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1. Experimental simulation of martian gully forms

Author

K. A. Coleman, Vincent Chevrier, L. A. Roe, K. L. Howe, and John C. Dixon

Subjects
Martian, geography, geography.geographical_feature_category, Astronomy and Astrophysics, Mars Exploration Program, Grain size, Volumetric flow rate, Flume, Space and Planetary Science, Rotameter, Scaling, Geomorphology, Geology, Channel (geography)
Abstract

Gullies are widespread on slopes on the surface of Mars and have been investigated by numerous authors, yet their formation processes remain elusive. In an attempt to understand the possibility of a water-based origin for these forms, we undertook a series of flume experiments at Earth surface temperatures and pressures. Our objectives were to produce forms that resemble those most commonly observed on Mars, documenting their morphometric characteristics and identifying any statistically significant relationships between form and controlling factors of slope and flow rate. Experiments were conducted in a 1×1.5 m2 flume filled with medium grain size sand. The experiments were run over a slope angle range of 10–30°, corresponding to the range for gullies on Mars. Water from a constant-head tank fed through 5 mm silicone hose to a rotameter and then released just below the surface at the top of the slope. Gullies were produced at slope angle values of 10°, 20°, and 30° and flow rate values of 445, 705, 965, and 1260 mL min−1 at each angle. Eighteen parameters were identified and subsequently measured on each gully produced in the flume. Gully forms were successfully reproduced and displayed development of the fundamental morphological components observed on Mars: alcove, channel, and apron. Slope–gully form relationships for each component revealed the following results: higher slope angles formed shorter gullies with thicker apron deposits. Moreover, longer gullies were seen at higher flow rates. We concluded that forms visually similar to those observed on Mars can be created by water in the laboratory flume under terrestrial conditions. Morphometric parameters can be measured and permit identification of controlling factors. Experimental simulation of gullies appears possible with proper scaling of experimental parameters. Although not directly scalable to Mars, flume gully parameters may be used to develop numerical models in the future.

Published
2009
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2. The DNA sequence and analysis of human chromosome 13

Author

A, Dunham, L H, Matthews, J, Burton, J L, Ashurst, K L, Howe, K J, Ashcroft, D M, Beare, D C, Burford, S E, Hunt, S, Griffiths-Jones, M C, Jones, S J, Keenan, K, Oliver, C E, Scott, R, Ainscough, J P, Almeida, K D, Ambrose, D T, Andrews, R I S, Ashwell, A K, Babbage, C L, Bagguley, J, Bailey, R, Bannerjee, K F, Barlow, K, Bates, H, Beasley, C P, Bird, S, Bray-Allen, A J, Brown, J Y, Brown, W, Burrill, C, Carder, N P, Carter, J C, Chapman, M E, Clamp, S Y, Clark, G, Clarke, C M, Clee, S C M, Clegg, V, Cobley, J E, Collins, N, Corby, G J, Coville, P, Deloukas, P, Dhami, I, Dunham, M, Dunn, M E, Earthrowl, A G, Ellington, L, Faulkner, A G, Frankish, J, Frankland, L, French, P, Garner, J, Garnett, J G R, Gilbert, C J, Gilson, J, Ghori, D V, Grafham, S M, Gribble, C, Griffiths, R E, Hall, S, Hammond, J L, Harley, E A, Hart, P D, Heath, P J, Howden, E J, Huckle, P J, Hunt, A R, Hunt, C, Johnson, D, Johnson, M, Kay, A M, Kimberley, A, King, G K, Laird, C J, Langford, S, Lawlor, D A, Leongamornlert, D M, Lloyd, C, Lloyd, J E, Loveland, J, Lovell, S, Martin, M, Mashreghi-Mohammadi, S J, McLaren, A, McMurray, S, Milne, M J F, Moore, T, Nickerson, S A, Palmer, A V, Pearce, A I, Peck, S, Pelan, B, Phillimore, K M, Porter, C M, Rice, S, Searle, H K, Sehra, R, Shownkeen, C D, Skuce, M, Smith, C A, Steward, N, Sycamore, J, Tester, D W, Thomas, A, Tracey, A, Tromans, B, Tubby, M, Wall, J M, Wallis, A P, West, S L, Whitehead, D L, Willey, L, Wilming, P W, Wray, M W, Wright, L, Young, A, Coulson, R, Durbin, T, Hubbard, J E, Sulston, S, Beck, D R, Bentley, J, Rogers, and M T, Ross

Subjects
RNA, Untranslated, Multidisciplinary, Chromosomes, Human, Pair 13, Genes, Genetics, Medical, Chromosome Mapping, Humans, Sequence Analysis, DNA, Physical Chromosome Mapping, Pseudogenes, Article
Abstract

Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.

Published
2004
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3. The Pfam Protein Families Database

Author

A, Bateman, E, Birney, R, Durbin, S R, Eddy, K L, Howe, and E L, Sonnhammer

Subjects
Quality Control, Internet, Genome, Databases, Factual, Genetics, Information Storage and Retrieval, Proteins, Article
Abstract

Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at http://www.sanger.ac.uk/Software/Pfam/ , in Sweden at http://www.cgr.ki.se/Pfam/ and in the US at http://pfam.wustl.edu/ . The latest version (4.3) of Pfam contains 1815 families. These Pfam families match 63% of proteins in SWISS-PROT 37 and TrEMBL 9. For complete genomes Pfam currently matches up to half of the proteins. Genomic DNA can be directly searched against the Pfam library using the Wise2 package.

Published
2000
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4. The DNA sequence and biological annotation of human chromosome 1

Author

S G, Gregory, K F, Barlow, K E, McLay, R, Kaul, D, Swarbreck, A, Dunham, C E, Scott, K L, Howe, K, Woodfine, C C A, Spencer, M C, Jones, C, Gillson, S, Searle, Y, Zhou, F, Kokocinski, L, McDonald, R, Evans, K, Phillips, A, Atkinson, R, Cooper, C, Jones, R E, Hall, T D, Andrews, C, Lloyd, R, Ainscough, J P, Almeida, K D, Ambrose, F, Anderson, R W, Andrew, R I S, Ashwell, K, Aubin, A K, Babbage, C L, Bagguley, J, Bailey, H, Beasley, G, Bethel, C P, Bird, S, Bray-Allen, J Y, Brown, A J, Brown, D, Buckley, J, Burton, J, Bye, C, Carder, J C, Chapman, S Y, Clark, G, Clarke, C, Clee, V, Cobley, R E, Collier, N, Corby, G J, Coville, J, Davies, R, Deadman, M, Dunn, M, Earthrowl, A G, Ellington, H, Errington, A, Frankish, J, Frankland, L, French, P, Garner, J, Garnett, L, Gay, M R J, Ghori, R, Gibson, L M, Gilby, W, Gillett, R J, Glithero, D V, Grafham, C, Griffiths, S, Griffiths-Jones, R, Grocock, S, Hammond, E S I, Harrison, E, Hart, E, Haugen, P D, Heath, S, Holmes, K, Holt, P J, Howden, A R, Hunt, S E, Hunt, G, Hunter, J, Isherwood, R, James, C, Johnson, D, Johnson, A, Joy, M, Kay, J K, Kershaw, M, Kibukawa, A M, Kimberley, A, King, A J, Knights, H, Lad, G, Laird, S, Lawlor, D A, Leongamornlert, D M, Lloyd, J, Loveland, J, Lovell, M J, Lush, R, Lyne, S, Martin, M, Mashreghi-Mohammadi, L, Matthews, N S W, Matthews, S, McLaren, S, Milne, S, Mistry, M J F, Moore, T, Nickerson, C N, O'Dell, K, Oliver, A, Palmeiri, S A, Palmer, A, Parker, D, Patel, A V, Pearce, A I, Peck, S, Pelan, K, Phelps, B J, Phillimore, R, Plumb, J, Rajan, C, Raymond, G, Rouse, C, Saenphimmachak, H K, Sehra, E, Sheridan, R, Shownkeen, S, Sims, C D, Skuce, M, Smith, C, Steward, S, Subramanian, N, Sycamore, A, Tracey, A, Tromans, Z, Van Helmond, M, Wall, J M, Wallis, S, White, S L, Whitehead, J E, Wilkinson, D L, Willey, H, Williams, L, Wilming, P W, Wray, Z, Wu, A, Coulson, M, Vaudin, J E, Sulston, R, Durbin, T, Hubbard, R, Wooster, I, Dunham, N P, Carter, G, McVean, M T, Ross, J, Harrow, M V, Olson, S, Beck, J, Rogers, D R, Bentley, R, Banerjee, S P, Bryant, D C, Burford, W D H, Burrill, S M, Clegg, P, Dhami, O, Dovey, L M, Faulkner, S M, Gribble, C F, Langford, R D, Pandian, K M, Porter, and E, Prigmore

Subjects
Sequence analysis, DNA Replication Timing, Molecular Sequence Data, Locus (genetics), Biology, Structural variation, Open Reading Frames, Chromosome 19, Gene Duplication, Humans, Disease, Selection, Genetic, Genetics, Recombination, Genetic, Multidisciplinary, Gene map, Base Sequence, Genetic Variation, Genome project, Genomics, Sequence Analysis, DNA, Genes, Chromosomes, Human, Pair 1, Human genome, Chromosome 21, Pseudogenes
Abstract

The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.

Published
2005

5. The DNA sequence and analysis of human chromosome 6

Author

A. J. Mungall, S. A. Palmer, S. K. Sims, C. A. Edwards, J. L. Ashurst, L. Wilming, M. C. Jones, R. Horton, S. E. Hunt, C. E. Scott, J. G. R. Gilbert, M. E. Clamp, G. Bethel, S. Milne, R. Ainscough, J. P. Almeida, K. D. Ambrose, T. D. Andrews, R. I. S. Ashwell, A. K. Babbage, C. L. Bagguley, J. Bailey, R. Banerjee, D. J. Barker, K. F. Barlow, K. Bates, D. M. Beare, H. Beasley, O. Beasley, C. P. Bird, S. Blakey, S. Bray-Allen, J. Brook, A. J. Brown, J. Y. Brown, D. C. Burford, W. Burrill, J. Burton, C. Carder, N. P. Carter, J. C. Chapman, S. Y. Clark, G. Clark, C. M. Clee, S. Clegg, V. Cobley, R. E. Collier, J. E. Collins, L. K. Colman, N. R. Corby, G. J. Coville, K. M. Culley, P. Dhami, J. Davies, M. Dunn, M. E. Earthrowl, A. E. Ellington, K. A. Evans, L. Faulkner, M. D. Francis, A. Frankish, J. Frankland, L. French, P. Garner, J. Garnett, M. J. R. Ghori, L. M. Gilby, C. J. Gillson, R. J. Glithero, D. V. Grafham, M. Grant, S. Gribble, C. Griffiths, M. Griffiths, R. Hall, K. S. Halls, S. Hammond, J. L. Harley, E. A. Hart, P. D. Heath, R. Heathcott, S. J. Holmes, P. J. Howden, K. L. Howe, G. R. Howell, E. Huckle, S. J. Humphray, M. D. Humphries, A. R. Hunt, C. M. Johnson, A. A. Joy, M. Kay, S. J. Keenan, A. M. Kimberley, A. King, G. K. Laird, C. Langford, S. Lawlor, D. A. Leongamornlert, M. Leversha, C. R. Lloyd, D. M. Lloyd, J. E. Loveland, J. Lovell, S. Martin, M. Mashreghi-Mohammadi, G. L. Maslen, L. Matthews, O. T. McCann, S. J. McLaren, K. McLay, A. McMurray, M. J. F. Moore, J. C. Mullikin, D. Niblett, T. Nickerson, K. L. Novik, K. Oliver, E. K. Overton-Larty, A. Parker, R. Patel, A. V. Pearce, A. I. Peck, B. Phillimore, S. Phillips, R. W. Plumb, K. M. Porter, Y. Ramsey, S. A. Ranby, C. M. Rice, M. T. Ross, S. M. Searle, H. K. Sehra, E. Sheridan, C. D. Skuce, S. Smith, M. Smith, L. Spraggon, S. L. Squares, C. A. Steward, N. Sycamore, G. Tamlyn-Hall, J. Tester, A. J. Theaker, D. W. Thomas, A. Thorpe, A. Tracey, A. Tromans, B. Tubby, M. Wall, J. M. Wallis, A. P. West, S. S. White, S. L. Whitehead, H. Whittaker, A. Wild, D. J. Willey, T. E. Wilmer, J. M. Wood, P. W. Wray, J. C. Wyatt, L. Young, R. M. Younger, D. R. Bentley, A. Coulson, R. Durbin, T. Hubbard, J. E. Sulston, I. Dunham, J. Rogers, and S. Beck

Subjects
Multidisciplinary, Genes, RNA, Transfer, HLA-B Antigens, Genetic Diseases, Inborn, Animals, Humans, Chromosomes, Human, Pair 6, Exons, Sequence Analysis, DNA, Physical Chromosome Mapping, Pseudogenes
Abstract

Chromosome 6 is a metacentric chromosome that constitutes about 6% of the human genome. The finished sequence comprises 166,880,988 base pairs, representing the largest chromosome sequenced so far. The entire sequence has been subjected to high-quality manual annotation, resulting in the evidence-supported identification of 1,557 genes and 633 pseudogenes. Here we report that at least 96% of the protein-coding genes have been identified, as assessed by multi-species comparative sequence analysis, and provide evidence for the presence of further, otherwise unsupported exons/genes. Among these are genes directly implicated in cancer, schizophrenia, autoimmunity and many other diseases. Chromosome 6 harbours the largest transfer RNA gene cluster in the genome; we show that this cluster co-localizes with a region of high transcriptional activity. Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome.

Published
2003

6. Dermatofibrosarcoma protuberans in two patients with acquired immunodeficiency syndrome

Author

A N, Sapadin, J M, Gelfand, K L, Howe, R G, Phelps, D, Grand, and D, Rudikoff

Subjects
Adult, Male, Acquired Immunodeficiency Syndrome, Skin Neoplasms, Dermatofibrosarcoma, Humans, Female, Middle Aged
Abstract

Dermatofibrosarcoma protuberans (DFSP) is a locally aggressive cutaneous tumor of intermediate malignancy. Most commonly, it arises as an asymptomatic, indurated plaque on the trunk within which protuberant nodules develop over time. We describe its occurrence in two patients with human immunodeficiency virus, a previously unreported association. The first patient, a 41-year-old woman, complained of painful lesions around the left shoulder that developed within a scar from previous trauma to the area. The second patient, a 50-year-old man, developed a recurrent DFSP within the scar from a previous surgical procedure. Dermatofibrosarcoma protuberans was confirmed in both cases by the histopathologic and immunohistochemical findings.

Published
2000

7. Erratum: The DNA sequence and biological annotation of human chromosome 1

Author

S. G. Gregory, K. F. Barlow, K. E. McLay, R. Kaul, D. Swarbreck, A. Dunham, C. E. Scott, K. L. Howe, K. Woodfine, C. C. A. Spencer, M. C. Jones, C. Gillson, S. Searle, Y. Zhou, F. Kokocinski, L. McDonald, R. Evans, K. Phillips, A. Atkinson, R. Cooper, C. Jones, R. E. Hall, T. D. Andrews, C. Lloyd, R. Ainscough, J. P. Almeida, K. D. Ambrose, F. Anderson, R. W. Andrew, R. I. S. Ashwell, K. Aubin, A. K. Babbage, C. L. Bagguley, J. Bailey, R. Banerjee, H. Beasley, G. Bethel, C. P. Bird, S. Bray-Allen, J. Y. Brown, A. J. Brown, S. P. Bryant, D. Buckley, D. C. Burford, W. D. H. Burrill, J. Burton, J. Bye, C. Carder, J. C. Chapman, S. Y. Clark, G. Clarke, C. Clee, S. M. Clegg, V. Cobley, R. E. Collier, N. Corby, G. J. Coville, J. Davies, R. Deadman, P. Dhami, O. Dovey, M. Dunn, M. Earthrowl, A. G. Ellington, H. Errington, L. M. Faulkner, A. Frankish, J. Frankland, L. French, P. Garner, J. Garnett, L. Gay, M. R. J. Ghori, R. Gibson, L. M. Gilby, W. Gillett, R. J. Glithero, D. V. Grafham, S. M. Gribble, C. Griffiths, S. Griffiths-Jones, R. Grocock, S. Hammond, E. S. I. Harrison, E. Hart, E. Haugen, P. D. Heath, S. Holmes, K. Holt, P. J. Howden, A. R. Hunt, S. E. Hunt, G. Hunter, J. Isherwood, R. James, C. Johnson, D. Johnson, A. Joy, M. Kay, J. K. Kershaw, M. Kibukawa, A. M. Kimberley, A. King, A. J. Knights, H. Lad, G. Laird, C. F. Langford, S. Lawlor, D. A. Leongamornlert, D. M. Lloyd, J. Loveland, J. Lovell, M. J. Lush, R. Lyne, S. Martin, M. Mashreghi-Mohammadi, L. Matthews, N. S. W. Matthews, S. McLaren, S. Milne, S. Mistry, M. J. F. M. oore, T. Nickerson, C. N. O'Dell, K. Oliver, A. Palmeiri, S. A. Palmer, R. D. Pandian, A. Parker, D. Patel, A. V. Pearce, A. I. Peck, S. Pelan, K. Phelps, B. J. Phillimore, R. Plumb, K. M. Porter, E. Prigmore, J. Rajan, C. Raymond, G. Rouse, C. Saenphimmachak, H. K. Sehra, E. Sheridan, R. Shownkeen, S. Sims, C. D. Skuce, M. Smith, C. Steward, S. Subramanian, N. Sycamore, A. Tracey, A. Tromans, Z. Van Helmond, M. Wall J. M. Wallis, S. White, S. L. Whitehead, J. E. Wilkinson, D. L. Willey, H. Williams, L. Wilming, P. W. Wray, Z. Wu, A. Coulson, M. Vaudin, J. E. Sulston, R. Durbin, T. Hubbard, R. Wooster, I. Dunham, N. P. Carter, G. McVean, M. T. Ross, J. Harrow, M. V. Olson, S. Beck, J. Rogers, and D. R. Bentley

Subjects
Genetics, Annotation, Multidisciplinary, Chromosome (genetic algorithm), Gribble, Biology, biology.organism_classification, DNA sequencing
Abstract

Nature 441, 315–321 (2006) We inadvertently omitted the names of the following authors: R. Banerjee, S. P. Bryant, D. C. Burford, W. D. H. Burrill, S. M. Clegg, P. Dhami, O. Dovey, L. M. Faulkner, S. M. Gribble, C. F. Langford, R. D. Pandian, K. M. Porter and E. Prigmore.

Published
2006
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8. Electric power in the wood-products industry

Author

K. L. Howe and C. E. Carey

Subjects
Engineering, Electric energy, Electric power system, Drilling machines, Geographic area, business.industry, Mechanical engineering, Agricultural engineering, Electric power, Raw material, business
Abstract

THIS paper deals with electric power in those industries in the Pacific Northwest which use forest wood as raw material for manufacture. It covers briefly the electric power requirements of these industries, and presents some statistics as to electric power consumption. During the past two decades the electric energy consumed in t he lumber, pulp, and paper industries of this district has grown to a value comparable to the total amount generated by all of the central stations operating within the same geographic area.

Published
1931
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