Search

Your search keyword '"Affara, Nabeel A"' showing total 404 results
Start Over Author "Affara, Nabeel A"
404 results on '"Affara, Nabeel A"'

7. Identification of methylation changes associated with positive and negative growth deviance in Gambian infants using a targeted methyl sequencing approach of genomic DNA

Author

Quilter, Claire R., primary, Harvey, Kerry M., additional, Bauer, Julien, additional, Skinner, Benjamin M., additional, Gomez, Maria, additional, Shrivastava, Manu, additional, Doel, Andrew M., additional, Drammeh, Saikou, additional, Dunger, David B., additional, Moore, Sophie E., additional, Ong, Ken K., additional, Prentice, Andrew M., additional, Bernstein, Robin M., additional, Sargent, Carole A., additional, and Affara, Nabeel A., additional

Published
2021
Full Text
View/download PDF

8. A Novel method for the identification and quantification of weight faltering

Author

Naumenko, Daniel J., primary, Dykes, James, additional, O'Connor, G. Kesler, additional, Stanley, Zofia, additional, Affara, Nabeel, additional, Doel, Andrew M., additional, Drammeh, Saikou, additional, Dunger, David B., additional, Faal, Abdoulie, additional, Ong, Ken K., additional, Sosseh, Fatou, additional, Prentice, Andrew M., additional, Moore, Sophie E., additional, and Bernstein, Robin M., additional

Published
2021
Full Text
View/download PDF

19. An improved pig reference genome sequence to enable pig genetics and genomics research

Author

Warr, Amanda, primary, Affara, Nabeel, primary, Aken, Bronwen, primary, Beiki, Hamid, primary, Bickhart, Derek M, primary, Billis, Konstantinos, primary, Chow, William, primary, Eory, Lel, primary, Finlayson, Heather A, primary, Flicek, Paul, primary, Girón, Carlos G, primary, Griffin, Darren K, primary, Hall, Richard, primary, Hannum, Greg, primary, Hourlier, Thibaut, primary, Howe, Kerstin, primary, Hume, David A, primary, Izuogu, Osagie, primary, Kim, Kristi, primary, Koren, Sergey, primary, Liu, Haibou, primary, Manchanda, Nancy, primary, Martin, Fergal J, primary, Nonneman, Dan J, primary, O'Connor, Rebecca E, primary, Phillippy, Adam M, primary, Rohrer, Gary A, primary, Rosen, Benjamin D, primary, Rund, Laurie A, primary, Sargent, Carole A, primary, Schook, Lawrence B, primary, Schroeder, Steven G, primary, Schwartz, Ariel S, primary, Skinner, Ben M, primary, Talbot, Richard, primary, Tseng, Elizabeth, primary, Tuggle, Christopher K, primary, Watson, Mick, primary, Smith, Timothy P L, primary, and Archibald, Alan L, primary

Published
2020
Full Text
View/download PDF

20. Timing of the Infancy-Childhood Growth Transition in Rural Gambia

Author

Bernstein, Robin M., primary, O'Connor, G. Kesler, additional, Vance, Eric A., additional, Affara, Nabeel, additional, Drammeh, Saikou, additional, Dunger, David B., additional, Faal, Abdoulie, additional, Ong, Ken K., additional, Sosseh, Fatou, additional, Prentice, Andrew M., additional, and Moore, Sophie E., additional

Published
2020
Full Text
View/download PDF

24. A conserved requirement forFbxo7during male germ cell cytoplasmic remodelling

Author

Rathje, Claudia Cattoni, Randle, Suzanne J, Al Rawi, Sara, Skinner, Benjamin Matthew, Nelson, David E, Majumdar, Antara, Johnson, Emma EP, Bacon, Joanne, Vlazaki, Myrto, Affara, Nabeel A, Ellis, Peter J.I., and Laman, Heike

Subjects
0303 health sciences, Cell type, biology, Spermatid, Spermiogenesis, Cell cycle, Chromatin, Ubiquitin ligase, Cell biology, 03 medical and health sciences, 0302 clinical medicine, medicine.anatomical_structure, Proteasome, biology.protein, medicine, 030217 neurology & neurosurgery, Germ cell, 030304 developmental biology
Abstract

Fbxo7 is the substrate-recognition subunit of an SCF-type ubiquitin E3 ligase complex. It has physiologically important functions in regulating mitophagy, proteasome activity and the cell cycle in multiple cell types, like neurons, lymphocytes and erythrocytes. Here, we show that in addition to the previously known Parkinsonian and hematopoietic phenotypes, male mice with reduced Fbxo7 expression are sterile. In these males, despite successful meiosis, nuclear elongation and eviction of histones from chromatin, the developing spermatids are phagocytosed by Sertoli cells during late spermiogenesis, as the spermatids undergo cytoplasmic remodeling. Surprisingly, despite the loss of all germ cells, there was no evidence of the symplast formation and cell sloughing that is typically associated with spermatid death in other mouse sterility models, suggesting that novel cell death and/or cell disposal mechanisms may be engaged in Fbxo7 mutant males. Mutation of the Drosophila Fbxo7 ortholog, nutcracker (ntc) also leads to sterility with germ cell death during cytoplasmic remodeling, indicating that the requirement for Fbxo7 at this stage is conserved. The ntc phenotype was attributed to decreased levels of the proteasome regulator, DmPI31 and reduced proteasome activity. Consistent with the fly model, we observe a reduction in PI31 levels in mutant mice; however, there is no alteration in proteasome activity in whole mouse testes. Our results are consistent with findings that Fbxo7 regulates PI31 protein levels, and indicates that a defect at the late stages of spermiogenesis, possibly due to faulty spatial dynamics of proteasomes during cytoplasmic remodeling, may underlie the fertility phenotype in mice.

Published
2019

26. Genetic analysis of meiotic recombination in humans by use of sperm typing: reduced recombination within a heterozygous paracentric inversion of chromosome 9q32-q34.3

Author

Brown, Graeme M., Leversha, Margaret, Hulten, Maj, Ferguson-Smith, Malcom A., Affara, Nabeel A., and Furlong, Robert A.

Subjects
Genetic disorders -- Research, Chromosome mapping -- Usage, Meiosis -- Research, Spermatozoa -- Analysis, Genetic recombination -- Research, Crossing over (Genetics) -- Research, Biological sciences
Abstract

To investigate patterns of genetic recombination in a heterozygous paracentric inversion of chromosome 9q32-q34.3, sperm typing has been carried out using a series of polymorphic microsatellite markers going across the inversion region. Two donors with cytogenticlly normal chromsomes 9 were tested as well, One of them was heterozygous for a pericentric chromosome 2 inversion. Distal to the telomeric breakpoint an increase in recombination was seen in the inversion patient. In the inversion recombination was dramatically lower, but several apparent double recombinants were seen.

Published
1998

29. Automated nuclear cartography reveals conserved sperm chromosome territory localization across 2 million years of mouse evolution

Author

Skinner, Benjamin M., Bacon, Joanne, Rathje, Claudia C., Larson, Erica L., Kopania, Emily E. K., Good, Jeffrey M., Affara, Nabeel A., Ellis, Peter J.I., Skinner, Benjamin M., Bacon, Joanne, Rathje, Claudia C., Larson, Erica L., Kopania, Emily E. K., Good, Jeffrey M., Affara, Nabeel A., and Ellis, Peter J.I.

Abstract

Measurements of nuclear organization in asymmetric nuclei in 2D images have traditionally been manual. This is exemplified by attempts to measure chromosome position in sperm samples, typically by dividing the nucleus into zones, and manually scoring which zone a FISH signal lies in. This is time consuming, limiting the number of nuclei that can be analyzed, and prone to subjectivity. We have developed a new approach for automated mapping of FISH signals in asymmetric nuclei, integrated into an existing image analysis tool for nuclear morphology. Automatic landmark detection defines equivalent structural regions in each nucleus, then dynamic warping of the FISH images to a common shape allows us to generate a composite of the signal within the entire cell population. Using this approach, we mapped the positions of the sex chromosomes and two autosomes in three mouse lineages (Mus musculus domesticus, Mus musculus musculus and Mus spretus). We found that in all three, chromosomes 11 and 19 tend to interact with each other, but are shielded from interactions with the sex chromosomes. This organization is conserved across 2 million years of mouse evolution.

Published
2019

30. A high-throughput method for unbiased quantitation and categorisation of nuclear morphology

Author

Skinner, Benjamin M., Rathje, Claudia C., Bacon, Joanne, Johnson, Emma P. S., Larson, Erica L., Kopania, Emily E. K., Good, Jeffrey M., Yousafzai, G., Affara, Nabeel A., Ellis, Peter J.I., Skinner, Benjamin M., Rathje, Claudia C., Bacon, Joanne, Johnson, Emma P. S., Larson, Erica L., Kopania, Emily E. K., Good, Jeffrey M., Yousafzai, G., Affara, Nabeel A., and Ellis, Peter J.I.

Abstract

The physical arrangement of chromatin in the nucleus is cell type and species specific; a fact particularly evident in sperm, in which most of the cytoplasm has been lost. Analysis of the characteristic falciform (‘hook shaped’) sperm in mice is important in studies of sperm development, hybrid sterility, infertility and toxicology. However, quantification of sperm shape differences typically relies on subjective manual assessment, rendering comparisons within and between samples difficult. We have developed an analysis program for morphometric analysis of asymmetric nuclei and characterised the sperm of mice from a range of inbred, outbred and wild-derived mouse strains. We find that laboratory strains have elevated sperm shape variability both within and between samples in comparison to wild-derived inbred strains, and that sperm shape in F1 offspring from a cross between CBA and C57Bl6J strains is subtly affected by the direction of the cross. We further show that hierarchical clustering can discriminate distinct sperm shapes with greater efficiency and reproducibility than even experienced manual assessors, and is useful both to distinguish between samples and also to identify different morphological classes within a single sample. Our approach allows for the analysis of nuclear shape with unprecedented precision and scale and will be widely applicable to different species and different areas of biology.

Published
2019

34. Regions of XY homology in the pig X chromosome and the boundary of the pseudoautosomal region

Author

Skinner Benjamin M, Lachani Kim, Sargent Carole A, and Affara Nabeel A

Subjects
X-chromosome, Genome, Porcine, Evolution, Microarray, Pseudoautosomal, Genetics, QH426-470
Abstract

Abstract Background Sex chromosomes are subject to evolutionary pressures distinct from the remainder of the genome, shaping their structure and sequence content. We are interested in the sex chromosomes of domestic pigs (Sus scrofa), how their structure and gene content compares and contrasts with other mammalian species, and the role of sex-linked genes in fertility. This requires an understanding of the XY-homologous sequence on these chromosomes. To this end, we performed microarray-based comparative genomic hybridisation (array-CGH) with male and female Duroc genomic DNA on a pig X-chromosome BAC tiling-path microarray. Putative XY-homologous BACs from regions of interest were subsequently FISH mapped. Results We show that the porcine PAR is approximately 6.5-6.9 Mb at the beginning of the short arm of the X, with gene content reflective of the artiodactyl common ancestor. Our array-CGH data also shows an XY-homologous region close to the end of the X long arm, spanning three X BACs. These BACs were FISH mapped, and paint the entire long arm of SSCY. Further clones of interest revealed X-autosomal homology or regions containing repetitive content. Conclusions This study has identified regions of XY homology in the pig genome, and defined the boundary of the PAR on the X chromosome. This adds to our understanding of the evolution of the sex chromosomes in different mammalian lineages, and will prove valuable for future comparative genomic work in suids and for the construction and annotation of the genome sequence for the sex chromosomes. Our finding that the SSCYq repetitive content has corresponding sequence on the X chromosome gives further insight into structure of SSCY, and suggests further functionally important sequences remain to be discovered on the X and Y.

Published
2013
Full Text
View/download PDF

40. Contributors

Author

Affara, Nabeel A., primary, Beitel, Lenore K., additional, Cate, Richard L., additional, Cooper, Desmond W., additional, Crawford, Christopher, additional, Cronmiller, Claire, additional, Donahoe, Patricia K., additional, Ferguson-Smith, Malcolm A., additional, Graves, Jennifer A. Marshall, additional, Gubbay, John, additional, Gustafson, Michael L., additional, Hampikian, Gregory K., additional, Imbeaud, Sandrine, additional, Josso, Nathalie, additional, Kaufman, Morris, additional, Lovell-Badge, Robin, additional, Lyon, Mary F., additional, McLaren, Anne, additional, Müller, Ulrich, additional, Nagamine, Claude M., additional, Neely, E. Kirk, additional, New, Maria I., additional, Ohno, Susumu, additional, Picard, Jean-Yves, additional, Pinsky, Leonard, additional, Rosenfeld, Ron G., additional, Salz, Helen K., additional, Simpson, Joe Leigh, additional, Sinclair, Andrew H., additional, Tiersch, Terrence R., additional, Trifiro, Mark, additional, Wachtel, Stephen S., additional, and Zachmann, Milo, additional

Published
1994
Full Text
View/download PDF

42. A Conserved Requirement for Fbxo7 During Male Germ Cell Cytoplasmic Remodeling

Author

Rathje, Claudia C., primary, Randle, Suzanne J., additional, Al Rawi, Sara, additional, Skinner, Benjamin M., additional, Nelson, David E., additional, Majumdar, Antara, additional, Johnson, Emma E. P., additional, Bacon, Joanne, additional, Vlazaki, Myrto, additional, Affara, Nabeel A., additional, Ellis, Peter J., additional, and Laman, Heike, additional

Published
2019
Full Text
View/download PDF

45. An improved pig reference genome sequence to enable pig genetics and genomics research

Author

Warr, Amanda, primary, Affara, Nabeel, additional, Aken, Bronwen, additional, Beiki, H., additional, Bickhart, Derek M., additional, Billis, Konstantinos, additional, Chow, William, additional, Eory, Lel, additional, Finlayson, Heather A., additional, Flicek, Paul, additional, Girón, Carlos G., additional, Griffin, Darren K., additional, Hall, Richard, additional, Hannum, Greg, additional, Hourlier, Thibaut, additional, Howe, Kerstin, additional, Hume, David A., additional, Izuogu, Osagie, additional, Kim, Kristi, additional, Koren, Sergey, additional, Liu, Haibou, additional, Manchanda, Nancy, additional, Martin, Fergal J., additional, Nonneman, Dan J., additional, O’Connor, Rebecca E., additional, Phillippy, Adam M., additional, Rohrer, Gary A., additional, Rosen, Benjamin D., additional, Rund, Laurie A., additional, Sargent, Carole A., additional, Schook, Lawrence B., additional, Schroeder, Steven G., additional, Schwartz, Ariel S., additional, Skinner, Ben M., additional, Talbot, Richard, additional, Tseng, Elizabeth, additional, Tuggle, Christopher K., additional, Watson, Mick, additional, Smith, Timothy P. L., additional, and Archibald, Alan L., additional

Published
2019
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results