Employing a systematic approach to biobanking and analyzing clinical and genetic data for advancing COVID-19 research

Within the GEN-COVID Multicenter Study, biospecimens from more than 1000 SARS-CoV-2 positive individuals have thus far been collected in the GEN-COVID Biobank (GCB). Sample types include whole blood, plasma, serum, leukocytes, and DNA. The GCB links samples to detailed clinical data available in the GEN-COVID Patient Registry (GCPR). It includes hospitalized patients (74.25%), broken down into intubated, treated by CPAP-biPAP, treated with O₂ supplementation, and without respiratory support (9.5%, 18.4%, 31.55% and 14.8, respectively); and non-hospitalized subjects (25.75%), either pauci- or asymptomatic. More than 150 clinical patient-level data fields have been collected and binarized for further statistics according to the organs/systems primarily affected by COVID-19: heart, liver, pancreas, kidney, chemosensors, innate or adaptive immunity, and clotting system. Hierarchical clustering analysis identified five main clinical categories: (1) severe multisystemic failure with either thromboembolic or pancreatic variant; (2) cytokine storm type, either severe with liver involvement or moderate; (3) moderate heart type, either with or without liver damage; (4) moderate multisystemic involvement, either with or without liver damage; (5) mild, either with or without hyposmia. GCB and GCPR are further linked to the GCGDR, which includes data from whole-exome sequencing and high-density SNP genotyping. The data are available for sharing through the Network for Italian Genomes, found within the COVID-19 dedicated section. The study objective is to systematize this comprehensive data collection and begin identifying multi-organ involvement in COVID-19, defining genetic parameters for infection susceptibility within the population, and mapping genetically COVID-19 severity and clinical complexity among patients.Subject terms: Genetics research, Viral infection     

Is the structure of anatomy curriculum adequate for safe medical practice?

IntroductionAnatomy has been considered a core subject within the medical education curriculum. In the current setting of ever-changing diagnostic and treatment modalities, the opinion of both students and trainers is crucial for the design of an anatomy curriculum which fulfils the criteria required for safe medical practice.MethodsMedical students, trainees and specialist trainee doctors and specialists from the London (England) area were surveyed to investigate the how curriculum changes have affected the relevance of anatomical knowledge to clinical practice and to identify recommendations for optimum teaching methods. The survey employed 5-point Likert scales and multiple-choice questions. Where the effect of training level was statistically significant (p < 0.05), post-hoc analysis was carried out using Mann–Whitney U tests. Significance levels were modified according to the Bonferroni method.ResultsTwo hundred and twenty-eight individuals completed the survey giving a response rate of 53%. Medical students, trainees and specialists all agreed (mean Likert score 4.51, 4.79, 4.69 respectively) that knowledge of anatomy is important for medical practice. Most of the trainees (88.4%) and specialists (81.3%) used dissection to learn anatomy, but only 61.4% of medical students used this approach. Dissection was the most commonly recommended approach for learning anatomy across all the groups (41.7%–69.3%).ConclusionsKnowledge of anatomy is perceived to be important for safe clinical practice. Anatomy should be taught with other relevant system or clinical modules. Newer tools for anatomy teaching need further validation before incorporation into the curriculum.     

Leukaemia incidence in Welsh children linked with low level radiation--making sense of some erroneous results published in the media.

A series of self-published epidemiological reports purporting to show a major excess risk of leukaemia in pre-school children living near the Irish Sea coast of Wales have been presented in the media as evidence of the harmful effects of low level radiation arising from Sellafield. The Welsh Cancer Intelligence and Surveillance Unit (WCISU), the body responsible for population-based cancer information in Wales, can provide insights into the validity of these reports, which appear to be a consequence of various mistakes. This raises important questions about the research governance of such reports and the communication of scientific findings via the mass media. Without suitable safeguards the media are in danger of promulgating misinformation.     

Relationship of skeletal muscle metaboreceptors in the upper and lower limbs with the respiratory control in patients with heart failure.

Increased activity of muscle metaboreceptors (afferents sensitive to muscle contraction that are responsible for the ventilatory responses to exercise) has been proposed in patients with chronic heart failure (CHF) to constitute a missing link between muscle metabolic abnormalities and exercise overventilation. We looked at this reflex overactivation to determine if it is systemic or limited to a single muscle region in the same human subject. This was done by comparing the metaboreflex response of ventilatory control in the lower and upper limbs in CHF patients and healthy controls. Groups of 15 stable CHF patients (63.7+/-2.7 years) and eight control subjects (69.8+/-1.8 years) performed both leg and arm metaboreflex tests. These metaboreflex tests involved two 5 min episodes of bicycle or handgrip exercise: on one occasion after the exercise the subjects recovered normally, while on the other occasion tourniquet cuffs were inflated around the exercising limb to supra-systolic pressure at the onset of recovery to obtain a regional circulatory occlusion, which isolates and maintains the stimulation of the metaboreflex after exercise. The contribution of the metaboreflex to exercise ventilation was computed as the absolute increment of peak ventilation that was maintained by regional circulatory occlusion. The metaboreceptor contribution to the ventilatory response to both leg exercise (patients, 5.3+/-1.6 litres/min; controls, 0.2+/-0.7 litres/min) and arm exercise (patients, 3.7+/-1.0 litres/min; controls, 0.02+/-0.4 litres/min) was significantly higher in CHF patients (P<0.05). A significant correlation was present between metaboreflex responses to arm and leg exercises (r=0.4, P<0.05). Metaboreflex responses during both types of exercise were inversely correlated with peak oxygen uptake (leg, r=-0.43, P<0.05; arm, r=-0.633, P=0.0009), but only the reflex during arm exercise was correlated with the .V(E) (ventilation)/.V(CO)(2) (CO(2) production) slope (r=0.576, P<0.005). Thus the metaboreflex system is systemically overactive and may potentially contribute to exercise intolerance during both lower- and upper-limb efforts in CHF. This suggests a unique mechanism responsible for overactivation of this system in the skeletal muscle of heart failure patients.     

Antibiotic resistance of mixed biofilms in cystic fibrosis: impact of emerging microorganisms on treatment of infection

Cystic fibrosis (CF) is a genetic disorder associated with multispecies infections where interactions between classical and newly identified bacteria might be crucial to understanding the persistent colonisation in CF lungs. This study investigated the interactions between two emerging species, Inquilinus limosus and Dolosigranulum pigrum, and the conventional CF pathogen Pseudomonas aeruginosa by evaluating the ability to develop biofilms of mixed populations and then studying their susceptibility patterns to eight different antimicrobials. Monospecies biofilms formed by I. limosus and D. pigrum produced significantly less biomass than P. aeruginosa and displayed greater sensitivity to antimicrobials. However, when in dual-species biofilms with P. aeruginosa, the emerging species I. limosus and D. pigrum were crucial in increasing tolerance of the overall consortia to most antibiotics, even without a change in the number of biofilm-encased cells. These results may suggest that revising these and other species interactions in CF might enable the development of more suitable and effective therapies in the future.     

Copper and quaternary ammonium cations exert synergistic bactericidal and antibiofilm activity against Pseudomonas aeruginosa

Biofilms are slimy aggregates of microbes that are likely responsible for many chronic infections as well as for contamination of clinical and industrial environments. Pseudomonas aeruginosa is a prevalent hospital pathogen that is well known for its ability to form biofilms that are recalcitrant to many different antimicrobial treatments. We have devised a high-throughput method for testing combinations of antimicrobials for synergistic activity against biofilms, including those formed by P. aeruginosa. This approach was used to look for changes in biofilm susceptibility to various biocides when these agents were combined with metal ions. This process identified that Cu²⁺ works synergistically with quaternary ammonium compounds (QACs; specifically benzalkonium chloride, cetalkonium chloride, cetylpyridinium chloride, myristalkonium chloride, and Polycide) to kill P. aeruginosa biofilms. In some cases, adding Cu²⁺ to QACs resulted in a 128-fold decrease in the biofilm minimum bactericidal concentration compared to that for single-agent treatments. In combination, these agents retained broad-spectrum antimicrobial activity that also eradicated biofilms of Escherichia coli, Staphylococcus aureus, Salmonella enterica serovar Cholerasuis, and Pseudomonas fluorescens. To investigate the mechanism of action, isothermal titration calorimetry was used to show that Cu²⁺ and QACs do not interact in aqueous solutions, suggesting that each agent exerts microbiological toxicity through independent biochemical routes. Additionally, Cu²⁺ and QACs, both alone and in combination, reduced the activity of nitrate reductases, which are enzymes that are important for normal biofilm growth. Collectively, the results of this study indicate that Cu²⁺ and QACs are effective combinations of antimicrobials that may be used to kill bacterial biofilms.     

Neurotoxic effects of homocysteine on cerebellar Purkinje neurons in vitro

Whilst a plethora of studies that describe the toxicity of homocysteine to CNS neurons have been published, the effects of homocysteine on the Purkinje neurons of the cerebellum that play a vital role in motor function remain wholly unexplored. We have therefore established cultures of embryonic cerebellar Purkinje neurons and exposed them to a range of concentrations of homocysteine and determined its effects on their survival. The experiments revealed that all concentrations of homocysteine studied, from 50 to 500microM, caused a significant decrease in cerebellar Purkinje neuron number. This loss could be counteracted by the pan-caspase inhibitor z-VAD-fmk in the first 24h following homocysteine exposure, revealing that the initial loss was apoptotic. However, z-VAD-fmk could not prevent homocysteine-mediated loss of cerebellar Purkinje neurons in the longer term, after 6 days in vitro. In addition to its effects on Purkinje neuron survival, homocysteine markedly reduced both the overall magnitude and the complexity of the neurite arbor extended by the cerebellar Purkinje neurons, following 6 days incubation with this agent in vitro. Taken together our data reveal that homocysteine is toxic to cerebellar Purkinje neurons in vitro, inhibiting both their survival and the outgrowth of neurites.     

Putative contribution of prostaglandin and bradykinin to muscle reflex hyperactivity in patients on Ace-inhibitor therapy for chronic heart failure.

AIMS: In patients with chronic heart failure (CHF), an overactive muscle ergoreceptor reflex (chemo-afferents sensitive to the products of muscle work) is thought to play an important role in the origin of dyspnoea. We sought to investigate whether raised intra-muscular prostaglandins (PG) and bradykinin, as estimated by levels within the venous effluent from exercising skeletal muscle may be involved in symptom generation through the stimulation of the ergoreflex. METHODS AND RESULTS: In 19 stable CHF patients and 12 normal controls, cardiopulmonary exercise capacity (peak O2 consumption [peak VO2]) and the ergoreflex contribution to ventilation (post-handgrip regional circulatory occlusion method) were measured. Venous resting and exercise plasma PGE2, PGF1alpha and bradykinin concentrations were assessed. Eleven patients on angiotensin converting enzyme inhibitors and 10 controls were challenged with ketoprofen infusion (to inhibit PG synthesis and bradykinin activity). Patients vs. controls presented lower exercise tolerance (peak VO2 15.9+/-0.7 vs. 33.0+/-1.3 mL/kg/min), an increased ventilatory response to exercise (VE/VCO2 slope 43+/-2 vs. 27+/-0.9) (p<0.0001 for all comparisons). The overactive ergoreflex of CHF (5.1+/-1.3 vs. 0.1+/-0.3 L/min) was significantly related to the increase in PGF1alpha (adjusted R2=0.34, p<0.005) but not PGE2 (adjusted R2=0.16, p>0.05). The increased PG and bradykinin productions both at rest and during exercise in CHF were attenuated after ketoprofen infusion, associated with ergoreflex reduction (-5.1+/-2.2 L/min, p<0.05 vs. saline). CONCLUSION: In CHF, overactive muscle ergoreflex is associated with elevated blood concentration of PG and bradykinin. Modulation of these metabolite concentrations acutely reduces the muscle ergoreflex activity, which suggests a causative role in triggering and/or mediating the ergoreflex response.