The Big Questions

  • Why are there introns? At the most basic level, introns are surprising and unexpected. Bacteria (and archaea) get along fine without them, and many of them come and go in eukaryotic evolution, suggesting that many introns are dispensable. Moreover, even for those introns that do perform vital functions (most famously, alternative splicing to generate multiple products from the same gene -- see below), the introns themselves generally appeared in evolution long before these functions (thus these functions cannot explain the origin of the intron themselves!) Thus there is a fundamental question as to why introns exist -- in general, are introns beneficial or harmful (or just neutral) to an organism's fitness?

  • Why do different species have such different intron-exon structures? While (nearly) all eukaryotic species have some spliceosomal introns, intron-exon structures vary strikingly across species, with huge differences in intron number, intron length, incidence and mode of alternative splicing, and intron sequences. These imply very different evolutionary histories of different species since the common ancestor of eukaryotes. What explains these qualitative differences in intron-exon structure across species?

  • How does alternative splicing evolve? Alternative splicing involves differential splicing of portions of RNA transcripts from a single gene, leading to multiple different products. Alternative splicing performs a dizzying array of functions in animals and other eukaryotes, and understanding how these novel functions arise is a central question of comparative and evolutionary genomics. We are working on reconstructing the evolutionary history of alternative splicing in metazoans and reconstructing evolution in deep animal ancestors. In addition, we are interested in the evolution of the networks by which alternative splicing is regulated.

News

Current Work

  • Population genomics of intron loss and gain. Understanding the mechanisms and evolutionary forces that govern intron loss and gain requires identifying and studying recent changes in intron-exon structures. We are using comparative genomics to study very recent changes -- those that are so recent that they differ between members of the same species. Studying these changes allows us to understand how intron-exon structures change, and how and why selection is acting on them.

  • Diversity of intron-exon structures. We are studying intron-exon structures in a wide variety of eukaryotic lineages (mostly protists) to understand the diversity of intron-exon structures across species. Discoveries have included trans-spliced introns in the intestinal parasite Giardia lamblia, novel splicing mechanisms in the intracellular parasite Encephalitozoon cuniculi, and emergence of two novel classes of introns in another species (yet unpublished).

  • Evolution of splicing networks. We are studying the evolution of splicing regulation in metazoans by reconstructing the evolutionary history of key regulatory networks. For example, we studied history of Nova, a family of proteins that regulates splicing of hundreds of genes in the vertebrate brain. We found that Nova is actually a very ancient splicing regulator, and that the brain-specific function of Nova is a relatively recent innovation. We are currently expanding this work to different species and different networks.

Lab Members

  • Scott Roy
    - Assistant Professor of Cell and Molecular Biology at SFSU -
    - Assistant Adjunct Professor at UCM -

    I am interested in the evolution of genome structures and the evolutionary origins of the pronounced differences in genome structure between different species. To study these questions, I study genomic sequences from a wide variety of species (and sometimes from different individuals within a species) to reconstruct evolution. I am interested in a wide variety of questions, and I encourage interested students to contact me to talk about possible projects.

  • Graham Larue
    - Ph.D. Student at UCM -

    My current work focuses on the evolutionary origin and dynamics of the minor spliceosomal (U12) introns across diverse eukaryotic lineages. Other research interests of mine include UTR introns, lncRNA and the evolution of eukaryotic gene structure. I do most of my work using Python and Bash, and will—albeit with deep, existential resentment—write the occasional regular expression.
    Github: https://github.com/glarue

  • Noelle Anderson
    - Ph.D. Student at UCM -

    I’m interested in a lot of things! At the moment, I’m focusing on how selection shapes parts of the genome that are under different conditions (using X chromosome versus autosome comparisons) and how/the degree to which mutational dominance plays into this. Outside of this, I’m interested in other aspects of population genetics, genomic architecture, phylogenetics, genomic conflict, and just about anything weird. In my “free time,” I enjoy gardening and roller skating.
    Email: nanderson8 at ucmerced dot edu
    Twitter: noelle_and

  • Brad Bowser
    - Ph.D. Student at UCM -

    I am interested in the evolution of the spliceosomal proteins and how structural changes can lead to altered splicing behaviors. Further, I am interested in the connection between intron number and the spliceosome itself. I am also interested in viruses and their various splicing strategies. I like sports, the beach, San Francisco, working out, and I manage to cook the exact same meals nearly every day.

  • Swadha Singh
    - Ph.D. Student at UCM -

    I am currently working on Hi-C data to study the whole chromatin architecture of various eukaryotes, in order to test the hypothesis that splicing of rare ‘minor’ type introns are facilitated by clustering of these introns (and their host genes) in the 3D genome.
    Email: ssingh235 at ucmerced dot edu

  • Brooke Weinstein
    - Graduate Student at SFSU -

    I'm fascinated with genome complexity and evolving diversity. I particularly enjoy thinking about male pregnancy in syngathid fishes (seahorses, pipefishes, pipehorses and seadragons) as well as deep and difficult phylogenomic questions such as the root of the animal tree. I love being underwater, horseback riding, and all critters.

  • Cameron
    - Graduate Student at SFSU -

    I’m a graduate student working on eukaryotic transcriptomics, conservation of miRNAs, and early eukaryotic evolution. I enjoy programming/ building pipelines, Linux, and systems administration.

  • Gerid Ollison
    - Graduate Student at SFSU -

    Every living organism on earth -bacteria, yeast, human, etc.- has a genome, albeit diversely endowed with abilities and phenotypes. The genome of an organism only represents the organism’s genetic potential. However, when placed into the context of other genomes from different organisms of different species that presumably evolved at different times, we learn the evolutionary history of a species genetic potential. I am a genomic historian, currently tracing the evolutionary history of a novel splicing network that was assembled in Drosophila.
    Website: theolligist.com

  • Jeanice Nyung
    - Graduate Student at SFSU -

    I am a second year Master's student in Dr. Roy's lab currently investigating the role of alternative splicing in plants. I'm broadly interested in plant biology and genetics and hope to use my bioinformatics skills to enhance my future career as a teacher.

  • Jordan Berry
    - Graduate Student at SFSU -

    I'm a Navy veteran who graduated from SF State with a bachelor's degree in cell and molecular biology in 2017. From 2012 to 2016 I conducted molecular genetics research, focusing primarily on the proteins involved in sperm meiosis. I joined the Roy lab in Spring 2017 and will continue in his lab for my master's degree program. I am currently investigating alternative splicing in genes containing U12 minor spliceosomal introns.

Publications

Roy, S. W. (2017). Genomic and Transcriptomic Analysis Reveals Spliced Leader Trans-Splicing in Cryptomonads. Genome biology and evolution, 9(3), 468.

Roy, S. W. (2017). Transcriptomic analysis of diplomonad parasites reveals a trans-spliced intron in a helicase gene in Giardia. PeerJ, 5, e2861.

Huff, J. T., Zilberman, D., & Roy, S. W. (2016). Mechanism for DNA transposons to generate introns on genomic scales. Nature, 538(7626), 533-536.

Roy, S. W. (2016). Is mutation random or targeted?: No evidence for hypermutability in snail toxin genes. Molecular biology and evolution, 33(10), 2642-2647.

Roy, S. W. (2016). Is genome complexity a consequence of inefficient selection? Evidence from intron creation in non-recombining regions. Molecular biology and evolution, msw172.

Roy, S. W. (2016). How common is parallel intron gain? Rapid evolution versus independent creation in recently created introns in Daphnia. Molecular biology and evolution, 33(8), 1902-1906.

McDevitt, S. L., Bredeson, J. V., Roy, S. W., Lane, J. A., & Noble, J. A. (2016). HAPCAD: An open-source tool to detect PCR crossovers in next-generation sequencing generated HLA data. Human immunology, 77(3), 257-263.

Roy, S. W. (2016). Probing the mechanisms of intron creation in a fast-evolving mite. bioRxiv, 051292.

Roy, S. W. (2016). Origins and evolution of trans-splicing of bursicon in mosquitos. bioRxiv, 050625.

Contact

From Wikipedia, the free encyclopedia.

Contact
is a word-guessing game for three or more players.
In Contact, one person (the "wordmaster" or "target word person") thinks of a word (the "target word"), and the objective of the other players is to guess that target word, one letter at a time, by giving clues hard enough to stump the wordmaster but easy enough that another player can "make contact" with the clue. Some amount of cooperation is needed among the other players, because a guess must be seconded by another player (by stating "Contact!") in order to be "challenged" by the wordmaster.

Rules
Play begins when one person chooses a target word (generally restricted to improper nouns), and announces the first letter. Other players then think of words that begin with that letter, and one may propose a clue for a not-yet-guessed such word (the "guess word" or "clued word"). Several versions of Contact exist, differing in the characteristics of these clues: In the most common version of Contact, a clue can comprise any actions, words, or sounds that all players can hear and (if necessary) see. In another version, the clue must ask whether the target word has certain characteristics. In another version, the clue must be a definition for the clued word. The wordmaster then attempts to identify the clued word. If the wordmaster thinks of a word that satisfies the clue, the wordmaster will say "It's not [guessed word]," and a new clue must be given. There are variations how closely the wordmaster's guesses must satisfy the clue: The wordmaster must think of the clued word. The protection against vague clues is that another player must get the same word. The wordmaster can give any word that fits the clue. These versions are actually equivalent, since if the clue-giver in the second version wishes, he can repeat his clue until the wordmaster guesses the clued word or gives up. Given their functional equivalence, the first version is more common since it does not require frequent repetition of "I repeat my clue." Simultaneously, all other players attempt to identify ("make contact with") the clued word, and any players who think they know the clued word can say "Contact!" If the wordmaster cannot identify the clued word (indicated by saying "challenge") and at least one "Contact!" occurs, the "contacted" guessers (including the initiator) simultaneously say their words. The wordmaster must say the next letter of his word if, depending on the version: At least one of the contacted guessers says the same word as the initiator. All of the contacted guessers say the same word as the initiator (although this discourages multiple contacts). A majority of the contacted guessers say the same word as the initiator. At least two respondents say the same word. If the target word is ever said by any player, the players win and the game is over. The wordmaster cannot win. The player who first guesses the target word usually becomes the wordmaster for the next round. Other variations include: Once at least one player has made contact, the wordmaster may be limited to a fixed number of guesses, usually three. Once at least one player has made contact, the wordmaster may be limited to a fixed time, usually one minute. The players may be limited to a fixed number of clues, usually twenty. The wordmaster wins if the players do not guess the target word by this time. The players may be limited to a fixed number of clues, usually ten, per letter given by the wordmaster. The wordmaster wins if the players do not earn another letter of the target word by this time. For each "contact" beyond the first that is correct when the wordmaster cannot identify the guess, and additional letter in the target word is given. No letters are given if multiple contacts are offered and they are not all the same, even if at least one is correct. Play continues in this fashion until the target word is completely revealed or said by anyone playing.

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i = 0;

while (!deck.isInOrder()) {
    print 'Iteration ' + i;
    deck.shuffle();
    i++;
}

print 'It took ' + i + ' iterations to sort the deck.';

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  • Felis enim feugiat.

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  2. Etiam vel felis viverra.
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  6. Felis enim et feugiat.

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100.00

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Item One Ante turpis integer aliquet porttitor. 29.99
Item Two Vis ac commodo adipiscing arcu aliquet. 19.99
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