Braided Channels • Braided Channels - In streams having highly variable discharge and easily eroded banks, sediment gets deposited to form bars and islands that are exposed during periods of low discharge. In such a stream the water flows in a braided pattern around the islands and bars, dividing and reuniting as it flows downstream. Such a channel is termed a braided channel. During periods of high discharge, the entire stream channel may contain water and the islands are covered to become submerged bars. During such high discharge, some of the islands could erode, but the sediment would be re-deposited as the discharge decreases, forming new islands or submerged bars. Islands may become resistant to erosion if they become inhabited by vegetation
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• Definition: Land that has water on all sides • Two Types: Continental islands and Oceanic islands • Continental islands are ones that lie close to a continent • Oceanic islands are islands found in the middle of the ocean • Island activity!! Menu
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Implications • Terrestrial species on these islands won’t have many relatives nearby. • Neighboring islands will have close relatives – but new terrestrial species won’t arrive on these islands from the South American mainland very often. – most of the island species have had plenty of time to differentiate from their nearest living relatives. • Another way of saying this is that there is very little gene flow between the islands and the mainland. 4
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Sites of Cytosine Methylation 1. CpG islands: regions of more than 200 bases (average of 1000 bases) with a G+C content of at least 50% (approximately 1% of the human genome, 60% of human gene promoters are associated with CpG islands.) CpG islands in promoters are usually unmethylated in normal cells. 6% become methylated in a tissue specific manner during early development or in differentiated tissues. 2. CpG island shores: regions of lower CpG density that lie in close proximity (2kb) of CpG islands. Most of the tissue –specific DNA methylation occurs in CpG island shores. 70% of the differentially methylated regions in reprogramming are associated with CpG island shores. 3. Gene body: seen in ubiquitously expressed genes, associated with transcriptional elongation. 4. Repetitive elements: protects chromosomal integrity by preventing reactivation of endoparasitic sequences that cause chromosomal instability, translocations, and gene disruption.
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Example Application CpG islands CG dinucleotides are rarer in eukaryotic genomes than expected given the marginal probabilities of C and G but the regions upstream of genes are richer in CG dinucleotides than elsewhere – CpG islands useful evidence for finding genes Application: Predict CpG islands with Markov chains one to represent CpG islands one to represent the rest of the genome 9/13/2006 Bio-sequence analysis Mining Biological Data KU EECS 800, Luke Huan, Fall’06 slide41
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Solving a problem swim • This is a video of a 3rd attempt to swim from the Farallon Islands to San Francisco on April 14th, 2011. A successful attempt was made May 20, 2011 taking 14:45:08 hours going the other direction. Distance is 27 statute miles (43 kilometers). • First problem is lack of nautical familiarity. The boat is tied to the dock and the cameraman who is the narrator suggest they “hoist the anchor” to cast off. • At 7:55 minutes into the video, the harbor entrance buoy is identified as “Large Navigational Buoy”. Later the swim stalls 10 miles or so outside the harbor due to the flood current. Flood current usually flow into a harbor…even in San Francisco. • Finally, the last scene show the skipper explaining what he thinks went wrong with the swim which you can’t hear because the video editor turned the music up. You learn from your mistakes… Reference tidal info @ http://wolfweb.unr.edu/homepage/edc/tides.html
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2. Farallon Islands
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3. Murres on Farallon Islands
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CQ1: Limited gene flow means: A: Birds rarely move between the mainland and the islands. B: Birds on the island have the same genes as birds on the mainland. C: Birds on the mainland don’t like birds from the islands. D: Birds on the mainland won’t evolve, but birds on the islands might. 5
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Subpart F Suppose in the preceding slide, USC is actually selling its product to various customers throughout the world. The Cayman Islands sub is a sales agent (paper corporation) that technically buys from USC for $600,000 and sells to USC’s customers for $1,000,000. The products are shipped directly to USC’s customers and USC actually handles the billing, etc. If CSub does not produce in the Cayman Islands and does not sell in the Cayman Islands, Subpart F comes into play. Subpart F. USC is treated as receiving a distribution of CSub earnings on the last day of the year. See bottom of page 9-22+
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Effect of Strain in the Simulation Morphologies Elastic energies Detachment rate Adatom concentration op row: Compressive strain=1% ottom row: Compressive strain=5% • With increasing compressive strain, islands become more regular, because i) small islands are more likely to break up, and ii) growth of large islands slows down. Christian Ratsch, UCLA CSCAMM, October 27, 2010
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Personalization Ontology-Based Preference Representation C C Topics C Politics C Sports C Leisure visit C Travel C Island Travel C Movies C Music C Techno C Classical C Pop C Region Geographical Region C Islands C Spanish Islands C USA Islands I Hawaii Hawaii Tourist Guide Political Region C America C NorthAmerica C Canada C USA locatedIn C Florida C
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Markov Chains for Discrimination Suppose we want to distinguish CpG islands from other sequence regions Given sequences from CpG islands, and sequences from other regions, we can construct a model to represent CpG islands a null model to represent the other regions can then score a test sequence by: Pr( x | CpGModel ) score ( x) log Pr( x | nullModel ) 9/13/2006 Bio-sequence analysis Mining Biological Data KU EECS 800, Luke Huan, Fall’06 slide42
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Convergent Plate Boundaries  Types of convergent boundaries  Oceanic-oceanic convergence    When two oceanic slabs converge, one descends beneath the other Often forms volcanoes on the ocean floor If the volcanoes emerge as islands, a volcanic island arc is formed (Japan, Aleutian Islands, Tonga Islands)
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Octree Drawbacks • Objects cross islands – octree has to be constantly updated – not so bad • Objects straddle islands – collision detection may involve objects from multiple islands – can be a headache
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