal strand separation. By allowing copied strands to dissociate, this heterogeneity may have been one of the essential features that allowed RNA to emerge as the first biopolymer.},
author = {Engelhart, Aaron E and Powner, Matthew W and Szostak, Jack W},
doi = {10.1038/nchem.1623},
file = {:Users/damascus/Documents/Mendeley\_papers/Engelhart, Powner, Szostak - 2013 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
keywords = {Base Sequence,Models,Nucleic Acid Conformation,RNA,RNA: chemistry,Theoretical},
month = may,
number = {5},
pages = {390--4},
pmid = {23609089},
publisher = {Nature Publishing Group},
title = {{Functional RNAs exhibit tolerance for non-heritable 2'-5' versus 3'-5' backbone heterogeneity.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4088963\&tool=pmcentrez\&rendertype=abstract},
volume = {5},
year = {2013}
}
@article{Eschenmoser1999,
author = {Eschenmoser, A.},
doi = {10.1126/science.284.5423.2118},
file = {:Users/damascus/Documents/Mendeley\_papers/Eschenmoser - 1999 - Science.pdf:pdf},
issn = {00368075},
journal = {Science},
month = jun,
number = {5423},
pages = {2118--2124},
title = {{Chemical Etiology of Nucleic Acid Structure}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.284.5423.2118},
volume = {284},
year = {1999}
}
@article{Fox2010,
abstract = {The modern ribosome was largely formed at the time of the last common ancestor, LUCA. Hence its earliest origins likely lie in the RNA world. Central to its development were RNAs that spawned the modern tRNAs and a symmetrical region deep within the large ribosomal RNA, (rRNA), where the peptidyl transferase reaction occurs. To understand pre-LUCA developments, it is argued that events that are coupled in time are especially useful if one can infer a likely order in which they occurred. Using such timing events, the relative age of various proteins and individual regions within the large rRNA are inferred. An examination of the properties of modern ribosomes strongly suggests that the initial peptides made by the primitive ribosomes were likely enriched for l-amino acids, but did not completely exclude d-amino acids. This has implications for the nature of peptides made by the first ribosomes. From the perspective of ribosome origins, the immediate question regarding coding is when did it arise rather than how did the assignments evolve. The modern ribosome is very dynamic with tRNAs moving in and out and the mRNA moving relative to the ribosome. These movements may have become possible as a result of the addition of a template to hold the tRNAs. That template would subsequently become the mRNA, thereby allowing the evolution of the code and making an RNA genome useful. Finally, a highly speculative timeline of major events in ribosome history is presented and possible future directions discussed.},
author = {Fox, George E},
doi = {10.1101/cshperspect.a003483},
file = {:Users/damascus/Documents/Mendeley\_papers/Fox - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Evolution, Molecular,RNA, Ribosomal,RNA, Ribosomal: genetics,RNA, Ribosomal: physiology,RNA, Transfer,RNA, Transfer: genetics,RNA, Transfer: physiology,Ribosomes,Ribosomes: genetics,Ribosomes: physiology},
month = sep,
number = {9},
pages = {a003483},
pmid = {20534711},
title = {{Origin and evolution of the ribosome.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2926754\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Gaucher2010,
abstract = {The Darwinian concept of biological evolution assumes that life on Earth shares a common ancestor. The diversification of this common ancestor through speciation events and vertical transmission of genetic material implies that the classification of life can be illustrated in a tree-like manner, commonly referred to as the Tree of Life. This article describes features of the Tree of Life, such as how the tree has been both pruned and become bushier throughout the past century as our knowledge of biology has expanded. We present current views that the classification of life may be best illustrated as a ring or even a coral with tree-like characteristics. This article also discusses how the organization of the Tree of Life offers clues about ancient life on Earth. In particular, we focus on the environmental conditions and temperature history of Precambrian life and show how chemical, biological, and geological data can converge to better understand this history."You know, a tree is a tree. How many more do you need to look at?"--Ronald Reagan (Governor of California), quoted in the Sacramento Bee, opposing expansion of Redwood National Park, March 3, 1966.},
author = {Gaucher, Eric a and Kratzer, James T and Randall, Ryan N},
doi = {10.1101/cshperspect.a002238},
file = {:Users/damascus/Documents/Mendeley\_papers/Gaucher, Kratzer, Randall - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Adaptation, Physiological,Biological Evolution,Environment,Escherichia coli,Escherichia coli: metabolism,History, Ancient,Paleontology,Paleontology: methods,Phylogeny,Temperature,Thermus,Thermus: metabolism},
month = jan,
number = {1},
pages = {a002238},
pmid = {20182607},
title = {{Deep phylogeny--how a tree can help characterize early life on Earth.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2827910\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Goldman2010,
abstract = {Delivery of prebiotic compounds to early Earth from an impacting comet is thought to be an unlikely mechanism for the origins of life because of unfavourable chemical conditions on the planet and the high heat from impact. In contrast, we find that impact-induced shock compression of cometary ices followed by expansion to ambient conditions can produce complexes that resemble the amino acid glycine. Our ab initio molecular dynamics simulations show that shock waves drive the synthesis of transient C-N bonded oligomers at extreme pressures and temperatures. On post impact quenching to lower pressures, the oligomers break apart to form a metastable glycine-containing complex. We show that impact from cometary ice could possibly yield amino acids by a synthetic route independent of the pre-existing atmospheric conditions and materials on the planet.},
author = {Goldman, Nir and Reed, Evan J and Fried, Laurence E and {William Kuo}, I-F and Maiti, Amitesh},
doi = {10.1038/nchem.827},
file = {:Users/damascus/Documents/Mendeley\_papers/Goldman et al. - 2010 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
keywords = {Earth (Planet),Glycine,Glycine: analysis,Meteoroids,Molecular Dynamics Simulation},
month = nov,
number = {11},
pages = {949--54},
pmid = {20966951},
publisher = {Nature Publishing Group},
title = {{Synthesis of glycine-containing complexes in impacts of comets on early Earth.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20966951},
volume = {2},
year = {2010}
}
@article{Gollihar2014,
author = {Gollihar, Jimmy and Levy, Matthew and Ellington, Andrew D},
doi = {10.1126/science.1246704},
file = {:Users/damascus/Documents/Mendeley\_papers/Gollihar, Levy, Ellington - 2014 - Science (New York, N.Y.).pdf:pdf},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
keywords = {Biogenesis,Carbohydrates,Carbohydrates: chemistry,Earth (Planet),Ligases,Ligases: chemistry,Mars,RNA, Catalytic,RNA, Catalytic: chemistry,Ribose,Ribose: chemistry},
month = jan,
number = {6168},
pages = {259--60},
pmid = {24436411},
title = {{Biochemistry. Many paths to the origin of life.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24436411},
volume = {343},
year = {2014}
}
@article{Hazen2010,
abstract = {Crystalline surfaces of common rock-forming minerals are likely to have played several important roles in life's geochemical origins. Transition metal sulfides and oxides promote a variety of organic reactions, including nitrogen reduction, hydroformylation, amination, and Fischer-Tropsch-type synthesis. Fine-grained clay minerals and hydroxides facilitate lipid self-organization and condensation polymerization reactions, notably of RNA monomers. Surfaces of common rock-forming oxides, silicates, and carbonates select and concentrate specific amino acids, sugars, and other molecular species, while potentially enhancing their thermal stabilities. Chiral surfaces of these minerals also have been shown to separate left- and right-handed molecules. Thus, mineral surfaces may have contributed centrally to the linked prebiotic problems of containment and organization by promoting the transition from a dilute prebiotic "soup" to highly ordered local domains of key biomolecules.},
author = {Hazen, Robert M and Sverjensky, Dimitri a},
doi = {10.1101/cshperspect.a002162},
file = {:Users/damascus/Documents/Mendeley\_papers/Hazen, Sverjensky - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Biogenesis,Crystallization,Minerals,Minerals: chemistry,Surface Properties},
month = may,
number = {5},
pages = {a002162},
pmid = {20452963},
title = {{Mineral surfaces, geochemical complexities, and the origins of life.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2857174\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Hein2011,
abstract = {The single-handedness of biological molecules is critical for molecular recognition and replication processes and would seem to be a prerequisite for the origin of life. A drawback of recently reported synthetic routes to RNA is the requirement for enantioenriched reactants, which fails to address the puzzle of how the single chirality of biological molecules arose. Here, we report the synthesis of highly enantioenriched RNA precursor molecules from racemic starting materials, with the molecular asymmetry derived solely from a small initial imbalance of the amino-acid enantiomers present in the reaction mixture. Acting as spectators to the main reaction chemistry, the amino acids orchestrate a sequence of physical and chemical amplification processes. The emergence of molecules of single chirality from complex, multi-component mixtures supports the robustness of this synthesis process under potential prebiotic conditions and provides a plausible explanation for the single-handedness of biological molecules before the emergence of self-replicating informational polymers.},
author = {Hein, Jason E and Tse, Eric and Blackmond, Donna G},
doi = {10.1038/nchem.1108},
file = {:Users/damascus/Documents/Mendeley\_papers/Hein, Tse, Blackmond - 2011 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
keywords = {Amino Acids,Amino Acids: chemistry,Glyceraldehyde,Glyceraldehyde: chemistry,Oxazoles,Oxazoles: chemistry,RNA Precursors,RNA Precursors: chemical synthesis,RNA Precursors: chemistry,RNA Precursors: genetics,Stereoisomerism},
month = sep,
number = {9},
pages = {704--6},
pmid = {21860459},
publisher = {Nature Publishing Group},
title = {{A route to enantiopure RNA precursors from nearly racemic starting materials.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21860459},
volume = {3},
year = {2011}
}
@article{Hernandez2013,
author = {Hern\'{a}ndez, Armando R and Piccirilli, Joseph a},
doi = {10.1038/nchem.1636},
file = {:Users/damascus/Documents/Mendeley\_papers/Hern\'{a}ndez, Piccirilli - 2013 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
keywords = {Models, Theoretical,Prebiotics,RNA,RNA: chemistry},
month = may,
number = {5},
pages = {360--2},
pmid = {23609081},
publisher = {Nature Publishing Group},
title = {{Chemical origins of life: Prebiotic RNA unstuck.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23609081},
volume = {5},
year = {2013}
}
@article{Hormoz2011,
abstract = {Recent experimental advances have opened up the possibility of equilibrium self-assembly of functionalized nanoblocks with a high degree of controllable specific interactions. Here, we propose design principles for selecting the short-range interactions between self-assembling components to maximize yield. We illustrate the approach with an example from colloidal engineering. We construct an optimal set of local interactions for eight colloidal particles (coated, e.g., with DNA strands) to assemble into a particular polytetrahedral cluster. Maximum yield is attained when the interactions between the colloids follow the design rules: All energetically favorable interactions have the same strength, as do all unfavorable ones, and the number of components and energies fall within the proposed range. In general, it might be necessary to use more component than strictly required for enforcing the ground state configuration. The results motivate design strategies for engineering components that can reliably self-assemble.},
author = {Hormoz, Sahand and Brenner, Michael P},
doi = {10.1073/pnas.1014094108},
file = {:Users/damascus/Documents/Mendeley\_papers/Hormoz, Brenner - 2011 - Proceedings of the National Academy of Sciences of the United States of America.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Colloids,Colloids: chemistry,Models, Molecular,Molecular Structure,Nanostructures,Nanostructures: chemistry},
month = mar,
number = {13},
pages = {5193--8},
pmid = {21383135},
title = {{Design principles for self-assembly with short-range interactions.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3069168\&tool=pmcentrez\&rendertype=abstract},
volume = {108},
year = {2011}
}
@article{Ichihashi2010,
abstract = {Understanding the origin of life requires knowledge not only of the origin of biological molecules such as amino acids, nucleotides and their polymers, but also the manner in which those molecules are integrated into the organized systems that characterize cellular life. In this article, we introduce a constructive approach to understand how biological molecules can be arranged to achieve a higher-order biological function: replication of genetic information.},
author = {Ichihashi, Norikazu and Matsuura, Tomoaki and Kita, Hiroshi and Sunami, Takeshi and Suzuki, Hiroaki and Yomo, Tetsuya},
doi = {10.1101/cshperspect.a004945},
file = {:Users/damascus/Documents/Mendeley\_papers/Ichihashi et al. - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Biological Evolution,DNA Replication,DNA Replication: genetics,Gene Regulatory Networks,Liposomes,Models, Genetic,Templates, Genetic},
month = jun,
number = {6},
pages = {a004945},
pmid = {20516136},
title = {{Constructing partial models of cells.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2869526\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Koga2011,
abstract = {Although phospholipid bilayers are ubiquitous in modern cells, their impermeability, lack of dynamic properties, and synthetic complexity are difficult to reconcile with plausible pathways of proto-metabolism, growth and division. Here, we present an alternative membrane-free model, which demonstrates that low-molecular-weight mononucleotides and simple cationic peptides spontaneously accumulate in water into microdroplets that are stable to changes in temperature and salt concentration, undergo pH-induced cycles of growth and decay, and promote $\alpha$-helical peptide secondary structure. Moreover, the microdroplets selectively sequester porphyrins, inorganic nanoparticles and enzymes to generate supramolecular stacked arrays of light-harvesting molecules, nanoparticle-mediated oxidase activity, and enhanced rates of glucose phosphorylation, respectively. Taken together, our results suggest that peptide-nucleotide microdroplets can be considered as a new type of protocell model that could be used to develop novel bioreactors, primitive artificial cells and plausible pathways to prebiotic organization before the emergence of lipid-based compartmentalization on the early Earth.},
author = {Koga, Shogo and Williams, David S and Perriman, Adam W and Mann, Stephen},
doi = {10.1038/nchem.1110},
file = {:Users/damascus/Documents/Mendeley\_papers/Koga et al. - 2011 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
keywords = {Artificial Cells,Artificial Cells: chemistry,Catalysis,Nanoparticles,Nanoparticles: chemistry,Nucleotides,Nucleotides: chemistry,Peptides,Peptides: chemistry},
month = sep,
number = {9},
pages = {720--4},
pmid = {21860462},
publisher = {Nature Publishing Group},
title = {{Peptide-nucleotide microdroplets as a step towards a membrane-free protocell model.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21860462},
volume = {3},
year = {2011}
}
@article{Kurihara2011,
abstract = {The construction of a protocell from a materials point of view is important in understanding the origin of life. Both self-reproduction of a compartment and self-replication of an informational substance have been studied extensively, but these processes have typically been carried out independently, rather than linked to one another. Here, we demonstrate the amplification of DNA (encapsulated guest) within a self-reproducible cationic giant vesicle (host). With the addition of a vesicular membrane precursor, we observe the growth and spontaneous division of the giant vesicles, accompanied by distribution of the DNA to the daughter giant vesicles. In particular, amplification of the DNA accelerated the division of the giant vesicles. This means that self-replication of an informational substance has been linked to self-reproduction of a compartment through the interplay between polyanionic DNA and the cationic vesicular membrane. Our self-reproducing giant vesicle system therefore represents a step forward in the construction of an advanced model protocell.},
author = {Kurihara, Kensuke and Tamura, Mieko and Shohda, Koh-Ichiroh and Toyota, Taro and Suzuki, Kentaro and Sugawara, Tadashi},
doi = {10.1038/nchem.1127},
file = {:Users/damascus/Documents/Mendeley\_papers/Kurihara et al. - 2011 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
keywords = {Artificial Cells,Artificial Cells: chemistry,Artificial Cells: metabolism,Biogenesis,DNA,DNA: metabolism,Lipid Bilayers,Lipid Bilayers: chemistry,Lipid Bilayers: metabolism,Phosphatidylcholines,Phosphatidylcholines: chemistry,Phosphatidylglycerols,Phosphatidylglycerols: chemistry,Polymerase Chain Reaction,Rhodamines,Rhodamines: chemistry},
month = oct,
number = {10},
pages = {775--81},
pmid = {21941249},
publisher = {Nature Publishing Group},
title = {{Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21941249},
volume = {3},
year = {2011}
}
@article{Lazcano2010,
abstract = {Following the publication of the Origin of Species in 1859, many naturalists adopted the idea that living organisms were the historical outcome of gradual transformation of lifeless matter. These views soon merged with the developments of biochemistry and cell biology and led to proposals in which the origin of protoplasm was equated with the origin of life. The heterotrophic origin of life proposed by Oparin and Haldane in the 1920s was part of this tradition, which Oparin enriched by transforming the discussion of the emergence of the first cells into a workable multidisciplinary research program. On the other hand, the scientific trend toward understanding biological phenomena at the molecular level led authors like Troland, Muller, and others to propose that single molecules or viruses represented primordial living systems. The contrast between these opposing views on the origin of life represents not only contrasting views of the nature of life itself, but also major ideological discussions that reached a surprising intensity in the years following Stanley Miller's seminal result which showed the ease with which organic compounds of biochemical significance could be synthesized under putative primitive conditions. In fact, during the years following the Miller experiment, attempts to understand the origin of life were strongly influenced by research on DNA replication and protein biosynthesis, and, in socio-political terms, by the atmosphere created by Cold War tensions. The catalytic versatility of RNA molecules clearly merits a critical reappraisal of Muller's viewpoint. However, the discovery of ribozymes does not imply that autocatalytic nucleic acid molecules ready to be used as primordial genes were floating in the primitive oceans, or that the RNA world emerged completely assembled from simple precursors present in the prebiotic soup. The evidence supporting the presence of a wide range of organic molecules on the primitive Earth, including membrane-forming compounds, suggests that the evolution of membrane-bounded molecular systems preceded cellular life on our planet, and that life is the evolutionary outcome of a process, not of a single, fortuitous event.},
author = {Lazcano, Antonio},
doi = {10.1101/cshperspect.a002089},
file = {:Users/damascus/Documents/Mendeley\_papers/Lazcano - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Biogenesis,Biological Evolution,Biology,Biology: history,History, 19th Century,History, 20th Century},
month = nov,
number = {11},
pages = {a002089},
pmid = {20534710},
title = {{Historical development of origins research.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2964185\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Li2014,
abstract = {The five-membered furanose ring is a central component of the chemical structure of biological nucleic acids. The conformations of the furanose ring can be analytically described using the concept of pseudorotation, and for RNA and DNA they are dominated by the C2'-endo and C3'-endo conformers. While the free energy difference between these two conformers can be inferred from NMR measurements, a free energy landscape of the complete pseudorotation cycle of nucleic acids in solution has remained elusive. Here, we describe a new free energy calculation method for molecular dynamics (MD) simulations using the two pseudorotation parameters directly as the collective variables. To validate our approach, we calculated the free energy surface of ribose pseudorotation in guanosine and 2'-deoxyguanosine. The calculated free energy landscape reveals not only the relative stability of the different pseudorotation conformers, but also the main transition path between the stable conformations. Applying this method to a standard A-form RNA duplex uncovered the expected minimum at the C3'-endo state. However, at a 2'-5' linkage, the minimum shifts to the C2'-endo conformation. The free energy of the C3'-endo conformation is 3 kcal/mol higher due to a weaker hydrogen bond and a reduced base stacking interaction. Unrestrained MD simulations suggest that the conversion from C3'-endo to C2'-endo and vice versa is on the nanosecond and microsecond time scale, respectively. These calculations suggest that 2'-5' linkages may enable folded RNAs to sample a wider spectrum of their pseudorotation conformations.},
author = {Li, Li and Szostak, Jack W},
doi = {10.1021/ja412079b},
file = {:Users/damascus/Documents/Mendeley\_papers/Li, Szostak - 2014 - Journal of the American Chemical Society.pdf:pdf},
issn = {1520-5126},
journal = {Journal of the American Chemical Society},
month = feb,
number = {7},
pages = {2858--65},
pmid = {24499340},
title = {{The free energy landscape of pseudorotation in 3'-5' and 2'-5' linked nucleic acids.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3982932\&tool=pmcentrez\&rendertype=abstract},
volume = {136},
year = {2014}
}
@article{Luisi2011,
author = {Luisi, Pier Luigi and Stano, Pasquale},
doi = {10.1038/nchem.1156},
file = {:Users/damascus/Documents/Mendeley\_papers/Luisi, Stano - 2011 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
keywords = {Artificial Cells,Artificial Cells: metabolism,DNA,DNA: metabolism,Lipid Bilayers,Lipid Bilayers: chemistry},
month = oct,
number = {10},
pages = {755--6},
pmid = {21941243},
publisher = {Nature Publishing Group},
title = {{Synthetic biology: minimal cell mimicry.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21941243},
volume = {3},
year = {2011}
}
@article{Mansy2010,
abstract = {Although model protocellular membranes consisting of monoacyl lipids are similar to membranes composed of contemporary diacyl lipids, they differ in at least one important aspect. Model protocellular membranes allow for the passage of polar solutes and thus can potentially support cell-to functions without the aid of transport machinery. The ability to transport polar molecules likely stems from increased lipid dynamics. Selectively permeable vesicle membranes composed of monoacyl lipids allow for many lifelike processes to emerge from a remarkably small set of molecules.},
author = {Mansy, Sheref S},
doi = {10.1101/cshperspect.a002188},
file = {:Users/damascus/Documents/Mendeley\_papers/Mansy - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Biological Evolution,Biological Transport,Cell Membrane,Cell Membrane: metabolism,Diffusion,Fatty Acids,Fatty Acids: chemistry,Lipids,Lipids: chemistry,Membrane Lipids,Membrane Lipids: metabolism,Models, Biological,Models, Chemical,Permeability,Protein Transport,Solubility},
month = aug,
number = {8},
pages = {a002188},
pmid = {20679338},
title = {{Membrane transport in primitive cells.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2908771\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{McKay2010,
abstract = {Evidence of past liquid water on the surface of Mars suggests that this world once had habitable conditions and leads to the question of life. If there was life on Mars, it would be interesting to determine if it represented a separate origin from life on Earth. To determine the biochemistry and genetics of life on Mars requires that we have access to an organism or the biological remains of one-possibly preserved in ancient permafrost. A way to determine if organic material found on Mars represents the remains of an alien biological system could be based on the observation that biological systems select certain organic molecules over others that are chemically similar (e.g., chirality in amino acids).},
author = {McKay, Christopher P},
doi = {10.1101/cshperspect.a003509},
file = {:Users/damascus/Documents/Mendeley\_papers/McKay - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Biogenesis,Exobiology,Mars,Water},
month = apr,
number = {4},
pages = {a003509},
pmid = {20452949},
title = {{An origin of life on Mars.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2845199\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Pizzarello2010,
abstract = {Carbon-containing meteorites provide a natural sample of the extraterrestrial organic chemistry that occurred in the solar system ahead of life's origin on the Earth. Analyses of 40 years have shown the organic content of these meteorites to be materials as diverse as kerogen-like macromolecules and simpler soluble compounds such as amino acids and polyols. Many meteoritic molecules have identical counterpart in the biosphere and, in a primitive group of meteorites, represent the majority of their carbon. Most of the compounds in meteorites have isotopic compositions that date their formation to presolar environments and reveal a long and active cosmochemical evolution of the biogenic elements. Whether this evolution resumed on the Earth to foster biogenesis after exogenous delivery of meteoritic and cometary materials is not known, yet, the selective abundance of biomolecule precursors evident in some cosmic environments and the unique L-asymmetry of some meteoritic amino acids are suggestive of their possible contribution to terrestrial molecular evolution.},
author = {Pizzarello, Sandra and Shock, Everett},
doi = {10.1101/cshperspect.a002105},
file = {:Users/damascus/Documents/Mendeley\_papers/Pizzarello, Shock - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Biogenesis,Carbon,Carbon: chemistry,Chemistry, Organic,Chemistry, Organic: methods,Earth (Planet),Evolution, Chemical,Extraterrestrial Environment,Meteoroids,Solar System},
month = mar,
number = {3},
pages = {a002105},
pmid = {20300213},
title = {{The organic composition of carbonaceous meteorites: the evolutionary story ahead of biochemistry.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2829962\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Powner2013,
author = {Powner, Matthew},
doi = {10.1038/nchem.1629},
file = {:Users/damascus/Documents/Mendeley\_papers/Powner - 2013 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
month = may,
number = {5},
pages = {355--7},
pmid = {23609075},
title = {{Asking original questions. Interview by Stephen Davey.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23609075},
volume = {5},
year = {2013}
}
@article{Ritson2012,
abstract = {A recent synthesis of activated pyrimidine ribonucleotides under prebiotically plausible conditions relied on mixed oxygenous and nitrogenous systems chemistry. As it stands, this synthesis provides support for the involvement of RNA in the origin of life, but such support would be considerably strengthened if the sugar building blocks for the synthesis--glycolaldehyde and glyceraldehyde--could be shown to derive from one carbon feedstock molecules using similarly mixed oxygenous and nitrogenous systems chemistry. Here, we show that these sugars can be formed from hydrogen cyanide by ultraviolet irradiation in the presence of cyanometallates in a remarkable systems chemistry process. Using copper cyanide complexes, the process operates catalytically to disproportionate hydrogen cyanide, first generating the sugars and then sequestering them as simple derivatives.},
author = {Ritson, Dougal and Sutherland, John D},
doi = {10.1038/nchem.1467},
file = {:Users/damascus/Documents/Mendeley\_papers/Ritson, Sutherland - 2012 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
keywords = {Carbohydrates,Carbohydrates: chemical synthesis,Carbohydrates: chemistry,Chemistry Techniques,Hydrogen Cyanide,Hydrogen Cyanide: chemistry,Oxidation-Reduction,Photochemical Processes,Prebiotics,Synthetic},
month = nov,
number = {11},
pages = {895--9},
pmid = {23089863},
publisher = {Nature Publishing Group},
title = {{Prebiotic synthesis of simple sugars by photoredox systems chemistry.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3589744\&tool=pmcentrez\&rendertype=abstract},
volume = {4},
year = {2012}
}
@article{Rodrigo2012,
abstract = {A grand challenge in synthetic biology is to use our current knowledge of RNA science to perform the automatic engineering of completely synthetic sequences encoding functional RNAs in living cells. We report here a fully automated design methodology and experimental validation of synthetic RNA interaction circuits working in a cellular environment. The computational algorithm, based on a physicochemical model, produces novel RNA sequences by exploring the space of possible sequences compatible with predefined structures. We tested our methodology in Escherichia coli by designing several positive riboregulators with diverse structures and interaction models, suggesting that only the energy of formation and the activation energy (free energy barrier to overcome for initiating the hybridization reaction) are sufficient criteria to engineer RNA interaction and regulation in bacteria. The designed sequences exhibit nonsignificant similarity to any known noncoding RNA sequence. Our riboregulatory devices work independently and in combination with transcription regulation to create complex logic circuits. Our results demonstrate that a computational methodology based on first-principles can be used to engineer interacting RNAs with allosteric behavior in living cells.},
author = {Rodrigo, Guillermo and Landrain, Thomas E and Jaramillo, Alfonso},
doi = {10.1073/pnas.1203831109},
file = {:Users/damascus/Documents/Mendeley\_papers/Rodrigo, Landrain, Jaramillo - 2012 - Proceedings of the National Academy of Sciences of the United States of America.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Automation,Chemistry, Physical,Chemistry, Physical: methods,Computational Biology,Computational Biology: methods,Escherichia coli,Escherichia coli: genetics,Escherichia coli: metabolism,Evolution, Molecular,Flow Cytometry,Flow Cytometry: methods,Genes, Reporter,Genetic Engineering,Genetic Engineering: methods,Models, Genetic,Nucleic Acid Conformation,Plasmids,Plasmids: metabolism,Promoter Regions, Genetic,RNA,RNA Processing, Post-Transcriptional,RNA Processing, Post-Transcriptional: genetics,RNA: chemistry,RNA: genetics,Spectrometry, Fluorescence,Spectrometry, Fluorescence: methods,Synthetic Biology,Synthetic Biology: methods,Thermodynamics},
month = sep,
number = {38},
pages = {15271--6},
pmid = {22949707},
title = {{De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3458397\&tool=pmcentrez\&rendertype=abstract},
volume = {109},
year = {2012}
}
@article{Schoning2000,
author = {Schoning, K.-U. and Scholz, P. and Guntha, S. and Wu, X. and Krishnamurthy, R. and Eschenmoser, A.},
doi = {10.1126/science.290.5495.1347},
file = {:Users/damascus/Documents/Mendeley\_papers/Schoning et al. - 2000 - Science.pdf:pdf},
issn = {00368075},
journal = {Science},
month = nov,
number = {5495},
pages = {1347--1351},
title = {{Chemical Etiology of Nucleic Acid Structure: The alpha -Threofuranosyl-(3'rightarrow 2') Oligonucleotide System}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.290.5495.1347},
volume = {290},
year = {2000}
}
@article{Schrum2010,
abstract = {Understanding the origin of cellular life on Earth requires the discovery of plausible pathways for the transition from complex prebiotic chemistry to simple biology, defined as the emergence of chemical assemblies capable of Darwinian evolution. We have proposed that a simple primitive cell, or protocell, would consist of two key components: a protocell membrane that defines a spatially localized compartment, and an informational polymer that allows for the replication and inheritance of functional information. Recent studies of vesicles composed of fatty-acid membranes have shed considerable light on pathways for protocell growth and division, as well as means by which protocells could take up nutrients from their environment. Additional work with genetic polymers has provided insight into the potential for chemical genome replication and compatibility with membrane encapsulation. The integration of a dynamic fatty-acid compartment with robust, generalized genetic polymer replication would yield a laboratory model of a protocell with the potential for classical Darwinian biological evolution, and may help to evaluate potential pathways for the emergence of life on the early Earth. Here we discuss efforts to devise such an integrated protocell model.},
author = {Schrum, Jason P and Zhu, Ting F and Szostak, Jack W},
doi = {10.1101/cshperspect.a002212},
file = {:Users/damascus/Documents/Mendeley\_papers/Schrum, Zhu, Szostak - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Artificial Cells,Artificial Cells: chemistry,Biogenesis,Cell Membrane,Cell Membrane: chemistry,Evolution, Chemical,Fatty Acids,Fatty Acids: chemistry},
month = sep,
number = {9},
pages = {a002212},
pmid = {20484387},
title = {{The origins of cellular life.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2926753\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Sheng2014,
abstract = {The mixture of 2'-5' and 3'-5' linkages generated during the nonenzymatic replication of RNA has long been regarded as a central problem for the origin of the RNA world. However, we recently observed that both a ribozyme and an RNA aptamer retain considerable functionality in the presence of prebiotically plausible levels of linkage heterogeneity. To better understand the RNA structure and function in the presence of backbone linkage heterogeneity, we obtained high-resolution X-ray crystal structures of a native 10-mer RNA duplex (1.32 \AA) and two variants: one containing one 2'-5' linkage per strand (1.55 \AA) and one containing three such linkages per strand (1.20 \AA). We found that RNA duplexes adjust their local structures to accommodate the perturbation caused by 2'-5' linkages, with the flanking nucleotides buffering the disruptive effects of the isomeric linkage and resulting in a minimally altered global structure. Although most 2'-linked sugars were in the expected 2'-endo conformation, some were partially or fully in the 3'-endo conformation, suggesting that the energy difference between these conformations was relatively small. Our structural and molecular dynamic studies also provide insight into the diminished thermal and chemical stability of the duplex state associated with the presence of 2'-5' linkages. Our results contribute to the view that a low level of 2'-5' substitution would not have been fatal in an early RNA world and may in contrast have been helpful for both the emergence of nonenzymatic RNA replication and the early evolution of functional RNAs.},
author = {Sheng, Jia and Li, Li and Engelhart, Aaron E and Gan, Jianhua and Wang, Jiawei and Szostak, Jack W},
doi = {10.1073/pnas.1317799111},
file = {:Users/damascus/Documents/Mendeley\_papers/Sheng et al. - 2014 - Proceedings of the National Academy of Sciences of the United States of America.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Base Sequence,Crystallography, X-Ray,Models, Molecular,Molecular Dynamics Simulation,Nucleic Acid Conformation,Nucleic Acid Heteroduplexes,Nucleic Acid Heteroduplexes: chemistry,Oligonucleotides,Oligonucleotides: genetics,RNA,RNA: chemistry},
month = feb,
number = {8},
pages = {3050--5},
pmid = {24516151},
title = {{Structural insights into the effects of 2'-5' linkages on the RNA duplex.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3939906\&tool=pmcentrez\&rendertype=abstract},
volume = {111},
year = {2014}
}
@article{Sleep2010,
abstract = {A sparse geological record combined with physics and molecular phylogeny constrains the environmental conditions on the early Earth. The Earth began hot after the moon-forming impact and cooled to the point where liquid water was present in approximately 10 million years. Subsequently, a few asteroid impacts may have briefly heated surface environments, leaving only thermophile survivors in kilometer-deep rocks. A warm 500 K, 100 bar CO(2) greenhouse persisted until subducted oceanic crust sequestered CO(2) into the mantle. It is not known whether the Earth's surface lingered in a approximately 70 degrees C thermophile environment well into the Archaean or cooled to clement or freezing conditions in the Hadean. Recently discovered approximately 4.3 Ga rocks near Hudson Bay may have formed during the warm greenhouse. Alkalic rocks in India indicate carbonate subduction by 4.26 Ga. The presence of 3.8 Ga black shales in Greenland indicates that S-based photosynthesis had evolved in the oceans and likely Fe-based photosynthesis and efficient chemical weathering on land. Overall, mantle derived rocks, especially kimberlites and similar CO(2)-rich magmas, preserve evidence of subducted upper oceanic crust, ancient surface environments, and biosignatures of photosynthesis.},
author = {Sleep, Norman H},
doi = {10.1101/cshperspect.a002527},
file = {:Users/damascus/Documents/Mendeley\_papers/Sleep - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Earth (Planet),Environment,Evolution, Planetary,Geologic Sediments,Geologic Sediments: chemistry,Minerals,Minerals: chemistry},
month = jun,
number = {6},
pages = {a002527},
pmid = {20516134},
title = {{The Hadean-Archaean environment.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2869525\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Strulson2012,
abstract = {RNA performs important cellular functions in contemporary life forms. Its ability to act both as a catalyst and a storage mechanism for genetic information is also an important part of the RNA world hypothesis. Compartmentalization within modern cells allows the local concentration of RNA to be controlled and it has been suggested that this was also important in early life forms. Here, we mimic intracellular compartmentalization and macromolecular crowding by partitioning RNA in an aqueous two-phase system (ATPS). We show that the concentration of RNA is enriched by up to 3,000-fold in the dextran-rich phase of a polyethylene glycol/dextran ATPS and demonstrate that this can lead to approximately 70-fold increase in the rate of ribozyme cleavage. This rate enhancement can be tuned by the relative volumes of the two phases in the ATPS. Our observations support the importance of compartmentalization in the attainment of function in an RNA World as well as in modern biology.},
author = {Strulson, Christopher a and Molden, Rosalynn C and Keating, Christine D and Bevilacqua, Philip C},
doi = {10.1038/nchem.1466},
file = {:Users/damascus/Documents/Mendeley\_papers/Strulson et al. - 2012 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
keywords = {Biocatalysis,Biomimetics,Catalytic,Catalytic: metabolism,Cell Compartmentation,Dextrans,Dextrans: chemistry,Intracellular Space,Intracellular Space: metabolism,Polyethylene Glycols,Polyethylene Glycols: chemistry,RNA,Water,Water: chemistry},
month = nov,
number = {11},
pages = {941--6},
pmid = {23089870},
publisher = {Nature Publishing Group},
title = {{RNA catalysis through compartmentalization.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23089870},
volume = {4},
year = {2012}
}
@article{Sutherland2010,
abstract = {It has normally been assumed that ribonucleotides arose on the early Earth through a process in which ribose, the nucleobases, and phosphate became conjoined. However, under plausible prebiotic conditions, condensation of nucleobases with ribose to give beta-ribonucleosides is fraught with difficulties. The reaction with purine nucleobases is low-yielding and the reaction with the canonical pyrimidine nucleobases does not work at all. The reasons for these difficulties are considered and an alternative high-yielding synthesis of pyrimidine nucleotides is discussed. Fitting the new synthesis to a plausible geochemical scenario is a remaining challenge but the prospects appear good. Discovery of an improved method of purine synthesis, and an efficient means of stringing activated nucleotides together, will provide underpinning support to those theories that posit a central role for RNA in the origins of life.},
author = {Sutherland, John D},
doi = {10.1101/cshperspect.a005439},
file = {:Users/damascus/Documents/Mendeley\_papers/Sutherland - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Biogenesis,Evolution, Chemical,Ribonucleotides,Ribonucleotides: biosynthesis,Ribonucleotides: chemistry,Ribonucleotides: genetics},
month = apr,
number = {4},
pages = {a005439},
pmid = {20452951},
title = {{Ribonucleotides.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2845210\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Walker2014,
author = {Walker, Sara},
doi = {10.3390/info5030424},
file = {:Users/damascus/Documents/Mendeley\_papers/Walker - 2014 - Information.pdf:pdf},
issn = {2078-2489},
journal = {Information},
keywords = {"origin of life,emergence,origin of life,top-down causation,top-down causation"},
month = jul,
number = {3},
pages = {424--439},
title = {{Top-Down Causation and the Rise of Information in the Emergence of Life}},
url = {http://www.mdpi.com/2078-2489/5/3/424/},
volume = {5},
year = {2014}
}
@article{Xayaphoummine2007,
abstract = {RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions (UTRs). Yet, the underlying mechanisms and coding requirements for efficient co-transcriptional folding remain unclear. Traditional approaches have intrinsic limitations to dissect RNA folding paths, as they rely on sequence mutations or circular permutations that typically perturb both RNA folding paths and equilibrium structures. Here, we show that exploiting sequence symmetries instead of mutations can circumvent this problem by essentially decoupling folding paths from equilibrium structures of designed RNA sequences. Using bistable RNA switches with symmetrical helices conserved under sequence reversal, we demonstrate experimentally that native and transiently formed helices can guide efficient co-transcriptional folding into either long-lived structure of these RNA switches. Their folding path is controlled by the order of helix nucleations and subsequent exchanges during transcription, and may also be redirected by transient antisense interactions. Hence, transient intra- and inter-molecular base pair interactions can effectively regulate the folding of nascent RNA molecules into different native structures, provided limited coding requirements, as discussed from an information theory perspective. This constitutive coupling between RNA synthesis and RNA folding regulation may have enabled the early emergence of autonomous RNA-based regulation networks.},
author = {Xayaphoummine, a and Viasnoff, V and Harlepp, S and Isambert, H},
doi = {10.1093/nar/gkl1036},
file = {:Users/damascus/Documents/Mendeley\_papers/Xayaphoummine et al. - 2007 - Nucleic acids research.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Base Sequence,Molecular Sequence Data,Nucleic Acid Conformation,RNA,RNA: chemistry,Regulatory Sequences, Ribonucleic Acid,Sequence Alignment,Transcription, Genetic},
month = jan,
number = {2},
pages = {614--22},
pmid = {17178750},
title = {{Encoding folding paths of RNA switches.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1802593\&tool=pmcentrez\&rendertype=abstract},
volume = {35},
year = {2007}
}
@article{Yu2012,
abstract = {The pre-RNA world hypothesis postulates that RNA was preceded in the evolution of life by a simpler genetic material, but it is not known if such systems can fold into structures capable of eliciting a desired function. Presumably, whatever chemistry gave rise to RNA would have produced other RNA analogues, some of which may have preceded or competed directly with RNA. Threose nucleic acid (TNA), a potentially natural derivative of RNA, has received considerable interest as a possible RNA progenitor due to its chemical simplicity and ability to exchange genetic information with itself and RNA. Here, we have applied Darwinian evolution methods to evolve, in vitro, a TNA receptor that binds to an arbitrary target with high affinity and specificity. This demonstration shows that TNA has the ability to fold into tertiary structures with sophisticated chemical functions, which provides evidence that TNA could have served as an ancestral genetic system during an early stage of life.},
author = {Yu, Hanyang and Zhang, Su and Chaput, John C},
doi = {10.1038/nchem.1241},
file = {:Users/damascus/Documents/Mendeley\_papers/Yu, Zhang, Chaput - 2012 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
keywords = {Animals,Aptamers, Nucleotide,Aptamers, Nucleotide: chemistry,Aptamers, Nucleotide: genetics,Base Sequence,Cattle,DNA,DNA: chemistry,DNA: genetics,DNA: metabolism,Evolution, Molecular,Gene Library,Humans,Models, Genetic,Molecular Sequence Data,Protein Binding,RNA,RNA: chemistry,RNA: genetics,RNA: metabolism,Serum Albumin, Bovine,Serum Albumin, Bovine: chemistry,Serum Albumin, Bovine: genetics,Streptavidin,Streptavidin: chemistry,Streptavidin: genetics,Tetroses,Tetroses: chemistry,Tetroses: genetics,Thrombin,Thrombin: chemistry,Thrombin: genetics},
month = mar,
number = {3},
pages = {183--7},
pmid = {22354431},
publisher = {Nature Publishing Group},
title = {{Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22354431},
volume = {4},
year = {2012}
}
@article{Zahnle2010,
abstract = {Earth is the one known example of an inhabited planet and to current knowledge the likeliest site of the one known origin of life. Here we discuss the origin of Earth's atmosphere and ocean and some of the environmental conditions of the early Earth as they may relate to the origin of life. A key punctuating event in the narrative is the Moon-forming impact, partly because it made Earth for a short time absolutely uninhabitable, and partly because it sets the boundary conditions for Earth's subsequent evolution. If life began on Earth, as opposed to having migrated here, it would have done so after the Moon-forming impact. What took place before the Moon formed determined the bulk properties of the Earth and probably determined the overall compositions and sizes of its atmospheres and oceans. What took place afterward animated these materials. One interesting consequence of the Moon-forming impact is that the mantle is devolatized, so that the volatiles subsequently fell out in a kind of condensation sequence. This ensures that the volatiles were concentrated toward the surface so that, for example, the oceans were likely salty from the start. We also point out that an atmosphere generated by impact degassing would tend to have a composition reflective of the impacting bodies (rather than the mantle), and these are almost without exception strongly reducing and volatile-rich. A consequence is that, although CO- or methane-rich atmospheres are not necessarily stable as steady states, they are quite likely to have existed as long-lived transients, many times. With CO comes abundant chemical energy in a metastable package, and with methane comes hydrogen cyanide and ammonia as important albeit less abundant gases.},
author = {Zahnle, Kevin and Schaefer, Laura and Fegley, Bruce},
doi = {10.1101/cshperspect.a004895},
file = {:Users/damascus/Documents/Mendeley\_papers/Zahnle, Schaefer, Fegley - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor perspectives in biology},
keywords = {Atmosphere,Atmosphere: chemistry,Biogenesis,Earth (Planet),Moon},
month = oct,
number = {10},
pages = {a004895},
pmid = {20573713},
title = {{Earth's earliest atmospheres.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2944365\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2010}
}
@article{Zeravcic2014,
author = {Zeravcic, Z and Brenner, M P},
doi = {10.1073/pnas.1313601111},
file = {:Users/damascus/Desktop/toRead/Brenner.pdf:pdf},
journal = {Proceedings of the National Academy of Sciences},
month = jan,
number = {13},
pages = {1--6},
title = {{Self-replicating colloidal clusters}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1313601111},
volume = {2013},
year = {2014}
}
@misc{,
file = {:Users/damascus/Documents/Mendeley\_papers/Unknown - Unknown - Unknown(3).pdf:pdf},
title = {{Isambert\_1.pdf}}
}
@article{,
doi = {10.1038/nchem.1647},
file = {:Users/damascus/Documents/Mendeley\_papers/Unknown - 2013 - Nature chemistry.pdf:pdf},
issn = {1755-4349},
journal = {Nature chemistry},
month = may,
number = {5},
pages = {349},
pmid = {23609072},
title = {{The ascent of molecules.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23609072},
volume = {5},
year = {2013}
}

repository: pfdamasceno/shakespeare

repo_name: pfdamasceno/shakespeare


text:
@article{
  moore,
  author={Moore, Gordon E.},
  title={Cramming More Components onto Integrated Circuits},
  journal={Electronics},
  year={1965},
  month={April},
  pages={114-117}
}

@article{
  dennard,
  author={Dennard, Robert H. and Gaensslen, Fritz H. and Yu, Hwa-Nien and Rideout, Leo and Bassous, Ernest and Leblanc, Andre R.},
  title={Design of Ion-Implanted MOSFETs with Very Small Physical Dimensions},
  journal={IEEE Journal of Solid State Circuits},
  volume={SC-9},
  year={1974},
  month={October},
  pages={256-268}
}

@misc{
  karlrupp,
  author={Rupp, Karl},
  title={42 Years of Microprocessor Trend Data},
  howpublished={\url{https://www.karlrupp.net/2018/02/42-years-of-microprocessor-trend-data/}},
  note={Accessed: 2019-02-01}
}

@article{
  darksilicon,
  author={Esmaeilzadeh, Hadi and Blem, Emily and St. Amant, Ren\'{e}e and Sankaralingam, Karthikeyan and Burger, Doug},
  title={Dark Silicon and the End of Multicore Scaling},
  journal={IEEE Micro},
  volume={32},
  year={2012},
  month={June},
  pages={122-134}
}

@inproceedings{
  four-horsemen,
  author={Taylor, Michael B.},
  booktitle={DAC Design Automation Conference 2012},
  title={Is dark silicon useful? {Harnessing} the four horsemen of the coming dark silicon apocalypse},
  year={2012},
  pages={1131-1136},
  month={June}
}

@article{
  greendroid,
  author={Taylor, Michael B. and Swanson, Steven},
  title={{GreenDroid}: {Exploring} the Next Evolution in Smartphone Application Processors},
  journal={IEEE Communications Magazine},
  volume={49},
  year={2011},
  month={April},
  pages={112-119}
}

@phdthesis{
  arnone-thesis,
  author={Arnone, Antonio},
  title={Feasibility of Accelerator Generation to Alleviate Dark Silicon in a Novel Architecture},
  school={University of York},
  year={2017},
  month={June}
}

@inproceedings{
  high-performance-microarchitecture,
  author={Razdan, Rahul and Smith, Michael D.},
  booktitle={27th Annual International Symposium on Microarchitecture},
  title={A High-Performance Microarchitecture with Hardware-Programmable Functional Units},
  year={1994},
  pages={172-180},
  month={November}
}

@inproceedings{
  garp,
  author={Hauser, John R. and Wawrzynek, John},
  booktitle={5th Annual IEEE Symposium on Field-Programmable Custom Computing Machines},
  title={Garp: A MIPS Processor with a Reconfigurable Coprocessor},
  year={1997},
  pages={12-21},
  month={April}
}

@article{
  c-cores,
  author = {Venkatesh, Ganesh and Sampson, Jack and Goulding, Nathan and Garcia, Saturnino and Bryksin, Vladyslav and Lugo-Martinez, Jose and Swanson, Steven and Taylor, Michael Bedford},
  title = {Conservation Cores: Reducing the Energy of Mature Computations},
  journal = {SIGARCH Computer Architecture News},
  volume = {38},
  month = {March},
  year = {2010},
  pages = {205-218}
}

@inproceedings{
  eco-cores,
  author={Sampson, Jack and Venkatesh, Ganesh and Goulding-Hotta, Nathan and Garcia, Saturnino and Swanson, Steven and Taylor, Michael B.},
  booktitle={2011 IEEE 17th International Symposium on High Performance Computer Architecture},
  title={Efficient Complex Operators for Irregular Codes},
  year={2011},
  pages={491-502},
  month={February},
}

@misc{
  microblaze,
  author={{Xilinx Inc.}},
  title={{The Xilinx MicroBlaze soft processor core}},
  howpublished={\url{https://www.xilinx.com/products/design-tools/microblaze.html}},
  note={Accessed: 2019-02-02}
}

@misc{
  microblaze-ref,
  author={{Xilinx Inc.}},
  title={MicroBlaze Processor Reference Guide},
  howpublished={\url{https://www.xilinx.com/support/documentation/sw_manuals/mb_ref_guide.pdf}},
  year={2008},
  note={Accessed: 2019-02-16}
}

@book{
  computer-arch,
  auther={Hennessy, John L. and Patterson, David A.},
  title={Computer Architecture: A Quantitative Approach},
  edition={2},
  publisher={Morgan Kaufmann Publishers, Inc.},
  year={1996}
}

@misc{
  sha256,
  author={{Alain Mosnier}},
  title={{SHA-256 Algorithm Implementation}},
  howpublished={\url{https://github.com/amosnier/sha-2}},
  note={Accessed: 2019-03-02}
}

@misc{
  fft,
  author={{Author unknown}},
  title={{Fixed-Point Fast Fourier Transform Algorithm Implementation}},
  howpublished={\url{https://gist.github.com/Tomwi/3842231}},
  note={Accessed: 2019-03-10}
}

@misc{
  power,
  author={{EE Herald}},
  title={{Low Power VLSI Chip Design: Circuit Design Techniques}},
  howpublished={\url{http://www.eeherald.com/section/design-guide/Low-Power-VLSI-Design.html}},
  note={Accessed: 2019-04-28}
}

license: MIT

repository: jayvalentine/code-to-silicon

license_type: permissive

repo_name: jayvalentine/code-to-silicon

branch_name: refs/heads/master

extension: bib


text:
@misc{imagewang,
  author    = "Jeremy Howard",
  title     = "Imagewang",
  url       = "https://github.com/fastai/imagenette/"
}

repository: tensorflow/datasets

repo_name: tensorflow/datasets

gha_language: Python


text:
@article{unwin2020state,
  title={State-level tracking of COVID-19 in the United States},
  author={Unwin, H Juliette T and Mishra, Swapnil and Bradley, Valerie C and Gandy, Axel and Mellan, Thomas A and Coupland, Helen and Ish-Horowicz, Jonathan and Vollmer, Michaela AC and Whittaker, Charles and Filippi, Sarah L and others},
  journal={Nature communications},
  volume={11},
  number={1},
  pages={1--9},
  year={2020},
  publisher={Nature Publishing Group}
}

repository: MJHutchinson/personal-website

repo_name: MJHutchinson/personal-website


text:
# SPDX-Licence-Identifier: MIT

SUMMARY = ""
LICENSE = "MIT"

# In this example, all of the sources are within a TAR file. BitBake will
# automatically extract the archive. The contents of this archive do not have
# any leading paths; this will be important with repsect to the source
# directory.
#
# Another common pattern you will notice here is adding patches on top of an
# unpacked archive -- it wouldn't be typical for a source archive to contain
# patches. The utility of this is that we can alter an otherwise complete code
# base for things like security, hardening, and making it easier to build with
# BitBake, among others.

SRC_URI = " \
	file://helloworld-tar-1.0.0.tgz \
    file://0000-patch-main.patch \
"

LIC_FILES_CHKSUM = "file://LICENSE;md5=c6640a3f1119eaec9540d5a4c69d5aef"

# As alluded to in the SRC_URI comment, you may need to consider what the value
# of the source directory should be. In this case, since there are no directory
# prefixes within the archive, once again, the source directory is the same as
# the working directory. However, it is much more common to have archives with
# files that have a leading path of the archive name. The consideration here is
# that this prefix must be appended to the WORKDIR to form S. For example, out
# archive could have the files (relative to the archive root):
#
#    /helloworld-tar
#
# Or with a version specified:
#
#    /helloworld-tar-1.0.0
#
# In any of the cases, this directory must be added. e.g
#
#    S = "${WORKDIR}/helloworld-tar-1.0.0"

S = "${WORKDIR}"

#CPPFLAGS += " -std=c++17 -O2"

do_compile() {
    ${CXX} ${CPPFLAGS} ${LDFLAGS} ${S}/main.cpp -o ${B}/helloworld_tar
}

do_install() {
    install -d ${D}${bindir}
    install -m 0755 ${B}/helloworld_tar ${D}${bindir}/helloworld_tar
}

FILES_${PN} = "${bindir}"

repository: NetworkGradeLinux/meta-mion

repo_name: NetworkGradeLinux/meta-mion

branch_name: refs/heads/dunfell

gha_license_id: MIT

gha_language: C

extension: bb


text:
@inproceedings{Lunn2008,
 abstract = {The World Wide Web (Web) is a visually complex, dynamic, multimedia system that can be inaccessible to people with visual impairments. SADIe uses semantic annotations of a Website's Cascading Style Sheet (CSS) to drive a transformation process that can improve access to content for visually impaired users. The original process of annotating the CSS involved the use of an upper ontology, extended by a site specific lower ontology. While this approach provided rich annotation of the CSS terms, experience suggests that components within the model were inappropriate for the interactive system we were developing. This experience has led to a more pragmatic approach that still provides the necessary semantics required to drive the SADIe transcoding tool, but in a more lightweight manner. This paper describes the lessons learnt from building the ontological models for the SADIe platform, highlighting pitfalls that developers of ontologies in interactive systems should be wary of. © 2008 IEEE.},
 author = {Lunn, D. and Bechhofer, S. and Harper, S.},
 booktitle = {Proceedings - 1st International Workshop on Ontologies in Interactive Systems, ONTORACT 2008},
 doi = {10.1109/ONTORACT.2008.9},
 isbn = {9780769535425},
 title = {Experiences of exposing semantics to drive transcoding},
 year = {2008}
}

repository: sharpic/academic-kickstart

repo_name: sharpic/academic-kickstart


text:
@PATENT{Cao2011,  author = {Nan Cao and Shixia Liu and Hao Lu and Xi Jun Ma and Martin M. Wattenberg},
  title = {Method and apparatus for improving the visibility of a {Treemap}},
  number = {US 7870509 B2},
  year = {2011},
  abstract = {The visibility of a treemap is improved by offsetting the area of a parent node relative to a bounding box containing all of its child nodes while constructing the treemap, so that a part of the bounding box lies outside the area of the parent node, and the area of each child node in the bounding box is located entirely or partially within the area of the parent node. The present invention highlights the parent-child relationships in the treemap with a cascading effect to make the structural information therein more apparent and easier to recognize.},
  url = {http://www.freepatentsonline.com/7870509.html}
}

repository: vis-au/treevisnet

repo_name: vis-au/treevisnet

gha_language: TeX


text:
@misc{garay_social_2021,
 address = {Virtual Meeting},
 author = {Garay, Candelaria and Simison, Emilia},
 month = {July},
 title = {Social Mobilization and Social Policy in Latin America},
 year = {2021}
}

repository: emisimison/academic-kickstart

repo_name: emisimison/academic-kickstart


text:
require openvpn.inc

PR = "r2"

SRC_URI[md5sum] = "60745008b90b7dbe25fe8337c550fec6"
SRC_URI[sha256sum] = "347c551e7c88affc1f4b7a4b715080253c9298dcc512ed29fe8ca5cd26d015d9"


text:
@inproceedings{yixue_zhao_decree_2019,
 author = {Zhao, Yixue},
 title = {Mobile-app Analysis and Instrumentation Techniques Reimagined with DECREE},
 booktitle = {Proceedings of the 41st International Conference on Software Engineering: Companion Proceedings},
 series = {ICSE '19},
 year = {2019},
 location = {Montreal, Quebec, Canada},
 pages = {218--221},
 numpages = {4},
 url = {https://doi.org/10.1109/ICSE-Companion.2019.00086},
 doi = {10.1109/ICSE-Companion.2019.00086},
 acmid = {3339755},
 publisher = {IEEE Press},
 address = {Piscataway, NJ, USA},
}

repository: felicitia/HugoAcademicWebsite

repo_name: felicitia/HugoAcademicWebsite


text:
@article{liu2021transcription,
  title={Transcription factor competition at the $\gamma$-globin promoters controls hemoglobin switching},
  author={Liu, Nan and Xu, Shuqian and Yao, Qiuming and Zhu, Qian and Kai, Yan and Hsu, Jonathan Y and Sakon, Phraew and Pinello, Luca and Yuan, Guo-Cheng and Bauer, Daniel E and others},
  journal={Nature Genetics},
  volume={53},
  number={4},
  pages={511--520},
  year={2021},
  publisher={Nature Publishing Group}
}


text:
@manual{Anleitung,
author = {TU Dortmund},
title = {Versuch 601: Franck-Hertz-Versuch},
url={http://129.217.224.2/HOMEPAGE/PHYSIKER/BACHELOR/AP/SKRIPT/V601.pdf},
urldate={2017-05-21},
year = 2016
}
@online{bla,
author = {Universität Siegen},
title = {Flächenträgheitsmomente einiger Querschnitte},
	urldate={2017-01-18},
	url={http://www.bau.uni-siegen.de/subdomains/bauinformatik/lehre/tm2/arbeitsblaetter/arbeitsblatt_08_flaechentraegheitsmomente_bsp.pdf},
}
@online{gott,
author = {Georg-August-Universität Göttingen},
title = {Der Franck-Hertz-Versuch},
	urldate={2017-05-22},
	url={https://lp.uni-goettingen.de/get/text/1612},
}
@online{ion,
author = {National Institute of Standards and Technology(NIST)},
title = {Atomic Data for Mercury (Hg)},
	urldate={2017-05-23},
	url={http://physics.nist.gov/PhysRefData/Handbook/Tables/mercurytable1.htm},
}
@online{G,
author = {Physikalisch-Technische Bundesanstalt (PTB)},
title = {Gravity Information System of PTB},
	urldate={2017-01-20},
	url={http://www.ptb.de/cartoweb3/SISproject.php},
}
@manual{V102,
	author = {TU Dortmund},
	title = {Versuch 102: Drehschwingungen},
	year = 2016
}
@book{Hans,
  author={Horst Czichos and Manfred Hennecke},
title={Das Ingenieurwissen},
publisher={Springer-Verlag},
year={2007},
address = {Akademischer Verein Hütte e.V., Berlin},
edition = {33}
}
@online{c,
title = {CODATA value: speed of light in vacuum},
work={The NIST reference on Constants, Units, and Uncertainty},
publisher={National Institute of Standards and Technology|NIST},
urldate={2017-05-21},
url={http://physics.nist.gov/cgi-bin/cuu/Value?c},
}
@online{h,
title = {CODATA value: Planck constant},
work={The NIST reference on Constants, Units, and Uncertainty},
publisher={National Institute of Standards and Technology|NIST},
urldate={2017-05-21},
url={http://physics.nist.gov/cgi-bin/cuu/Value?h},
}
@online{e,
title = {CODATA value: elementary charge},
work={The NIST reference on Constants, Units, and Uncertainty},
publisher={National Institute of Standards and Technology|NIST},
urldate={2017-05-15},
url={http://physics.nist.gov/cgi-bin/cuu/Value?e},
}

repository: nsalewski/laboratory

repo_name: nsalewski/laboratory


text:
SUMMARY = "PyOTA: The IOTA Python API Library "
DESCRIPTION = "This is the official Python library for the IOTA Core. It implements both the official API, as well as functionality such as signing, bundles, utilities and conversion."

HOMEPAGE = "https://pyota.readthedocs.io/en/latest/"
LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://${COMMON_LICENSE_DIR}/MIT;md5=0835ade698e0bcf8506ecda2f7b4f302"

PYPI_PACKAGE = "PyOTA"
SRC_URI[md5sum] = "ebbc883496c986bbfdb1dc503ee14459"

RDEPENDS_${PN} = "\
	${PYTHON_PN}-setuptools \
	${PYTHON_PN}-misc \
	${PYTHON_PN}-phx-filters \
        ${PYTHON_PN}-six \
        ${PYTHON_PN}-requests \
	${PYTHON_PN}-pysha3 \
        ${PYTHON_PN}-typing \
	${PYTHON_PN}-pycparser \
	${PYTHON_PN}-ipython \
	${PYTHON_PN}-pydoc \
"

inherit pypi setuptools3


text:
@article{varfolomeev2016modeling20131412,
 address = {United States},
 author = {Kots, E. D. and Khrenova, M. G. and Lushchekina, S. V. and Varfolomeev, S. D. and Grigorenko, B. L. and Nemukhin, A. V.},
 doi = {10.1021/acs.jpcb.6b02542},
 issn = {1089-5647; 1520-6106},
 journal = {Journal of Physical Chemistry B},
 language = {english},
 number = {18},
 pages = {4221--4231},
 publisher = {United States},
 title = {Modeling the complete catalytic cycle of aspartoacylase},
 volume = {120},
 year = {2016}
}

repository: polyakoviv/LCC

repo_name: polyakoviv/LCC

branch_name: refs/heads/main


text:
@article{fu2019lidar,
  title={LiDAR--Camera Calibration under Arbitrary Configurations: Observability and Methods},
  author={Fu, Bo and Wang, Yue and Ding, Xiaqing and Jiao, Yanmei and Tang, Li and Xiong, Rong},
  journal={IEEE Transactions on Instrumentation and Measurement},
  year={2019},
  publisher={IEEE}
}

repository: slinkle/academic-kickstart

repo_name: slinkle/academic-kickstart


text:
@article{schonlau2017text,
  title={Text mining with n-gram variables},
  author={Schonlau, Matthias and Guenther, Nick and Sucholutsky, Ilia},
  journal={The Stata Journal},
  volume={17},
  number={4},
  pages={866--881},
  year={2017},
  publisher={SAGE Publications Sage CA: Los Angeles, CA}
}

@article{sucholutsky2018convart,
  title={ConvART: Improving Adaptive Resonance Theory for Unsupervised Image Clustering},
  author={Sucholutsky, Ilia and Schonlau, Matthias},
  journal={Journal of Computational Vision and Imaging Systems},
  volume={4},
  number={1},
  pages={3--4},
  year={2018}
}

@article{ourrestorer,
  title={Pay attention and you won’t lose it: a deep learning approach to sequence imputation},
  author={Sucholutsky, Ilia and Narayan, Apurva and Schonlau, Matthias and Fischmeister, Sebastian},
  journal={PeerJ Computer Science},
  volume={5},
  pages={e210},
  year={2019},
  month={August},
  publisher={PeerJ Inc.},
  url={https://peerj.com/articles/cs-210/}
}

@inproceedings{
ourlstm,
Author = {Ilia Sucholutsky and Apurva Narayan and Matthias Schonlau and Sebastian Fischmeister},
Title = {Deep Learning for System Trace Restoration},
Year = {2019},
month={July},
booktitle={2019 International Joint Conference on Neural Networks (IJCNN)},
organization={IEEE},
doi={10.1109/IJCNN.2019.8852116},
note = {Pre-print at arXiv:1904.05411},
url={https://arxiv.org/abs/1904.05411}
}

@article{idd,
    title={Soft-Label Dataset Distillation and Text Dataset Distillation},
    author={Ilia Sucholutsky and Matthias Schonlau},
    year={2019},
    journal={2021 International Joint Conference on Neural Networks (IJCNN)},
    Note={Forthcoming. Pre-print available at arXiv:1910.02551},
    url={https://arxiv.org/abs/1910.02551}
}

@inproceedings{sucholutsky2020less,
  title={`{L}ess Than One'-Shot Learning: Learning {N} Classes From {M}$<$ {N} Samples},
  author={Sucholutsky, Ilia and Schonlau, Matthias},
  booktitle={Proceedings of the AAAI Conference on Artificial Intelligence},
  note={Forthcoming. Pre-print available at arXiv:2009.08449},
  url={https://arxiv.org/abs/2009.08449},
  year={2021}
}

@article{sucholutsky2020optimal, title={Optimal 1-{NN} prototypes for pathological geometries}, volume={7}, DOI={10.7717/peerj-cs.464}, journal={PeerJ Computer Science}, author={Sucholutsky, Ilia and Schonlau, Matthias}, url={https://peerj.com/articles/cs-464/}, year={2021}}

@inproceedings{sucholutsky2020secdd,
  title={Sec{DD}: Efficient and Secure Method for Remotely Training Neural Networks {(Student Abstract)}},
  author={Sucholutsky, Ilia and Schonlau, Matthias},
  booktitle={Proceedings of the AAAI Conference on Artificial Intelligence},
  note={Forthcoming. Pre-print available at arXiv:2009.09155},
  url={https://arxiv.org/abs/2009.09155},
  year={2021}
}

@article{sucholutsky2021one,
  title={One Line To Rule Them All: Generating {LO}-Shot Soft-Label Prototypes},
  author={Sucholutsky, Ilia and Kim, Nam-Hwui and Browne, Ryan P and Schonlau, Matthias},
  journal={2021 International Joint Conference on Neural Networks (IJCNN)},
  Note={Forthcoming. Pre-print available at arXiv:2102.07834},
  url={https://arxiv.org/abs/2102.07834},
  year={2021}
}


text:
SUMMARY = "Plugin providing hotcorners"
LICENSE = "GPLv2"
LIC_FILES_CHKSUM = "file://README.md;beginline=48;endline=53;md5=2c694b8e0f73274b13465b509e4f5427"

inherit xfce-panel-plugin cmake

DEPENDS += "libwnck3"

SRC_URI = "https://github.com/brianhsu/${BPN}/releases/download/${PV}/${BPN}-${PV}.tar.gz \
           file://0001-CMakeLists.txt-fix-library-install-path.patch"
SRC_URI[md5sum] = "ac31b45cda1867cb6bd69bb285638263"
SRC_URI[sha256sum] = "942684c92f96a158e1417e597947f822769ac56aa1993a8c9f166ee633ef2b8d"

EXTRA_OECMAKE = "-DBASE_LIB_PATH=${baselib}"


text:
@article{kathleen2004hyperdisease,
 author = {Kathleen Lyons, S and Smith, Felisa A and Wagner, Peter J and White, Ethan P and Brown, James H},
 journal = {Ecology Letters},
 number = {9},
 pages = {859--868},
 publisher = {Wiley Online Library},
 title = {Was a ‘hyperdisease’responsible for the late Pleistocene megafaunal extinction?},
 volume = {7},
 year = {2004}
}

repository: weecology/website

repo_name: weecology/website


text:
KBRANCH ?= "dev-5.10"
LINUX_VERSION ?= "5.10.39"

SRCREV="45c6dc0de963bfdd8b468dceeea24f56a8e51424"

require linux-aspeed.inc