Prevalence of multidrug resistance in Escherichia coli in the immediate calves' environment in Swiss dairy farms

In dairy farms, calves are the animal group that carries the fecal flora with the highest prevalence of antimicrobial resistance (AMR). Calves' age and antimicrobial exposure are major factors affecting AMR prevalence. The calves' housing environment is suspected to be a reservoir of resistant bacteria, acting as a source of colonization of the calves' gut and maintenance of AMR in farms. Aims To describe the prevalence of AMR and multidrug resistance (MDR) in Escherichia coli isolated from preweaned calves' housing environment in Swiss dairy farms To explore factors associated with AMR and MD

The impact of percutaneous epididymal sperm aspiration on sperm quality in mice

In laboratory mice, sperm quality is usually assessed in spermatozoa collected from the cauda epididymidis of freshly sacrificed males. Percutaneous epididymal sperm aspiration (PESA) is a non-terminal alternative that would allow repeated sperm collection for sperm quality assessment in living males. To test whether PESA is a suitable method to assess sperm quality, we compared sperm traits between samples collected by PESA vs the commonly applied terminal cauda epididymidis dissection. The collected sperm samples were analyzed using computer-assisted sperm analysis and various parameters, including sperm motility, swimming velocity and morphology, were determined. We were able to retrieve motile sperm from all mice using PESA and the terminal cauda epididymidis dissection. Based on computer-assisted sperm analysis, however, sperm motility and swimming velocity were significantly lower after PESA compared to samples obtained by cauda epididymidis dissection. In addition, we found significantly more morphological abnormalities in PESA samples, probably induced as a side effect of the sampling technique. Although sperm samples collected by PESA are successfully used for in vitro fertilization, we cannot recommend PESA as a suitable method to assess sperm quality in mice, since the procedure seems to impair various sperm traits

Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell immunoprofiling

Introduction: SARS-CoV-2 infection results in varying disease severity, ranging from asymptomatic infection to severe illness. A detailed understanding of the immune response to SARS-CoV-2 is critical to unravel the causative factors underlying differences in disease severity and to develop optimal vaccines against new SARS-CoV-2 variants. Methods: We combined single-cell RNA and T cell receptor sequencing with CITE-seq antibodies to characterize the CD8+ T cell response to SARS-CoV-2 infection at high resolution and compared responses between mild and severe COVID-19. Results: We observed increased CD8+ T cell exhaustion in severe SARS-CoV-2 infection and identified a population of NK-like, terminally differentiated CD8+ effector T cells characterized by expression of FCGR3A (encoding CD16). Further characterization of NK-like CD8+ T cells revealed heterogeneity among CD16+ NK-like CD8+ T cells and profound differences in cytotoxicity, exhaustion, and NK-like differentiation between mild and severe disease conditions. Discussion: We propose a model in which differences in the surrounding inflammatory milieu lead to crucial differences in NK-like differentiation of CD8+ effector T cells, ultimately resulting in the appearance of NK-like CD8+ T cell populations of different functionality and pathogenicity. Our in-depth characterization of the CD8+ T cell-mediated response to SARS-CoV-2 infection provides a basis for further investigation of the importance of NK-like CD8+ T cells in COVID-19 severity.</p

γ-H2AX in recognition and signaling of DNA double-strand breaks in the context of chromatin

DNA double-strand breaks (DSBs) are extremely dangerous lesions with severe consequences for cell survival and the maintenance of genomic stability. In higher eukaryotic cells, DSBs in chromatin promptly initiate the phosphorylation of the histone H2A variant, H2AX, at Serine 139 to generate γ-H2AX. This phosphorylation event requires the activation of the phosphatidylinositol-3-OH-kinase-like family of protein kinases, DNA-PKcs, ATM, and ATR, and serves as a landing pad for the accumulation and retention of the central components of the signaling cascade initiated by DNA damage. Regions in chromatin with γ-H2AX are conveniently detected by immunofluorescence microscopy and serve as beacons of DSBs. This has allowed the development of an assay that has proved particularly useful in the molecular analysis of the processing of DSBs. Here, we first review the role of γ-H2AX in DNA damage response in the context of chromatin and discuss subsequently the use of this modification as a surrogate marker for mechanistic studies of DSB induction and processing. We conclude with a critical analysis of the strengths and weaknesses of the approach and present some interesting applications of the resulting methodology

LTR Retrotransposons in Fungi

Transposable elements with long terminal direct repeats (LTR TEs) are one of the best studied groups of mobile elements. They are ubiquitous elements present in almost all eukaryotic genomes. Their number and state of conservation can be a highlight of genome dynamics. We searched all published fungal genomes for LTR-containing retrotransposons, including both complete, functional elements and remnant copies. We identified a total of over 66,000 elements, all of which belong to the Ty1/Copia or Ty3/Gypsy superfamilies. Most of the detected Gypsy elements represent Chromoviridae, i.e. they carry a chromodomain in the pol ORF. We analyzed our data from a genome-ecology perspective, looking at the abundance of various types of LTR TEs in individual genomes and at the highest-copy element from each genome. The TE content is very variable among the analyzed genomes. Some genomes are very scarce in LTR TEs (<50 elements), others demonstrate huge expansions (>8000 elements). The data shows that transposon expansions in fungi usually involve an increase both in the copy number of individual elements and in the number of element types. The majority of the highest-copy TEs from all genomes are Ty3/Gypsy transposons. Phylogenetic analysis of these elements suggests that TE expansions have appeared independently of each other, in distant genomes and at different taxonomical levels. We also analyzed the evolutionary relationships between protein domains encoded by the transposon pol ORF and we found that the protease is the fastest evolving domain whereas reverse transcriptase and RNase H evolve much slower and in correlation with each other

Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell immunoprofiling

IntroductionSARS-CoV-2 infection results in varying disease severity, ranging from asymptomatic infection to severe illness. A detailed understanding of the immune response to SARS-CoV-2 is critical to unravel the causative factors underlying differences in disease severity and to develop optimal vaccines against new SARS-CoV-2 variants.MethodsWe combined single-cell RNA and T cell receptor sequencing with CITE-seq antibodies to characterize the CD8+ T cell response to SARS-CoV-2 infection at high resolution and compared responses between mild and severe COVID-19.ResultsWe observed increased CD8+ T cell exhaustion in severe SARS-CoV-2 infection and identified a population of NK-like, terminally differentiated CD8+ effector T cells characterized by expression of FCGR3A (encoding CD16). Further characterization of NK-like CD8+ T cells revealed heterogeneity among CD16+ NK-like CD8+ T cells and profound differences in cytotoxicity, exhaustion, and NK-like differentiation between mild and severe disease conditions.DiscussionWe propose a model in which differences in the surrounding inflammatory milieu lead to crucial differences in NK-like differentiation of CD8+ effector T cells, ultimately resulting in the appearance of NK-like CD8+ T cell populations of different functionality and pathogenicity. Our in-depth characterization of the CD8+ T cell-mediated response to SARS-CoV-2 infection provides a basis for further investigation of the importance of NK-like CD8+ T cells in COVID-19 severity

Quality assessment of murine spermatozoa obtained by percutaneous epididymal sperm aspiration (PESA)

Diplomarbeit - Veterinärmedizinische Universität Wien - 2021Diese Studie wurde durchgeführt um zu testen, ob die perkutane epididymale Spermienaspiration (PESA) als zuverlässliche Methode für Spermienqualitätsbestimmungen in Labormäusen herangezogen werden kann. Dafür haben wir Qualitätsmerkmale einerseits von Spermien, die via PESA gewonnen wurden und andererseits von Spermien, die via chirurgische Extraktion der Nebenhodenschwänze (SECE) erworben wurden, miteinander verglichen. Die erhaltenen Spermienproben wurden mittels Computerunterstützer Spermienanalyse (CASA) evaluiert, wobei verschiedene Parameter, unter anderem Spermienmotilität, Schwimmgeschwindigkeit und Morphologie bestimmt wurden. Im Rahmen dieser Studie konnten wir von allen Mäusen sowohl mittels PESA als auch durch chirurgische Präparation der Nebenhoden motile Spermien gewinnen. PESA Proben zeigten grundsätzlich eine geringere Spermienkonzentration als auch eine geringere Motilität und Schwimmgeschwindigkeit. Eine hohe Variabilität zwischen den einzelnen Tieren konnten in PESA Proben beobachtet werden. Zusätzlich konnten in PESA gewonnen Proben signifikant mehr morphologische Veränderungen von der Norm beobachtet werden. Unter Anbetracht der Ergebnisse ist PESA keine zuverlässige Methode zur Spermien-Qualitätsbestimmung bei Labormäusen.Diploma thesis - University of Veterinary Medicine Vienna - 2021To test whether percutaneous epididymal sperm aspiration (PESA) can be applied as a reliable method to assess sperm quality in laboratory mice, we compared sperm quality traits between PESA sperm samples and sperm aliquots obtained by the standard sperm retrieval method, surgical epididymis extraction (SECE). The collected sperm samples were analyzed using computer assisted sperm analysis (CASA) and various sperm parameters, including sperm motility, swimming velocity and morphology were assessed. In this study, we were able to retrieve motile sperm from all mice by using both PESA and SECE techniques. PESA sperm generally provided a lower total number of spermatozoa and showed significantly lower sperm motility and swimming velocity with a wide range of variation between individuals. Also, there were significantly more morphological deformities in PESA samples compared to sperm samples gained via SECE. Therefore, we cannot recommend PESA to measure sperm quality in laboratory mice

Cognitive Assessments in Acute Geriatrics: Presentation of the main Psychometric Properties and Experiences of Occupational Therapists

Hintergrund: Aufgrund von Multimorbidität und erhöhter Vulnerabilität im hohen Alter drohen Verlust der Selbständigkeit sowie funktionelle, psychische oder kognitive Einschränkungen, die zu einer Aufnahme auf der Akutgeriatrie führen können. Ein geriatrisches Assessment, darin auch Assessments zur kognitiven Beurteilung, ermittelt Ressourcen und Defizite der*des Patient*in als Basis für eine bedarfsgerechte Behandlung. Gespräche mit einer Ergotherapeutin, die auf einer Akutgeriatrie arbeitet, ergaben, dass die Durchführung kognitiver Assessments häufig mit Verunsicherung und Belastung des*der Patient*in verbunden ist. Ziel: Das Ziel dieser Bachelorarbeit ist es, die Hauptgütekriterien kognitiver Assessments, welche von Ergotherapeut*innen und/oder anderen Berufsgruppen auf Akutgeriatrien verwendet werden, anhand der Studienlage darzustellen. Die Arbeit soll zur Anregung einer kritischen Auseinandersetzung bei der Verwendung kognitiver Assessments auf der Akutgeriatrie in Österreich beitragen. Methodik: Eine Literaturrecherche zu den Hauptgütekriterien erfolgte in den Datenbanken Pubmed, Cinahl und Cochrane Library sowie per Handrecherche. Acht Studien wurden zusammengefasst, kritisch bewertet und verglichen. Die empirische Erhebung erfolgte mittels Online-Fragebogen an Ergotherapeut*innen, die auf Akutgeriatrien in Österreich arbeiten. Ergebnisse: Auf den Akutgeriatrien in Österreich wird eine Vielzahl an kognitiven Assessments verwendet. Ergotherapeut*innen berichten von unterschiedlichen Reaktionen, die auch negativ ausfallen. Am häufigsten findet der Mini-Mental Status Test (MMSE) Anwendung. Der Studienvergleich ergab keine höhere Validität oder Reliabilität des MMSE im Vergleich zu den anderen kognitiven Assessments. Conclusio: Um Verunsicherung und Belastung des*der Patient*in während der Durchführung kognitiver Assessments zu reduzieren, sind Beziehungsaufbau und entsprechende Aufklärung von Bedeutung. Weitere Forschung wird empfohlen, um geeignete valide sowie reliable kognitive Assessments für das akutgeriatrische Setting zu ermitteln.Background: Due to multimorbidity and increased vulnerability in old age, there is a risk of loss of independence and functional, mental or cognitive decline, which may lead to admission to acute geriatrics. A geriatric assessment, including assessments for cognitive evaluation, identifies patient's resources and deficits as a basis for an appropriate therapy. Conversations with an occupational therapist who works in acute geriatrics revealed that the conduct of cognitive assessments is often associated with uncertainty and stress for the patient. Aim: The aim of this bachelor thesis is to present the main psychometric properties of cognitive assessments used by occupational therapists and/or other professions in acute geriatrics, on the basis of available evidence. The thesis is intended to encourage a critical approach on the use of cognitive assessments in acute geriatrics in Austria. Methods: A literature search on the main psychometric properties was carried out in the databases Pubmed, Cinahl and Cochrane Library as well as by hand search. Eight studies were summarized, critically evaluated and compared. The empirical survey was carried out by means of an online questionnaire addressed to occupational therapists working in acute geriatrics in Austria. Results: A variety of cognitive assessments are used in acute geriatrics in Austria. Occupational therapists report different reactions, some of which are negative. The Mini-Mental State Examination (MMSE) is the most commonly used. The study comparison did not demonstrate a higher validity or reliability of the MMSE compared to other cognitive assessments. Conclusions: Building rapport and providing adequate information are important in order to reduce uncertainty and stress on the patient during the conduct of cognitive assessments. Further research is recommended to identify suitable valid as well as reliable cognitive assessments for the acute geriatric setting