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- Ritter, Camila, et al.
(författare)
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Advancing biodiversity assessments with environmental DNA: Long-read technologies help reveal the drivers of Amazonian fungal diversity
- 2020
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 10:14, s. 7509-7524
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Tidskriftsartikel (refereegranskat)abstract
- Fungi are a key component of tropical biodiversity. However, due to their inconspicuous and largely subterranean nature, they are usually neglected in biodiversity inventories. The goal of this study was to identify the key determinants of fungal richness, community composition, and turnover in tropical rainforests. We tested specifically for the effect of soil properties, habitat, and locality in Amazonia. For these analyses, we used high-throughput sequencing data of short and long reads of fungal DNA present in soil and organic litter samples, combining existing and novel genomic data. Habitat type (phytophysiognomy) emerges as the strongest factor explaining fungal community composition. Naturally open areas-campinas-are the richest habitat overall. Soil properties have different effects depending on the soil layer (litter or mineral soil) and the choice of genetic marker. We suggest that campinas could be a neglected hotspot of fungal diversity. An underlying cause for their rich diversity may be the overall low soil fertility, which increases the reliance on biotic interactions essential for nutrient absorption in these environments, notably ectomycorrhizal fungi-plant associations. Our results highlight the advantages of using both short and long DNA reads produced through high-throughput sequencing to characterize fungal diversity. While short reads can suffice for diversity and community comparison, long reads add taxonomic precision and have the potential to reveal population diversity.
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| 2. |
- Tjon-Kon-Fat, Lee-Ann, et al.
(författare)
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Platelets harbor prostate cancer biomarkers and the ability to predict therapeutic response to abiraterone in castration resistant patients
- 2018
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Ingår i: The Prostate. - : Wiley-Blackwell. - 0270-4137 .- 1097-0045. ; 78:1, s. 48-53
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Novel therapies for castration resistant prostate cancer (CRPC) have been introduced in the clinic with possibilities for individualized treatment plans. Best practice of those expensive drugs requires predictive biomarker monitoring. This study used circulating biomarker analysis to follow cancer-derived transcripts implicated in therapy resistance.METHOD: The isolated platelet population of blood samples and digital-PCR were used to identify selected biomarker transcripts in patients with CRPC prior chemo- or androgen synthesis inhibiting therapy.RESULTS: Fifty patients received either docetaxel (n = 24) or abiraterone (n = 26) therapy, with therapy response rates of 54% and 48%, respectively. Transcripts for the PC-associated biomarkers kallikrein-related peptidase-2 and -3 (KLK2, KLK3), folate hydrolase 1 (FOLH1), and neuropeptide-Y (NPY) were uniquely present within the platelet fraction of cancer patients and not detected in healthy controls (n = 15). In the abiraterone treated cohort, the biomarkers provided information on therapy outcome, demonstrating an association between detectable biomarkers and short progression free survival (PFS) (FOLH1, P < 0.01; KLK3, P < 0.05; and NPY, P < 0.05). Patients with biomarker-negative platelets had the best outcome, while FOLH1 (P < 0.05) and NPY (P = 0.05) biomarkers provided independent predictive information in a multivariate analysis regarding PFS. KLK2 (P < 0.01), KLK3 (P < 0.001), and FOLH1 (P < 0.05) biomarkers were associated with short overall survival (OS). Combining three biomarkers in a panel (KLK3, FOLH1, and NPY) made it possible to separate long-term responders from short-term responders with 87% sensitivity and 82% specificity.CONCLUSION: Analyzing tumor-derived biomarkers in platelets of CRPC patients enabled prediction of the outcome after abiraterone therapy with higher accuracy than baseline serum PSA or PSA response.
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| 3. |
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| 4. |
- Malm, Johan, et al.
(författare)
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Blood Plasma Reference Material – A Global Resource for Proteomic Research
- 2013
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 12:7, s. 3087-3092
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Tidskriftsartikel (refereegranskat)abstract
- There is an ever-increasing awareness and interest within the clinical research field that has creating a large demand for blood fraction samples as well as other clinical samples. The translational research area is another field that demanding for blood samples, used widely in proteomics, genomics, as well as metabolomics. Blood samples are the global most common biological samples that find its use in a broad variety of applications in Life Science. We hereby introduce a new reference blood plasma (EDTA) that is aimed as a global resource for the Proteomics community. We have developed these reference plasma standards by defining the Control group as those with CRP levels <3mg/L and a Disease group with CRP ranges >30 mg/L. In these references we have used both newborn children 1-2 weeks, as well as youngsters 10-15 years, and middle aged 30-50 years, and elderly patients at the ages of 65+. The total number of these reference plasma pools was 80 patients in each group. We provide data on the developments and characteristics of the reference blood plasma standards, as well as what is used by the team members at the respective laboratories. The standards have been evaluated by pilot sample processing in biobanking operations, and are currently a resource that allows the Proteomic society to perform quantitative proteomic studies. By the use of high quality reference plasma samples, global initiatives, such as the Chromosome Human Proteome Project (C-HPP), will benefit as one scientific program when the entire human proteome is mapped and linked to human diseases.
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| 5. |
- Malm, Johan, et al.
(författare)
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Large Scale Biobanking of Blood – The Importance of High Density Sample Processing Procedures
- 2012
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Ingår i: Journal of Proteomics. - : Elsevier BV. - 1874-3919. ; 76:1, s. 116-124
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Tidskriftsartikel (refereegranskat)abstract
- We introduce a novel automated sample-processing concept that will be of mandatory importance to proteomics and future clinical research, performing patient studies from resulting blood fractions in various disease areas. Biobank storage of small sample volumes allows for high replicate numbers to be processed and aliquoted, where each sample aliquot can be used for a dedicated clinical analysis and end-point measurement. In order to preserve sample integrity and value over time, the principle of single usage is gaining recognition. We hereby present a 384-format sample tube system for the preservation and archiving of clinical patient samples that will form the basis for future proteomics studies. This high density scaling allows for reproducible aliquoting 70-µL volumes of blood fractions. Blood plasma with EDTA, Li-heparin, and citrate, as anti-coagulants, are fractioned along with the buffy coat and the erythrocyte fraction, in addition to the serum fraction. We demonstrate an automated sample handling for biobanking: samples from patients were processed and aliquoted in both 96- and 384-sample racks by liquid handling robotics and Laboratory Intelligence Management System (LIMS) overview and control. Within this study, the blood samples were analyzed by the Clinical Chemistry department at the Southern University Hospital in Malmö, using standard biomarker assays, quantifying 23 common markers used in everyday healthcare around the world. We were able to prove that the 384-format using an aluminum foil with a thin polymer film coating for sealing, is stable and can reproducibly be processed for automated biobank freezer units.
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