Ines Yang

Hannover Medical School | MHH · Clinic for Dental Prosthetics

Bacterial adhesion to dental implants is the onset for the development of pathological biofilms. Reliable characterization of this initial process is the basis towards the development of anti-biofilm strategies. In the present study, single-cell force spectroscopy (SCFS), by means of an atomic force microscope connected to a microfluidic pressure c...

Background Peri-implant mucositis and peri-implantitis are highly prevalent biofilm-associated diseases affecting the tissues surrounding dental implants. As antibiotic treatment is ineffective to fully cure biofilm mediated infections, antimicrobial modifications of implants to reduce or prevent bacterial colonization are called for. Preclinical i...

The RNA helicase RIG-I plays a key role in sensing pathogen-derived RNA. Double-stranded RNA structures bearing 5'-tri- or diphosphates are commonly referred to as activating RIG-I ligands. However, endogenous RNA fragments generated during viral infection via RNase L also activate RIG-I. Of note, RNase-digested RNA fragments bear a 5'-hydroxyl gro...

Objectives The aim of this study was to evaluate volume, vitality and diversity of biofilms on the abutment materials zirconia and titanium as a function of time using an in vivo model for the biofilm formation. Materials and methods The development of biofilms on zirconia and titanium grade 4 test specimens in the human oral cavity over time was...

Aim SLC26A3 (DRA) mediates the absorption of luminal Cl‐ in exchange for HCO3‐ in the distal intestine. Its expression is lost in congenital chloride diarrhoea (CLD) and strongly decreased in the presence of intestinal inflammation. To characterize the consequences of a loss of Slc26a3 beyond disturbed electrolyte transport, colonic mucus synthesis...

To combat implant-associated infections, there is a need for novel materials which effectively inhibit bacterial biofilm formation. In the present study, the antiadhesive properties of titanium surface functionalization based on the "slippery liquid-infused porous surfaces" (SLIPS) principle were demonstrated and the underlying mechanism was analyz...

Aggregatibacter and Haemophilus species are relevant human commensals and opportunistic pathogens. Consequently, their bacteriophages may have significant impact on human microbial ecology and pathologies. Our aim was to reveal the prevalence and diversity of bacteriophages infecting Aggregatibacter and Haemophilus species that colonize the human b...

Infection with the emerging pathogen Clostridioides (Clostridium) difficile might lead to colonization of the gastrointestinal tract of humans and mammals eventually resulting in antibiotic-associated diarrhea, which can be mild to possibly life-threatening. Recurrences after antibiotic treatment have been described in 15–30% of the cases and are e...

Background & aims: Helicobacter pylori is remarkable for its genetic variation. Yet little isknown about its genetic changes during early stages of human infection, as the bacteria adapt to their new environment. We analyzed genome and methylome variations in a fully virulent strain of H pylori strain during experimental infection. Methods: We p...

Recombination plays a dominant role in the evolution of the bacterial pathogenHelicobacterpylori, but its dynamics remain incompletely understood. Here we use anin vitrotransformation system combined with genome sequencing to study chromosomal integrationpatterns after natural transformation. A single transformation cycle results in up to 21imports...

Supplementary Figures 1-7, Supplementary Tables 1-6 and Supplementary References

Inhabitants of Túquerres in the Colombian Andes have a 25-fold higher risk of gastric cancer than inhabitants of the coastal town Tumaco, despite similar H. pylori prevalences. The gastric microbiota was recently shown in animal models to accelerate the development of H. pylori-induced precancerous lesions. 20 individuals from each town, matched fo...

The human diarrheal pathogens Campylobacter jejuni and Campylobacter coli interfere with host innate immune signaling by different means, and their flagellins, FlaA and FlaB, have a low intrinsic property to activate the innate immune receptor Toll-like receptor 5 (TLR5). We have investigated here the hypothesis that the unusual secreted, flagellin...

The epithelium is the main entry point for many viruses, but the processes that protect barrier surfaces against viral infections are incompletely understood. Here we identified interleukin 22 (IL-22) produced by innate lymphoid cell group 3 (ILC3) as an amplifier of signaling via interferon-λ (IFN-λ), a synergism needed to curtail the replication...

Recent results indicate a significant contribution of innate immune signaling to maintain mucosal homeostasis, but the precise underlying signal transduction pathways are ill-defined. By comparative analysis of intestinal epithelial cells isolated from conventionally raised and germ-free mice, as well as animals deficient in the adaptor molecules M...

Antimicrobial peptides (AMP) provide protection from infection by pathogenic microorganisms and restrict bacterial growth at epithelial surfaces to maintain mucosal homeostasis. In addition, they exert a significant anti-inflammatory activity. Here we analysed the anatomical distribution and biological activity of an orally administered AMP in the...

The mouse pathobiont Helicobacter hepaticus can induce typhlocolitis in interleukin-10-deficient mice, and H. hepaticus infection of immunodeficient mice is widely used as a model to study the role of pathogens and commensal bacteria in the pathogenesis of inflammatory bowel disease. C57BL/6J Il10(-/-) mice kept under specific pathogen-free conditi...

Genera as identified by RDP classifier, including distribution among individual samples. (XLS)

OTU classification according to (1) 80% consensus of classification of individual sequences and (2) classification of OTU consensus sequences (3) final OTU classification. (XLS)

Normalized mutual information (NMI) value between species and OTUs obtained for 30 difference levels using ESPRIT-Tree. NMI = 1 would indicate complete agreement between species and OTU boundaries for all sequences analyzed. For this dataset, NMI peaks at OTU cutoff 0.08 and an NMI score of 0.98. (DOC)

List of Schaedler Flora sequences classified according to the criteria also employed for the experimental sequences. (XLS)

Comparison of primer pairs 8F-338R and 8F-541R according to SILVA TestPrime results. Included groups correspond to the taxonomic identification of OTUs identified as restricted to one animal facility or significantly more abundant in one set of samples. (XLS)

Distribution of OTUs among individual samples after subsampling to 1227 sequences per sample, including OTU classification. (XLS)

OTU overview, including OTU classification, aggregate information on OTU distribution among sample sets, and results of Metastats comparisons between sample sets (p< = 0.05). (XLS)

Helicobacter pylori infects the stomachs of one in two humans and can cause sequelae that include ulcers and cancer. Here we sequenced the genomes of 97 H. pylori isolates from 52 members of two families living in rural conditions in South Africa. From each of 45 individuals, two H. pylori strains were isolated from the antrum and corpus parts of t...

The human stomach is a formidable barrier to orally ingested microorganisms, and was long thought to be sterile. The discovery of Helicobacter pylori, a carcinogenic bacterial pathogen that infects the stomach mucosa of more than one half of all humans globally has started a major paradigm shift in our understanding of the stomach as an ecological...

The ichthyotoxic and mixotrophic prymnesiophyte Prymnesium parvum is known to produce dense virtually monospecific blooms in marine coastal, brackish, and inshore waters. Fish-killing Pyrmnesium blooms are often associated with macronutrient imbalanced conditions based upon shifts in ambient nitrogen (N):phosphorus (P) ratios. We therefore investig...

A long standing debate amongst diatomists has been the separation of Fragilaria from Synedra. Many genera have been separated from both Fragilaria and Synedra based on morphological grounds alone. SSU analysis has now shown that Fragilaria and Synedra sensu stricto are good monophyletic sister clades. However, all new genera separated from Fragilar...

Fosmid library contig list with annotations. (XLS)

Gel electrophoresis of restriction digested fosmid clones. (XLS)

Overview of stop codon usages in dinoflgellate and other chromalveolates. (XLS)

The complete SL-containing EST sets of A. ostenfeldii , A. minutum , A. catenella and A. tamarense . (FAS)

BAC library contig list with annotations. (XLS)

Overview of RepeatMasker results of A. ostenfeldii genomic sequences (BAC and fosmid data combined). (TIF)

Alignment of repeat motif 1, 3, and 4. (XLS)

Overview of RepeatMasker results of one completely sequenced fosmid clone. (TIF)

Many dinoflagellate species are notorious for the toxins they produce and ecological and human health consequences associated with harmful algal blooms (HABs). Dinoflagellates are particularly refractory to genomic analysis due to the enormous genome size, lack of knowledge about their DNA composition and structure, and peculiarities of gene regula...

The toxigenic marine dinoflagellate Alexandrium minutum forms toxic blooms causing paralytic shellfish poisoning (PSP), primarily in coastal waters, throughout the world. We examined effects on physiology and gene expression patterns associated with growth and nutrient starvation in a toxic strain of A. minutum. Bloom-relevant factors, including gr...

The cosmopolitan marine dinoflagellate Alexandrium minutum is known to produce toxins causing paralytic shellfish poisoning (PSP). As has recently been shown, this toxicity can be enhanced by the presence of certain copepod species. Inducible defences are known from a variety of marine organisms, but the associated transcriptomic changes have only...

The dinoflagellate Alexandrium minutum typically produces paralytic shellfish poisoning (PSP) toxins, which are known only from cyanobacteria and dinoflagellates. While a PSP toxin gene cluster has recently been characterized in cyanobacteria, the genetic background of PSP toxin production in dinoflagellates remains elusive. We constructed and anal...

Rarefaction curve. Generated ESTs and assembled cluster as contigs were analysed using http://www.biology.ualberta.ca/jbrzusto/rarefact.php#Calculator.

List of differentially expressed genes. Table of contigs identified as differentially expressed between both toxic strains and the non-toxic strain at two time-points during light phase. Included are contig IDs, microarray-based gene expression data, characterisation of the contigs, manual annotation and results of various database searches.

Primer tables and respective PCR conditions. All primers used and the respective PCR protocols of the study are listed in this file.

Phyml-based likelihood trees with bootstrap support values. 14 phylogenies of A. minutum EST contigs that produced significant (e < 10-4) BLAST hits with cyanobacterial sxt-related genes. Phylogenies were calculated including the A. minutum contig sequence, the corresponding cyanobacterial gene, and their closest SwissProt matches as identified by...

Dinoflagellates of the A. minutum species complex are widely distributed bloomforming, photosynthetic protists typically producing potent neurotoxins which cause paralytic shellfish poisoning (PSP). Human intoxications usually occur via the ingestion of filter-feeding bivalves, but intoxications after consumption of predatory crabs have also been r...

The separation of Fragilaria and Synedra has been the subject of a long standing debate amongst diatomists. For those advocating keeping the two genera separate, several additional genera have been separated from both Fragilaria and Synedra based on morphological grounds alone. A molecular analysis has now been applied to evaluate the status of sev...

In the present study, two abundant epiphytic diatom taxa were isolated from the assimilation hairs of the brown macroalga Chordaria flagelliformis collected in the Arctic Kongsfjorden (Spitsbergen, Norway), established as unialgal cultures and their growth rates determined under controlled photon fluence rate and temperature conditions. Using morph...