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288 results on '"Prost, S."'

7. A chromosome-scale high-contiguity genome assembly of the cheetah (Acinonyx jubatus)

Author

Winter, S. (Sven), Meißner, R. (René), Greve, C. (Carola), Ben Hamadou, A. (Alexander), Horin, P. (Petr), Prost, S. (Stefan), Burger, P. A. (Pamela A.), Winter, S. (Sven), Meißner, R. (René), Greve, C. (Carola), Ben Hamadou, A. (Alexander), Horin, P. (Petr), Prost, S. (Stefan), and Burger, P. A. (Pamela A.)

Abstract

The cheetah (Acinonyx jubatus, SCHREBER 1775) is a large felid and is considered the fastest land animal. Historically, it inhabited open grassland across Africa, the Arabian Peninsula, and southwestern Asia; however, only small and fragmented populations remain today. Here, we present a de novo genome assembly of the cheetah based on PacBio continuous long reads and Hi-C proximity ligation data. The final assembly (VMU_Ajub_asm_v1.0) has a total length of 2.38 Gb, of which 99.7% are anchored into the expected 19 chromosome-scale scaffolds. The contig and scaffold N50 values of 96.8 Mb and 144.4 Mb, respectively, a BUSCO completeness of 95.4% and a k-mer completeness of 98.4%, emphasize the high quality of the assembly. Furthermore, annotation of the assembly identified 23,622 genes and a repeat content of 40.4%. This new highly contiguous and chromosome-scale assembly will greatly benefit conservation and evolutionary genomic analyses and will be a valuable resource, e.g., to gain a detailed understanding of the function and diversity of immune response genes in felids.

Published
2023

8. An introduction to illegal wildlife trade and its effects on biodiversity and society

Author

Mozer, A. (Annika), Prost, S. (Stefan), Mozer, A. (Annika), and Prost, S. (Stefan)

Abstract

Illegal Wildlife Trade (IWT) is among the most lucrative illegal industries in the world. Its consequences go far beyond direct effects on the species in trade. In this review, we outline the basics of IWT and discuss its cascading consequences on environments, human lives and communities, national stability, and the economy. In addition, we outline structures used in IWT, from subsistence and local use to more complicated configurations, which can include multiple players. Furthermore, while a small fraction of poaching is opportunistic, most of the international IWT is run by organised crime groups. We outline how IWT can be associated with many different crimes like drug trafficking, corruption, or whitewashing. Additionally, many studies have observed a rapidly increasing trend of online trade with endangered and protected species. Moreover, this review gives a short overview of the situation in the European Union (EU) regarding laws and implementation of CITES and highlights that the EU acts as a major source, transit hub, and consumer in IWT. To address the highly dynamic and complicated problem of IWT, research, knowledge exchange, funding, and collaborations in all fields are necessary.

Published
2023

13. Simulated genetic efficacy of metapopulation management and conservation value of captive reintroductions in a rapidly declining felid.

Author

Magliolo, M., Naude, V. N., van der Merwe, V. C., Prost, S., Orozco‐terWengel, P., Burger, P. A., Kotze, A., Grobler, J. P., and Dalton, D. L.

Subjects
GENETIC drift, INBREEDING, WILDLIFE reintroduction, PRINCIPAL components analysis, CHEETAH, SINGLE nucleotide polymorphisms, GENETIC variation
Abstract

In South Africa, cheetahs (Acinonyx jubatus) occur as a relictual, unmanaged population of 'free‐roamers', a managed metapopulation across fenced reserves, and in various captive facilities. To ensure that the Cheetah Metapopulation Project (CMP) is not at risk of losing overall genetic variation to drift or inbreeding, we propose various interventions, including exchanges between free‐roamers and the metapopulation or supplementation with unrelated individuals from captivity. Simulated trajectories of genetic diversity under such intervention strategies over time could directly inform conservation action and policy towards securing the long‐term genetic integrity of the CMP. Single Nucleotide Polymorphisms (SNPs) were genotyped for 172 adult cheetahs across the free‐roamer population, the metapopulation, and three major captive facilities. Management intervention trajectory models were tested including, (1) no intervention, (2) genetic exchange between free‐roamers and the metapopulation, (3) translocation from a single captive facility and (4) translocation from several captive facilities into the metapopulation. Discriminant Analysis of Principal Components (DAPC) showed that two captive populations are highly differentiated from the metapopulation and each other, whilst the third captive and free‐roamer populations are genetically more similar to the metapopulation. Simulated genetic variation over 25 generations indicated that models 1 and 2 show significant losses of heterozygosity due to genetic drift and present a proportional increase in the frequencies of 1st‐ and 2nd‐degree relatives, whilst this variation and pairwise relatedness remain relatively constant under models 3 and 4. We emphasise the potential importance of captive facilities as reservoirs of genetic diversity in metapopulation management and threatened species recovery. [ABSTRACT FROM AUTHOR]

Published
2023
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17. Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations

Author

von Seth, J, Dussex, N, Diez-del-Molino, D, van der Valk, T, Kutschera, V E, Kierczak, M, Steiner, C C, Liu, S L, Gilbert, M T P, Sinding, M H S, Prost, S, Guschanski, K, Nathan, S K S S, Brace, S, Chan, Y L, Wheat, C W, Skoglund, P, Ryder, O A, Goossens, B, Gotherstrom, A, Dalen, L, von Seth, J, Dussex, N, Diez-del-Molino, D, van der Valk, T, Kutschera, V E, Kierczak, M, Steiner, C C, Liu, S L, Gilbert, M T P, Sinding, M H S, Prost, S, Guschanski, K, Nathan, S K S S, Brace, S, Chan, Y L, Wheat, C W, Skoglund, P, Ryder, O A, Goossens, B, Gotherstrom, A, and Dalen, L

Published
2021
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24. Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

Author

Krehenwinkel, H., Pomerantz, A., Henderson, J.B., Kennedy, S.R., Lim, J.Y., Swamy, V., Shoobridge, J.D., Graham, N., Patel, N.H., Gillespie, R.G., and Prost, S.

Subjects
Oxford Nanopore Technologies, purl.org/pe-repo/ocde/ford#1.02.03 [https], eukaryotes, ribosomal, metabarcoding, MinION, long DNA barcodes, purl.org/pe-repo/ocde/ford#1.02.01 [https], biodiversity
Abstract

BACKGROUND: In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies). FINDINGS: Using a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed Nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates. CONCLUSIONS: Sequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost-effective, portable, and universal approach for eukaryote DNA barcoding. Although bulk community analyses using long-amplicon approaches may introduce biases, the long rDNA amplicons approach signifies a powerful tool for enabling the accurate recovery of taxonomic and phylogenetic diversity across biological communities.

Published
2019

27. What are the challenges in 2016 regarding resistance to tyrosine kinase inhibitors in chronic myeloid leukemia and cancer?

Author

Lewis, M, Copland, M, Soverini, S, Sadovnik, I, Bedel, A, Prost, S, Italiano, A, Mahon, Fx., Lewis, M, Copland, M, Soverini, S, Sadovnik, I, Bedel, A, Prost, S, Italiano, A, and Mahon, Fx.

Subjects
chronic myeloid leukemia, hemic and lymphatic diseases, Leukemia, Myelogenous, Chronic, BCR-ABL Positive, tyrosine kinase inhibitors, Humans, leukemic stem cell, History, 21st Century, Protein Kinase Inhibitors, resistance to treatment
Abstract

In the past decade, the treatment of chronic myeloid leukemia (CML) has undergone a drastic evolution. The discovery and success of imatinib and second-generation tyrosine kinase inhibitors have substantially increased the outcome for CML patients. The next step in medical and scientific research is to better understand the malignancy so as to eventually find a cure to eliminate all leukemic cells from patients. One of the key issues is about the resistance of the leukemic stem cells to tyrosine kinase inhibitors. Here, we briefly describe our current studies on CML resistance, and leukemic stem cell modeling and characterization.

Published
2016

28. Outcomes of surgical treatments of spinal metastases: a prospective study.

Author

Bouthors, C., Prost, S., Court, C., Blondel, B., Charles, Y. P., Fuentes, S., Mousselard, H. P., Mazel, C., Flouzat-Lachaniette, C. H., Bonnevialle, P., Saihlan, F., and SOFCOT

Subjects
*LAMINECTOMY, *PROPORTIONAL hazards models, *KARNOFSKY Performance Status, *METASTASIS, *BONE metastasis, *LONGITUDINAL method, *PAIN management, *DISEASE progression, *RESEARCH, *PAIN, *RESEARCH methodology, *LUNG tumors, *RETROSPECTIVE studies, *CANCER relapse, *EVALUATION research, *MEDICAL cooperation, *TREATMENT effectiveness, *COMPARATIVE studies, *SPINAL tumors, *BREAST tumors, *SPINE
Abstract

Background: Owing to recent advances in cancer therapy, updated data are required for clinicians counselling patients on treatment of spinal metastases.Objective: To analyse the outcomes of surgical treatments of spinal metastases.Methods: Prospective and multicentric study that included consecutively patients operated on for spinal metastases between January 2016 and January 2017. Overall survival was calculated with the Kaplan-Meier method. Cox proportional hazard model was used to calculate hazard ratio (HR) analysing mortality risk according to preoperative Karnofsky performance status (KPS), mobility level and neurological status.Results: A total of 252 patients were included (145 males, 107 females) aged a mean 63.3 years. Median survival was 450 days. Primary cancer sites were lung (21%) and breast (19%). Multiple spinal metastases involved 122 patients (48%). Concomitant skeletal and visceral metastases were noted in 90 patients (36%). Main procedure was laminectomy and posterior fixation (57%). Overall, pain and mobility level were improved postoperatively. Most patients had normal preoperative motor function (50%) and remained so postoperatively. Patients "bedbound" on admission were the less likely to recover. In-hospital death rate was 2.4% (three disease progression, one septic shock, one pneumonia, one pulmonary embolism). Complication rate was 33%, deep wound infection was the most frequent aetiology. Higher mortality was observed in patients with poorest preoperative KPS (KPS 0-40%, HR = 3.1, p < 0.001) and mobility level ("bedbound", HR = 2.16, p < 0.001). Survival seemed also to be linked to preoperative neurological function.Conclusion: Surgical treatments helped maintain reasonable condition for patients with spinal metastases. Intervention should be offered before patients' condition worsen to ensure better outcomes. [ABSTRACT FROM AUTHOR]

Published
2020
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29. Ancient mitogenomes of Phoenicians from Sardinia and Lebanon: A story of settlement, integration, and female mobility

Author

Matisoo-Smith, E., primary, Gosling, A. L., additional, Platt, D., additional, Kardailsky, O., additional, Prost, S., additional, Cameron-Christie, S., additional, Collins, C. J., additional, Boocock, J., additional, Kurumilian, Y., additional, Guirguis, M., additional, Pla Orquín, R., additional, Khalil, W., additional, Genz, H., additional, Abou Diwan, G., additional, Nassar, J., additional, and Zalloua, P., additional

Published
2018
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30. Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe

Author

Horn, S, Prost, S, Stiller, M, Makowiecki, D, Kuznetsova, T, Benecke, N, Pucher, E, Hufthammer, AK, Schouwenburg, C, Shapiro, B, and Hofreiter, M

Subjects
Conservation Biology, Population, Population Genetics - Empirical, Rodentia, Genetic, Models, parasitic diseases, Genetics, otorhinolaryngologic diseases, Animals, Phylogeny, Institut für Biochemie und Biologie, Evolutionary Biology, Fossils, Nucleic Acid Hybridization, Genetic Variation, Bayes Theorem, DNA, Extinction, Biological Sciences, Biological, Mitochondrial, Europe, Phylogeography, Conservation Genetics, Sequence Analysis
Abstract

After centuries of human hunting, the Eurasian beaver Castor fiber had disappeared from most of its original range by the end of the 19th century. The surviving relict populations are characterized by both low genetic diversity and strong phylogeographical structure. However, it remains unclear whether these attributes are the result of a human-induced, late Holocene bottleneck or already existed prior to this reduction in range. To investigate genetic diversity in Eurasian beaver populations during the Holocene, we obtained mitochondrial control region DNA sequences from 48 ancient beaver samples and added 152 modern sequences from GenBank. Phylogeographical analyses of the data indicate a differentiation of European beaver populations into three mitochondrial clades. The two main clades occur in western and eastern Europe, respectively, with an early Holocene contact zone in eastern Europe near a present-day contact zone. A divergent and previously unknown clade of beavers from the Danube Basin survived until at least 6000 years ago, but went extinct during the transition to modern times. Finally, we identify a recent decline in effective population size of Eurasian beavers, with a stronger bottleneck signal in the western than in the eastern clade. Our results suggest that the low genetic diversity and the strong phylogeographical structure in recent beavers are artefacts of human hunting-associated population reductions. While beaver populations have been growing rapidly since the late 19th century, genetic diversity within modern beaver populations remains considerably reduced compared to what was present prior to the period of human hunting and habitat reduction. © 2014 John Wiley & Sons Ltd.

Published
2014

33. Transplantation of Macaca cynomolgus iPS-derived hematopoietic cells in NSG immunodeficient mice

Author

Abed, S., primary, Tubsuwan, A., additional, Chaichompoo, P., additional, Park, I. H., additional, Pailleret, A., additional, Benyoucef, A., additional, Tosca, L., additional, De Dreuzy, E., additional, Paulard, A., additional, Granger-Locatelli, M., additional, Relouzat, F., additional, Prost, S., additional, Tachdjian, G., additional, Fucharoen, S., additional, Daley, G. Q., additional, Payen, E., additional, Chretien, S., additional, Leboulch, P., additional, and Maouche-Chretien, L., additional

Published
2015
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46. Hepatitis B x protein inhibits p53-dependent DNA repair in primary mouse hepatocytes.

Author

Prost, S, Ford, J M, Taylor, C, Doig, J, and Harrison, D J

Abstract

The mechanisms by which the hepatitis B x protein (HBx) contributes to hepatocarcinogenesis remain unclear. However, interaction with the tumor suppressor gene p53 and inhibition of p53-dependent cellular functions, including nucleotide excision repair, could be central to this process. We studied the levels of global repair (removal of cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts) and transcription-coupled repair (removal of CPDs in both strands of the dihydrofolate reductase gene) in primary wild-type and p53-null mouse hepatocytes. We show that global repair of CPDs appears to be more efficient in mouse hepatocytes than in other commonly studied rodent cells and approaches the levels of human cells and that p53 is required for global genomic DNA repair of CPDs but not for transcription-coupled repair. We then investigated the effect of HBx expression on hepatocyte nucleotide excision repair. We demonstrate that HBx expression affects DNA repair in a p53-dependent manner. Transient HBx expression reduces global DNA repair in wild-type cells to the level of p53-null hepatocytes and has no effect on the repair of a transfected damaged plasmid. Therefore, in viral hepatitis, the hepatitis B virus could inhibit the p53-dependent component of global repair leading, over time, to accumulation of genetic defects and fostering carcinogenesis.

Published
1998

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