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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, et alFitzgerald 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] [Show More Authors] [Citation(s) in RCA: 834] [Impact Index Per Article: 83.4] [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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Fu B, Bakker E, Yun JH, Yang VC, Meyerhoff ME. Response mechanism of polymer membrane-based potentiometric polyion sensors. Anal Chem 1994; 66:2250-9. [PMID: 8080104 DOI: 10.1021/ac00086a009] [Citation(s) in RCA: 137] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The potentiometric response mechanism of a previously reported polymer membrane-based electrode sensitive to the polyanion heparin is established. Based on transport and extraction studies, the heparin response is attributed to a nonequilibrium change in the phase boundary potential at the sample/membrane interface. While true equilibrium polyion response, obtained for low heparin concentrations only after very long equilibration times (> 20 h), yields the expected Nernstian response slope of < 1 mV/decade, the observed large and reproducible EMF response to clinically relevant heparin concentrations (approximately 10(-7) M) during typical measurement periods (2-5 min) is ascribed to a steady-state kinetic process defined by the flux of the polyion both to the surface and into the bulk of the polymer membrane. A model describing this nonequilibrium response is presented. With this model, the uniqueness of the polymer membrane composition (e.g., very low plasticizer content, strictly controlled cationic site concentration, etc.) required to achieve analytically useful heparin response becomes clear. Practical working conditions and limitations of the sensor are discussed. To support the generality of the steady-state model proposed, corresponding EMF response data for a newly developed membrane electrode sensitive to a polycationic protein (protamine) are also presented. It is shown that the protamine-responsive membrane electrode appears to operate via the exact same kinetic mechanism as the heparin sensing system.
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Lee YN, Zhou X, Kleinman LI, Nunnermacker LJ, Springston SR, Daum PH, Newman L, Keigley WG, Holdren MW, Spicer CW, Young V, Fu B, Parrish DD, Holloway J, Williams J, Roberts JM, Ryerson TB, Fehsenfeld FC. Atmospheric chemistry and distribution of formaldehyde and several multioxygenated carbonyl compounds during the 1995 Nashville/Middle Tennessee Ozone Study. ACTA ACUST UNITED AC 1998. [DOI: 10.1029/98jd01251] [Citation(s) in RCA: 131] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Yang F, Alkalaeva EZ, Perelman PL, Pardini AT, Harrison WR, O'Brien PCM, Fu B, Graphodatsky AS, Ferguson-Smith MA, Robinson TJ. Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype. Proc Natl Acad Sci U S A 2003; 100:1062-6. [PMID: 12552116 PMCID: PMC298726 DOI: 10.1073/pnas.0335540100] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2002] [Indexed: 11/18/2022] Open
Abstract
The Afrotheria, a supraordinal grouping of mammals whose radiation is rooted in Africa, is strongly supported by DNA sequence data but not by their disparate anatomical features. We have used flow-sorted human, aardvark, and African elephant chromosome painting probes and applied reciprocal painting schemes to representatives of two of the Afrotherian orders, the Tubulidentata (aardvark) and Proboscidea (elephants), in an attempt to shed additional light on the evolutionary affinities of this enigmatic group of mammals. Although we have not yet found any unique cytogenetic signatures that support the monophyly of the Afrotheria, embedded within the aardvark genome we find the strongest evidence yet of a mammalian ancestral karyotype comprising 2n = 44. This karyotype includes nine chromosomes that show complete conserved synteny to those of man, six that show conservation as single chromosome arms or blocks in the human karyotype but that occur on two different chromosomes in the ancestor, and seven neighbor-joining combinations (i.e., the synteny is maintained in the majority of species of the orders studied so far, but which corresponds to two chromosomes in humans). The comparative chromosome maps presented between human and these Afrotherian species provide further insight into mammalian genome organization and comparative genomic data for the Afrotheria, one of the four major evolutionary clades postulated for the Eutheria.
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Meyerhoff ME, Fu B, Bakker E, Yun JH, Yang VC. Polyion-sensitive membrane electrodes for biomedical analysis. Anal Chem 1996; 68:168A-175A. [PMID: 8779438 DOI: 10.1021/ac9618536] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Li HL, Yuan HX, Fu B, Xing XP, Sun BJ, Tang WH. First Report of Fusarium pseudograminearum Causing Crown Rot of Wheat in Henan, China. PLANT DISEASE 2012; 96:1065. [PMID: 30727237 DOI: 10.1094/pdis-01-12-0007-pdn] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Fusarium pseudograminearum (O'Donnell & Aoki), a residue-borne pathogen, is responsible for crown rot of wheat (Triticum aestivum L.). Since its first detection in Queensland, Australia in 1951, it has been reported in many other countries, but not China (2). In May 2011, a crown rot disease was observed in wheat cv. Aikang 58 in a wheat-maize rotation, irrigable and loam field in Henan Province, China. Diseased wheat plants showed honey brown discoloration in the stem bases and whitehead in some plants, which are symptoms of crown rot with about 70% incidence in a surveyed field (2). The pathogen was isolated from diseased stem base on potato dextrose agar (PDA) after being surface-disinfested with 5% NaClO solution for 2 min. Pure cultures were established on carnation leaf agar (CLA) through a single spore technique and identified by morphological and molecular methods according to protocols described previously (1,3,4). Macroconidia of F. pseudograminearum were formed in abundant sporodochia on CLA cultures grown under the BLB light. Macroconidia were usually five septate (about three to seven) and 27 to 91 × 2.7 to 5.5 μm. Colonies grown on PDA from a single conidium in the dark at 25°C had average radial growth rates of ~4.7 to 9.9 mm per day. Colony pigment on PDA grown under light varied from rose to burgundy, while mycelium ranged from rose to yellow white. Two isolates (WZ-8A and WZ-2B) were selected for molecular identification. The translation elongation factor 1-α gene and rDNA ITS gene were amplified by PCR using the specific primers described previously (4). PCR products were sequenced (GenBank Accession Nos. JN862232 to JN862235). Phylogenic analysis of the sequence indicated that the isolates were identified as F. pseudograminearum. The identification was further confirmed by the F. pseudograminearum species-specific PCR primers (Fp1-1: CGGGGTAGTTTCACATTTCCG and Fp1-2: GAGAATGTGATGACGACAATA) (1). The expected PCR products of 520 bp were produced only in F. pseudograminearum. Isolates WZ-2B and WZ-8A were deposited in the Agriculture Culture Collection of China as ACCC38067 and ACCC 38068, respectively. Pathogenicity tests were conducted by inoculating winter wheat cultivar Wenmai 19 with isolates WZ-8A and WZ-2B through soil inoculation. Inoculum was prepared by growing cultures on sterilized wheat bran and chopped wheat-straw (4:1, v/v) after incubation at 25°C for 2 weeks. This inoculum was added to sterilized soil at 1% by volume and no inoculum was added in control treatment. Five seeds were planted in a 15 cm wide pot in a 20 to 25°C greenhouse, with six replications. Seedling death and crown browning occurred in the inoculated wheat plants after 4 weeks with over 90% incidence, while no symptoms developed in the control plants. The fungus was reisolated from inoculated plants, fulfilling Koch's postulates. To our knowledge, this is the first report of F. pseudograminearum causing crown rot of wheat in China. Considering Henan is the largest wheat production province in China with over 5 million hectares planting area, and the soil and climate conditions are suitable for this disease, it will be a important pathogen of wheat in Henan in the future. References: (1) T. Aoki et al. Mycologia 91:597, 1999. (2) L. W. Burgess. Page 271 in: Crown Rot of Wheat: Fusarium. B. A. Summerell et al., eds. APS Press, St. Paul, MN, 2001. (3) R. G. Francis et al. Trans. Brit. Mycol. Soc. 68:421, 1977. (4) J. B. Scott et al. Mycol. Res. 110:1413, 2006.
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Luo Q, Zhang L, Li X, Fu B, Deng Z, Qing C, Su R, Xu J, Guo Y, Huang Z, Li J. Identification of circular RNAs hsa_circ_0044235 in peripheral blood as novel biomarkers for rheumatoid arthritis. Clin Exp Immunol 2018; 194:118-124. [PMID: 30216431 PMCID: PMC6156811 DOI: 10.1111/cei.13181] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2018] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNAs) are a new class of RNAs that can be used as biomarkers in clinical blood samples. However, little is known about circRNAs' diagnostic values for rheumatoid arthritis (RA). In this study, the hsa_circ_0054189, hsa_circ_0008675, hsa_circ_0082689, hsa_circ_0082688, hsa_circ_0010932, hsa_circ_0002473 and hsa_circ_0044235 in peripheral blood were determined by quantitative reverse transcription–polymerase chain reaction (qRT–PCR). For hsa_circ_0044235, only one abnormal expression circRNAs in peripheral blood was selected as a targeted circRNA to explore the diagnostic value for RA. Our work demonstrated that the hsa_circ_0044235 in peripheral blood was decreased significantly in RA patients. The hsa_circ_0044235 in peripheral blood from RA patients did not correlate with C‐reactive protein (CRP), erythrocyte sedimentation rate (ESR), rheumatoid factor (RF), anti‐citrullinated protein antibodies (ACPA) or disease activity score 28 (DAS28). Receiver operating characteristic (ROC) curve analysis suggested that the hsa_circ_0044235 in peripheral blood has significant value in the diagnosis of RA. The risk score based on hsa_circ_0044235 in peripheral blood also distinguished significantly the patients with RA from systemic lupus erythematosus (SLE). This study suggests that the hsa_circ_0044235 in peripheral blood may be a potential biomarker of patients with RA.
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O'Shaughnessy KM, Fu B, Ferraro F, Lewis I, Downing S, Morris NH. Factor V Leiden and thermolabile methylenetetrahydrofolate reductase gene variants in an East Anglian preeclampsia cohort. Hypertension 1999; 33:1338-41. [PMID: 10373212 DOI: 10.1161/01.hyp.33.6.1338] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Preeclampsia is a heritable condition that develops as a result of widespread vascular endothelial dysfunction. The thrombotic tendency in this condition has suggested a number of candidate genes, and there have been recent reports of positive association with the Leiden variant of factor V and the thermolabile variant of methylenetetrahydrofolate reductase. We attempted to reproduce these results in a large cohort of well-characterized women with preeclampsia, recruited prospectively within the East Anglian region of the United Kingdom. Women in the preeclampsia cohort (n=283) were genotyped for both the Leiden variant (G1691A) of factor V and the thermolabile variant (C677T) of methylenetetrahydrofolate reductase. Genotype and allele frequencies were compared with those of 2 control groups, one consisting of women recruited prospectively (n=100) from the same maternity hospital as the subjects and another consisting of normotensive women (n=100) from East Anglia. No significant differences were detected. Specifically, the carrier rate for the Leiden variant was 5.3% in the preeclampsia group and 5. 5% in the combined control group. T677 homozygotes for methylenetetrahydrofolate reductase were 11% and 11.5% in the 2 groups, respectively. We conclude that there is no evidence of association of preeclampsia with either of these 2 polymorphisms in our study population.
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Li K, Guo Q, Zhang X, Dong X, Liu W, Zhang A, Li Y, Yan J, Jia G, Zheng Z, Tang W, Pan L, An M, Zhang B, Liu S, Fu B. Oral cancer-associated tertiary lymphoid structures: gene expression profile and prognostic value. Clin Exp Immunol 2019; 199:172-181. [PMID: 31652350 DOI: 10.1111/cei.13389] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2019] [Indexed: 02/06/2023] Open
Abstract
Tertiary lymphoid structure (TLS) provides a local and critical microenvironment for both cellular and humoral immunity and supports effective antigen presentation and lymphocyte activation. However, the gene expression profile and prognostic significance of TLS in oral cancer remain largely unrevealed. In this study, we found the presence of both intratumoral and peritumoral TLSs in a series of 65 patients with oral cancer treated by surgical resection, with positive detection rates of 33.8 and 75.4%, respectively. The presence of intratumoral TLSs, but not peritumoral TLSs, was significantly associated with decreased P53 and Ki67 scores (P = 0·027 and 0·047, respectively). The survival analyses revealed that oral cancer patients with higher grades of TLSs was associated with improved disease-free survival (DFS) and overall survival (OS) (P = 0·037 and 0·031, respectively). Gene expression profiling analysis of the cytokines and chemokines responsible for lymph-node neogenesis identified a three-up-regulated-gene set, i.e. IL7, LTB and CXCL13, which was shown to be correlated with human oral cancer-associated TLSs. This study provides a framework for better understanding of oral cancer-associated TLSs and for delineating future innovative prognostic biomarkers and immune therapeutic strategies for oral cancer.
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Yang F, Fu B, O'Brien PCM, Robinson TJ, Ryder OA, Ferguson-Smith MA. Karyotypic relationships of horses and zebras: results of cross-species chromosome painting. Cytogenet Genome Res 2004; 102:235-43. [PMID: 14970709 DOI: 10.1159/000075755] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2003] [Accepted: 08/05/2003] [Indexed: 11/19/2022] Open
Abstract
Complete sets of chromosome-specific painting probes, derived from flow-sorted chromosomes of human (HSA), Equus caballus (ECA) and Equus burchelli (EBU) were used to delineate conserved chromosomal segments between human and Equus burchelli, and among four equid species, E. przewalskii (EPR), E. caballus, E. burchelli and E. zebra hartmannae (EZH) by cross-species chromosome painting. Genome-wide comparative maps between these species have been established. Twenty-two human autosomal probes revealed 48 conserved segments in E. burchelli. The adjacent segment combinations HSA3/21, 7/16p, 16q/19q, 14/15, 12/22 and 4/8, presumed ancestral syntenies for all eutherian mammals, were also found conserved in E. burchelli. The comparative maps of equids allow for the unequivocal characterization of chromosomal rearrangements that differentiate the karyotypes of these equid species. The karyotypes of E. przewalskii and E. caballus differ by one Robertsonian translocation (ECA5 = EPR23 + EPR24); numerous Robertsonian translocations and tandem fusions and several inversions account for the karyotypic differences between the horses and zebras. Our results shed new light on the karyotypic evolution of Equidae.
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Robinson TJ, Fu B, Ferguson-Smith MA, Yang F. Cross-species chromosome painting in the golden mole and elephant-shrew: support for the mammalian clades Afrotheria and Afroinsectiphillia but not Afroinsectivora. Proc Biol Sci 2004; 271:1477-84. [PMID: 15306319 PMCID: PMC1691750 DOI: 10.1098/rspb.2004.2754] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cross-species painting (fluorescence in situ hybridization) with 23 (human Homo sapiens (HSA)) chromosome-specific painting probes (HSA 1-22 and the X) was used to delimit regions of homology on the chromosomes of the golden mole (Chrysochloris asiaticus) and elephant-shrew (Elephantulus rupestris). A cladistic interpretation of our data provides evidence of two unique associations, HSA 1/19p and 5/21/3, that support Afrotheria. The recognition of HSA 5/3/21 expands on the 3/21 synteny originally designated as an ancestral state for all eutherians. We have identified one adjacent segment combination (HSA2/8p/4) that is supportive of Afroinsectiphillia (aardvark, golden mole, elephant-shrew). Two segmental combinations (HSA 10q/17 and HSA 3/20) unite the aardvark and elephant-shrews as sister taxa. The finding that segmental syntenies in evolutionarily distant taxa can improve phylogenetic resolution suggests that they may be useful for testing sequence-based phylogenies of the early eutherian mammals. They may even suggest clades that sequence trees are not recovering with any consistency and thus encourage the search for additional rare genomic changes among afrotheres.
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Graphodatsky AS, Yang F, Perelman PL, O'Brien PCM, Serdukova NA, Milne BS, Biltueva LS, Fu B, Vorobieva NV, Kawada SI, Robinson TJ, Ferguson-Smith MA. Comparative molecular cytogenetic studies in the order Carnivora: mapping chromosomal rearrangements onto the phylogenetic tree. Cytogenet Genome Res 2003; 96:137-45. [PMID: 12438790 DOI: 10.1159/000063032] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We have made a set of chromosome-specific painting probes for the American mink by degenerate oligonucleotide primed-PCR (DOP-PCR) amplification of flow-sorted chromosomes. The painting probes were used to delimit homologous chromosomal segments among human, red fox, dog, cat and eight species of the family Mustelidae, including the European mink, steppe and forest polecats, least weasel, mountain weasel, Japanese sable, striped polecat, and badger. Based on the results of chromosome painting and G-banding, comparative maps between these species have been established. The integrated map demonstrates a high level of karyotype conservation among mustelid species. Comparative analysis of the conserved chromosomal segments among mustelids and outgroup species revealed 18 putative ancestral autosomal segments that probably represent the ancestral chromosomes, or chromosome arms, in the karyotype of the most recent ancestor of the family Mustelidae. The proposed 2n = 38 ancestral Mustelidae karyotype appears to have been retained in some modern mustelids, e.g., Martes, Lutra, Ictonyx, and Vormela. The derivation of the mustelid karyotypes from the putative ancestral state resulted from centric fusions, fissions, the addition of heterochromatic arms, and occasional pericentric inversions. Our results confirm many of the evolutionary conclusions suggested by other data and strengthen the topology of the carnivore phylogenetic tree through the inclusion of genome-wide chromosome rearrangements.
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Tian F, Zhou L, Zhang Z, Niu L, Zhang L, Chen C, Zhou J, Yang H, Wang X, Fu B, Huang C, Pashley DH, Tay FR. Paucity of Nanolayering in Resin-Dentin Interfaces of MDP-based Adhesives. J Dent Res 2015; 95:380-7. [PMID: 26701351 DOI: 10.1177/0022034515623741] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Self-assembled nanolayering structures have been reported in resin-dentin interfaces created by adhesives that contain 10-methacryloyloxydecyl dihydrogen phosphate (10-MDP). These structures have been hypothesized to contribute to bond durability. The objective of the present study was to determine the extent of nanolayering in resin-dentin interfaces after application of commercialized 10-MDP-containing self-etch and universal adhesives to human dentin. Seven commercialized adhesives were examined: Adhese Universal (Ivoclar-Vivadent), All-Bond Universal (Bisco, Inc.), Clearfil SE Bond 2, Clearfil S3 Bond Plus, Clearfil Universal Bond (all from Kuraray Noritake Dental Inc.), G-Premio Bond (GC Corp.), and Scotchbond Universal (3M ESPE). Each adhesive was applied in the self-etch mode on midcoronal dentin according to the respective manufacturer's instructions. Bonded specimens (n = 6) were covered with flowable resin composite, processed for transmission electron microscopy, and examined at 30 random sites without staining. Thin-film glancing angle X-ray diffraction (XRD) was used to detect the characteristic peaks exhibited by nanolayering (n = 4). The control consisted of 15%wt, 10%wt, and 5%wt 10-MDP (DM Healthcare Products, Inc.) dissolved in a mixed solvent (ethanol and water weight ratio 9:8, with photoinitiators). Experimental primers were applied to dentin for 20 s, covered with hydrophobic resin layer, and examined in the same manner. Profuse nanolayering with highly ordered periodicity (~3.7 nm wide) was observed adjacent to partially dissolved apatite crystallites in dentin treated with the 15% 10-MDP primer. Three peaks in the 2θ range of 2.40° (3.68 nm), 4.78° (1.85 nm), and 7.18° (1.23 nm) were identified from thin-film XRD. Reduction in the extent of nanolayering was observed in the 10% and 5% 10-MDP experimental primer-dentin interface along with lower intensity XRD peaks. Nanolayering and characteristic XRD peaks were rarely observed in specimens prepared from the commercialized adhesives. The sparsity of nanolayering in resin-dentin interfaces created by commercialized adhesives challenges its clinical effectiveness as a mechanism for improving bond longevity in dentin bonding.
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Fu B, Curry FR, Adamson RH, Weinbaum S. A model for interpreting the tracer labeling of interendothelial clefts. Ann Biomed Eng 1997; 25:375-97. [PMID: 9084841 DOI: 10.1007/bf02648050] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We extended the model describing the low molecular weight electron dense tracer wake in the interendothelial cleft and surrounding tissue to describe the time-dependent transport of intermediate size solutes of 1.0-3.5 nm radius by convection and diffusion in an interendothelial cleft containing a fiber matrix. This model provides a quantitative basis on which to reinterpret electron microscopic studies of the distribution of tracers such as horseradish peroxidase (HRP; molecular weight = 40,000; Stokes radius = 3.0 nm) along the interendothelial cell cleft from the lumen to the tissue. For example, we show that, in contrast to our results with low molecular weight tracers, the wake of large molecular weight tracers on the abluminal side of the junctional strand is not likely to be detected, because the concentration of the tracer is predicted to be very low in most experiments. Thus the lack of a tracer such as HRP on the abluminal side of the junctional strand and in the tissue is not as strong evidence against the presence of a cleft pathway as suggested previously. The model does provide the basis for the design of experiments to locate both the principal molecular sieve and breaks in the junctional strand from the standing gradient on the luminal side of the junctional strand. An important experimental variable is the pressure in the vessel lumen which can be varied between 0 and 30 cm H2O to change the contributions of diffusive and convective transport to transcapillary exchange through he interendothelial cleft. This approach will also allow the testing of models for transcapillary pathways for large molecules by measuring the distribution of fluorescent traces across the microvessel wall and in the tissue surrounding the microvessel using confocal microscopy.
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Chi J, Fu B, Nie W, Wang J, Graphodatsky AS, Yang F. New insights into the karyotypic relationships of Chinese muntjac (Muntiacus reevesi), forest musk deer (Moschus berezovskii) and gayal (Bos frontalis). Cytogenet Genome Res 2005; 108:310-6. [PMID: 15627750 DOI: 10.1159/000081520] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2004] [Accepted: 07/18/2004] [Indexed: 11/19/2022] Open
Abstract
To investigate the karyotypic relationships between Chinese muntjac (Muntiacus reevesi), forest musk deer (Moschus berezovskii) and gayal (Bos frontalis), a complete set of Chinese muntjac chromosome-specific painting probes has been assigned to G-banded chromosomes of these three species. Sixteen autosomal probes (i.e. 6-10, 12-22) of the Chinese muntjac each delineated one pair of conserved segments in the forest musk deer and gayal, respectively. The remaining six autosomal probes (1-5, and 11) each delineated two to five pairs of conserved segments. In total, the 22 autosomal painting probes of Chinese muntjac delineated 33 and 34 conserved chromosomal segments in the genomes of forest musk deer and gayal, respectively. The combined analysis of comparative chromosome painting and G-band comparison reveals that most interspecific homologous segments show a high degree of conservation in G-banding patterns. Eleven chromosome fissions and five chromosome fusions differentiate the karyotypes of Chinese muntjac and forest musk deer; twelve chromosome fissions and six fusions are required to convert the Chinese muntjac karyotype to that of gayal; one chromosome fission and one fusion separate the forest musk deer and gayal. The musk deer has retained a highly conserved karyotype that closely resembles the proposed ancestral pecoran karyotype but shares none of the rearrangements characteristic for the Cervidae and Bovidae. Our results substantiate that chromosomes 1-5 and 11 of Chinese muntjac originated through exclusive centromere-to-telomere fusions of ancestral acrocentric chromosomes.
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Research Support, Non-U.S. Gov't |
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Li YL, Zheng YF, Fu B, Zhou JB, Wei CS. Oxygen isotope composition of quartz-vein in ultrahigh-pressure eclogite from Dabieshan and implications for transport of high-pressure metamorphic fluid. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1464-1895(01)00120-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Ao L, Gu X, Feng Q, Wang J, O'Brien PCM, Fu B, Mao X, Su W, Wang Y, Volleth M, Yang F, Nie W. Karyotype relationships of six bat species (Chiroptera, Vespertilionidae) from China revealed by chromosome painting and G-banding comparison. Cytogenet Genome Res 2006; 115:145-53. [PMID: 17065796 DOI: 10.1159/000095235] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Accepted: 04/25/2006] [Indexed: 11/19/2022] Open
Abstract
The Vespertilionidae is the largest family in the order Chiroptera and has a worldwide distribution in the temperate and tropical regions. In order to further clarify the karyotype relationships at the lower taxonomic level in Vespertilionidae, genome-wide comparative maps have been constructed between Myotis myotis (MMY, 2n = 44) and six vesper bats from China: Myotis altarium (MAL, 2n = 44), Hypsugo pulveratus (HPU, 2n = 44), Nyctalus velutinus (NVE, 2n = 36), Tylonycteris robustula (TRO, 2n = 32), Tylonycteris sp. (TSP, 2n = 30)and Miniopterus fuliginosus (MFU, 2n = 46) by cross-species chromosome painting with a set of painting probes derived from flow-sorted chromosomes of Myotis myotis. Each Myotis myotis autosomal probe detected a single homologous chromosomal segment in the genomes of these six vesper bats except for MMY chromosome 3/4 paint which hybridized onto two chromosomes in the genome of M. fuliginosus. Our results show that Robertsonian translocation is the main mode of karyotype evolution in Vespertilionidae and that the addition of heterochromatic material also plays an important role in the karyotypic evolution of the genera Tylonycteris and Nyctalus. Two conserved syntenic associations (MMY9 + 23 and 18 + 19) could be the synapomorphic features for the genus Tylonycteris. The integration of our maps with the published maps has enabled us to deduce chromosomal homologies between human and these six vesper bats and provided new insight into the karyotype evolution of the family Vespertilionidae.
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Tang GX, Yan PP, Yan CL, Fu B, Zhu SJ, Zhou LQ, Huang X, Wang Y, Lei J. Determinants of suicidal ideation in gynecological cancer patients. Psychooncology 2015; 25:97-103. [PMID: 26103593 DOI: 10.1002/pon.3880] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 05/14/2015] [Accepted: 05/19/2015] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Gynecological cancer survivors are at increased risk of psychological problems including suicide risk. Suicidal ideation, which was thought to be precursor to suicide attempts, has not been well studied. This study aimed to investigate the prevalence, and determinants of suicidal ideation for women with gynecological cancer, and then to assess the effect of coping style and social support on suicidal ideation. METHODS Patients with cervical, ovarian and endometrial cancers seen at Hunan Provincial Tumor Hospital from September 2012 to June 2013 were consecutively recruited and were asked to complete the Zung Self-Rating Depression Scale, Suicidal Ideation of Self-rating Scale, Medical Coping Modes Questionnaire and Social Support Rating Scale. Path analysis was used to examine the relationship among coping style, social support, depression symptoms and suicidal ideation. RESULTS A total of 579 (579/623, 93.0%) gynecological cancer patients were enrolled in this study and completed all investigations between September 2012 and June 2013. Among them, 105 (18.1%) patients reported suicidal ideation, with the highest rate in patients with ovarian cancer (30.16%). Suicidal ideation was associated with depression symptoms, care providers, chemotherapy history and acceptance-resignation. Path analysis showed that the acceptance-resignation affected suicidal ideation directly as well as mediated by social support and depression symptoms, while confrontation and avoidance affected suicidal ideation entirely through social support and depression symptoms. CONCLUSIONS Suicidal ideation is high among patients with gynecological cancer, especially among ovarian cancer patients. Coping strategies such as confrontation and avoidance, and social support may be helpful for preventing suicidal ideation among them.
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Research Support, Non-U.S. Gov't |
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Li W, Ye Y, Fu B, Wang J, Yu L, Ichiki T, Inagami T, Ichikawa I, Chen X. Genetic deletion of AT2 receptor antagonizes angiotensin II-induced apoptosis in fibroblasts of the mouse embryo. Biochem Biophys Res Commun 1998; 250:72-6. [PMID: 9735334 DOI: 10.1006/bbrc.1998.9189] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To examine whether angiotensin II (Ang II) can trigger apoptosis via Ang II type 2 (AT2) receptor, two genotypes of skin fibroblasts cultured from the AT2 receptor gene targeting homozygous (AT2-/-) and wild-type (AT2+/+) mouse embryos, respectively, were studied when exposed to Ang II. In the AT2+/+ fibroblasts, mRNA expression of the AT2 receptor was modulated by Ang II in a dose-dependent manner and apoptosis appeared with the convincing features of internucleosomal DNA fragmentation and DNA content decrease after stimulation with Ang II, whereas Ang II had no significant impact on the AT2-/- fibroblasts due to the AT2 receptor gene deletion. This is the first report using a gene targeting study to demonstrate that Ang II induces apoptosis through the AT2 receptor in the fibroblasts of the mouse embryo.
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Yu X, Liang B, Jin X, Fu B, Hannig M. Comparative In Vivo Study on the Desensitizing Efficacy of Dentin Desensitizers and One-bottle Self-etching Adhesives. Oper Dent 2010; 35:279-86. [DOI: 10.2341/09-346-c] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Clinical Relevance
Dentin desensitizers and one-bottle self-etching adhesives can significantly reduce dentin hypersensitivity. Clinical desensitizing effectiveness depends on the individual dentin desensitizers/adhesives used.
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Fu B, Wang YK, Xu P, Yan K, Li M. Value of ecosystem hydropower service and its impact on the payment for ecosystem services. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 472:338-46. [PMID: 24291631 DOI: 10.1016/j.scitotenv.2013.11.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 11/01/2013] [Accepted: 11/03/2013] [Indexed: 05/04/2023]
Abstract
Hydropower is an important service provided by ecosystems. We surveyed all the hydropower plants in the Zagunao River Basin, Southwest China. Then, we assessed the hydropower service by using the InVEST (The Integrated Value and Tradeoff of Ecosystem Service Tools) model. Finally, we discussed the impact on ecological compensation. The results showed that: 1) hydropower service value of ecosystems in the Zagunao River Basin is 216.29 Euro/hm(2) on the average, of which the high-value area with more than 475.65 Euro/hm(2) is about 750.37 km(2), accounting for 16.12% of the whole watershed, but it provides 53.47% of the whole watershed service value; 2) ecosystem is an ecological reservoir with a great regulation capacity. Dams cannot completely replace the reservoir water conservation function of ecosystems, and has high economic and environmental costs that must be paid as well. Compensation for water conservation services should become an important basis for ecological compensation of hydropower development. 3) In the current PES cases, the standard of compensation is generally low. Cascade development makes the value of upstream ecosystem services become more prominent, reflecting the differential rent value, and the value of ecosystem services should be based on the distribution of differentiated ecological compensation.
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Li H, Fu B, Wang MA, Li N, Liu WJ, Xie ZQ, Ma YQ, Qin Z. Total Synthesis and Biological Activity of (±)-Rocaglamide and Its 2,3-Di-epi Analogue. European J Org Chem 2008. [DOI: 10.1002/ejoc.200700905] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wang GX, Zhan YA, Hu HL, Wang Y, Fu B. Mesenchymal stem cells modified to express interferon-β inhibit the growth of prostate cancer in a mouse model. J Int Med Res 2012; 40:317-27. [PMID: 22429371 DOI: 10.1177/147323001204000132] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE This study investigated use of mesenchymal stem cells (MSCs) genetically engineered to produce interferon-β (IFN-β) as a gene delivery system to treat prostate cancer in an animal model. METHODS To measure the effects on tumour cell growth in vitro, IFN-β-producing MSCs (IFN-β-MSCs) were co-cultured with the prostate cancer cell line PC-3. The in vivo migration of intravenously injected fluorescently-labelled MSCs to healthy tissues and PC-3 xenograft tumours grown in immuno-deficient mice was determined by fluorescence microscopy. The antitumour effects of intravenously injected IFN-β-MSCs on PC-3 xenograft growth and animal survival were also investigated. RESULTS IFN-β-MSCs inhibited the growth of PC-3 cells in vitro. Fluorescently-labelled MSCs migrated to the margins and centre of tumour masses but not into healthy tissues. Intravenously injected IFN-β-MSCs significantly reduced PC-3 xenograft tumour weight and increased animal survival compared with controls. CONCLUSIONS Intravenously injected IFN-β-MSCs inhibited PC-3 xenograft growth. This could be an effective gene delivery system for treatment of solid human tumours.
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Research Support, Non-U.S. Gov't |
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Pardini A, O'Brien P, Fu B, Bonde R, Elder F, Ferguson-Smith M, Yang F, Robinson T. Chromosome painting among Proboscidea, Hyracoidea and Sirenia: support for Paenungulata (Afrotheria, Mammalia) but not Tethytheria. Proc Biol Sci 2007; 274:1333-40. [PMID: 17374594 PMCID: PMC1914331 DOI: 10.1098/rspb.2007.0088] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite marked improvements in the interpretation of systematic relationships within Eutheria, particular nodes, including Paenungulata (Hyracoidea, Sirenia and Proboscidea), remain ambiguous. The combination of a rapid radiation, a deep divergence and an extensive morphological diversification has resulted in a limited phylogenetic signal confounding resolution within this clade both at the morphological and nucleotide levels. Cross-species chromosome painting was used to delineate regions of homology between Loxodonta africana (2n=56), Procavia capensis (2n=54), Trichechus manatus latirostris (2n=48) and an outgroup taxon, the aardvark (Orycteropus afer, 2n=20). Changes specific to each lineage were identified and although the presence of a minimum of 11 synapomorphies confirmed the monophyly of Paenungulata, no change characterizing intrapaenungulate relationships was evident. The reconstruction of an ancestral paenungulate karyotype and the estimation of rates of chromosomal evolution indicate a reduced rate of genomic repatterning following the paenungulate radiation. In comparison to data available for other mammalian taxa, the paenungulate rate of chromosomal evolution is slow to moderate. As a consequence, the absence of a chromosomal character uniting two paenungulates (at the level of resolution characterized in this study) may be due to a reduced rate of chromosomal change relative to the length of time separating successive divergence events.
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Zhong N, Ju W, Xu W, Ye L, Shen Y, Wu G, Chen SH, Jin R, Hu XF, Yang A, Liu X, Poon P, Pang C, Zheng Y, Song L, Zhao P, Fu B, Gu H, Brown WT. Frequency of the fragile X syndrome in Chinese mentally retarded populations is similar to that in Caucasians. AMERICAN JOURNAL OF MEDICAL GENETICS 1999; 84:191-4. [PMID: 10331588 DOI: 10.1002/(sici)1096-8628(19990528)84:3<191::aid-ajmg3>3.0.co;2-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Fragile X syndrome is recognized as the most common inherited cause of mental retardation in western countries. The prevalence of the fragile X syndrome in Asian populations is uncertain. We report a multi-institutional collaborative study of molecular screening for the fragile X syndrome from 1,127 Chinese mentally retarded (MR) individuals. We found that 2.8% of the Chinese MR population screened by DNA analysis had the fragile X full mutation. Our screening indicated that the fragile X syndrome prevalence was very close to that of Caucasian subjects. In addition, we found that 62.5% of fragile X chromosomes had a single haplotype for DXS548-FRAXAC1 (21-18 repeats) which was present in only 9.7% of controls. This unique distribution of microsatellite markers flanking the FMR1 CGG repeats suggests that the fragile X syndrome in Chinese populations, as in the Caucasian, may also be derived from founder chromosomes.
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