ORCID Profile
0000-0002-2354-3003
Current Organisations
Birkbeck, University of London
,
North Carolina State University
,
University of Pittsburgh
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Publisher: Cold Spring Harbor Laboratory
Date: 05-07-2022
DOI: 10.1101/2022.06.30.498290
Abstract: Microbial strains have closely related genomes but may have different phenotypes in the same environment. Shotgun metagenomic sequencing can capture the genomes of all strains present in a community but strain-resolved analysis from shotgun sequencing alone remains difficult. We developed an approach to identify and interrogate strain-level differences in groups of metagenomes. We use this approach to perform a meta-analysis of stool microbiomes from in iduals with and without inflammatory bowel disease (IBD Crohn’s disease, ulcerative colitis n = 605), a disease for which there are not specific microbial biomarkers but some evidence that microbial strain variation may stratify by disease state. We first developed a machine learning classifier based on compressed representations of complete metagenomes (FracMinHash sketches) and identified genomes that correlate with IBD subtype. To rescue variation that may not have been present in the genomes, we then used assembly graph genome queries to recover strain variation for correlated genomes. Lastly, we developed a novel differential abundance framework that works directly on the assembly graph to uncover all sequence variants correlated with IBD. We refer to this approach as dominating set differential abundance analysis and have implemented it in the spacegraphcats software package . Using this approach, we identified five bacterial strains that are associated with Crohn’s disease. Our method captures variation within the entire sequencing data set, allowing for discovery of previously hidden disease associations.
Publisher: Springer Science and Business Media LLC
Date: 23-05-2004
DOI: 10.1038/NG1367
Publisher: Oxford University Press (OUP)
Date: 09-2007
DOI: 10.1634/STEMCELLS.2007-0143
Abstract: Spermatogonial stem cells (SSCs) are at the foundation of mammalian spermatogenesis. Whereas rare Asingle spermatogonia comprise the rodent SSC pool, primate spermatogenesis arises from more abundant Adark and Apale spermatogonia, and the identity of the stem cell is subject to debate. The fundamental differences between these models highlight the need to investigate the biology of primate SSCs, which have greater relevance to human physiology. The alkylating chemotherapeutic agent, busulfan, ablates spermatogenesis in rodents and causes infertility in humans. We treated adult rhesus macaques with busulfan to gain insights about its effects on SSCs and spermatogenesis. Busulfan treatment caused acute declines in testis volume and sperm counts, indicating a disruption of spermatogenesis. One year following high-dose busulfan treatment, sperm counts remained undetectable, and testes were depleted of germ cells. Similar to rodents, rhesus spermatogonia expressed markers of germ cells (VASA, DAZL) and stem rogenitor spermatogonia (PLZF and GFRα1), and cells expressing these markers were depleted following high-dose busulfan treatment. Furthermore, fresh or cryopreserved germ cells from normal rhesus testes produced colonies of spermatogonia, which persisted as chains on the basement membrane of mouse seminiferous tubules in the primate to nude mouse xenotransplant assay. In contrast, testis cells from animals that received high-dose busulfan produced no colonies. These studies provide basic information about rhesus SSC activity and the impact of busulfan on the stem cell pool. In addition, the germ cell-depleted testis model will enable autologous/homologous transplantation to study stem cell/niche interactions in nonhuman primate testes. Disclosure of potential conflicts of interest is found at the end of this article.
Location: United Kingdom of Great Britain and Northern Ireland
Location: Germany
Location: United Kingdom of Great Britain and Northern Ireland
Location: United States of America
No related grants have been discovered for Felix Reidl.