Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds

This article is dedicated to the memory of Cyrus Chothia, who was a leading light in the world of protein structure evolution. His elegant analyses of protein families and their mechanisms of structural and functional evolution provided important evolutionary and biological insights and firmly established the value of structural perspectives. He was a mentor and supervisor to many other leading scientists who continued his quest to characterise structure and function space. He was also a generous and supportive colleague to those applying different approaches. In this article we review some of his accomplishments and the history of protein structure classifications, particularly SCOP and CATH. We also highlight some of the evolutionary insights these two classifications have brought. Finally, we discuss how the expansion and integration of protein sequence data into these structural families helps reveal the dark matter of function space and can inform the emergence of novel functions in Metazoa. Since we cover 25 years of structural classification, it has not been feasible to review all structure based evolutionary studies and hence we focus mainly on those undertaken by the SCOP and CATH groups and their collaborators

Drug-associated gastropathy: diagnostic criteria

Drugs are widely used to treat different diseases in modern medicine, but they are often associated with adverse events. Those located in the gastrointestinal tract are common and often mild, but they can be serious or life-threatening and determine the continuation of treatment. The stomach is often affected not only by drugs taken orally but also by those administered parenterally. Here, we review the mechanisms of damage, risk factors and specific endoscopic, histopathological and clinical features of those drugs more often involved in gastric damage, namely NSAIDs, aspirin, anticoagulants, glucocorticosteroids, anticancer drugs, oral iron preparations and proton pump inhibitors. NSAID- and aspirin-associated forms of gastric damage are widely studied and have specific features, although they are often hidden by the coexistence of Helicobacter pylori infection. However, the damaging effect of anticoagulants and corticosteroids or oral iron therapy on the gastric mucosa is controversial. At the same time, the increased use of new antineoplastic drugs, such as checkpoint inhibitors, has opened up a new area of gastrointestinal damage that will be seen more frequently in the near future. We conclude that there is a need to expand and understand drug-induced gastrointestinal damage to prevent and recognize drug-associated gastropathy in a timely manner

Human neutrophil alloantigens systems

Neutrophil alloantigens are involved in a variety of clinical conditions including immune neutropenias, transfusion-related acute lung injury (TRALI), refractoriness to granulocyte transfusions and febrile transfusion reactions. In the last decade, considerable progress has been made in the characterization of the implicated antigens. Currently, seven antigens are assigned to five human neutrophil antigen (HNA) systems. The HNA-1a, HNA-1b and HNA-1c antigens have been identified as polymorphic forms of the neutrophil Fcγ receptor IIIb (CD16b), encoded by three alleles. Recently, the primary structure of the HNA-2a antigen was elucidated and the HNA-2a-bearing glycoprotein was identified as a member of the Ly-6/uPAR superfamily, which has been clustered as CD177. The HNA-3a antigen is located on a 70-95 kDa glycoprotein; however, its molecular basis is still unknown. Finally, the HNA-4a and HNA-5a antigens were found to be caused by single nucleotide mutations in the αM (CD11b) and αL (CD11a) subunits of the leucocyte adhesion molecules (β2 integrins). Molecular and biochemical characterization of neutrophil antigenshave expanded our diagnostic tools by the introduction of genotyping techniques and immunoassays for antibody identification. Further studies in the field of neutrophil immunology will facilitate the prevention and management of transfusion reactions and immune diseases caused by neutrophil antibodies.Os aloantígenos de neutrófilos estão associados a várias condições clínicas como neutropenias imunes, insuficiência pulmonar relacionada à transfusão (TRALI), refratariedade à transfusão de granulócitos, e reações transfusionais febris. Na última década, foi observado considerável progresso na caracterização dos aloantígenos envolvidos nestas condições clínicas. Atualmente sete antígenos estão incluídos em cinco sistemas de antígenos de neutrófilo humano (HNA). Os antígenos HNA-1a, HNA-1b e HNA-1c foram identificados como formas polimórficas do receptor Fcγ RIIIb (CD16b), codificados por três alelos. Recentemente, a estrutura primária do antígeno HNA-2a foi elucidada e a glicoproteína carreadora do antígeno foi identificada como um membro da superfamília Ly-6/uPARe designada como CD177. O antígeno HNA-3a está localizadoem uma glicoproteína de 70-90 kDa, entretanto sua base molecular ainda é desconhecida. Finalmente, os antígenos HNA-4ae HNA-5a são resultantes de mutações de um único nucleotídeo nas subunidades αM (CD11b) and αL (CD11a) das moléculas de adesão de leucócitos (β2 integrinas). A caracterização molecular e bioquímica dos antígenos neutrofílicos permitiu a expansão das ferramentas diagnósticas pela introdução de técnicas de genotipagem e imunoensaios para a identificação de anticorpos. Novos estudos envolvendo a imunologia de granulócitos serão de grande valor para a prevenção e tratamento de reações transfusionais e doenças imunes causadas por aloanticorpos de neutrófilos.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Universidade Federal de São Paulo (UNIFESP)UNIFESPSciEL

SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms

Abstract We modeled 3D structures of all SARS‐CoV‐2 proteins, generating 2,060 models that span 69% of the viral proteome and provide details not available elsewhere. We found that ˜6% of the proteome mimicked human proteins, while ˜7% was implicated in hijacking mechanisms that reverse post‐translational modifications, block host translation, and disable host defenses; a further ˜29% self‐assembled into heteromeric states that provided insight into how the viral replication and translation complex forms. To make these 3D models more accessible, we devised a structural coverage map, a novel visualization method to show what is—and is not—known about the 3D structure of the viral proteome. We integrated the coverage map into an accompanying online resource (https://aquaria.ws/covid) that can be used to find and explore models corresponding to the 79 structural states identified in this work. The resulting Aquaria‐COVID resource helps scientists use emerging structural data to understand the mechanisms underlying coronavirus infection and draws attention to the 31% of the viral proteome that remains structurally unknown or dark

The person-centred approach to an ageing society

Modern care is often based on investigations such as laboratory markers and imaging - for example, X-ray or ultrasound. The results contribute to a diagnosis and, if judged necessary, treatment is initiated. This diseased-oriented approach is the prevailing mode of management in modern medicine. In contrast, person-centered care (PCC) takes the point of departure from each person\ub4s subjective experience of illness and its impact on daily life. A patient is considered as a person with emotions and feelings. PCC is considered present within clinical care according to a definition articulated by the Centre for Person Centred Care at the University of Gothenburg (GPCC) when three core components are present: elicitation of a detailed patient narrative; formulated partnership between caregiver and patient and documentation of the partnership in the patient record. Accordingly, when there is an illness requiring care and the person is attended using these components, PCC is being applied. In most situations today, PCC is not applied in terms of the narrative and is not fully elicited or the partnership and/or the documentation are not included. It is proposed that the challenge to Society arising from changing demographics can be addressed by implementing PCC and creating an alternative to existing healthcare. The importance and benefits of such an approach on a wider scale is not yet clear as research has been limited to date. Studies in selected patient populations (heart failure and hip fractures), however, have shown promising results. As the population ages, there will be a dramatic increase in healthcare consumption. Even with technological developments, there will be a need for tremendous resources to be dedicated to care. A new organization and attitude from healthcare policymakers and providers above and beyond the present model appears required in order to respond to this demand. As part of such change, person-centred care, with the interaction between healthcare providers and the person of the patient, can facilitate, compensate and develop more effective healthcare services for the future

MCT1 and MCT4 kinetic of mRNA expression in different tissues after aerobic exercise at maximal lactate steady state workload

We evaluate the mRNA expression of monocarboxylate transporters 1 and 4 (MCT1 and MCT4) in skeletal muscle (soleus, red and white gastrocnemius), heart and liver tissues in mice submitted to a single bout of swimming exercise at the maximal lactate steady state workload (MLSSw). After 72 h of MLSS test, the animals were submitted to a swimming exercise session for 25 min at individual MLSSw. Tissues and muscle samples were obtained at rest (control, n=5), immediately (n=5), 5 h (n=5) and 10 h (n=5) after exercise for determination of the MCT1 and MCT4 mRNA expression (RT-PCR). The MCT1 mRNA expression in liver increased after 10 h in relation to the control, immediate and 5 h groups, but the MCT4 remained unchanged. The MCT1 mRNA expression in heart increased by 31 % after 10 h when compared to immediate, but no differences were observed in relation to the control group. No significant differences were observed for red gastrocnemius in MCT1 and MCT4 mRNA expression. However, white gastrocnemius increased MCT1 mRNA expression immediately when compared to rest, 5 and 10 h test groups. In soleus muscle, the MCT1 mRNA expression increased immediately, 5 and 10 h after exercise when compared to the control. In relation to MCT4 mRNA expression, the soleus increased immediately and 10 h after acute exercise when compared to the control group. The soleus, liver and heart were the main tissues that showed improved the MCT1 mRNA expression, indicating its important role in controlling MLSS concentration in mice.644513522CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQCOORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPsem informaçãosem informação04/06643-1FAP-UNIME

Ballistic InSb Nanowires and Networks via Metal-Sown Selective Area Growth

Selective area growth is a promising technique to realize semiconductor-superconductor hybrid nanowire networks, potentially hosting topologically protected Majorana-based qubits. In some cases, however, such as the molecular beam epitaxy of InSb on InP or GaAs substrates, nucleation and selective growth conditions do not necessarily overlap. To overcome this challenge, we propose a metal-sown selective area growth (MS SAG) technique, which allows decoupling selective deposition and nucleation growth conditions by temporarily isolating these stages. It consists of three steps: (i) selective deposition of In droplets only inside the mask openings at relatively high temperatures favoring selectivity, (ii) nucleation of InSb under Sb flux from In droplets, which act as a reservoir of group III adatoms, done at relatively low temperatures, favoring nucleation of InSb, and (iii) homoepitaxy of InSb on top of the formed nucleation layer under a simultaneous supply of In and Sb fluxes at conditions favoring selectivity and high crystal quality. We demonstrate that complex InSb nanowire networks of high crystal and electrical quality can be achieved this way. We extract mobility values of 10※000-25※000 cm V s consistently from field-effect and Hall mobility measurements across single nanowire segments as well as wires with junctions. Moreover, we demonstrate ballistic transport in a 440 nm long channel in a single nanowire under a magnetic field below 1 T. We also extract a phase-coherent length of ∼8 μm at 50 mK in mesoscopic rings

Antibiotic resistance prevalence and trends in patients infected with helicobacter pylori in the period 2013–2020: Results of the european registry on h. pylori management (hp-eureg)

Background: Bacterial antibiotic resistance changes over time depending on multiple factors; therefore, it is essential to monitor the susceptibility trends to reduce the resistance impact on the effectiveness of various treatments. Objective: To conduct a time-trend analysis of Helicobacter pylori resistance to antibiotics in Europe. Methods: The international prospective European Registry on Heli-cobacter pylori Management (Hp-EuReg) collected data on all infected adult patients diagnosed with culture and antimicrobial susceptibility testing positive results that were registered at AEG-REDCap e-CRF until December 2020. Results: Overall, 41,562 patients were included in the Hp-EuReg. Culture and antimicrobial susceptibility testing were performed on gastric biopsies of 3974 (9.5%) patients, of whom 2852 (7%) were naive cases included for analysis. The number of positive cultures decreased by 35% from the period 2013–2016 to 2017–2020. Concerning naïve patients, no antibiotic resistance was found in 48% of the cases. The most frequent resistances were reported against metronidazole (30%), clarithromycin (25%), and levofloxacin (20%), whereas resistances to tetracycline and amoxicillin were below 1%. Dual and triple resistances were found in 13% and 6% of the cases, respectively. A decrease (p < 0.001) in the metronidazole resistance rate was observed between the 2013–2016 (33%) and 2017–2020 (24%) periods. Conclusion: Culture and antimicrobial susceptibility testing for Helicobacter pylori are scarcely performed (<10%) in Europe. In naïve patients, Helicobacter pylori resistance to clarithromycin remained above 15% throughout the period 2013–2020 and resistance to levofloxacin, as well as dual or triple resistances, were high. A progressive decrease in metronidazole resistance was observed

Features of the Parameters of 24-Hours pH-Impedance and High-Resolution Esophageal Manometry in Patients with Barrett's Esophagus on Proton Pump Inhibitors

Аim: to identify predictors of insufficient effectiveness of proton pump inhibitors based on the evaluation of the results of 24-hour pH-impedance and high-resolution esophageal manometry in patients with Barrett's esophagus.Materials and methods. 52 patients with histologically confirmed Barrett's esophagus who are on therapy with proton pump inhibitors were examined. All patients underwent daily pH-impedance and high-resolution esophageal manometry.Results. According to daily pH-impedance, group 1 consisted of 37 patients who responded satisfactorily to antisecretory therapy, group 2 of 15 patients who demonstrated insufficient response to acid-suppressive therapy, 11 of whom had no clinical manifestations. The total number of reflux averaged 55 in group 1 and 106 in group 2. The average number of acid reflux in group 1 was 5.68, in group 2 — 48.5. The average number of non-acid reflux prevailed in patients of group 2 and averaged 58, in group 1 the indicator averaged 47. Evaluation of the results of high-resolution esophageal manometry showed that violations of the structure and function of the esophago-gastric junction were detected in 21 patients out of 52. Disorders of the motility of the thoracic esophagus were detected in 31 patients out of 52. When comparing the frequency of motor disorders from the thoracic esophagus in groups 1 and 2, no significant differences were obtained. However, significantly more frequent registration of violations of the structure and/or function of the esophago-gastric junction was found in the group with unsatisfactory effectiveness of proton pump inhibitors.Conclusion. In a number of patients with Barrett's esophagus, there is an insufficient effect of acid-suppressive therapy and at the same time an asymptomatic course of the disease, which may increase the risk of its progression. Predictors of insufficiently successful treatment of patients with Barrett's esophagus may be both insufficient pharmacological effect of proton pump inhibitors themselves, and motility disorders that cause the presence of non-acid reflux, decreased esophageal clearance, which in turn may cause the patient's symptoms to persist and adversely affect the condition of the esophageal mucosa