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- ItemConsensusPrime—A Bioinformatic Pipeline for Ideal Consensus Primer Design(Basel : MDPI, 2022) Collatz, Maximilian; Braun, Sascha D.; Monecke, Stefan; Ehricht, RalfBackground: High-quality oligonucleotides for molecular amplification and detection procedures of diverse target sequences depend on sequence homology. Processing input sequences and identifying homogeneous regions in alignments can be carried out by hand only if they are small and contain sequences of high similarity. Finding the best regions for large and inhomogeneous alignments needs to be automated. Results: The ConsensusPrime pipeline was developed to sort out redundant and technical interfering data in multiple sequence alignments and detect the most homologous regions from multiple sequences. It automates the prediction of optimal consensus primers for molecular analytical and sequence-based procedures/assays. Conclusion: ConsensusPrime is a fast and easy-to-use pipeline for predicting optimal consensus primers that is executable on local systems without depending on external resources and web services. An implementation in a Docker image ensures platform-independent executability and installability despite the combination of multiple programs. The source code and installation instructions are publicly available on GitHub.
- ItemWhat the Phage: a scalable workflow for the identification and analysis of phage sequences(Oxford : Oxford University Press, 2022) Marquet, Mike; Hölzer, Martin; Pletz, Mathias W; Viehweger, Adrian; Makarewicz, Oliwia; Ehricht, Ralf; Brandt, ChristianPhages are among the most abundant and diverse biological entities on earth. Phage prediction from sequence data is a crucial first step to understanding their impact on the environment. A variety of bacteriophage prediction tools have been developed over the years. They differ in algorithmic approach, results, and ease of use. We, therefore, developed "What the Phage"(WtP), an easy-to-use and parallel multitool approach for phage prediction combined with an annotation and classification downstream strategy, thus supporting the user's decision-making process by summarizing the results of the different prediction tools in charts and tables. WtP is reproducible and scales to thousands of datasets through a workflow manager (Nextflow). WtP is freely available under a GPL-3.0 license (https://github.com/replikation/What_the_Phage).
- ItemComplete genome sequence of a new clostridium sp. isolated from anaerobic digestion and biomethanation(Washington, DC : American Society for Microbiology, 2020) Hahnke, Sarah; Abendroth, Christian; Pascual, Javier; Langer, Thomas; Ramm, Patrice; Klocke, Michael; Luschnig, Olaf; Porcar, ManuelHere, we present the genome sequence and annotation of the bacterial strain HV4-5-A1G, a potentially new Clostridium species. Based on its genomic data, this strain may act as a keystone microorganism in the hydrolysis of complex polymers, as well as in the different acidogenesis and acetogenesis steps during anaerobic digestion. © 2020 Hahnke et al.
- ItemA “built-up” composite film with synergistic functionalities on Mg–2Zn–1Mn bioresorbable stents improves corrosion control effects and biocompatibility([Bejing] : KeAi Publishing, 2023) Dou, Zhenglong; Chen, Shuiling; Wang, Jiacheng; Xia, Li; Maitz, Manfred F.; Tu, Qiufen; Zhang, Wentai; Yang, Zhilu; Huang, NanControl of premature corrosion of magnesium (Mg) alloy bioresorbable stents (BRS) is frequently achieved by the addition of rare earth elements. However, limited long-term experience with these elements causes concerns for clinical application and alternative methods of corrosion control are sought after. Herein, we report a “built-up” composite film consisting of a bottom layer of MgF2 conversion coating, a sandwich layer of a poly (1, 3-trimethylene carbonate) (PTMC) and 3-aminopropyl triethoxysilane (APTES) co-spray coating (PA) and on top a layer of poly (lactic-co-glycolic acid) (PLGA) ultrasonic spray coating to decorate the rare earth element-free Mg–2Zn–1Mn (ZM21) BRS for tailoring both corrosion resistance and biological functions. The developed “built-up” composite film shows synergistic functionalities, allowing the compression and expansion of the coated ZM21 BRS on an angioplasty balloon without cracking or peeling. Of special importance is that the synergistic corrosion control effects of the “built-up” composite film allow for maintaining the mechanical integrity of stents for up to 3 months, where complete biodegradation and no foreign matter residue were observed about half a year after implantation in rabbit iliac arteries. Moreover, the functionalized ZM21 BRS accomplished re-endothelialization within one month.
- ItemInternational transfers of personal data for health research following Schrems II: a problem in need of a solution(Basingstoke : Stockton Press, 2021) Hallinan, Dara; Bernier, Alexander; Cambon-Thomsen, Anne; Crawley, Francis P.; Dimitrova, Diana; Bauzer Medeiros, Claudia; Nilsonne, Gustav; Parker, Simon; Pickering, Brian; Rennes, StéphanieOn 16 July 2020, the Court of Justice of the European Union issued their decision in the Schrems II case concerning Facebook's transfers of personal data from the EU to the US. The decision may have significant effects on the legitimate transfer of personal data for health research purposes from the EU. This article aims: (i) to outline the consequences of the Schrems II decision for the sharing of personal data for health research between the EU and third countries, particularly in the context of the COVID-19 pandemic; and, (ii) to consider certain options available to address the consequences of the decision and to facilitate international data exchange for health research moving forward.
- ItemPhoto-functionalized TiO2 nanotubes decorated with multifunctional Ag nanoparticles for enhanced vascular biocompatibility(Bejing : KeAi Publishing, 2021) Chen, Jiang; Dai, Sheng; Liu, Luying; Maitz, Manfred F.; Liao, Yuzhen; Cui, Jiawei; Zhao, Ansha; Yang, Ping; Huang, Nan; Wang, YunbingTitanium dioxide (TiO2) has a long history of application in blood contact materials, but it often suffers from insufficient anticoagulant properties. Recently, we have revealed the photocatalytic effect of TiO2 also induces anticoagulant properties. However, for long-term vascular implant devices such as vascular stents, besides anticoagulation, also anti-inflammatory, anti-hyperplastic properties, and the ability to support endothelial repair, are desired. To meet these requirements, here, we immobilized silver nanoparticles (AgNPs) on the surface of TiO2 nanotubes (TiO2-NTs) to obtain a composite material with enhanced photo-induced anticoagulant property and improvement of the other requested properties. The photo-functionalized TiO2-NTs showed protein-fouling resistance, causing the anticoagulant property and the ability to suppress cell adhesion. The immobilized AgNPs increased the photocatalytic activity of TiO2-NTs to enhances its photo-induced anticoagulant property. The AgNP density was optimized to endow the TiO2-NTs with anti-inflammatory property, a strong inhibitory effect on smooth muscle cells (SMCs), and low toxicity to endothelial cells (ECs). The in vivo test indicated that the photofunctionalized composite material achieved outstanding biocompatibility in vasculature via the synergy of photo-functionalized TiO2-NTs and the multifunctional AgNPs, and therefore has enormous potential in the field of cardiovascular implant devices. Our research could be a useful reference for further designing of multifunctional TiO2 materials with high vascular biocompatibility.
- ItemAnatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research(London : BioMed Central, 2022) Vogt, Lars; Mikó, István; Bartolomaeus, ThomasBackground: In times of exponential data growth in the life sciences, machine-supported approaches are becoming increasingly important and with them the need for FAIR (Findable, Accessible, Interoperable, Reusable) and eScience-compliant data and metadata standards. Ontologies, with their queryable knowledge resources, play an essential role in providing these standards. Unfortunately, biomedical ontologies only provide ontological definitions that answer What is it? questions, but no method-dependent empirical recognition criteria that answer How does it look? questions. Consequently, biomedical ontologies contain knowledge of the underlying ontological nature of structural kinds, but often lack sufficient diagnostic knowledge to unambiguously determine the reference of a term. Results: We argue that this is because ontology terms are usually textually defined and conceived as essentialistic classes, while recognition criteria often require perception-based definitions because perception-based contents more efficiently document and communicate spatial and temporal information—a picture is worth a thousand words. Therefore, diagnostic knowledge often must be conceived as cluster classes or fuzzy sets. Using several examples from anatomy, we point out the importance of diagnostic knowledge in anatomical research and discuss the role of cluster classes and fuzzy sets as concepts of grouping needed in anatomy ontologies in addition to essentialistic classes. In this context, we evaluate the role of the biological type concept and discuss its function as a general container concept for groupings not covered by the essentialistic class concept. Conclusions: We conclude that many recognition criteria can be conceptualized as text-based cluster classes that use terms that are in turn based on perception-based fuzzy set concepts. Finally, we point out that only if biomedical ontologies model also relevant diagnostic knowledge in addition to ontological knowledge, they will fully realize their potential and contribute even more substantially to the establishment of FAIR and eScience-compliant data and metadata standards in the life sciences.
- ItemGlobal data on earthworm abundance, biomass, diversity and corresponding environmental properties(London : Nature Publ. Group, 2021) Phillips, Helen R. P.; Bach, Elizabeth M.; Bartz, Marie L. C.; Bennett, Joanne M.; Beugnon, Rémy; Briones, Maria J. I.; Brown, George G.; Ferlian, Olga; Gongalsky, Konstantin B.; Guerra, Carlos A.; König-Ries, Birgitta; López-Hernández, Danilo; Loss, Scott R.; Marichal, Raphael; Matula, Radim; Minamiya, Yukio; Moos, Jan Hendrik; Moreno, Gerardo; Morón-Ríos, Alejandro; Motohiro, Hasegawa; Muys, Bart; Krebs, Julia J.; Neirynck, Johan; Norgrove, Lindsey; Novo, Marta; Nuutinen, Visa; Nuzzo, Victoria; Mujeeb Rahman, P.; Pansu, Johan; Paudel, Shishir; Pérès, Guénola; Pérez-Camacho, Lorenzo; Orgiazzi, Alberto; Ponge, Jean-François; Prietzel, Jörg; Rapoport, Irina B.; Rashid, Muhammad Imtiaz; Rebollo, Salvador; Rodríguez, Miguel Á.; Roth, Alexander M.; Rousseau, Guillaume X.; Rozen, Anna; Sayad, Ehsan; Ramirez, Kelly S.; van Schaik, Loes; Scharenbroch, Bryant; Schirrmann, Michael; Schmidt, Olaf; Schröder, Boris; Seeber, Julia; Shashkov, Maxim P.; Singh, Jaswinder; Smith, Sandy M.; Steinwandter, Michael; Russell, David J.; Szlavecz, Katalin; Talavera, José Antonio; Trigo, Dolores; Tsukamoto, Jiro; Uribe-López, Sheila; de Valença, Anne W.; Virto, Iñigo; Wackett, Adrian A.; Warren, Matthew W.; Webster, Emily R.; Schwarz, Benjamin; Wehr, Nathaniel H.; Whalen, Joann K.; Wironen, Michael B.; Wolters, Volkmar; Wu, Pengfei; Zenkova, Irina V.; Zhang, Weixin; Cameron, Erin K.; Eisenhauer, Nico; Wall, Diana H.; Brose, Ulrich; Decaëns, Thibaud; Lavelle, Patrick; Loreau, Michel; Mathieu, Jérôme; Mulder, Christian; van der Putten, Wim H.; Rillig, Matthias C.; Thakur, Madhav P.; de Vries, Franciska T.; Wardle, David A.; Ammer, Christian; Ammer, Sabine; Arai, Miwa; Ayuke, Fredrick O.; Baker, Geoff H.; Baretta, Dilmar; Barkusky, Dietmar; Beauséjour, Robin; Bedano, Jose C.; Birkhofer, Klaus; Blanchart, Eric; Blossey, Bernd; Bolger, Thomas; Bradley, Robert L.; Brossard, Michel; Burtis, James C.; Capowiez, Yvan; Cavagnaro, Timothy R.; Choi, Amy; Clause, Julia; Cluzeau, Daniel; Coors, Anja; Crotty, Felicity V.; Crumsey, Jasmine M.; Dávalos, Andrea; Cosín, Darío J. Díaz; Dobson, Annise M.; Domínguez, Anahí; Duhour, Andrés Esteban; van Eekeren, Nick; Emmerling, Christoph; Falco, Liliana B.; Fernández, Rosa; Fonte, Steven J.; Fragoso, Carlos; Franco, André L. C.; Fusilero, Abegail; Geraskina, Anna P.; Gholami, Shaieste; González, Grizelle; Gundale, Michael J.; López, Mónica Gutiérrez; Hackenberger, Branimir K.; Hackenberger, Davorka K.; Hernández, Luis M.; Hirth, Jeff R.; Hishi, Takuo; Holdsworth, Andrew R.; Holmstrup, Martin; Hopfensperger, Kristine N.; Lwanga, Esperanza Huerta; Huhta, Veikko; Hurisso, Tunsisa T.; Iannone, Basil V.; Iordache, Madalina; Irmler, Ulrich; Ivask, Mari; Jesús, Juan B.; Johnson-Maynard, Jodi L.; Joschko, Monika; Kaneko, Nobuhiro; Kanianska, Radoslava; Keith, Aidan M.; Kernecker, Maria L.; Koné, Armand W.; Kooch, Yahya; Kukkonen, Sanna T.; Lalthanzara, H.; Lammel, Daniel R.; Lebedev, Iurii M.; Le Cadre, Edith; Lincoln, Noa K.Earthworms are an important soil taxon as ecosystem engineers, providing a variety of crucial ecosystem functions and services. Little is known about their diversity and distribution at large spatial scales, despite the availability of considerable amounts of local-scale data. Earthworm diversity data, obtained from the primary literature or provided directly by authors, were collated with information on site locations, including coordinates, habitat cover, and soil properties. Datasets were required, at a minimum, to include abundance or biomass of earthworms at a site. Where possible, site-level species lists were included, as well as the abundance and biomass of individual species and ecological groups. This global dataset contains 10,840 sites, with 184 species, from 60 countries and all continents except Antarctica. The data were obtained from 182 published articles, published between 1973 and 2017, and 17 unpublished datasets. Amalgamating data into a single global database will assist researchers in investigating and answering a wide variety of pressing questions, for example, jointly assessing aboveground and belowground biodiversity distributions and drivers of biodiversity change.
- ItemPhenotypic and Molecular Detection of Biofilm Formation in Staphylococcus aureus Isolated from Different Sources in Algeria(Basel : MDPI, 2020) Achek, Rachid; Hotzel, Helmut; Nabi, Ibrahim; Kechida, Souad; Mami, Djamila; Didouh, Nassima; Tomaso, Herbert; Neubauer, Heinrich; Ehricht, Ralf; Monecke, Stefan; El-Adawy, HosnyStaphylococcus aureus is an opportunistic bacterium causing a wide variety of diseases. Biofilm formation of Staphylococcus aureus is of primary public and animal health concern. The purposes of the present study were to investigate the ability of Staphylococcus aureus isolated from animals, humans, and food samples to form biofilms and to screen for the presence of biofilmassociated and regulatory genes. In total, 55 Staphylococcus aureus isolated from sheep mastitis cases (n = 28), humans (n = 19), and from food matrices (n = 8) were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The ability of Staphylococcus aureus for slime production and biofilm formation was determined quantitatively. A DNA microarray examination was performed to detect adhesion genes (icaACD and biofilmassociated protein gene (bap)), genes encoding microbial surface components recognizing adhesive matrix molecules (MSCRAMMs), regulatory genes (accessory gene regulator (agr) and staphylococcal accessory regulator (sarA)), and the staphylococcal cassette chromosome mec elements (SCCmec). Out of 55 Staphylococcus aureus isolates, 39 (71.0%) and 23 (41.8%) were producing slime and biofilm, respectively. All Staphylococcus aureus strains isolated from food showed biofilm formation ability. 52.6% of the Staphylococcus aureus strains isolated from sheep with mastitis, and 17.9% of isolates from humans, were able to form a biofilm. Microarray analysis typed the Staphylococcus aureus into 15 clonal complexes. Among all Staphylococcus aureus isolates, four of the human isolates (21.1%) harbored the mecA gene (SCCmec type IV) typed into 2 clonal complexes (CC22-MRSA-IV and CC80-MRSA-IV) and were considered as methicillin-resistant, while two of them were slime-producing. None of the isolates from sheep with mastitis harbored the cna gene which is associated with biofilm production. The fnbB gene was found in 100%, 60% and 40% of biofilm-producing Staphylococcus aureus isolated from food, humans, and sheep with mastitis, respectively. Three agr groups were present and agr group III was predominant with 43.6%, followed by agr group I (38.2%), and agr group II (18.2%). This study revealed the capacity of Staphylococcus aureus isolates to form biofilms and highlighted the genetic background displayed by Staphylococcus aureus isolates from different sources in Algeria. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
- ItemFormer Training Relieves the Later Development of Behavioral Inflexibility in an Animal Model Overexpressing the Dopamine Transporter(Totowa, NJ : Humana Press, 2022) Edemann-Callesen, Henriette; Glienke, Maximilian; Akinola, Esther Olubukola; Lieser, Maike Kristin; Habelt, Bettina; Hadar, Ravit; Bernhardt, Nadine; Winter, ChristineA range of dopamine-dominating neuropsychiatric disorders present with cognitive deficits. In accordance, the dopamine transporter overexpressing rat model (DAT-tg rat) displays cognitive deficits by means of behavioral inflexibility and learning disabilities. It remains to be investigated when cognitive deficits emerge, due to the inherent DA irregularities, during the life course of the DAT-tg rat and what may relieve symptoms. The Morris water maze (MWM) was used to assess cognitive abilities in three cohorts of DAT-tg rats. In the first cohort, the development of cognitive deficits was assessed by repeatedly testing animals in the MWM at postnatal day (PND) 35, 60, and 90. In the second and third cohort, pharmacological interventions and transcranial direct current stimulation (tDCS) were tested in adult animals to understand what drives, and thus relieves, the deficits. Minor differences were observed between DAT-tg rats and control rats at PND 35 and 60, whereas cognitive deficits fully emerged at PND 90. A high dosage of methylphenidate diminished both behavioral inflexibility and improved learning abilities in adult rats. Interestingly, rats subjected early in life to the MWM also displayed improved behavioral flexibility as compared to rats naïve to the paradigm. Cognitive deficits gradually develop over time and fully emerge in adulthood. Pharmacological modulation of the ubiquitous DAT overexpression overall improves deficits in adult rats, whereas early training decreases later development of behavioral inflexibility. Thus, former training may constitute a preventive avenue that alters some aspects of cognitive deficits resulting from inherent DA abnormalities.