A comparative survey of the influence of small self-cleaving ribozymes on gene expression in human cell culture.

Self-cleaving ribozymes are versatile tools for synthetic biologists when it comes to controlling gene expression. Up to date, 12 different classes are known, and over the past decades more and more details about their structure, cleavage mechanisms and natural environments have been uncovered. However, when these motifs are applied to mammalian gene expression constructs, the outcome can often be unexpected. A variety of factors, such as surrounding sequences and positioning of the ribozyme influences the activity and hence performance of catalytic RNAs. While some information about the efficiency of individual ribozymes (each tested in specific contexts) is known, general trends obtained from standardized, comparable experiments are lacking, complicating decisions such as which ribozyme to choose and where to insert it into the target mRNA. In many cases, application-specific optimization is required, which can be very laborious. Here, we systematically compared different classes of ribozymes within the 3'-UTR of a given reporter gene. We then examined position-dependent effects of the best-performing ribozymes. Moreover, we tested additional variants of already widely used hammerhead ribozymes originating from various organisms. We were able to identify functional structures suited for aptazyme design and generated highly efficient hammerhead ribozyme variants originating from the human genome. The present dataset will aide decisions about how to apply ribozymes for affecting gene expression as well as for developing ribozyme-based switches for controlling gene expression in human cells.

Outcome of parasitological examinations in dogs in Germany: a retrospective survey.

Dog faecal samples examined from January 2019 to December 2019 were retrospectively analysed for frequency of endoparasites. The examinations were performed with several different methods: 29,219 samples were examined by flotation method and sodium acetate-acetic acid-formalin concentration (SAFC) technique, 1,330 samples by Baermann-Wetzel migration technique, 12,221 samples using a Giardia coproantigen enzyme-linked-immunosorbent assay (ELISA), 1,180 samples using a Cryptosporidium coproantigen ELISA, 1,671 samples by polymerase chain reaction (PCR) testing for Giardia duodenalis and 447 samples by PCR testing for Cryptosporidium spp.. A total of 7.1% of the samples were positive for parasites in the microscopical examination using the flotation method and SAFC technique. The parasites found included Cystoisospora spp. (2.8%), Giardia duodenalis (2.3%), Ancylostomatidae (1.8%), Toxocara canis (1.6%), Trichuris vulpis (0.7%), Toxascaris leonina (0.5%), Capillaria spp. (0.2%), Angiostrongylus vasorum (0.2%), Crenosoma vulpis (0.1%), Taeniidae (0.1%), Sarcocystis spp. (0.03%), Dipylidium caninum (0.01%), Diphyllobothrium latum (< 0.01%), Spirurida (< 0.01%) and Opisthorchiidae (< 0.01%). Using the Baermann-Wetzel migration technique, Angiostrongylus vasorum was found in 0.75% and Crenosoma vulpis in 0.3% of the samples. ELISAs for Giardia duodenalis and Cryptosporidium spp. revealed 13.9% and 1.0% positive faecal samples, and Giardia duodenalis and Cryptosporidium spp. PCRs 19.4% and 2.0%, respectively. Dogs in the first year of life were more frequently infected with parasites than older animals. In the microscopic examination using flotation method and SAFC technique, the significantly highest detection rates were found in dogs up to six months of age (p < 0.001).

Imaging of retina cellular and subcellular structures using ptychographic hard X-ray tomography.

Ptychographic hard X-ray computed tomography (PXCT) is a recent method allowing imaging with quantitative electron-density contrast. Here, we imaged, at cryogenic temperature and without sectioning, cellular and subcellular structures of a chemically fixed and stained wild-type mouse retina, including axons and synapses, with complete isotropic 3D information over tens of microns. Comparison with tomograms of degenerative retina from a mouse model of retinitis pigmentosa illustrates the potential of this method for analyzing disease processes like neurodegeneration at sub-200 nm resolution. As a non-destructive imaging method, PXCT is very suitable for correlative imaging. Within the outer plexiform layer containing the photoreceptor synapses, we identified somatic synapses. We used a small region inside the X-ray-imaged sample for further high-resolution focused ion beam/scanning electron microscope tomography. The subcellular structures of synapses obtained with the X-ray technique matched the electron microscopy data, demonstrating that PXCT is a powerful scanning method for tissue volumes of more than 60 cells and sensitive enough for identification of regions as small as 200 nm, which remain available for further structural and biochemical investigations.

Robust and Easy-to-Use One-Pot Workflow for Label-Free Single-Cell Proteomics.

The analysis of ultralow input samples or even individual cells is essential to answering a multitude of biomedical questions, but current proteomic workflows are limited in their sensitivity and reproducibility. Here, we report a comprehensive workflow that includes improved strategies for all steps, from cell lysis to data analysis. Thanks to convenient-to-handle 1 µL sample volume and standardized 384-well plates, the workflow is easy for even novice users to implement. At the same time, it can be performed semi-automatized using CellenONE, which allows for the highest reproducibility. To achieve high throughput, ultrashort gradient lengths down to 5 min were tested using advanced µ-pillar columns. Data-dependent acquisition (DDA), wide-window acquisition (WWA), data-independent acquisition (DIA), and commonly used advanced data analysis algorithms were benchmarked. Using DDA, 1790 proteins covering a dynamic range of four orders of magnitude were identified in a single cell. Using DIA, proteome coverage increased to more than 2200 proteins identified from single-cell level input in a 20 min active gradient. The workflow enabled differentiation of two cell lines, demonstrating its suitability to cellular heterogeneity determination.

Gait is not Affected by Hemispherotomy-Case Report from Two Children.

In children with therapy refractory epilepsy, the functional disconnection of one hemisphere (hemispherotomy) may be considered as a treatment option. The visual field defects and hand function effects associated with the procedure have been extensively studied. However, the effect of the hemispherotomy on gait pattern has thus far only been analyzed qualitatively, and there is limited quantitative data. At the Children's Hospital, we regularly perform standardized quantitative gait analysis studies and care for children with complex epilepsies. During the standard routine of care for two children with structural therapy refractory epilepsy, gait analysis was performed prior to and after hemispherotomy. Both patients had prenatal ischemic brain lesions, had developed severe epilepsy during the first 3 years of life, and were treated with the hemispherotomy at about 7 years of age. Interestingly, one patient did not show any changes in gait pattern, while for the other patient, differences could be observed by means of three-dimensional gait analysis. However, greater deviations to controls postoperatively may also be related to day-to-day variability.

High-resolution non-destructive three-dimensional imaging of integrated circuits.

Modern nanoelectronics has advanced to a point at which it is impossible to image entire devices and their interconnections non-destructively because of their small feature sizes and the complex three-dimensional structures resulting from their integration on a chip. This metrology gap implies a lack of direct feedback between design and manufacturing processes, and hampers quality control during production, shipment and use. Here we demonstrate that X-ray ptychography-a high-resolution coherent diffractive imaging technique-can create three-dimensional images of integrated circuits of known and unknown designs with a lateral resolution in all directions down to 14.6 nanometres. We obtained detailed device geometries and corresponding elemental maps, and show how the devices are integrated with each other to form the chip. Our experiments represent a major advance in chip inspection and reverse engineering over the traditional destructive electron microscopy and ion milling techniques. Foreseeable developments in X-ray sources, optics and detectors, as well as adoption of an instrument geometry optimized for planar rather than cylindrical samples, could lead to a thousand-fold increase in efficiency, with concomitant reductions in scan times and voxel sizes.

Metabolic changes associated with two endocrine abnormalities in dogs: elevated fructosamine and low thyroxine.

INTRODUCTION: Metabolomics studies in canine endocrine abnormalities are sparse and basic information on these abnormalities must be generated. OBJECTIVES: To characterize the metabolic changes associated with elevated fructosamine, reflecting poor glycemic control, and low thyroxine, a thyroid hormone controlling metabolism. METHODS: Leftovers of clinical serum samples; 25 controls, 79 high fructosamine, and 47 low thyroxine, were analyzed using 1H NMR and differences were evaluated using Firth logistic regression. RESULTS: Both high fructosamine and low thyroxine were associated with changes in concentrations of multiple metabolites, including glycoprotein acetyls and lipids. CONCLUSION: These findings suggest promising makers for further research and clinical validation.

Screening of Antimicrobial Activity of Essential Oils against Bovine Respiratory Pathogens - Focusing on Pasteurella multocida.

Administration of essential oils as natural plant products with antimicrobial activity might be an alternative to antibiotic treatment of bovine respiratory disease. The aim of this study was to analyse the in vitro antimicrobial activity of 11 essential oils against Pasteurella multocida isolated from the respiratory tract of calves using microdilution with determination of minimum inhibitory and bactericidal concentration as well as agar disc diffusion. Additionally, antimicrobial activity against Mannheimia haemolytica and bacteria in the Mannheimia clade was assessed by agar disc diffusion. Seven essential oil mixtures were also tested against all bacterial isolates. P. multocida was strongly inhibited by cinnamon cassia and lemongrass oil followed by coriander, winter savory, thyme, clove, and peppermint oil in the microdilution assays. Eucalyptus, wintergreen, spruce, and star anise oil showed lower activity. Comparison of both methods revealed an underestimation of cinnamon cassia oil activity by agar disc diffusion and conflicting results for wintergreen oil in microdilution, which precipitated in broth. Cinnamon cassia, thyme, wintergreen, lemongrass, and winter savory oil all showed strong antimicrobial activity against M. haemolytica. Bacteria in the Mannheimia clade were mostly inhibited by cinnamon cassia and thyme oil. Pasteurella isolates were more susceptible to inhibition by essential oils than Mannheimia isolates. Essential oil mixtures did not show stronger antibacterial activity than single essential oils. In conclusion, cinnamon cassia and lemongrass as well as coriander, winter savory, and thyme oil are promising candidates for treatment of P. multocida-associated bovine respiratory infections.

SARS-CoV-2-Specific Antibodies in Domestic Cats during First COVID-19 Wave, Europe.

We conducted a severe acute respiratory syndrome coronavirus 2 antibody seroprevalence study among >2,000 domestic cats from 4 countries during the first coronavirus disease wave in Europe. We found 4.4% seroprevalence using a virus neutralization test and 4.3% using a receptor-binding domain ELISA, demonstrating probable human-to-cat transmission.

Serum NMR metabolomics uncovers multiple metabolic changes in phenobarbital-treated dogs.

INTRODUCTION: Phenobarbital is a commonly used anticonvulsant for the treatment of canine epileptic seizures. In addition to its central nervous system (CNS) depressing effects, long-term phenobarbital administration affects liver function. However, broader metabolic consequences of phenobarbital treatment are poorly characterized. OBJECTIVES: To identify metabolic changes in the sera of phenobarbital-treated dogs and to investigate the relationship between serum phenobarbital concentration and metabolite levels. METHODS: Leftovers of clinical samples were used: 58 cases with phenobarbital concentrations ranging from 7.8 µg/mL to 50.8 µg/mL, and 25 controls. The study design was cross-sectional. The samples were analyzed by a canine-specific 1H NMR metabolomics platform. Differences between the case and control groups were evaluated by logistic regression. The linear relationship between metabolite and phenobarbital concentrations was evaluated using linear regression. RESULTS: Increasing concentrations of glycoprotein acetyls, LDL particle size, palmitic acid, and saturated fatty acids, and decreasing concentrations of albumin, glutamine, histidine, LDL particle concentration, multiple HDL measures, and polyunsaturated fatty acids increased the odds of the sample belonging to the phenobarbital-treated group, having a p-value < .0033, and area under the curve (AUC) > .7. Albumin and glycoprotein acetyls had the best discriminative ability between the groups (AUC: .94). No linear associations between phenobarbital and metabolite concentrations were observed. CONCLUSION: The identified metabolites are known to associate with, for example, liver and CNS function, inflammatory processes and drug binding. The lack of a linear association to phenobarbital concentration suggests that other factors than the blood phenobarbital concentration contribute to the magnitude of metabolic changes.

DETECTION OF TESTADENOVIRUSES AND ATADENOVIRUSES IN TORTOISES AND TURTLES IN EUROPE.

Adenoviruses have been regularly detected in squamate reptiles; evidence of infection in chelonians is described much less frequently. The adenoviruses found in turtles and tortoises have been genetically diverse, and have included members of the genus Siadenovirus, a proposed testadenovirus genus, and, in a single case, an Atadenovirus. In this study, samples from 949 chelonians submitted to a diagnostic laboratory were screened for the presence of adenoviruses by polymerase chain reaction (PCR) targeting a portion of the DNA polymerase gene. Adenoviruses were detected in 22 (2.3%) chelonians of different species. Adenovirus-positive species included Hermann's tortoises (Testudo hermanni), spur-thighed tortoises (T. graeca), Horsfield's tortoises (T. horsfieldii), sliders (Trachemys spp.), box turtles (Terrapene spp.) and a black pond turtle (Geochlemys hamiltonii). Sequencing and phylogenetic analyses of the obtained PCR products revealed that the majority of the detected adenoviruses (72.7%) cluster with members of the proposed testadenovirus genus, while the rest (27.3%) cluster with the atadenoviruses. This study significantly expands the known host range of both the proposed testadenoviruses and the atadenoviruses in different chelonian species and families.

CLINICAL CHEMISTRY, VITAMIN, ELECTROPHORESIS, AND HEMATOLOGIC ANALYTES OF BLACK-HEADED IBIS (THRESKIORNIS MELANOCEPHALUS).

The evaluation of laboratory blood analytes is an important tool for health assessment in avian medicine. Unfortunately, there is a lack of suitable reference values for many zoo bird species. The goal of the present study was to establish reference intervals for a wide range of blood analytes in healthy black-headed ibis (Threskiornis melanocephalus) kept in a zoologic garden. Lithium heparinized blood samples from 15 individuals were collected, and 18 different clinical chemistry analytes were measured. New are especially the minimum and maximum values for bile acid (2.38-49.4 µmol/L), cholinesterase (439-1260 U/L), vitamin A (0.65-1.70 mg/L), vitamin E (26.3-52.5 mg/L), and capillary zone electrophoresis (prealbumin, 10.2-23.4%; albumin, 35.9-44.1%; A/G ratio, 1.07-1.69; α-, 15.7-20.0%; ß-, 13.5-19.1%; γ-globulin, 6.08-11.3%). The measured values for clinical chemistry, vitamin, electrophoresis, and hematologic analytes are a basis for further studies and for diagnostics and clinical treatment in this ibis species.

DETECTION OF MYCOPLASMA AND CHLAMYDIA IN PYTHONS WITH AND WITHOUT SERPENTOVIRUS INFECTION.

Serpentoviruses (order Nidovirales) are an important cause of respiratory disease in snakes. Although transmission studies have shown that serpentoviruses can cause respiratory disease in pythons, the possible role of additional potential pathogens is not yet understood. Very little information is available on the role of mycoplasma and chlamydia infections in disease in pythons. Diagnostic samples from 271 pythons of different genera submitted to a laboratory for detection of serpentoviruses were also screened for mycoplasma and chlamydia infections by PCR. Most of the samples were oral swabs. Almost 30% of the samples were positive for serpentoviruses, and mycoplasmas were detected in more than 60% of the pythons. The occurrence of these two pathogens correlated significantly (P < 0.001). Additionally, about 3% of the snakes tested positive for Chlamydia. This study found a high prevalence of mycoplasmas in the tested pythons and a correlation between infections with these bacteria and serpentoviruses in python samples submitted for diagnostic testing. Because the role mycoplasmas play in respiratory diseases of snakes is still largely unknown, further investigations are necessary to evaluate the role of mixed infections in disease.

Correlation between Oxygen Vacancies and Oxygen Evolution Reaction Activity for a Model Electrode: PrBaCo2 O5+δ.

The role of the perovskite lattice oxygen in the oxygen evolution reaction (OER) is systematically studied in the PrBaCo2 O5+δ family. The reduced number of physical/chemical variables combined with in-depth characterizations such as neutron dif-fraction, O K-edge X-ray absorption spectroscopy (XAS), electron energy loss spectroscopy (EELS), magnetization and scanning transmission electron microscopy (STEM) studies, helps investigating the complex correlation between OER activity and a single perovskite property, such as the oxygen content. Larger amount of oxygen vacancies appears to facilitate the OER, possibly contributing to the mechanism involving the oxidation of lattice oxygen, i.e., the lattice oxygen evolution reaction (LOER). Furthermore, not only the number of vacancies but also their local arrangement in the perovskite lattice influences the OER activity, with a clear drop for the more stable, ordered stoichiometry.

Bronchoalveolar lavage cytokines are of minor value to diagnose complications following lung transplantation.

Early diagnosis and treatment of acute cellular rejection (ACR) may improve long-term outcome for lung transplant recipients (LTRs). Cytokines have become valuable diagnostic tools in many medical fields. The role of bronchoalveolar lavage (BAL) cytokines is of unknown value to diagnose ACR and distinguish rejection from infection. We hypothesized that distinct cytokine patterns obtained by surveillance bronchoscopies during the first year after transplantation are associated with ACR and microbiologic findings. We retrospectively analyzed data from 319 patients undergoing lung transplantation at University Hospital Zurich from 1998 to 2016. We compared levels of IL-6, IL-8, IFN-γ and TNF-α in 747 BAL samples with transbronchial biopsies (TBB) and microbiologic results from surveillance bronchoscopies. We aimed to define reference values that would allow distinction between four specific groups "ACR", "infection", "combined ACR and infection" and "no pathologic process". No definitive pattern was identified. Given the overlap between groups, these four cytokines are not suitable diagnostic markers for ACR or infection after lung transplantation.

The immune microenvironment in typical carcinoid lung tumour, a brief report of four cases.

Pulmonary typical carcinoid (TC) is a low-grade, rare lung cancer of neuroendocrine origin. Currently, there is very little information available about the immune cell composition in TC tumours. Here, we analysed by flow cytometry resected tumours from four never-smoker female patients with TC. Twelve distinct immune cell types were identified in TC tumours. The most abundant immune cells were CD8+ T cells, CD4+ T cells, B cells and macrophages, which represented 19.8%, 17.7%, 11.5% and 11% of all tumour-infiltrating CD45+ leucocytes, respectively. Natural killer (NK) cells (8.8%) and neutrophils (3.9%) were also common. Three types of dendritic cells (DCs) were identified (plasmacytoid DCs, CD1c  DCs, and CD141  DCs) which together constituted 1.4% of all immune cells in TC tumours. Small populations of basophils (1.2%), mast cells (0.8%) and eosinophils (0.6%) were also present. Notably, the percentage of leucocytes (of all living cells) was much lower in TC tumours compared to high-grade non-small cell lung cancer (NSCLC) tumours and also compared to non-cancerous lung tissue. We conclude that TC tumours are relatively non-inflammatory, although the immune landscape was found to be very complex.

A methodological perspective on the cognitive outcome of epilepsy surgery in children and adolescents.

PURPOSE: The purpose of the study was to explore the impact of timing and test specificity of cognitive outcome measures after pediatric epilepsy surgery. METHODS: A consecutive national cohort of 114 children with medically resistant epilepsy having had resective epilepsy surgery were screened for children tested with a complete age-appropriate Wechsler Intelligence test at two or three time-points. This provided 43 children for analyses. Composite subscale scores were assessed in comparison to index and intelligence quotient (IQ) scores. RESULTS: We found a main effect of time in seizure-free children for full-scale IQ (FSIQ); F(2, 42) = 6.49 with higher T2 measures compared with T1 (MDiff = 5.46, p = .006). There was a difference in FSIQ scores between seizure-free and nonseizure-free children at T2; M = 7.31, 95% confidence interval (CI) [0.05 to 14.57], t(38) = 2.04, p = .049, favoring seizure-free children. A statistical difference between composite scale scores and index scores was found with medium to large effect. The correlation of medical treatment (anti-epileptic drug (AED)) change and score differences in FSIQ outcome was significant (p = .041), with less AED correlated with a higher FSIQ. All children with left-temporal surgery had a stable or improved verbal comprehension composite subscale score outcome at T2 regardless of seizure status. CONCLUSION: Our results correspond to some longitudinal studies with outcome measures >2 years, in contrast to short-term studies ≤2 years with a stable outcome. Our study supports the fact that the specificity of the used tests and the timing of assessments after pediatric epilepsy surgery are essential factors for the clinical validity of outcome measures. However, there are further needs of extensive longitudinal studies to provide a better understanding of life-long cognitive development and impact after childhood epilepsy surgery.

Treating osteosarcoma with CAR T cells.

Novel therapies to treat patients with solid cancers that have developed resistance to chemotherapy represent unmet needs of considerable dimensions. In the present review, we will address the attempts to develop chimeric antigen receptor (CAR) targeted immunotherapy against osteosarcoma (OS). This aggressive cancer displays its peak incidence in children and young adults. The main cause of patient death is lung metastases with a 5-year survival as low as 5%-10% in the primary metastatic setting and 30% in the relapse situation, respectively. Effective adjuvant combination chemotherapy introduced more than 40 years ago improved the survival rates from below 20% to around 60% in patients; however, since then, no major breakthroughs have been made. The use of immune checkpoint inhibitors has been disappointing in OS, while other types of immunotherapies such as CAR T cells remain largely unexplored. Indeed, for CAR T-cell therapy to be efficacious, two main criteria need to be fulfilled: (a) CAR T cells should target an epitope selectively expressed on the cell surface of OS in order to prevent toxicities in normal tissues and (b) the target should also be widely expressed on OS metastases. These challenges have already been undertaken in OS and illustrate the difficulties in developing tomorrow's CAR-T treatment in a solid tumour. We will discuss the experiences with CAR-T therapy development and efficacy to combat the clinical challenges in OS.

Comparison of three different PCR protocols for the detection of ferlaviruses.

BACKGROUND: Ferlaviruses are important pathogens in snakes often associated with respiratory and neurological disease. The detection of ferlaviral RNA by PCR is considered to be the most reliable method for the diagnosis of infection. The PCRs that have been used most commonly for this purpose have not been properly assessed to determine their sensitivity, specificity and ability to detect the known genetic diversity of this group of viruses. The aim of this study was to compare three published PCR protocols so that a single method could be recommended to laboratories that perform this testing. RESULTS: Comparisons were carried out using cell culture isolates and tissues from snakes infected with specific virus genotypes. A single round PCR targeting a short segment of the viral polymerase (L) gene provided the highest sensitivity and specificity, and detected isolated ferlaviruses from all four described genogroups, as well as from tissues of infected snakes. CONCLUSION: A broadly-reactive PCR for the detection of all known ferlaviruses was found to provide a good combination of detection limit, specificity and speed. Based on these criteria, this method is recommended for the diagnosis of ferlavirus infections.

Microbiota of the conjunctival sac of 120 healthy cats.

OBJECTIVES: To describe the bacterial and fungal microbiota of the conjunctiva and factors influencing these microbiota of healthy cats. To evaluate the antimicrobial resistance profile and discuss the use of appropriate antimicrobial drugs. ANIMALS STUDIED: One hundred and twenty healthy cats PROCEDURES: Conjunctival samples with dry or premoistened swabs were obtained from both eyes and cultured for aerobic and anaerobic bacteria and fungi. In vitro bacterial, susceptibility testing was performed. The effects of age, sex, breed, season, living environment, and sample collection technique on the frequency and composition of microbial isolation were evaluated. RESULTS: In 49 of 120 cats (40.8%) and 73 of 240 swabs (30.4%), microorganisms were isolated. Of the isolates, 71% (61/86) were Gram-positive bacteria, 26% (22/86) were Gram-negative bacteria, and 3% (3/86) were fungi. Staphylococcus felis (17/86; 19.8%) was the most commonly isolated species. Moraxella osloensis (5/86; 5.8%) was the most frequent Gram-negative species. The season had a statistically significant influence (P = 0.04) on the frequency of isolation. The use of premoistened swabs increased the rate of Gram-positive bacterial detection significantly (P = 0.03). The in vitro susceptibility testing showed high efficacy of chloramphenicol, gentamicin, pradofloxacin, and enrofloxacin. CONCLUSIONS: The isolated microbiota aligns with previous studies performed in other countries, although the microbiota of cats in the present study showed wider bacterial diversity, and more Gram-negative species were isolated. Swab sampling should be performed with premoistened swabs. The topical antimicrobials gentamicin and chloramphenicol are suitable therapeutics for first-line treatment.