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Singh S, Jighly A, Sehgal D, Burgueño J, Joukhadar R, Singh SK, Sharma A, Vikram P, Sansaloni CP, Govindan V, Bhavani S, Randhawa M, Solis-Moya E, Singh S, Pardo N, Arif MAR, Laghari KA, Basandrai D, Shokat S, Chaudhary HK, Saeed NA, Basandrai AK, Ledesma-Ramírez L, Sohu VS, Imtiaz M, Sial MA, Wenzl P, Singh GP, Bains NS. Direct introgression of untapped diversity into elite wheat lines. Nat Food 2021; 2:819-827. [PMID: 37117978 DOI: 10.1038/s43016-021-00380-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 08/27/2021] [Indexed: 04/30/2023]
Abstract
The effective utilization of natural variation has become essential in addressing the challenges that climate change and population growth pose to global food security. Currently adopted protracted approaches to introgress exotic alleles into elite cultivars need substantial transformation. Here, through a strategic three-way crossing scheme among diverse exotics and the best historical elites (exotic/elite1//elite2), 2,867 pre-breeding lines were developed, genotyped and screened for multiple agronomic traits in four mega-environments. A meta-genome-wide association study, selective sweeps and haplotype-block-based analyses unveiled selection footprints in the genomes of pre-breeding lines as well as exotic-specific associations with agronomic traits. A simulation with a neutrality assumption demonstrated that many pre-breeding lines had significant exotic contributions despite substantial selection bias towards elite genomes. National breeding programmes worldwide have adopted 95 lines for germplasm enhancement, and 7 additional lines are being advanced in varietal release trials. This study presents a great leap forwards in the mobilization of GenBank variation to the breeding pipelines.
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Affiliation(s)
- Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
- Geneshifters, Pullman, WA, USA.
| | - A Jighly
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, Australia
| | - D Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - J Burgueño
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - R Joukhadar
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, Australia
| | - S K Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - A Sharma
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | - P Vikram
- International Center for Biosaline Agriculture, Dubai, United Arab Emirates
| | - C P Sansaloni
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - V Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - S Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - M Randhawa
- CIMMYT-World Agroforestry Centre (ICRAF), Nairobi, Kenya
| | - E Solis-Moya
- Carretera Celaya-San Miguel de Allende, Celaya, México
| | - S Singh
- ICAR-National Institute of Plant Biotechnology, New Delhi, India
| | - N Pardo
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - M A R Arif
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - K A Laghari
- Nuclear Institute of Agriculture, Tando Jam, Pakistan
| | - D Basandrai
- CSK Himachal Pradesh Agricultural University Palampur, Palampur, India
| | - S Shokat
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
- Department of Plant and Environmental Sciences, Crop Science, University of Copenhagen, Taastrup, Denmark
| | - H K Chaudhary
- CSK Himachal Pradesh Agricultural University Palampur, Palampur, India
| | - N A Saeed
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - A K Basandrai
- CSK Himachal Pradesh Agricultural University Palampur, Palampur, India
| | | | - V S Sohu
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | | | - M A Sial
- Nuclear Institute of Agriculture, Tando Jam, Pakistan
| | | | - G P Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - N S Bains
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
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Singh S, Sehgal D, Kumar S, Arif MAR, Vikram P, Sansaloni CP, Fuentes-Dávila G, Ortiz C. GWAS revealed a novel resistance locus on chromosome 4D for the quarantine disease Karnal bunt in diverse wheat pre-breeding germplasm. Sci Rep 2020; 10:5999. [PMID: 32265455 PMCID: PMC7138846 DOI: 10.1038/s41598-020-62711-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 03/11/2020] [Indexed: 11/09/2022] Open
Abstract
This study was initiated to identify genomic regions conferring resistance to Karnal Bunt (KB) disease in wheat through a genome-wide association study (GWAS) on a set of 179 pre-breeding lines (PBLs). A GWAS of 6,382 high-quality DArTseq SNPs revealed 15 significant SNPs (P-value <10-3) on chromosomes 2D, 3B, 4D and 7B that were associated with KB resistance in individual years. In particular, two SNPs (chromosome 4D) had the maximum R2 values: SNP 1114200 | F | 0-63:T > C at 1.571 cM and R2 of 12.49% and SNP 1103052 | F | 0-61:C > A at 1.574 cM and R2 of 9.02%. These two SNPs displayed strong linkage disequilibrium (LD). An in silico analysis of SNPs on chromosome 4D identified two candidate gene hits, TraesCS4D02G352200 (TaNox8; an NADPH oxidase) and TraesCS4D02G350300 (a rhomboid-like protein belonging to family S54), with SNPs 1103052 | F | 0-61:C > A and 1101835 | F | 0-5:C > A, respectively, both of which function in biotic stress tolerance. The epistatic interaction analysis revealed significant interactions among 4D and 7B loci. A pedigree analysis of confirmed resistant PBLs revealed that Aegilops species is one of the parents and contributed the D genome in these resistant PBLs. These identified lines can be crossed with any elite cultivar across the globe to incorporate novel KB resistance identified on 4B.
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Affiliation(s)
- Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P. 56237, México. .,Geneshifters, 222 Mary Jena Lane, Pullman, WA, 99163, USA.
| | - D Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P. 56237, México
| | - S Kumar
- Centre of Excellence in Biotechnology, Anand Agricultural University (AAU), Anand, Gujarat, 388 110, India
| | - M A R Arif
- Nuclear Institute for Agriculture and Biology, Faislabad, 38000, Pakistan
| | - P Vikram
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P. 56237, México
| | - C P Sansaloni
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P. 56237, México
| | - G Fuentes-Dávila
- INIFAP-CIRNO, Campo Experimental Norman E. Borlaug, Apdo. Postal 155, Km 12 Norman E. Borlaug, Cd. Obregon, Sonora, CP 85000, Mexico
| | - C Ortiz
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P. 56237, México
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Abstract
The increasing availability of Single Nucleotide Polymorphisms (SNPs) discovered by Next Generation Sequencing will enable a range of new genetic analyses in crops, which was not possible before. Concomitantly, researchers will face the challenge of handling large data sets at the whole-genome level. By grouping thousands of SNPs into a few hundred haplotype blocks, complexity of the data can be reduced with fewer statistical tests and a lower probability of spurious associations. Owing to the strong genome structure present in breeding lines of most crops, the deployment of haplotypes could be a powerful complement to improve efficiency of marker-assisted and genomic selection. This review describes in brief the commonly used approaches to construct haplotype blocks and some examples in animals and crops are cited where haplotype-based dissection of traits were proven beneficial. Some important considerations and facts while working with haplotypes in crops are reviewed at the end.
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Affiliation(s)
- D. Sehgal
- International Center for Maize and Wheat Improvement (CIMMYT)
| | - S. Dreisigacker
- International Center for Maize and Wheat Improvement (CIMMYT)
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Korkaya H, Jameel S, Gupta D, Tyagi S, Kumar R, Zafrullah M, Mazumdar M, Lal SK, Xiaofang L, Sehgal D, Das SR, Sahal D. The ORF3 protein of hepatitis E virus binds to Src homology 3 domains and activates MAPK. J Biol Chem 2001; 276:42389-400. [PMID: 11518702 DOI: 10.1074/jbc.m101546200] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hepatitis E virus (HEV) is the causative agent of hepatitis E, an acute form of viral hepatitis. The biology and pathogenesis of HEV remain poorly understood. We have used in vitro binding assays to show that the HEV ORF3 protein (pORF3) binds to a number of cellular signal transduction pathway proteins. This includes the protein tyrosine kinases Src, Hck, and Fyn, the p85alpha regulatory subunit of phosphatidylinositol 3-kinase, phospholipase Cgamma, and the adaptor protein Grb2. A yeast two-hybrid assay was used to further confirm the pORF3-Grb2 interaction. The binding involves a proline-rich region in pORF3 and the src homology 3 (SH3) domains in the cellular proteins. Competition assays and computer-assisted modeling was used to evaluate the binding surfaces and interaction energies of the pORF3.SH3 complex. In pORF3-expressing cells, pp60(src) was found to associate with an 80-kDa protein, but no activation of the Src kinase was observed in these cells. However, there was increased activity and nuclear localization of ERK in the pORF3-expressing cells. These studies suggest that pORF3 is a viral regulatory protein involved in the modulation of cell signaling. The ORF3 protein of HEV appears to be the first example of a SH3 domain-binding protein encoded by a virus that causes an acute and primarily self-limited infection.
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Affiliation(s)
- H Korkaya
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
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Taylor ML, Dastych J, Sehgal D, Sundstrom M, Nilsson G, Akin C, Mage RG, Metcalfe DD. The Kit-activating mutation D816V enhances stem cell factor--dependent chemotaxis. Blood 2001; 98:1195-9. [PMID: 11493470 DOI: 10.1182/blood.v98.4.1195] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The D816V mutation of c-kit has been detected in patients with mastocytosis. This mutation leads to constitutive tyrosine kinase activation of Kit. Because stem cell factor (SCF), the ligand for Kit (CD117(+)), is a chemoattractant for CD117(+) cells and one feature of mastocytosis is an abnormal collection of mast cells in tissues derived from CD34(+)CD117(+) mast cell precursors, the hypothesis was considered that the D816V mutation would enhance chemotaxis of these precursor cells. Constructs encoding wild-type Kit or Kit bearing the D816V mutation were transfected into Jurkat cells, labeled with Calcein-AM, and migration to SCF assessed in the presence or absence of tyrosine kinase inhibitors. Chemotaxis to SCF was enhanced in D816V transfectants compared to wild-type Kit transfectants (P <.002). Migration of both transfectants was inhibited by tyrosine kinase inhibitors, although D816V transfectants were more sensitive. Chemotaxis was next performed on CD34(+)CD117(+) circulating mast cell precursors obtained from patients with mastocytosis. Analysis of prechemotaxis and migrated cells showed that whereas less than 10% in the prechemotaxis sample had the D816V mutation, 40% to 80% of migrated cells had this mutation. These results demonstrate that the D816V Kit mutation enhances chemotaxis of CD117(+) cells, offering one explanation for increased mast cells observed in tissues of patients with mastocytosis. (Blood. 2001;98:1195-1199)
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Affiliation(s)
- M L Taylor
- Laboratory of Allergic Diseases and Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1881, USA.
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Sehgal D, Schiaffella E, Anderson AO, Mage RG. Generation of heterogeneous rabbit anti-DNP antibodies by gene conversion and hypermutation of rearranged VL and VH genes during clonal expansion of B cells in splenic germinal centers. Eur J Immunol 2000; 30:3634-44. [PMID: 11169406 DOI: 10.1002/1521-4141(200012)30:12<3634::aid-immu3634>3.0.co;2-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The mechanisms described here account for development of the heterogeneous high-affinity anti-DNP antibodies that rabbits can produce. Rearranged immunoglobulin light and heavy chain genes from single DNP-specific splenic germinal center B cells were amplified by PCR. We found that in clonal lineages, rearranged V[kappa] and V[H] are further diversified by gene conversion and somatic hypermutation. The positive and negative selection of amino acids in complementarity-determining regions observed allows emergence of a variety of different combining site structures. A by-product of the germinal center reaction may be cells with sequences altered by gene conversion that no longer react with the immunizing antigen but are a source of new repertoire. The splenic germinal center would thus play an additional role in adults similar to that of the appendix and other gut-associated lymphoid tissues of young rabbits.
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Affiliation(s)
- D Sehgal
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892-1892, USA
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Mage RG, Sehgal D, Schiaffella E, Anderson AO. Gene-conversion in rabbit B-cell ontogeny and during immune responses in splenic germinal centers. Vet Immunol Immunopathol 1999; 72:7-15. [PMID: 10614487 DOI: 10.1016/s0165-2427(99)00110-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Combinatorial diversity is limited in rabbits because only a few V(H) genes rearrange. Most diversification of the primary repertoire is generated by somatic hypermutation and gene conversion-like changes of rearranged V(H) in B cells that migrate to appendix and other gut associated lymphoid tissues (GALT) of young rabbits. The changes are referred to as gene conversion-like because the non-reciprocal nature of the alterations introduced has not yet been demonstrated. There are many similarities between rabbits and chickens in how their B cells develop and diversify their repertoires. However, although the majority of rabbit B cells may have rearranged and diversified their V genes early in life, some B cells in adult rabbits have rearranged VH sequences that are identical or nearly identical to germline sequences. We found these cells in splenic germinal centers (GC) on days 7 and 10 after immunization of normal adult rabbits with DNP-BGG. By day 15, all rearranged V(H) sequences were diversified. We find an overall pattern of splenic precursor cells whose germline or near germline sequences change both by gene conversion and point mutations during early divisions and mainly by point mutations during later divisions. These events, in parallel with diversification of light chain sequences, may produce the diverse combining sites that serve as substrates for further affinity maturation by selection either within GC or later among emigrant cells in sites such as bone marrow. Some of the sequences altered by gene conversion in splenic germinal centers may also produce new members of the B-cell repertoire in adult rabbits comparable to those produced in GALT of neonatal rabbits.
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Affiliation(s)
- R G Mage
- National Institutes of Health, NIAID, Laboratory of Immunology, Bethesda, MD 20892-1892, USA.
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Sehgal D, Johnson G, Wu TT, Mage RG. Generation of the primary antibody repertoire in rabbits: expression of a diverse set of Igk-V genes may compensate for limited combinatorial diversity at the heavy chain locus. Immunogenetics 1999; 50:31-42. [PMID: 10541804 DOI: 10.1007/s002510050683] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In mouse and human, generation of combinatorial diversity through use of different heavy and light chain variable region genes in immunoglobulin rearrangements can be a major contributor to the primary antibody repertoire. In rabbits, the contribution of the combinatorial mechanism to heavy chain diversity is minimal, as only a few Igh-V genes are rearranged and expressed. To investigate the contribution of combinatorial diversity toward generation of the rabbit V(kappa) repertoire, we constructed five genomic libraries from rabbit kidney DNA and 1 cDNA library from the bone marrow of a 1-day-old rabbit using a series of polymerase chain reaction-based strategies. Our analyses indicate that most of the sequences that we recovered from our libraries belong to a single family and some are extremely similar. The actual number of germline Igk-V genes is potentially greater than our conservative estimate of at least 39, 28 of which we found expressed as mRNA. The germline Igk-V genes display different lengths of the coding region 3' of Cys 88 ranging from 7 to 12 amino acids, resulting in CDR3 length heterogeneity among functional V(kappa)J(kappa) sequences ranging from 8 to 15 amino acids. Some of the V(kappa)J(kappa) junctions had N and P nucleotide additions. Thus, in contrast to limited combinatorial diversity of its heavy chain, the rabbit can draw upon a diverse set of germline Igk-V genes. The kappa light chain has the potential to be a major contributor toward generation of the antibody specificities of the rabbit pre-immune repertoire.
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Affiliation(s)
- D Sehgal
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA
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Schiaffella E, Sehgal D, Anderson AO, Mage RG. Gene conversion and hypermutation during diversification of VH sequences in developing splenic germinal centers of immunized rabbits. J Immunol 1999; 162:3984-95. [PMID: 10201919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The young rabbit appendix and the chicken bursa of Fabricius are primary lymphoid organs where the B cell Ab repertoire develops in germinal centers (GCs) mainly by a gene conversion-like process. In human and mouse, V-gene diversification by somatic hypermutation in GCs of secondary lymphoid organs leads to affinity maturation. We asked whether gene conversion, somatic hypermutation, or both occur in rabbit splenic GCs during responses to the hapten DNP. We determined DNA sequences of rearranged heavy and light chain V region gene segments in single cells from developing DNP-specific GCs after immunization with DNP-bovine gamma-globulin and conclude that the changes at the DNA level that may lead to affinity maturation occur by both gene conversion and hypermutation. Selection was suggested by finding some recurrent amino acid replacements that may contribute increased affinity for antigen in the complementarity-determining region sequences of independently evolved clones, and a narrower range of complementarity-determining region 3 lengths at day 15. Some of the alterations of sequence may also lead to new members of the B cell repertoire in adult rabbits comparable with those produced in gut associated lymphoid tissues of young rabbits.
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Affiliation(s)
- E Schiaffella
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
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Abstract
The gene encoding the green fluorescent protein (gfp) under the control of the highly expressed Autographa californica nucleopolyhedrovirus (AcMNPV)-polyhedrin promoter has been introduced into the polyhedrin (polh) locus of Bombyx mori nucleopolyhedrovirus (BmNPV) by homologous recombination. The insect host larvae and the cultured cells infected with this recombinant virus (vBmGFP) showed high levels of expression of gfp. The larval tissues permissive to virus multiplication could be readily visualized using the tagged recombinant virus, thus providing a direct approach to study the progress of virus infection or its control in the animal host. The highly expressed recombinant protein, GFP, could be easily solubilized from fat bodies. Thus, the caterpillar-based expression could serve as an economic alternative method for the large-scale production of recombinant proteins, even when they are nonsecretory in nature. Further, if the recombinant vBmGFP is used as a parent in generating other recombinants, conversion of the fluorescent plaques to colorless plaques serves as an easy means for screening recombinants. Such a method is especially helpful for BmNPV-recombinant selections in the absence of the other simplified techniques as are available for the prototype baculovirus AcMNPV system.
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Affiliation(s)
- D Sehgal
- Indian Institute of Science, Bangalore, India
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Sehgal D, Schiaffella E, Anderson AO, Mage RG. Analyses of single B cells by polymerase chain reaction reveal rearranged VH with germline sequences in spleens of immunized adult rabbits: implications for B cell repertoire maintenance and renewal. J Immunol 1998; 161:5347-56. [PMID: 9820508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
We used PCR to amplify rearranged VHDJH genes in single cells collected by micromanipulation from splenic germinal centers of immunized adult rabbits. In the course of the study, the objective of which was to analyze diversification of rearranged VHDJH sequences, we were surprised to find cells 7 and 10 days after immunization with rearranged VH1a2 as well as a-negative (y33 and x32) sequences that were identical or close to germline (10 or fewer changes). About 58% (82/140) of the sequences had unique CDR3 regions and were unrelated. In seven different germinal centers, we found one to four different clones with two to seven members. Clonally related cells underwent diversification by hypermutation and gene conversion. We found that contrary to published reports, adult rabbits indeed have newly diversifying B cell receptors in splenic germinal centers. The attractive idea that the rabbit, like the chicken, develops its B cell repertoire early in life and depends upon self-renewing cells in the periphery to maintain its B lymphocyte pool throughout life, is challenged by the current finding. Although a major population of B lymphocytes may be generated early in life, diversified extensively, and maintained by self-renewal in the periphery, some sources of cells with sequences close to germline do exist in adult rabbits and appear in the developing germinal centers. Although considerable repertoire diversity is generated in young rabbits, mechanisms for continued generation of B cell receptor diversity are retained in adult life, where they may confer survival advantage.
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Affiliation(s)
- D Sehgal
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892-1892, USA
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Sehgal D, Mage RG, Schiaffella E. VH mutant rabbits lacking the VH1a2 gene develop a2+ B cells in the appendix by gene conversion-like alteration of a rearranged VH4 gene. J Immunol 1998; 160:1246-55. [PMID: 9570541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We investigated the molecular basis for the appearance of V(H)a2 allotype-bearing B cells in mutant Alicia rabbits. The mutation arose in an a2 rabbit; mutants exhibit altered expression of V(H) genes because of a small deletion encompassing V(H)1a2, the 3'-most gene in the V(H) locus. The V(H)1 gene is the major source of V(H)a allotype because this gene is preferentially rearranged in normal rabbits. In young homozygous ali/ali animals, the levels of a2 molecules found in the serum increase with age. In adult ali/ali rabbits, 20 to 50% of serum Igs and B cells bear a2 allotypic determinants. Previous studies suggested that positive selection results in expansion of a2 allotype-bearing B cells in the appendix of young mutant ali/ali rabbits. We separated appendix cells from a 6-wk-old Alicia rabbit by FACS based on the expression of surface IgM and a2 allotype. The VDJ portion of the expressed Ig mRNA was amplified from the IgM+ a2+ and IgM+ a2- populations by reverse transcriptase-PCR. The cDNAs from both populations were cloned and sequenced. Analysis of these sequences suggested that, in a2+ B cells, the first D proximal functional gene in Alicia rabbits, V(H)4a2, rearranged and was altered further by a gene conversion-like mechanism. Upstream V(H) genes were identified as potential gene sequence donors; V(H)9 was found to be the most frequently used gene donor. Among the a2- B cells, y33 was the most frequently rearranged gene.
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Affiliation(s)
- D Sehgal
- Molecular Immunogenetics Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
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Azam A, Paul J, Sehgal D, Prasad J, Bhattacharya S, Bhattacharya A. Identification of novel genes from Entamoeba histolytica by expressed sequence tag analysis. Gene 1996; 181:113-6. [PMID: 8973317 DOI: 10.1016/s0378-1119(96)00484-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Shotgun sequencing of cDNA clones is now an established approach to gain insight into the expressed nucleotide (nt) sequences in a given cell. We analysed 100 randomly picked cDNA clones of the protozoan parasite, Entamoeba histolytica, by nt sequencing, with a view to obtain novel gene sequences not detected so far by biochemical and genetic analyses. About 56% of the analysed clones showed significant homology with other genes in the database, including a number of genes whose presence may not be suspected in E. histolytica owing to its unusual subcellular organization. The results suggest that this approach can provide important clues to understand unique biochemical mechanisms in this parasite.
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Affiliation(s)
- A Azam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Sehgal D, Mittal V, Ramachandran S, Dhar SK, Bhattacharya A, Bhattacharya S. Nucleotide sequence organisation and analysis of the nuclear ribosomal DNA circle of the protozoan parasite Entamoeba histolytica. Mol Biochem Parasitol 1994; 67:205-14. [PMID: 7870125 DOI: 10.1016/0166-6851(94)00129-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have sequenced the extrachromsomal ribosomal DNA (rDNA) circle of the human protozoan parasite Entamoeba histolytica HM-1:IMSS and present here the complete sequence organisation of the 24.5-kb molecule. Each circle contains two 5.9-kb rDNA transcription units organised as inverted repeats. The regions downstream (3543 bp) and upstream (9216 bp) of the rDNAs contain various families of short tandem repeats. Some of the upstream repeats share extensive sequence homology with the downstream repeats. In addition to the rDNAs themselves, the rDNA circle appears to code for only one other transcript which is 0.7 kb in size as seen in Northern blots. From DNA sequence analysis, no open reading frame could be assigned to the transcript. Extrachromosomal rDNA circles also exist in other E. histolytica strains. Restriction enzyme maps of rDNA circles were constructed from E. histolytica strains 200:NIH, HK-9 and Rahman; and Entamoeba moshkovskii strain Laredo. Striking differences were observed in the organisation of some of them, e.g. the HK-9, Rahman and Laredo circles contained only one rDNA unit and lacked the 0.7-kb transcript sequence. The short repeat sequences upstream and downstream of rDNAs were present in HK-9 and Rahman but absent in Laredo. Circles with one rDNA unit may be derived from those with two units by homologous recombination at direct repeat sequences located upstream and downstream of the two rDNAs.
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Affiliation(s)
- D Sehgal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Indiana
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Abstract
Water-soluble carbodiimides are widely used for carboxyl-amine conjugation. However, extremely variable and low yields, obtained under a variety of conditions, have been a serious problem in the coupling. A simple method, optimizing various parameters of the coupling reaction, in which N-hydroxysuccinimide is included to assist the 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride-catalyzed amidation reaction is described. A product yield of up to 90% is routinely achieved.
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Affiliation(s)
- D Sehgal
- Department of Animal Sciences, University of Maryland, College Park 20742
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Sehgal D, Bhattacharya A, Bhattacharya S. Analysis of a polymorphic locus present upstream of rDNA transcription units in the extrachromosomal circle of Entamoeba histolytica. Mol Biochem Parasitol 1993; 62:129-30. [PMID: 8114815 DOI: 10.1016/0166-6851(93)90187-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- D Sehgal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Mittal V, Sehgal D, Bhattacharya A, Bhattacharya S. A second short repeat sequence detected downstream of rRNA genes in the Entamoeba histolytica rDNA episome. Mol Biochem Parasitol 1992; 54:97-100. [PMID: 1518536 DOI: 10.1016/0166-6851(92)90098-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- V Mittal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Mittal V, Ramachandran S, Sehgal D, Bhattacharya A, Bhattacharya S. Sequence analysis of a DNA fragment with yeast autonomously replicating sequence activity from the extrachromosomal ribosomal DNA circle of Entamoeba histolytica. Nucleic Acids Res 1991; 19:2777. [PMID: 2041750 PMCID: PMC328200 DOI: 10.1093/nar/19.10.2777] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- V Mittal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Katiyar GP, Sehgal D, Khare BB, Agarwal DK, Tripathi AM, Agarwal KN. Physical growth characteristics of upper socio-economic adolescent boys of Varanasi. Indian Pediatr 1985; 22:915-22. [PMID: 3837779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Sehgal D, Mulenga H, Chintu C. Thanatophoric dwarfism: a report of two infants. East Afr Med J 1983; 60:713-717. [PMID: 6671430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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Chintu C, Sehgal D, Bhagwat GP, Dube MK. Acute leukaemias in Zambian children. East Afr Med J 1983; 60:704-9. [PMID: 6608444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Bhat GJ, Hira SK, Ratnam AV, Sehgal D, Chintu C, Mulenga RC. Congenital syphilis in Lusaka--III. Incidence in the neonatal intensive-care unit. East Afr Med J 1982; 59:374-8. [PMID: 7173075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Hira SK, Ratnam AV, Sehgal D, Bhat GJ, Chintu C, Lulenga RC. Congenital syphilis in Lusaka--i. Incidence in a general nursery ward. East Afr Med J 1982; 59:241-6. [PMID: 7140609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Raghu MB, Sehgal D, Chintu C. The management of diabetes mellitus in children. Review and our experience in Zambian children and adolescents. Med J Zambia 1981; 15:77-80. [PMID: 6812306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Sehgal D, Raghu MB, Chintu C. Juvenile diabetes mellitus clinical spectrum in Zambian children. Med J Zambia 1981; 15:84-7. [PMID: 6812307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Sehgal D, Chawla V, Maguire MJ. Hereditary anhidrotic ectodermal dysplasia in a Zambian family. East Afr Med J 1981; 58:374-9. [PMID: 7285838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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