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1. A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival

Author

Abassah-Oppong, Samuel, Zoia, Matteo, Mannion, Brandon J., Rouco, Raquel, Tissières, Virginie, Spurrell, Cailyn H., Roland, Virginia, Darbellay, Fabrice, Itum, Anja, Gamart, Julie, Festa-Daroux, Tabitha A., Sullivan, Carly S., Kosicki, Michael, Rodríguez-Carballo, Eddie, Fukuda-Yuzawa, Yoko, Hunter, Riana D., Novak, Catherine S., Plajzer-Frick, Ingrid, Tran, Stella, Akiyama, Jennifer A., Dickel, Diane E., Lopez-Rios, Javier, Barozzi, Iros, Andrey, Guillaume, Visel, Axel, Pennacchio, Len A., Cobb, John, and Osterwalder, Marco

Published
2024
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2. Bat species assemblage predicts coronavirus prevalence

Author

Meyer, Magdalena, Melville, Dominik W., Baldwin, Heather J., Wilhelm, Kerstin, Nkrumah, Evans Ewald, Badu, Ebenezer K., Oppong, Samuel Kingsley, Schwensow, Nina, Stow, Adam, Vallo, Peter, Corman, Victor M., Tschapka, Marco, Drosten, Christian, and Sommer, Simone

Published
2024
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10. Defining global strategies to improve outcomes in sickle cell disease: a Lancet Haematology Commission

Author

Piel, Frédéric B, Rees, David C, DeBaun, Michael R, Nnodu, Obiageli, Ranque, Brigitte, Thompson, Alexis A, Ware, Russell E, Abboud, Miguel R, Abraham, Allistair, Ambrose, Emmanuela E, Andemariam, Biree, Colah, Roshan, Colombatti, Raffaella, Conran, Nicola, Costa, Fernando F, Cronin, Robert M, de Montalembert, Mariane, Elion, Jacques, Esrick, Erica, Greenway, Anthea L, Idris, Ibrahim M, Issom, David-Zacharie, Jain, Dipty, Jordan, Lori C, Kaplan, Zane S, King, Allison A, Lloyd-Puryear, Michele, Oppong, Samuel A, Sharma, Akshay, Sung, Lillian, Tshilolo, Leon, Wilkie, Diana J, and Ohene-Frempong, Kwaku

Published
2023
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14. A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival

Author

Abassah-Oppong, Samuel, Mannion, Brandon J, Zoia, Matteo, Rouco, Raquel, Tissieres, Virginie, Spurrell, Cailyn H, Roland, Virginia, Darbellay, Fabrice, Ljubojevic, Anja, Gamart, Julie, Festa-Daroux, Tabitha A, Sullivan, Carly S, Rodríguez-Carballo, Eddie, Fukuda-Yuzawa, Yoko, Hunter, Riana, Novak, Catherine S, Plajzer-Frick, Ingrid, Tran, Stella, Akiyama, Jennifer A, Dickel, Diane E, Lopez-Rios, Javier, Barozzi, Iros, Andrey, Guillaume, Visel, Axel, Pennacchio, Len A, Cobb, John, and Osterwalder, Marco

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Human Genome, Biotechnology, Congenital Structural Anomalies, Heart Disease, Pediatric, Cardiovascular, 1.1 Normal biological development and functioning, Generic health relevance
Abstract

ABSTRACT Gene deserts are defined as genomic regions devoid of protein coding genes and spanning more than 500 kilobases, collectively encompassing about 25% of the human genome. Approximately 30% of all gene deserts are enriched for conserved elements with cis -regulatory signatures. These are located predominantly near developmental transcription factors (TFs) but despite predicted critical functions, the transcriptional contributions and biological necessity of most gene deserts remain elusive. Here, we explore the cis -regulatory impact of a gene desert flanking the Shox2 gene, a TF indispensable for proximal limb, craniofacial and cardiac pacemaker development. Using a functional genomics approach in mouse embryos we identify the gene desert as a hub for numerous Shox2 -overlapping enhancers arranged in a globular chromatin domain with tissue-specific features. In accordance, using endogenous CRISPR deletion, we demonstrate that the gene desert interval is essential for Shox2 transcriptional control in developing limbs, craniofacial compartments, and the heart. Phenotypically, gene desert ablation leads to pacemaker-related embryonic lethality due to Shox2 depletion in the cardiac sinus venosus. We show that this role is partially mediated through a distal gene desert enhancer, providing evidence for intra-gene desert regulatory robustness. Finally, we uncover a multi-layered functional role of the gene desert by revealing an additional requirement for stylopod morphogenesis, mediated through an array of proximal limb enhancers (PLEs). In summary, our study establishes the Shox2 gene desert as a fundamental genomic unit that controls pleiotropic gene expression through modular arrangement and coordinated dynamics of tissue-specific enhancers.

Published
2020

24. Effects of different cutting heights on coppice response of forage shrubs in Ghana

Author

Oppong Samuel Kıngsley, Ammal Abukari, and Ziblim Abukari Imoro

Subjects
coppice, cutting height, dry matter, shrub, sprout, baltalık, kesim yüksekliği, kuru madde, çalı, filiz, Forestry, SD1-669.5
Abstract

This study aimed to determine the effect of cutting intensity on the recovery rate, growth, and biomass production of selected savanna forage shrub species. The study was conducted at the University for Development Studies (UDS), Nyankpala Campus in the Tolon District of the Northern Region of Ghana. Cajanus cajan, Stylosanthes mucronata, Tephrosia purpureum and Securinega virosa were cut at 15 cm, 30 cm, and 60 cm above ground level a month after a standardizing cut and number of days to sprout, the number of shoots, plant height, and root collar diameter was recorded. The experiment was a randomized complete block design with four replications. Shrubs cut at 60 cm used less mean number of days (4.25) for sprouting and those cut at 15 cm took a longer period (4.92) to sprout. Plant height, number of shoots, and root collar diameter after cutting were highest for shrubs cut at 60 cm. Securinega virosa used less mean number of days (4.00) to sprout while S. mucronata used the highest mean number of days (5.44) after cutting. Total dry matter yield was significantly highest (123.90 g/plant) for shrubs cut at 60 cm but lowest for those cut at 15 cm (91.20 g/plant). Cajanus cajan recorded a significantly higher total dry matter (116.30 g/plant) while S. virosa had the lowest (93.00 g/plant). Our results suggest that cutting height significantly influences the rate of sprouting of shrubs after cutting, and the response to the cutting effect is species-dependent.

Published
2021
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25. Response of benthic invertebrate assemblages to seasonal and habitat condition in the Wewe River, Ashanti region (Ghana)

Author

Oppong Samuel K., Nsor Collins Ayine, and Buabeng Gabriel Kwabena

Subjects
benthic invertebrates, stream condition, geometric series, rarefaction, hill numbers, canonical correspondence analysis, wewe river, Biology (General), QH301-705.5
Abstract

Aquatic macro-invertebrates play a vital role in the food chain of river ecosystem at several trophic guilds and consumer levels, and are used as biomonitoring tools for aquatic ecosystem health. However, hydrologic conditions of these ecosystems have been severely altered because of the increase in urban development and agricultural expansion. This study examined benthic invertebrate response to processes that structure their community in the Wewe River, segmented into intact, medium, and severe condition zones. We sampled in 100 stations in a period of 4 months in the wet (June–September, 2019) and 3 months in the dry (January–March, 2020) seasons. Geometric series, rarefaction, and Hill numbers models were used to quantify invertebrate assemblages, while ordination technique, canonical correspondence analysis, was used to evaluate the influence of predictive factors on their assemblages. A total of 2,075 individuals belonging to 20 family taxa were registered. There was no significant difference in benthic assemblages between the dry and wet seasons. Predictive factors accounted for 47.04 and 50.84% variances, respectively. Taxa distribution patterns differed significantly only in the severely disturbed zone during the wet season. Neptidae, Libellulidae, and Chironomidae were the most abundant taxa, indicating their broad range habitat preference and their ability to adapt to seasonal changes. Asellidae and Perlidae were the least detected, suggesting their sensitivity to elevated levels of some water quality parameters. The findings highlight the threats to the benthic community and overall functional state of the Wewe River, with the need to consider the proposed conservation interventions indicated in this study.

Published
2021
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29. A unique stylopod patterning mechanism by Shox2-controlled osteogenesis.

Author

Ye, Wenduo, Song, Yingnan, Huang, Zhen, Osterwalder, Marco, Ljubojevic, Anja, Xu, Jue, Bobick, Brent, Abassah-Oppong, Samuel, Ruan, Ningsheng, Shamby, Ross, Yu, Diankun, Zhang, Lu, Cai, Chen-Leng, Visel, Axel, Zhang, Yanding, Cobb, John, and Chen, YiPing

Subjects
Extremities, Animals, Mice, Homeodomain Proteins, Gene Expression Regulation, Developmental, Gene Deletion, Binding Sites, Base Sequence, Protein Binding, Cell Lineage, Body Patterning, Osteogenesis, Genome, Models, Biological, Core Binding Factor Alpha 1 Subunit, Enhancer Elements, Genetic, Mesenchymal Stromal Cells, Nucleotide Motifs, Limb, Patterning, Shox2, Skeleton, Stylopod, Mesenchymal Stem Cells, Gene Expression Regulation, Developmental, Models, Biological, Enhancer Elements, Genetic, Human Genome, Genetics, 1.1 Normal biological development and functioning, Biological Sciences, Medical and Health Sciences
Abstract

Vertebrate appendage patterning is programmed by Hox-TALE factor-bound regulatory elements. However, it remains unclear which cell lineages are commissioned by Hox-TALE factors to generate regional specific patterns and whether other Hox-TALE co-factors exist. In this study, we investigated the transcriptional mechanisms controlled by the Shox2 transcriptional regulator in limb patterning. Harnessing an osteogenic lineage-specific Shox2 inactivation approach we show that despite widespread Shox2 expression in multiple cell lineages, lack of the stylopod observed upon Shox2 deficiency is a specific result of Shox2 loss of function in the osteogenic lineage. ChIP-Seq revealed robust interaction of Shox2 with cis-regulatory enhancers clustering around skeletogenic genes that are also bound by Hox-TALE factors, supporting a lineage autonomous function of Shox2 in osteogenic lineage fate determination and skeleton patterning. Pbx ChIP-Seq further allowed the genome-wide identification of cis-regulatory modules exhibiting co-occupancy of Pbx, Meis and Shox2 transcriptional regulators. Integrative analysis of ChIP-Seq and RNA-Seq data and transgenic enhancer assays indicate that Shox2 patterns the stylopod as a repressor via interaction with enhancers active in the proximal limb mesenchyme and antagonizes the repressive function of TALE factors in osteogenesis.

Published
2016

30. Spatiotemporal dynamics of terrestrial invertebrate assemblages in the riparian zone of the Wewe river, Ashanti region, Ghana

Author

Nsor Collins Ayine, Oppong Samuel K., Danquah Emmanuel, Ochem Michael, and Antobre Osei Owusu

Subjects
habitat conditions, environmental disturbance, geometric series, rarefaction, renyi diversity ordering, canonical correspondence analysis, Biology (General), QH301-705.5
Abstract

This study assessed invertebrate response to disturbances in the riparian zone of the Wewe river, using geometric series, rarefaction, Renyi diversity, and CCA models. We sampled 2,077 individuals (dry season) and 2,282 (wet season) belonging to 16 invertebrate orders. The severely disturbed habitat registered the highest individuals (n = 1,999), while the least was the moderately disturbed habitat (n = 740). Seasonal assemblages were not significantly different. Fire, farming, tree felling, and erosion explained 66.8% and 60.55% in the dry and wet seasons, respectively, of variations in invertebrate assemblages. This suggests threats to the invertebrate community and the riparian ecosystem health by anthropogenic interventions.

Published
2020
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31. “If You Need a Psychiatrist, It’s BAD”: Stigma Associated with Seeking Mental Health Care Among Obstetric Providers in Ghana

Author

Lawrence,Emma, Parekh,Bela, Owusu-Antwi,Ruth, Newman,Noah, Russell,Colin, Beyuo,Titus, Yeboah,Michael, Oppong,Samuel, Moyer,Cheryl, Lawrence,Emma, Parekh,Bela, Owusu-Antwi,Ruth, Newman,Noah, Russell,Colin, Beyuo,Titus, Yeboah,Michael, Oppong,Samuel, and Moyer,Cheryl

Abstract

Emma R Lawrence,1 Bela J Parekh,2 Ruth Owusu-Antwi,3 Noah Newman,2 Colin B Russell,1 Titus K Beyuo,4,5 Michael Yeboah,6 Samuel A Oppong,4,5 Cheryl A Moyer1,7 1Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA; 2University of Michigan Medical School, Ann Arbor, MI, USA; 3Department of Behavioural Sciences, Kwame Nkrumah University of Science and Technology/ Psychiatry Unit, Komfo Anokye Teaching Hospital, Kumasi, Ghana; 4Department of Obstetrics and Gynecology, University of Ghana Medical School, Accra, Ghana; 5Department of Obstetrics and Gynecology, Korle Bu Teaching Hospital, Korle Bu, Accra, Ghana; 6Department of Obstetrics and Gynecology, Komfo Anokye Teaching Hospital, Kumasi, Ghana; 7Department of Learning Health Sciences, University of Michigan, Ann Arbor, MI, USACorrespondence: Ruth Owusu-Antwi, Department of Behavioural Sciences, Kwame Nkrumah University of Science and Technology/ Psychiatry Unit, Komfo Anokye Teaching Hospital, Accra Road, Kumasi, Ashanti Region, Ghana, Tel +233244650245, Email rucha_2001@yahoo.comPurpose: Globally, the COVID-19 pandemic has brought attention to the impact of negative patient outcomes on healthcare providers. In Ghana, obstetric providers regularly face maternal and neonatal mortality, yet limited research has focused on provision of mental health support for these providers. This study sought to understand how obstetric providers viewed seeking mental health support after poor clinical outcomes, with a focus on the role of mental health stigma.Patients and Methods: Participants were 52 obstetric providers (20 obstetrician/gynecologists and 32 midwives) at two tertiary care hospitals in Ghana. Five focus groups, led by a trained facilitator and lasting approximately two hours, were conducted to explore provider experiences and perceptions of support following poor maternal and neonatal outcomes. Discussions were audiotaped and transcribed verbatim, then analyzed qualitatively using grounde

Published
2024

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