Rupert De Wachter’s research while affiliated with University of Antwerp and other places

... Cloacal swabs were collected before arriving at the facility. DNA was extracted from the swabs using a Maxwell RSC Buccal swab kit (Promega) according to the manufacturer's instructions to confirm the absence of C. jejuni by PCR as described by Eyers et al. (51), which was also used to confirm the absence of C. hepaticus. The absence of S. Typhimurium was confirmed by PCR, as described below. ...

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Immunological and pathobiological characteristics of a novel live Salmonella Typhimurium-vectored Campylobacter vaccine candidate for layer chickens

... Gaps and missing or ambiguous data were ignored. Nucleotide substitution rates for each alignment were calibrated as described by Van de Peer and De Wachter [64,65] using TreeCon. ...

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Diversity of Peronosporomycete (Oomycete) Communities Associated with the Rhizosphere of Different Plant Species

... Notably, Zhao and colleagues reported that the m.1095T>C mutation was correlated with ototoxicity and non-syndromic hearing loss in three Chinese families affected by this condition (Zhao et al., 2005). This T-to-C substitution, located within the 12S rRNA gene, was found to disrupt the highly conserved stem-loop structure of helix 25 (Neefs et al., 1991). Significantly, the m.1095T>C mutation was identified in affected individuals, but not in 364 Chinese control subjects. ...

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An update on ototoxicity: from a genetic perspective

... The dearth of molecular data for frenulate species becomes even more conspicuous when considering the limited number of sequences available compared to the extensive catalog of described species. As highlighted by Sen et al. (2018), a few sequences from frenulate species have been recurrently utilized across molecular studies for an extended period (Winnepenninckx et al. 1995;Black et al. 1997;Halanych et al. 2001;Rousset et al. 2004;Halanych 2005). Notably, only sequences from 12 Frenulata species are present in GenBank, accounting for a mere 7.8% of all described species. ...

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Rescuing the history of siboglinids in Brazilian deep waters: Neotype designation for the species Siboglinum besnardi Tommasi, 1970 and Siboglinum nonatoi Tommasi, 1970 (Annelida: Siboglinidae)

... 3; 94% BP in Van de Peer and De Wachter (1997a); see also Wainright et al. 1993], by its unique possession of a large insertion in protein synthesis elongation factor-1 (EF-1), and by analyses of the conservative, taxonomically well-sampled proteins -tubulin -tubulin, EF-1, and actin (Fig. 4) (Baldauf 1999). Although SSU rRNA data seem to resolve fungal relationships consistently and with high bootstrap support for many major clades (e.g., Bruns et al. 1992; Van de Peer et al. 1995), the overall divergence order among animal taxa is not well resolved by these data (Adoutte and Philippe 1993; Abouheif et al. 1998). Nevertheless, some important conclusions about metazoan relationships can be drawn on the basis of SSU rRNA. ...

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An Updated and Comprehensive rRNA Phylogeny of (Crown) Eukaryotes Based on Rate-Calibrated Evolutionary Distances

... This uncertainty can pose a serious limitation on the applicability of Sanger sequencing in colony identication when there is potential for multispecies colony formation. 42 Nanopore sequencing technology is emerging fast in the landscape of sequencing and is being applied for an increasing range of applications, including whole genome sequencing, microbiome analysis, and transcriptome analysis. 34,36,37,51 Underlying the rapid growth and increased acceptance of this technology is a continual advancement in the sequencing platform and basecalling algorithm, increased availability of protocols and bioinformatics tools for analysis, along with benchmarking studies conrming the robustness and reliability of performance. ...

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Application of nanopore sequencing for accurate identification of bioaerosol-derived bacterial colonies

... The forward primer 5 0 -GAAACTGCGAATGGCTCATT-3 0 and reverse primer 5 0 -GACGGGCGGTGTGTACAAAGG-3 0 were used for PCR amplification of the 18S rRNA gene region (Winnepenninckx et al. 1994;Hadziavdic et al. 2014). Tks Gflex DNA polymerase (TaKaRa Bio, Shiga, Japan) was used for the PCR reaction in accordance with the manufacturer's instructions. ...

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Far‐red light acclimation in Phaeophila dendroides ( Ulvales, Ulvophyceae ) isolated from a coral skeleton

... During the development of the European Database on small ribosomal RNA and its variability maps [9], a new numbering system was established, and the nine variable regions (V1-V9) were re-numbered according to the position of the helices ( Figure 1). Moreover, this new nomenclature highlighted that one variable region was missing in prokaryotes (V4) and another in eukaryotes (V6) [10][11][12][13][14][15][16][17][18][19]. ...

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About the Analysis of 18S rDNA Sequence Data from Trypanosomes in Barcoding and Phylogenetics: Tracing a Continuation Error Occurring in the Literature

... However, this contamination could be valuable on its own and possibly contain information on the presence of leaf endophytes. In fact, previous studies that used a DNA sequencing approach to detect leaf endophytes in Rubiaceae (e.g., Van Oevelen et al., 2001;Lemaire et al., 2011b;Verstraete et al., 2013a) also extracted total DNA but then eliminated the plant DNA by targeting bacterial DNA. ...

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Metagenomics of African Empogona and Tricalysia (Rubiaceae) reveals the presence of leaf endophytes

... Ç Ì ‡ÒÚÓfl˘Â ‚ÂÏfl ‚ ÒÓÒÚ ‡‚ ˝ÛÍ ‡ËÓÚÓ‚ ËÁ‚Â-ÒÚÌÓ ·ÓΠ80 Ó·ÓÒÓ·ÎÂÌÌ˚ı "ÛÔÔ Ó" ‡ÌËÁÏÓ‚, Á ‡-ÒÎÛÊË‚ ‡˛˘Ëı ‚˚ÒÓÍÓ"Ó Ú ‡ÍÒÓÌÓÏ˘ÂÒÍÓ"Ó  ‡Ì" ‡ -ÓÚ ˆ ‡ÒÚ‚ ‡ Ë ‚˚¯Â ‡-ÚÓ‚, 1973;Walters, Erdmann, 1988;Margulis, Gurrero, 1991;Schliegel, 1991;Van de Peer, 1992;äÛÒ ‡ÍËÌ, ÑÓÁ‰Ó‚, 1994Lipscomb et al., 1998. èË  ‡ÒÒÏÓÚÂÌËË Ì ‡Á‚ ‡ÌÌ˚ı "ÛÔÔ Ï˚ Ì ÓÒ-Ú ‡Ì ‡‚ÎË‚ ‡ÂÏÒfl ÔÓ‰Ó·ÌÓ Ì ‡ Ë ‚ÌÛÚÂÌÌÂÈ ÒËÒÚÂ-Ï ‡ÚËÍÂ, Ó" ‡Ì˘˂ ‡flÒ¸ Î˯¸ ÔÂ˜ËÒÎÂÌËÂÏ Ú ‡Í-ÒÓÌÓ‚, ‚ıÓ‰fl˘Ëı Ëı ‚ ÒÓÒÚ ‡‚. ...

Reference:

Revolution in Megataxonomy: Prerequisites and Results