Biology subjects

Pieper, R.

Publications and source records attributed to Pieper, R..

7 recordsLinked to original sources

bioRxiv2026

Keratinizing Squamous and Intestinal Metaplasia in Urothelium of Long-term Catheterized Patients with Chronic Urinary Tract Infections

Purpose: Many spinal cord-injured (SCI) patients are recurrently catheterized to manage urinary retention and incontinence. Microbial pathogens colonize urethral catheter surfaces, persist in form of biofilms and trigger inflammatory responses in the bladder. Our objective was to determine bladder tissue changes due to long-term inflammation using LC-MS proteomics. Experimental Design: We examined longitudinal proteomic profiles from eight SCI patients, sampled over 2 to 6 months, in a patient-specific manner as well as compared with trauma patients diagnosed with acute urinary tract infections (UTI). The sample sources were urinary pellets (UP) from all subjects, and catheter biofilm extracts (CB) from SCI patients. Bioinformatic protein network and western blot analyses served to corroborate evidence of protein and cell differentiation changes in the urinary tract of SCI patients. Results: More than 50 proteins with functional or structural roles in the epidermal cornified envelope were quantitatively increased in proteomic profiles from three SCI patients. This included stress response keratins and proteins involved in keratin crosslinking, e.g. transglutaminases and small proline-rich proteins, suggesting occurrence of keratinizing squamous epithelial metaplasia. Protein co-expression network analyses supported epithelial trans-differentiation changes. Nearly thirty proteins with gastro-intestinal epithelial cell expression specificity were enriched in proteomic profiles from a single SCI patient. Among those were mucin-2 and sucrase-isomaltase, secreted proteins detected in samples for only that patient via western blots. This finding was consistent with intestinal epithelial metaplasia. Conclusions and clinical relevance: Without using invasive cystoscopy and histopathology, proteomic analyses from easily available UP and CB samples allowed us to infer cell differentiation changes in urothelial tissues of SCI patients with chronic infections, supporting a concept of clinical relevance for urothelial metaplasia screening, a precursor stage of urothelial neoplasms.

molecular biology↗

bioRxiv2024

Crosstalk of pathogens with human immune system in airway mucus profiled via machine learning-enhanced data-independent acquisition mass spectrometry

Withdrawal StatementThe authors have withdrawn their manuscript owing to Johnson & Johnson publication policies on online archives of unpublished manuscripts in the biological sciences. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

molecular biology↗

bioRxiv2024

A comparison of wild boar and domestic pig microbiota does not reveal a loss of microbial species but an increase in alpha diversity and opportunistic genera in domestic pigs

The microbiome of wild animals is believed to be co-evolved with host species, which may play an important role in host physiology. It has been hypothesized that the rigorous hygienic practice in combination with antibiotics and diets with simplified formulas used in the modern swine industry may negatively affect the establishment and development of the gut microbiome. In this study, we evaluated the fecal microbiome of 90 domestic pigs sampled from 9 farms in Canada and 39 wild pigs sampled from three different locations on two continents (North America and Europe) using 16S rRNA gene amplicon sequencing. Surprisingly, the gut microbiome in domestic pigs exhibited higher alpha-diversity indices than wild pigs (P<0.0001). The wild pig microbiome showed a lower Firmicutes to Bacteroidetes ratio and a higher presence of bacterial phyla Elusimicrobiota, Verrucomicrobiota, Cyanobacteria, and Fibrobacterota compared to their domestic counterparts. At the genus level, wild pig microbiome had enriched genera that were known for fibre degradation and short-chained fatty acids production. Interestingly, the phylum Fusobacteriota was only observed in domestic pigs. We identified 31 ASVs that were commonly found in the pig gut microbiome regardless of host sources, which could be recognized as members of the core gut microbiome. Interestingly, we found a few ASVs missing in domestic pigs that were prevalent in wild ones, whereas domestic pigs harbored 59 ASVs that were completely absent in wild pigs. The present study sheds light on the impact of domestication on the pig gut microbiome, including the gain of new genera. ImportanceThe microbiome of pigs plays a crucial role in shaping host physiology and health. This study looked to identify if domestication and current rearing practices have resulted in a loss of co-evolved bacterial species by comparing the microbiome of wild boar and conventionally raised pigs. It represents a comparison of domestic and wild pigs with the largest sample sizes, and is the first to examine wild boars from multiple sites and continents. We were able to identify core microbiome members that were shared between wild and domestic populations, and counter to expectation, few microbes were identified to be lost from wild boar. Nevertheless, the microbiome of wild boars was distinct from domestic pigs, with notably lower abundance of important pathogenic genera. The differences in microbial composition may identify an opportunity to shift the microbial community of domestic pigs towards that of wild boar with the intent to reduce pathogen load.

microbiology↗

bioRxiv2020

FLOWERING LOCUS T4 (HvFT4) delays flowering and decreases floret fertility in barley

FLOWERING LOCUS T-like genes (FT-like) control the photoperiodic regulation of flowering in many angiosperm plants. The family of FT-like genes is characterised by extensive gene duplication and subsequent diversification of FT functions which occurred independently in modern angiosperm lineages. In barley, there are 12 known FT-like genes (HvFT) but the function of most of them remains uncharacterised. This study aimed to characterise the role of HvFT4 in flowering time control and development in barley. The overexpression of HvFT4 in the spring cultivar Golden Promise delayed flowering time under long-day conditions. Microscopic dissection of the shoot apical meristem (SAM) revealed that overexpression of HvFT4 specifically delayed spikelet initiation and reduced the number of spikelet primordia and grains per spike. Furthermore, ectopic overexpression of HvFT4 was associated with floret abortion and with the downregulation of the barley MADS-box genes VRN-H1, HvBM3 and HvBM8 which promote floral development. This suggests that HvFT4 functions as a repressor of reproductive development in barley. Unraveling the genetic basis of FT-like genes can contribute to the identification of novel breeding targets to modify reproductive development and thereby spike morphology and grain yield. HighlightWe identify the FLOWERING LOCUS T (FT)-like gene HvFT4 as a negative regulator of reproductive development, spikelet initiation, floret fertility and grain number in barley.

developmental biology↗

bioRxiv2019

Nutritional Immunity and Antibiotic Drug Treatments Influence Microbial Composition but Fail to Eliminate Urethral Catheter Biofilms in Recurrently Catheterized Patients

Polymicrobial biofilms that form on indwelling urethral catheters used by neurogenic bladder patients are known to recur following catheter replacements. Uropathogens dominate in catheter biofilms (CBs), grow and disperse as multi-cellular aggregates. Their microbial complexity, the characteristics of host immune responses and the molecular crosstalk in this ecosystem are incompletely understood. By surveying eight patients over up to six months with meta-omics analysis methods, we shed new light on the longitudinal microbial dynamics in CBs and the microbial-host crosstalk. There was evidence of chronic innate immune responses in all patients. Pathogens dominated the microbial contents. Proteus mirabilis often out-competed other species in cases of salt encrustation of catheters. The examination of proteomes in CBs and associated urinary pellets revealed many abundant bacterial systems for transition metal ion (TMI) acquisition. TMIs are sequestered by effector proteins released by activated neutrophils and urothelial cells, such as lactotransferrin and calgranulins, which were abundant in the host proteomes. We identified positive quantitative correlations among systems responsible for siderophore biosynthesis, TMI/siderophore uptake and TMI cellular import in bacterial species, suggesting competition for TMIs to support their metabolism and growth in CBs. Enterococcus faecalis was prevalent as a cohabitant of CBs and expressed three lipoproteins with apparent TMI acquisition functions. Fastidious anaerobic bacteria such as Veillonella, Actinobaculum, and Bifidobacterium grew in CB communities that appeared to be oxygen starved. Finally, antibiotic drug treatments were shown to influence microbial composition of CBs but failed to prevent re-colonization of urethral catheters with persisting and/or drug-resistant newly emerging pathogens.

microbiology↗

bioRxiv2018

Longitudinal Surveys Show that Urethral Catheters Harbor Recurrent Polymicrobial Biofilms with Cooperative and Competitive Behaviors Among Cohabitating Pathogens

The analysis of catheter biofilms (CBs) from patients with neurogenic bladder disorders revealed persistent colonization by polymicrobial communities. The recurrence of bacterial species in the CBs of sequentially replaced catheters suggests urothelial reservoirs responsible for recolonization of the catheter surface. Proteomic data for CB samples were indicative of chronic inflammation in the patients urinary tracts via neutrophil and eosinophil infiltration and epithelial cell exfoliation. These host defense pathways, effective in killing pathogens during uncomplicated urinary tract infection, failed to eliminate CBs. Intermittent antibiotic drug treatment had different outcomes: either replacement of drug-susceptible by drug-tolerant bacteria or transient microbial biomass reduction followed by resurgence of the previously colonizing bacteria. Proteins that sequester iron and zinc such as lactotransferrin, lipocalin-2 and calprotectin were abundant in the patients CBs and urine sediments. Indicative of a host-pathogen battle for bivalent metal ions, acquisition and transport systems for such ions were highly expressed by many organisms residing in CBs. Species part of the Enterococcaceae and Aerococcaceae families, generally not well-characterized in their ability to synthesize siderophores, frequently cohabitated biofilms dominated by siderophore-producing Enterobacteriaceae. In support of metal acquisition cooperativity, we noticed positive abundance correlations for a Proteus mirabilis yersiniabactin-type siderophore system and two Enterococcus faecalis ABC transporters. Distinct bacterial strains highly expressed known or putative cytotoxins that appeared to compromise the survival of co-resident bacteria, e.g. a P. mirabilis hemolysin and Pseudomonas aeruginosa type 6 secretion and pyoverdin biosynthesis systems. In conclusion, there is support for cooperative and competitive behaviors among bacteria cohabitating CBs.

microbiology↗

bioRxiv2017

Microbial Metagenome Of Urinary Tract Infection

Urine culture and microscopy techniques are used to profile the bacterial species present in urinary tract infections. To gain insight into the urinary flora in infection and health, we analyzed clinical laboratory features and the microbial metagenome of 121 clean-catch urine samples. 16S rDNA gene signatures were successfully obtained for 116 participants, while whole genome shotgun sequencing data was successfully generated for samples from 49 participants. Analysis of these datasets supports the definition of the patterns of infection and colonization/contamination. Although 16S rDNA sequencing was more sensitive, whole genome shotgun sequencing allowed for a more comprehensive and unbiased representation of the microbial flora, including eukarya and viral pathogens, and of bacterial virulence factors. Urine samples positive by whole genome shotgun sequencing contained a plethora of bacterial (median 41 genera/sample), eukarya (median 2 species/sample) and viral sequences (median 3 viruses/sample). Genomic analyses revealed cases of infection with potential pathogens (e.g., Alloscardovia sp, Actinotignum sp, Ureaplasma sp) that are often missed during routine urine culture due to species specific growth requirements. We also observed gender differences in the microbial metagenome. While conventional microbiological methods are inadequate to identify a large diversity of microbial species that are present in urine, genomic approaches appear to comprehensively and quantitatively describe the urinary microbiome.

microbiology↗