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opencc-by-4.0Nov 2023View details →

Online Appendix for PhD Thesis Titled "Dissecting Causal Relationships and Molecular Mechanisms in Disease using Genetic Risk Profiles"

This repository contains 23 tables and two figures, which are too big to be included in the Appendix section of my thesis document. The second version includes additional summary statistics of metabolite-PGS associations which can be found at http://mrcieu.mrsoftware.org/metabolites_PRS_atlas/.

opencc-by-4.0Aug 2021View details →

Molecular characterization and genetic diversity of four undescribed novel oleaginous Mortierella alpina strains from Libya

A large number of undiscovered fungal species still exist on earth, which can be useful for bioprospecting, particularly for single cell oil (SCO) production. Mortierella is one of the significant genera in this field and contains about hundred species. Moreover, M. alpina is the main single cell oil producer / arachidonic acid producer at commercial scale under this genus.

opencc-by-4.0Sep 2021View details →

Dataset related to article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant".

The files contain raw data related to the article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant", available from <a href="https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/full">https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/ful</a>l. File "Genetic and clinical data": <ul> <li>In the sheet "485 aHUS patients" are reported data obtained from the screening of 485 unrelated patients with aHUS including rare variants (RVs) in complement disease-associated genes (CFH, CD46, CFI, C3, CFB and THBD), the presence of CFH-CFHR genomic rearrangements and/or anti-FH antibodies.</li> <li>In the sheet "Pedigrees with c.286+2T>G" are listed all pedigrees carrying the c.286+2T>G variant, the diseases status of all subjects and the age of disease onset of patients. In bold are indicated pedigrees (n=7) used to study the penetrance of aHUS in c.286+2T>G carriers.</li> <li>In the sheet "Haplotypes" are reported genotypes used to evaluate the association between the presence of CFH-H3 and CD46GGAAC risk haplotypes and aHUS. Results of this analysis are reported in Table 3 of the published paper.</li> <li>In the sheet "Raw data Fig.2" are reported data of "platelet count" and "serum creatinine" of the proband used to elaborate Figure 2.</li> </ul> In the file "C3 and C5b-9 deposition" is reported the quantification of serum-induced C3 and C5b-9 deposition on human microvascular endothelial cell line (HMEC-1). The fluorescent staining was evaluated with Image J and expressed as pixel2 per field analyzed. The fields with the lowest and highest values were excluded from calculation. These values were used to elaborate data included in Table 2 and in Figure 5. In the file "CD46 protein expression" are reported data of CD46 expression on peripheral blood mononuclear cells (PBMCs) isolated from the proband, his relatives and healthy volunteers. Data of specific expression of CD46 (evaluated for SCR1 or for SCR4 as reported in the materials and methods section) are indicated as median fluorescence intensity (MFI) percentage compared with the control. In the ppt file "cDNA amplification and sequencing results" is reported: <ul> <li>the agarose gel image of the amplified cDNA from the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> <li>Electropherograms obtained from the cDNA sequencing of the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> </ul> Additional data will be made available by the authors, without undue reservation, to any qualified researcher.

opencc-by-4.0Jul 2023View details →

Three systems of molecular markers reveal genetic differences between varieties sabina and balkanensis in the Juniperus sabina L. range

Genotypes of 94 Juniperus sabina samples from 14 populations at SNP (Jsabina_SNPs.txt) and SilicoDArT (Jsabina_SilicoDArTs.txt) loci investigated using the DArTseq technology developed by Diversity Array Technology Pty Ltd (DArT, Canberra, ACT, Australia)

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Data from: Drift happens: molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests

Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus FST = 0.32, FST' = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R2 = 0.51) and higher local inbreeding (R2 = 0.22). Populations varied greatly in levels of local inbreeding (FIS = 0.2 to 0.9) and FIS declined in smaller, more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.

opencc-zeroDec 2018View details →

FIGURE 17. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology

FIGURE 17. Hungarosoma bokori Verhoeff, 1928, female, vulvae (Driny Cave). Vulvae in posterior-ventral view (o = opercula) Not scaled.

FIGURE 19 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology

FIGURE 19. Distribution of the genus Hungarosoma Verhoeff, 1928. Empty dot: H. inexpectatum, solid dots: H. bokori. Distribution of H. bokori in Slovak-Aggtelek Karst drawn in higher scale.

FIGURE 18. A in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology

FIGURE 18. A Maximum-Likelihood tree (GTR + G + I model) based on the COI gene and rooted with Polyxenus lagurus. All data—except from H. bokori — were obtained from Genbank. Numbers refer to bootstrap values (1000 replicates). Scale bar = 0.02 substitutions / site. For origin of the H. bokori material, see Table 1.

FIGURES 12 – 14. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology

FIGURES 12 – 14. Hungarosoma bokori Verhoeff, 1928, male (Abaliget Cave). 12: Antenna. 13: Gonopod complex, anterior view. The right side of pair structures is slightly turned laterally. 14: Gonopods in right lateral view. Abbreviations: Letters a – h signal equivalent structures in both views. Anterior gonopods (legs 8): a = cheirite, b = brush-like arm, c = additive divided arm, d = hyaline process. Posterior gonopods (legs 9): e = gonopod, f = ventral hyaline prominence, g = claw shape process with long seta. Not scaled. Photos: Andrej Mock.

FIGURES 6 – 9. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology

FIGURES 6 – 9. Hungarosoma bokori Verhoeff, 1928, specimens from the Abaliget Cave, preserved in alcohol (not scaled). 6: Habitus of adult male in lateral view; the cheirites of anterior gonopods are visible. 7: Details of the dorsal part of the male trunk. 8: Ventral side of mid-body segments in detail. 9: Dorsal side of a juvenile of stadium III with the shape of the pleurotergites typical for the genus (all material from the Abaliget Cave, Hungary). Photos: Andrej Mock.

FIGURES 10 – 11. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology

FIGURES 10 – 11. Hungarosoma bokori Verhoeff, 1928, female from the Driny Cave, scanning electronic microscopy of details of the shape and surface of mid-body segments. 10: Dorsolateral view (left side). 11: A pleurotergite, dorsolateral view in detail. Photos: Andrej Mock & Karel Tajovský.

FIGURE 16. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology

FIGURE 16. Hungarosoma bokori Verhoeff, 1928, male, gonopods (Abaliget Cave). Right lateral view. Letters a – h signal equivalent structures in both views. Abbreviations: Letters a – h signal equivalent structures in both views. Anterior gonopods (legs 8): a = cheirite, b = brush-like arm, c = additive divided arm, d = hyaline process. Posterior gonopods (legs 9): e = gonopod, f = ventral hyaline prominence, g = claw shape process with long seta.

FIGURES 2 – 5. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology

FIGURES 2 – 5. Hungarosoma bokori Verhoeff, 1928, female, holotype (Abaliget Cave). 2: Head end of the body, right lateral view. 3: Tergite 15, dorsal view. 4: Antenna, lateral view. 5: Discernable vulvae in situ (v), right lateral view. Photos: Jörg Spelda.

FIGURE 15. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology

FIGURE 15. Hungarosoma bokori Verhoeff, 1928, male, gonopods (Abaliget Cave). Anterior view (right side of pair structures is slightly turned laterally). Abbreviations: Letters a – h signal equivalent structures in both views. Anterior gonopods (legs 8): a = cheirite, b = brush-like arm, c = additive divided arm, d = hyaline process. Posterior gonopods (legs 9): e = gonopod, f = ventral hyaline prominence, g = claw shape process with long seta.

FIGURE 1. Hungarosoma bokori Verhoeff, 1928 in Hungarosoma bokori Verhoeff, 1928 (Diplopoda: Chordeumatida): new insights into its taxonomy, systematics, molecular genetics, biogeography and ecology

FIGURE 1. Hungarosoma bokori Verhoeff, 1928, female, sampled at the entrance of the Baradla Cave, Hungary, 21. iii. 2013. Photo: Ľubomír Kováč & Andrej Mock.

Figure 6 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 6. Variation of the live adult male paratype GZNU20220705001 of Rana zhijinensis Luo, Xiao & Zhou, sp. nov. A. Dorsolateral view; B. Dorsal view; C. Ventral view.

Figure 1 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 1. Sampling localities of Rana zhijinensis Luo, Xiao & Zhou, sp. nov., R. culaiensis, R. hanluica, and R. omeimontis in Guizhou Province, China. A. Guiguo Town, Zhijin County; B. Supu Town, Qianxi County; C. Zhujianshan Nature Reserve, Huangping County; D. Leigongshan National Nature Reserve, Leishan County.

Figure 2 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 2. Phylogenetic tree based on three mitochondrial genes and six nuclear genes. A. Maternal tree; B. Nuclear gene tree. In both phylogenetic tree, ultrafast bootstrap support (UFB) values from ML analyses/Bayesian posterior probabilities (BPP) from BI analyses are given beside nodes. Scale bars denote nucleotide substitutions per sites for mitochondrial and nuclear genes.

Figure 5 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 5. Morphological features of the live adult male holotype GZNU2018081606 of Rana zhijinensis Luo, Xiao & Zhou, sp. nov. A. Dorsolateral view; B. Dorsal view; C. Ventral view; D. Egg cluster; E. Ventral view of hand and dark gray-blackish nuptial pad; F. Ventral view of foot.