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Hsiao K, Chapman P, Nilsen S, Eckman C, Harigaya Y, Younkin S, Yang F, Cole G. Correlative memory deficits, Abeta elevation, and amyloid plaques in transgenic mice. Science 1996; 274:99-102. [PMID: 8810256 DOI: 10.1126/science.274.5284.99] [Citation(s) in RCA: 3234] [Impact Index Per Article: 111.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Transgenic mice overexpressing the 695-amino acid isoform of human Alzheimer beta-amyloid (Abeta) precursor protein containing a Lys670 --> Asn, Met671 --> Leu mutation had normal learning and memory in spatial reference and alternation tasks at 3 months of age but showed impairment by 9 to 10 months of age. A fivefold increase in Abeta(1-40) and a 14-fold increase in Abeta(1-42/43) accompanied the appearance of these behavioral deficits. Numerous Abeta plaques that stained with Congo red dye were present in cortical and limbic structures of mice with elevated amounts of Abeta. The correlative appearance of behavioral, biochemical, and pathological abnormalities reminiscent of Alzheimer's disease in these transgenic mice suggests new opportunities for exploring the pathophysiology and neurobiology of this disease.
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Abstract
The crystal structure of recombinant wild-type green fluorescent protein (GFP) has been solved to a resolution of 1.9 A by multiwavelength anomalous dispersion phasing methods. The protein is in the shape of a cylinder, comprising 11 strands of beta-sheet with an alpha-helix inside and short helical segments on the ends of the cylinder. This motif, with beta-structure on the outside and alpha-helix on the inside, represents a new protein fold, which we have named the beta-can. Two protomers pack closely together to form a dimer in the crystal. The fluorophores are protected inside the cylinders, and their structures are consistent with the formation of aromatic systems made up of Tyr66 with reduction of its C alpha-C beta bond coupled with cyclization of the neighboring glycine and serine residues. The environment inside the cylinder explains the effects of many existing mutants of GFP and suggests specific side chains that could be modified to change the spectral properties of GFP. Furthermore, the identification of the dimer contacts may allow mutagenic control of the state of assembly of the protein.
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Yang F, Murugan R, Wang S, Ramakrishna S. Electrospinning of nano/micro scale poly(l-lactic acid) aligned fibers and their potential in neural tissue engineering. Biomaterials 2005; 26:2603-10. [PMID: 15585263 DOI: 10.1016/j.biomaterials.2004.06.051] [Citation(s) in RCA: 1085] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2004] [Accepted: 06/17/2004] [Indexed: 01/19/2023]
Abstract
Efficacy of aligned poly(l-lactic acid) (PLLA) nano/micro fibrous scaffolds for neural tissue engineering is described and their performance with random PLLA scaffolds is compared as well in this study. Perfectly aligned PLLA fibrous scaffolds were fabricated by an electrospinning technique under optimum condition and the diameter of the electrospun fibers can easily be tailored by adjusting the concentration of polymer solution. As the structure of PLLA scaffold was intended for neural tissue engineering, its suitability was evaluated in vitro using neural stem cells (NSCs) as a model cell line. Cell morphology, differentiation and neurite outgrowth were studied by various microscopic techniques. The results show that the direction of NSC elongation and its neurite outgrowth is parallel to the direction of PLLA fibers for aligned scaffolds. No significant changes were observed on the cell orientation with respect to the fiber diameters. However, the rate of NSC differentiation was higher for PLLA nanofibers than that of micro fibers and it was independent of the fiber alignment. Based on the experimental results, the aligned nanofibrous PLLA scaffold could be used as a potential cell carrier in neural tissue engineering.
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Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, McDonald LA, Feldblyum TV, Angiuoli S, Dickinson T, Hickey EK, Holt IE, Loftus BJ, Yang F, Smith HO, Venter JC, Dougherty BA, Morrison DA, Hollingshead SK, Fraser CM. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 2001; 293:498-506. [PMID: 11463916 DOI: 10.1126/science.1061217] [Citation(s) in RCA: 1054] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role. Approximately 5% of the genome is composed of insertion sequences that may contribute to genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the metabolism of polysaccharides and hexosamines provide a substantial source of carbon and nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif identified within the signal peptide of proteins is potentially involved in targeting these proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several surface-exposed proteins that may serve as potential vaccine candidates were identified. Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity.
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Fitzgerald TW, Gerety SS, Jones WD, van Kogelenberg M, King DA, McRae J, Morley KI, Parthiban V, Al-Turki S, Ambridge K, Barrett DM, Bayzetinova T, Clayton S, Coomber EL, Gribble S, Jones P, Krishnappa N, Mason LE, Middleton A, Miller R, Prigmore E, Rajan D, Sifrim A, Tivey AR, Ahmed M, Akawi N, Andrews R, Anjum U, Archer H, Armstrong R, Balasubramanian M, Banerjee R, Baralle D, Batstone P, Baty D, Bennett C, Berg J, Bernhard B, Bevan AP, Blair E, Blyth M, Bohanna D, Bourdon L, Bourn D, Brady A, Bragin E, Brewer C, Brueton L, Brunstrom K, Bumpstead SJ, Bunyan DJ, Burn J, Burton J, Canham N, Castle B, Chandler K, Clasper S, Clayton-Smith J, Cole T, Collins A, Collinson MN, Connell F, Cooper N, Cox H, Cresswell L, Cross G, Crow Y, D’Alessandro M, Dabir T, Davidson R, Davies S, Dean J, Deshpande C, Devlin G, Dixit A, Dominiczak A, Donnelly C, Donnelly D, Douglas A, Duncan A, Eason J, Edkins S, Ellard S, Ellis P, Elmslie F, Evans K, Everest S, Fendick T, Fisher R, Flinter F, Foulds N, Fryer A, Fu B, Gardiner C, Gaunt L, Ghali N, Gibbons R, Gomes Pereira SL, Goodship J, Goudie D, Gray E, Greene P, Greenhalgh L, Harrison L, Hawkins R, Hellens S, Henderson A, Hobson E, Holden S, Holder S, Hollingsworth G, Homfray T, Humphreys M, Hurst J, Ingram S, Irving M, Jarvis J, Jenkins L, Johnson D, Jones D, Jones E, Josifova D, Joss S, Kaemba B, Kazembe S, Kerr B, Kini U, Kinning E, Kirby G, Kirk C, Kivuva E, Kraus A, Kumar D, Lachlan K, Lam W, Lampe A, Langman C, Lees M, Lim D, Lowther G, Lynch SA, Magee A, Maher E, Mansour S, Marks K, Martin K, Maye U, McCann E, McConnell V, McEntagart M, McGowan R, McKay K, McKee S, McMullan DJ, McNerlan S, Mehta S, Metcalfe K, Miles E, Mohammed S, Montgomery T, Moore D, Morgan S, Morris A, Morton J, Mugalaasi H, Murday V, Nevitt L, Newbury-Ecob R, Norman A, O'Shea R, Ogilvie C, Park S, Parker MJ, Patel C, Paterson J, Payne S, Phipps J, Pilz DT, Porteous D, Pratt N, Prescott K, Price S, Pridham A, Procter A, Purnell H, Ragge N, Rankin J, Raymond L, Rice D, Robert L, Roberts E, Roberts G, Roberts J, Roberts P, Ross A, Rosser E, Saggar A, Samant S, Sandford R, Sarkar A, Schweiger S, Scott C, Scott R, Selby A, Seller A, Sequeira C, Shannon N, Sharif S, Shaw-Smith C, Shearing E, Shears D, Simonic I, Simpkin D, Singzon R, Skitt Z, Smith A, Smith B, Smith K, Smithson S, Sneddon L, Splitt M, Squires M, Stewart F, Stewart H, Suri M, Sutton V, Swaminathan GJ, Sweeney E, Tatton-Brown K, Taylor C, Taylor R, Tein M, Temple IK, Thomson J, Tolmie J, Torokwa A, Treacy B, Turner C, Turnpenny P, Tysoe C, Vandersteen A, Vasudevan P, Vogt J, Wakeling E, Walker D, Waters J, Weber A, Wellesley D, Whiteford M, Widaa S, Wilcox S, Williams D, Williams N, Woods G, Wragg C, Wright M, Yang F, Yau M, Carter NP, Parker M, Firth HV, FitzPatrick DR, Wright CF, Barrett JC, Hurles ME. Large-scale discovery of novel genetic causes of developmental disorders. Nature 2015; 519:223-8. [PMID: 25533962 PMCID: PMC5955210 DOI: 10.1038/nature14135] [Citation(s) in RCA: 826] [Impact Index Per Article: 82.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 12/04/2014] [Indexed: 12/23/2022]
Abstract
Despite three decades of successful, predominantly phenotype-driven discovery of the genetic causes of monogenic disorders, up to half of children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis. Particularly challenging are those disorders rare enough to have eluded recognition as a discrete clinical entity, those with highly variable clinical manifestations, and those that are difficult to distinguish from other, very similar, disorders. Here we demonstrate the power of using an unbiased genotype-driven approach to identify subsets of patients with similar disorders. By studying 1,133 children with severe, undiagnosed developmental disorders, and their parents, using a combination of exome sequencing and array-based detection of chromosomal rearrangements, we discovered 12 novel genes associated with developmental disorders. These newly implicated genes increase by 10% (from 28% to 31%) the proportion of children that could be diagnosed. Clustering of missense mutations in six of these newly implicated genes suggests that normal development is being perturbed by an activating or dominant-negative mechanism. Our findings demonstrate the value of adopting a comprehensive strategy, both genome-wide and nationwide, to elucidate the underlying causes of rare genetic disorders.
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Wang PJ, McCarrey JR, Yang F, Page DC. An abundance of X-linked genes expressed in spermatogonia. Nat Genet 2001; 27:422-6. [PMID: 11279525 DOI: 10.1038/86927] [Citation(s) in RCA: 599] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Spermatogonia are the self-renewing, mitotic germ cells of the testis from which sperm arise by means of the differentiation pathway known as spermatogenesis. By contrast with hematopoietic and other mammalian stem-cell populations, which have been subjects of intense molecular genetic investigation, spermatogonia have remained largely unexplored at the molecular level. Here we describe a systematic search for genes expressed in mouse spermatogonia, but not in somatic tissues. We identified 25 genes (19 of which are novel) that are expressed in only male germ cells. Of the 25 genes, 3 are Y-linked and 10 are X-linked. If these genes had been distributed randomly in the genome, one would have expected zero to two of the genes to be X-linked. Our findings indicate that the X chromosome has a predominant role in pre-meiotic stages of mammalian spermatogenesis. We hypothesize that the X chromosome acquired this prominent role in male germ-cell development as it evolved from an ordinary, unspecialized autosome.
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Tortorella MD, Burn TC, Pratta MA, Abbaszade I, Hollis JM, Liu R, Rosenfeld SA, Copeland RA, Decicco CP, Wynn R, Rockwell A, Yang F, Duke JL, Solomon K, George H, Bruckner R, Nagase H, Itoh Y, Ellis DM, Ross H, Wiswall BH, Murphy K, Hillman MC, Hollis GF, Newton RC, Magolda RL, Trzaskos JM, Arner EC. Purification and cloning of aggrecanase-1: a member of the ADAMTS family of proteins. Science 1999; 284:1664-6. [PMID: 10356395 DOI: 10.1126/science.284.5420.1664] [Citation(s) in RCA: 500] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We purified, cloned, and expressed aggrecanase, a protease that is thought to be responsible for the degradation of cartilage aggrecan in arthritic diseases. Aggrecanase-1 [a disintegrin and metalloproteinase with thrombospondin motifs-4 (ADAMTS-4)] is a member of the ADAMTS protein family that cleaves aggrecan at the glutamic acid-373-alanine-374 bond. The identification of this protease provides a specific target for the development of therapeutics to prevent cartilage degradation in arthritis.
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Kelly S, Jahanshad N, Zalesky A, Kochunov P, Agartz I, Alloza C, Andreassen OA, Arango C, Banaj N, Bouix S, Bousman CA, Brouwer RM, Bruggemann J, Bustillo J, Cahn W, Calhoun V, Cannon D, Carr V, Catts S, Chen J, Chen JX, Chen X, Chiapponi C, Cho KK, Ciullo V, Corvin AS, Crespo-Facorro B, Cropley V, De Rossi P, Diaz-Caneja CM, Dickie EW, Ehrlich S, Fan FM, Faskowitz J, Fatouros-Bergman H, Flyckt L, Ford JM, Fouche JP, Fukunaga M, Gill M, Glahn DC, Gollub R, Goudzwaard ED, Guo H, Gur RE, Gur RC, Gurholt TP, Hashimoto R, Hatton SN, Henskens FA, Hibar DP, Hickie IB, Hong LE, Horacek J, Howells FM, Hulshoff Pol HE, Hyde CL, Isaev D, Jablensky A, Jansen PR, Janssen J, Jönsson EG, Jung LA, Kahn RS, Kikinis Z, Liu K, Klauser P, Knöchel C, Kubicki M, Lagopoulos J, Langen C, Lawrie S, Lenroot RK, Lim KO, Lopez-Jaramillo C, Lyall A, Magnotta V, Mandl RCW, Mathalon DH, McCarley RW, McCarthy-Jones S, McDonald C, McEwen S, McIntosh A, Melicher T, Mesholam-Gately RI, Michie PT, Mowry B, Mueller BA, Newell DT, O'Donnell P, Oertel-Knöchel V, Oestreich L, Paciga SA, Pantelis C, Pasternak O, Pearlson G, Pellicano GR, Pereira A, Pineda Zapata J, Piras F, Potkin SG, Preda A, Rasser PE, Roalf DR, Roiz R, Roos A, Rotenberg D, Satterthwaite TD, Savadjiev P, Schall U, Scott RJ, Seal ML, Seidman LJ, Shannon Weickert C, Whelan CD, Shenton ME, Kwon JS, Spalletta G, Spaniel F, Sprooten E, Stäblein M, Stein DJ, Sundram S, Tan Y, Tan S, Tang S, Temmingh HS, Westlye LT, Tønnesen S, Tordesillas-Gutierrez D, Doan NT, Vaidya J, van Haren NEM, Vargas CD, Vecchio D, Velakoulis D, Voineskos A, Voyvodic JQ, Wang Z, Wan P, Wei D, Weickert TW, Whalley H, White T, Whitford TJ, Wojcik JD, Xiang H, Xie Z, Yamamori H, Yang F, Yao N, Zhang G, Zhao J, van Erp TGM, Turner J, Thompson PM, Donohoe G. Widespread white matter microstructural differences in schizophrenia across 4322 individuals: results from the ENIGMA Schizophrenia DTI Working Group. Mol Psychiatry 2018; 23:1261-1269. [PMID: 29038599 PMCID: PMC5984078 DOI: 10.1038/mp.2017.170] [Citation(s) in RCA: 479] [Impact Index Per Article: 68.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 05/02/2017] [Accepted: 06/07/2017] [Indexed: 12/15/2022]
Abstract
The regional distribution of white matter (WM) abnormalities in schizophrenia remains poorly understood, and reported disease effects on the brain vary widely between studies. In an effort to identify commonalities across studies, we perform what we believe is the first ever large-scale coordinated study of WM microstructural differences in schizophrenia. Our analysis consisted of 2359 healthy controls and 1963 schizophrenia patients from 29 independent international studies; we harmonized the processing and statistical analyses of diffusion tensor imaging (DTI) data across sites and meta-analyzed effects across studies. Significant reductions in fractional anisotropy (FA) in schizophrenia patients were widespread, and detected in 20 of 25 regions of interest within a WM skeleton representing all major WM fasciculi. Effect sizes varied by region, peaking at (d=0.42) for the entire WM skeleton, driven more by peripheral areas as opposed to the core WM where regions of interest were defined. The anterior corona radiata (d=0.40) and corpus callosum (d=0.39), specifically its body (d=0.39) and genu (d=0.37), showed greatest effects. Significant decreases, to lesser degrees, were observed in almost all regions analyzed. Larger effect sizes were observed for FA than diffusivity measures; significantly higher mean and radial diffusivity was observed for schizophrenia patients compared with controls. No significant effects of age at onset of schizophrenia or medication dosage were detected. As the largest coordinated analysis of WM differences in a psychiatric disorder to date, the present study provides a robust profile of widespread WM abnormalities in schizophrenia patients worldwide. Interactive three-dimensional visualization of the results is available at www.enigma-viewer.org.
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Abbaszade I, Liu RQ, Yang F, Rosenfeld SA, Ross OH, Link JR, Ellis DM, Tortorella MD, Pratta MA, Hollis JM, Wynn R, Duke JL, George HJ, Hillman MC, Murphy K, Wiswall BH, Copeland RA, Decicco CP, Bruckner R, Nagase H, Itoh Y, Newton RC, Magolda RL, Trzaskos JM, Burn TC. Cloning and characterization of ADAMTS11, an aggrecanase from the ADAMTS family. J Biol Chem 1999; 274:23443-50. [PMID: 10438522 DOI: 10.1074/jbc.274.33.23443] [Citation(s) in RCA: 365] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aggrecan is responsible for the mechanical properties of cartilage. One of the earliest changes observed in arthritis is the depletion of cartilage aggrecan due to increased proteolytic cleavage within the interglobular domain. Two major sites of cleavage have been identified in this region at Asn(341)-Phe(342) and Glu(373)-Ala(374). While several matrix metalloproteinases have been shown to cleave at Asn(341)-Phe(342), an as yet unidentified protein termed "aggrecanase" is responsible for cleavage at Glu(373)-Ala(374) and is hypothesized to play a pivotal role in cartilage damage. We have identified and cloned a novel disintegrin metalloproteinase with thrombospondin motifs that possesses aggrecanase activity, ADAMTS11 (aggrecanase-2), which has extensive homology to ADAMTS4 (aggrecanase-1) and the inflammation-associated gene ADAMTS1. ADAMTS11 possesses a number of conserved domains that have been shown to play a role in integrin binding, cell-cell interactions, and extracellular matrix binding. We have expressed recombinant human ADAMTS11 in insect cells and shown that it cleaves aggrecan at the Glu(373)-Ala(374) site, with the cleavage pattern and inhibitor profile being indistinguishable from that observed with native aggrecanase. A comparison of the structure and expression patterns of ADAMTS11, ADAMTS4, and ADAMTS1 is also described. Our findings will facilitate the study of the mechanisms of cartilage degradation and provide targets to search for effective inhibitors of cartilage depletion in arthritic disease.
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Yang F, Murugan R, Ramakrishna S, Wang X, Ma YX, Wang S. Fabrication of nano-structured porous PLLA scaffold intended for nerve tissue engineering. Biomaterials 2004; 25:1891-900. [PMID: 14738853 DOI: 10.1016/j.biomaterials.2003.08.062] [Citation(s) in RCA: 360] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Nerve tissue engineering (NTE) is one of the most promising methods to restore central nerve systems in human health care. Three-dimensional distribution and growth of cells within the porous scaffold are of clinical significance for NTE. In this study, an attempt was made to develop porous polymeric nano-fibrous scaffold using a biodegradable poly(L-lactic acid) (PLLA) for in vitro culture of nerve stem cells (NSCs). The processing of PLLA scaffold has been carried out by liquid-liquid phase separation method. The physico-chemical properties of the scaffold were fully characterized by using differential scanning calorimetry and scanning electron microscopy. These results confirmed that the prepared scaffold is highly porous and fibrous with diameters down to nanometer scale. As our nano-structured PLLA scaffold mimics natural extracellular matrix, we have intended this biodegradable scaffold as cell carrier in NTE. The in vitro performance of NSCs seeded on nano-fibrous scaffold is addressed in this study. The cell cultural tests showed that the NSCs could differentiate on the nano-structured scaffold and the scaffold acted as a positive cue to support neurite outgrowth. These results suggested that the nano-structured porous PLLA scaffold is a potential cell carrier in NTE.
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Research Support, Non-U.S. Gov't |
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360 |
11
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Yang F, He J, Lin X, Li Q, Pan D, Zhang X, Xu X. Complete genome sequence of the shrimp white spot bacilliform virus. J Virol 2001; 75:11811-20. [PMID: 11689662 PMCID: PMC114767 DOI: 10.1128/jvi.75.23.11811-11820.2001] [Citation(s) in RCA: 356] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the first complete genome sequence of a marine invertebrate virus. White spot bacilliform virus (WSBV; or white spot syndrome virus) is a major shrimp pathogen with a high mortality rate and a wide host range. Its double-stranded circular DNA genome of 305,107 bp contains 181 open reading frames (ORFs). Nine homologous regions containing 47 repeated minifragments that include direct repeats, atypical inverted repeat sequences, and imperfect palindromes were identified. This is the largest animal virus that has been completely sequenced. Although WSBV is morphologically similar to insect baculovirus, the two viruses are not detectably related at the amino acid level. Rather, some WSBV genes are more homologous to eukaryotic genes than viral genes. In fact, sequence analysis indicates that WSBV differs from all known viruses, although a few genes display a weak homology to herpesvirus genes. Most of the ORFs encode proteins that bear no homology to any known proteins, either suggesting that WSBV represents a novel class of viruses or perhaps implying a significant evolutionary distance between marine and terrestrial viruses. The most unique feature of WSBV is the presence of an intact collagen gene, a gene encoding an extracellular matrix protein of animal cells that has never been found in any viruses. Determination of the genome of WSBV will facilitate a better understanding of the molecular mechanism underlying the pathogenesis of the WSBV virus and will also provide useful information concerning the evolution and divergence of marine and terrestrial animal viruses at the molecular level.
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Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, White O. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res 2001; 29:41-3. [PMID: 11125044 PMCID: PMC29844 DOI: 10.1093/nar/29.1.41] [Citation(s) in RCA: 320] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional identification of proteins by sequence homology. We introduce the term 'equivalog' to describe members of a set of homologous proteins that are conserved with respect to function since their last common ancestor. Related proteins are grouped into equivalog families where possible, and otherwise into protein families with other hierarchically defined homology types. TIGRFAMs currently contains over 800 protein families, available for searching or downloading at www.tigr.org/TIGRFAMs. Classification by equivalog family, where achievable, complements classification by orthology, superfamily, domain or motif. It provides the information best suited for automatic assignment of specific functions to proteins from large-scale genome sequencing projects.
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320 |
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Zhang Q, Skepper JN, Yang F, Davies JD, Hegyi L, Roberts RG, Weissberg PL, Ellis JA, Shanahan CM. Nesprins: a novel family of spectrin-repeat-containing proteins that localize to the nuclear membrane in multiple tissues. J Cell Sci 2001; 114:4485-98. [PMID: 11792814 DOI: 10.1242/jcs.114.24.4485] [Citation(s) in RCA: 308] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In search of vascular smooth muscle cell differentiation markers, we identified two genes encoding members of a new family of type II integral membrane proteins. Both are ubiquitously expressed, and tissue-specific alternative mRNA initiation and splicing generate at least two major isoforms of each protein, with the smaller isoforms being truncated at the N-terminus. We have named these proteins nesprin-1 and -2 for nuclear envelope spectrin repeat, as they are characterized by the presence of multiple, clustered spectrin repeats, bipartite nuclear localization sequences and a conserved C-terminal, single transmembrane domain. Transient transfection of EGFP-fusion expression constructs demonstrated their localization to the nuclear membrane with a novel C-terminal, TM-domain-containing sequence essential for perinuclear localization. Using antibodies to nesprin-1, we documented its colocalization with LAP1, emerin and lamins at the nuclear envelope, and immunogold labeling confirmed its presence at the nuclear envelope and in the nucleus where it colocalized with heterochromatin. Nesprin-1 is developmentally regulated in both smooth and skeletal muscle and is re-localized from the nuclear envelope to the nucleus and cytoplasm during C2C12 myoblast differentiation. These data and structural analogies with other proteins suggest that nesprins may function as ‘dystrophins of the nucleus’ to maintain nuclear organization and structural integrity.
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MESH Headings
- Amino Acid Sequence
- Animals
- Biomarkers
- COS Cells
- Cell Differentiation/genetics
- Cells, Cultured
- Cytoskeletal Proteins
- DNA, Complementary/isolation & purification
- Humans
- Immune Sera/chemistry
- In Situ Hybridization, Fluorescence
- Membrane Proteins/chemistry
- Membrane Proteins/genetics
- Membrane Proteins/immunology
- Membrane Proteins/metabolism
- Mice
- Microfilament Proteins
- Molecular Sequence Data
- Multigene Family
- Muscle Proteins/chemistry
- Muscle Proteins/genetics
- Muscle Proteins/metabolism
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/metabolism
- Nerve Tissue Proteins
- Nuclear Envelope/metabolism
- Nuclear Localization Signals/genetics
- Nuclear Proteins/chemistry
- Nuclear Proteins/genetics
- Nuclear Proteins/immunology
- Nuclear Proteins/metabolism
- Organ Specificity/genetics
- Protein Structure, Tertiary/genetics
- Rats
- Repetitive Sequences, Amino Acid
- Sequence Homology, Amino Acid
- Spectrin/metabolism
- Subcellular Fractions/metabolism
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Abstract
The distal histidine residue, His64(E7), and the proximal histidine residue, His93(F8), in myoglobin (Mb) are important for the function of the protein. For example, the increase in the association rate constant for CO binding at low pH has been suggested to be caused by the protonation of these histidine residues. In order to investigate the influence of protonation on the structure of myoglobin, we determined the crystal structures of sperm whale myoglobin to 2.0 A or better in different states of ligation (MbCO, deoxyMb and metMb) at pH values of 4, 5 and 6. The most dramatic change found at low pH is that His64 swings out of the distal pocket in the MbCO structure at pH 4, opening a direct channel from the solvent to the iron atom. This rotation seems to be facilitated by conformational changes in the CD corner. The benzyl side-chain of Phe46(CD4), which has been suggested to be a critical residue in controlling the rotation of His64, moves away from His64 at pH 4 in the deoxyMb structure, allowing more free rotation of His64. Arg45(CD3) is also important for the dynamics of myoglobin, since it influences the pK(a) of His64 and forms a hydrogen bond lattice that hinders the rotation of His64 at neutral pH. This hydrogen-bond lattice disappears at low pH. Although His64 rotates out of the distal pocket in the MbCO structure at pH 4, leaving more space for the CO ligand, the Fe-C-O angle refines to about 130 degrees, the same as those at pH 5 and 6. In the MbCO structure at pH 4, significant conformational changes appear in the EF corner. The peptide plane between Lys79(EF2) and Gly80(EF3) flips about 150 degrees. The occupancy of this conformation in the MbCO structures increases with decreases in pH. On the proximal side of the heme, the bond between the heme iron atom and N(epsilon) of His93 remains intact under the experimental conditions in the MbCO and deoxyMb structures, but appears elongated in the metMb structure at pH 4, representing either a weakened bond or the breakage of the bond in some fraction of the molecules in the crystal.
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Yang F, de Villiers WJ, McClain CJ, Varilek GW. Green tea polyphenols block endotoxin-induced tumor necrosis factor-production and lethality in a murine model. J Nutr 1998; 128:2334-40. [PMID: 9868178 DOI: 10.1093/jn/128.12.2334] [Citation(s) in RCA: 295] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Green tea polyphenols are potent antioxidants. They have both anti-cancer and anti-inflammatory effects. However, their mechanisms of actions remain unclear. In inflammation, tumor necrosis factor-alpha(TNFalpha) plays a pivotal role. NF-KB, an oxidative stress -sensitive nuclear transcription factor, controls the expression of many genes including the TNFalpha gene. We postulated that green tea polyphenols regulate TNFalpha gene expression by modulating NF-KB activation through their antioxidant properties. In the macrophage cell line, RAW264.7, (-)epigallocatechin gallate (EGCG), the major green tea polyphenol, decreased lipopolysaccharide (LPS)-induced TNFalpha production in a dose-dependent fashion (50% inhibition at 100 mmol/L). EGCG also inhibited LPS-induced TNFalpha mRNA expression and nuclear NF-KB-binding activity in RAW264.7 cells (30-40% inhibition at 100 mmol/L). Similarly, EGCG inhibited LPS-induced TNFalpha production in elicited mouse peritoneal macrophages. In male BALB/c mice, green tea polyphenols (given by oral gavage 2 h prior to an i.p. injection of 40 mg LPS/kg body wt) decreased LPS-induced TNFalpha production in serum in a dose-responsive fashion. At a dose of 0.5 g green tea polyphenols/kg body wt, serum TNFalpha was reduced by 80% of control. Moreover, 0.5 g green tea polyphenols/kg body wt completely inhibited LPS-induced lethality in male BALB/c mice. We conclude that the anti-inflammatory mechanism of green tea polyphenols is mediated at least in part through down-regulation of TNFalpha gene expression by blocking NF-KB activation. These findings suggest that green tea polyphenols may be effective therapy for a variety of inflammatory processes.
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295 |
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Ning H, Yang F, Jiang M, Hu L, Feng K, Zhang J, Yu Z, Li B, Xu C, Li Y, Wang J, Hu J, Lou X, Chen H. The correlation between cotransplantation of mesenchymal stem cells and higher recurrence rate in hematologic malignancy patients: outcome of a pilot clinical study. Leukemia 2008; 22:593-9. [PMID: 18185520 DOI: 10.1038/sj.leu.2405090] [Citation(s) in RCA: 270] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this open-label randomized clinical trial, HLA-identical sibling-matched hematopoietic stem cells (HSC) were transplanted (non-MSCs group, n=15) or cotransplanted with mesenchymal stem cells (MSCs) (MSCs group, n=10) in hematologic malignancy patients. The median number of MSCs infused was 3.4 x 10(5) kg(-1) (range, 0.3-15.3 x 10(5) kg(-1)). MSCs infusions were well tolerated. The median time to neutrophil engraftment (absolute neutrophil count >0.5 x 10(9) l(-1)) was 16 days for MSCs group and 15 days for non-MSCs group. The median time to platelet engraftment (platelet count >50 x 10(9) l(-1)) was 30 and 27 days, respectively. Grades II-IV acute graft-versus-host disease (GVHD) was observed respectively, in one (11.1%) and eight (53.3%) evaluable patients. Chronic GVHD was found in one (14.3%) and four (28.6%) evaluable patients. The number of patients who relapsed were six (60.0%) and three (20.0%), and the 3-year disease-free survivals were 30.0 and 66.7%, respectively. Thus cotransplantation of MSCs and HSCs may prevent GVHD, but the relapse rate is obviously higher than the control group. We conclude that use of MSCs must be handled with extreme caution before a large-scale clinical trial is performed.
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Research Support, Non-U.S. Gov't |
17 |
270 |
17
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Yang F, Demma M, Warren V, Dharmawardhane S, Condeelis J. Identification of an actin-binding protein from Dictyostelium as elongation factor 1a. Nature 1990; 347:494-6. [PMID: 2215665 DOI: 10.1038/347494a0] [Citation(s) in RCA: 266] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Indirect evidence has implicated an interaction between the cytoskeleton and the protein synthetic machinery. Two recent reports have linked the elongation factor 1a (EF-1a) which is involved in protein synthesis, with the microtubular cytoskeleton. In situ hybridization has, however, revealed that the messages for certain cytoskeletal proteins are preferentially associated with actin filaments. ABP-50 is an abundant actin filament bundling protein of native relative molecular mass 50,000 (50K) isolated from Dictyostelium discoideum. Immunofluorescence studies show that ABP-50 is present in filopodia and other cortical regions that contain actin filament bundles. In addition, ABP-50 binds to monomeric actin in the cytosol of unstimulated cells and the association of ABP-50 with the actin cytoskeleton is regulated during chemotaxis. Through complementary DNA sequencing and subsequent functional analysis, we have identified ABP-50 as D. discoideum EF-1a. The ability of EF-1a to bind reversibly to the actin cytoskeleton upon stimulation could provide a mechanism for spatially and temporally regulated protein synthesis in eukaryotic cells.
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Comparative Study |
35 |
266 |
18
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Seiffert D, Bradley JD, Rominger CM, Rominger DH, Yang F, Meredith JE, Wang Q, Roach AH, Thompson LA, Spitz SM, Higaki JN, Prakash SR, Combs AP, Copeland RA, Arneric SP, Hartig PR, Robertson DW, Cordell B, Stern AM, Olson RE, Zaczek R. Presenilin-1 and -2 are molecular targets for gamma-secretase inhibitors. J Biol Chem 2000; 275:34086-91. [PMID: 10915801 DOI: 10.1074/jbc.m005430200] [Citation(s) in RCA: 248] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Presenilins are integral membrane protein involved in the production of amyloid beta-protein. Mutations of the presenilin-1 and -2 gene are associated with familial Alzheimer's disease and are thought to alter gamma-secretase cleavage of the beta-amyloid precursor protein, leading to increased production of longer and more amyloidogenic forms of A beta, the 4-kDa beta-peptide. Here, we show that radiolabeled gamma-secretase inhibitors bind to mammalian cell membranes, and a benzophenone analog specifically photocross-links three major membrane polypeptides. A positive correlation is observed among these compounds for inhibition of cellular A beta formation, inhibition of membrane binding and cross-linking. Immunological techniques establish N- and C-terminal fragments of presenilin-1 as specifically cross-linked polypeptides. Furthermore, binding of gamma-secretase inhibitors to embryonic membranes derived from presenilin-1 knockout embryos is reduced in a gene dose-dependent manner. In addition, C-terminal fragments of presenilin-2 are specifically cross-linked. Taken together, these results indicate that potent and selective gamma-secretase inhibitors block A beta formation by binding to presenilin-1 and -2.
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25 |
248 |
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Yang F, Lum JB, McGill JR, Moore CM, Naylor SL, van Bragt PH, Baldwin WD, Bowman BH. Human transferrin: cDNA characterization and chromosomal localization. Proc Natl Acad Sci U S A 1984; 81:2752-6. [PMID: 6585826 PMCID: PMC345148 DOI: 10.1073/pnas.81.9.2752] [Citation(s) in RCA: 223] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Transferrin (Tf) is the major iron binding protein in vertebrate serum. It shares homologous amino acid sequences with four other proteins: lactotransferrin, ovotransferrin, melanoma antigen p97, and HuBlym-1. Antigen p97 and the Tf receptor genes have been mapped on human chromosome 3. The goal of the study described here was to initiate the characterization of the Tf gene by identifying and characterizing its cDNA and mapping its chromosomal location. Recombinant plasmids containing human cDNA encoding Tf have been isolated by screening an adult human liver library with a mixed oligonucleotide probe. Within the 2.3 kilobase pairs of Tf cDNA analyzed, there is a probable leader sequence encoded by 57 nucleotides followed by 2037 nucleotides that encode the homologous amino and carboxyl domains. During evolution, three areas of the homologous amino and carboxyl domains have been strongly conserved, possibly reflecting functional constraints associated with iron binding. Chromosomal mapping by in situ hybridization and somatic cell hybrid analysis indicate that the Tf gene is located at q21-25 on human chromosome 3, consistent with linkage of the Tf, Tf receptor, and melanoma p97 loci.
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research-article |
41 |
223 |
20
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Yang F, O'Brien PC, Milne BS, Graphodatsky AS, Solanky N, Trifonov V, Rens W, Sargan D, Ferguson-Smith MA. A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic maps. Genomics 1999; 62:189-202. [PMID: 10610712 DOI: 10.1006/geno.1999.5989] [Citation(s) in RCA: 206] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cross-species reciprocal chromosome painting was used to delineate homologous chromosomal segments between domestic dog, red fox, and human. Whole sets of chromosome-specific painting probes for the red fox and dog were made by PCR amplification of flow-sorted chromosomes from established cell cultures. Based on their hybridization patterns, a complete comparative chromosome map of the three species has been built. Thirty-nine of the 44 synteny groups from the published radiation hybrid map and 33 of the 40 linkage groups in the linkage map of the dog have been assigned to specific chromosomes by fluorescence in situ hybridization and PCR-based genotyping. Each canine chromosome has at least one DNA marker assigned to it. The human-canid map shows that the canid karyotypes are among the most extensively rearranged karyotypes in mammals. Twenty-two human autosomal paints delineated 73 homologous regions on 38 canine autosomes, while paints from 38 dog autosomes detected 90 homologous segments in the human genome. Of the 22 human autosomes, only the syntenies of three chromosomes (14, 20, and 21) have been maintained intact in the canid genome. The dog-fox map and DAPI banding comparison demonstrate that the remarkable karyotype differences between fox (2n = 34 + 0-8 Bs) and dog (2n = 78) are due to 26 chromosomal fusion events and 4 fission events. It is proposed that the more easily karyotyped fox chromosomes can be used as a common reference and control system for future gene mapping in the DogMap project and CGH analysis of canine tumor DNA.
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Comparative Study |
26 |
206 |
21
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Hao S, Cui L, Jiang D, Han X, Ren Y, Jiang J, Liu Y, Liu Z, Mao S, Wang Y, Li Y, Ren X, Ding X, Wang S, Yu C, Shi X, Du M, Yang F, Zheng Y, Zhang Z, Li X, Brown DE, Li J. A Transforming Metal Nanocomposite with Large Elastic Strain, Low Modulus, and High Strength. Science 2013; 339:1191-4. [DOI: 10.1126/science.1228602] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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12 |
202 |
22
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Chen J, Qin HJ, Yang F, Liu J, Guan T, Qu FM, Zhang GH, Shi JR, Xie XC, Yang CL, Wu KH, Li YQ, Lu L. Gate-voltage control of chemical potential and weak antilocalization in Bi₂Se₃. PHYSICAL REVIEW LETTERS 2010; 105:176602. [PMID: 21231064 DOI: 10.1103/physrevlett.105.176602] [Citation(s) in RCA: 201] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Indexed: 05/30/2023]
Abstract
We report that Bi₂Se₃ thin films can be epitaxially grown on SrTiO₃ substrates, which allow for very large tunablity in carrier density with a back gate. The observed low field magnetoconductivity due to weak antilocalization (WAL) has a very weak gate-voltage dependence unless the electron density is reduced to very low values. Such a transition in WAL is correlated with unusual changes in longitudinal and Hall resistivities. Our results suggest a much suppressed bulk conductivity at large negative gate voltages and a possible role of surface states in the WAL phenomena.
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201 |
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Espy DD, Yang F, Bhatt T, Pai YC. Independent influence of gait speed and step length on stability and fall risk. Gait Posture 2010; 32:378-82. [PMID: 20655750 PMCID: PMC2943048 DOI: 10.1016/j.gaitpost.2010.06.013] [Citation(s) in RCA: 196] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Revised: 05/24/2010] [Accepted: 06/22/2010] [Indexed: 02/02/2023]
Abstract
With aging, individuals' gaits become slower and their steps shorter; both are thought to improve stability against balance threats. Recent studies have shown that shorter step lengths, which bring the center of mass (COM) closer to the leading foot, improve stability against slip-related falls. However, a slower gait, hence lower COM velocity, does the opposite. Due to the inherent coupling of step length and speed in spontaneous gait, the extent to which the benefit of shorter steps can offset the slower speed is unknown. The purpose of this study was to investigate, through decoupling, the independent effects of gait speed and step length on gait stability and the likelihood of slip-induced falls. Fifty-seven young adults walked at one of three target gait patterns, two of equal speed and two of equal step length; at a later trial, they encountered an unannounced slip. The results supported our hypotheses that faster gait as well as shorter steps each ameliorates fall risk when a slip is encountered. This appeared to be attributable to the maintenance of stability from slip initiation to liftoff of the recovery foot during the slip. Successful decoupling of gait speed from step length reveals for the first time that, although slow gait in itself leads to instability and falls (a one-standard-deviation decrease in gait speed increases the odds of fall by 4-fold), this effect is offset by the related decrease in step length (the same one-standard-deviation decrease in step length lowers fall risk by 6 times).
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research-article |
15 |
196 |
24
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Lu G, Yang F, Taylor JA, Stein JF. A comparison of photoplethysmography and ECG recording to analyse heart rate variability in healthy subjects. J Med Eng Technol 2009; 33:634-41. [DOI: 10.3109/03091900903150998] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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16 |
180 |
25
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Abstract
DNA sequencing shows that the intragenic duplication within the human haptoglobin Hp2 allele was formed by a non-homologous, probably random, crossing-over within different introns of two Hp1 genes, probably in an Hp1F / Hp1S heterozygote.
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41 |
179 |