Platform for isolation and characterization of SARS-CoV-2 variants enables rapid characterization of Omicron in Australia

Genetically distinct variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged since the start of the COVID-19 pandemic. Over this period, we developed a rapid platform (R-20) for viral isolation and characterization using primary remnant diagnostic swabs. This, combined with quarantine testing and genomics surveillance, enabled the rapid isolation and characterization of all major SARS-CoV-2 variants circulating in Australia in 2021. Our platform facilitated viral variant isolation, rapid resolution of variant fitness using nasopharyngeal swabs and ranking of evasion of neutralizing antibodies. In late 2021, variant of concern Omicron (B1.1.529) emerged. Using our platform, we detected and characterized SARS-CoV-2 VOC Omicron. We show that Omicron effectively evades neutralization antibodies and has a different entry route that is TMPRSS2-independent. Our low-cost platform is available to all and can detect all variants of SARS-CoV-2 studied so far, with the main limitation being that our platform still requires appropriate biocontainment

Cyanobacterial nitrogenases: phylogenetic diversity, regulation and functional predictions

Abstract Cyanobacteria is a remarkable group of prokaryotic photosynthetic microorganisms, with several genera capable of fixing atmospheric nitrogen (N2) and presenting a wide range of morphologies. Although the nitrogenase complex is not present in all cyanobacterial taxa, it is spread across several cyanobacterial strains. The nitrogenase complex has also a high theoretical potential for biofuel production, since H2 is a by-product produced during N2 fixation. In this review we discuss the significance of a relatively wide variety of cell morphologies and metabolic strategies that allow spatial and temporal separation of N2 fixation from photosynthesis in cyanobacteria. Phylogenetic reconstructions based on 16S rRNA and nifD gene sequences shed light on the evolutionary history of the two genes. Our results demonstrated that (i) sequences of genes involved in nitrogen fixation (nifD) from several morphologically distinct strains of cyanobacteria are grouped in similarity with their morphology classification and phylogeny, and (ii) nifD genes from heterocytous strains share a common ancestor. By using this data we also discuss the evolutionary importance of processes such as horizontal gene transfer and genetic duplication for nitrogenase evolution and diversification. Finally, we discuss the importance of H2 synthesis in cyanobacteria, as well as strategies and challenges to improve cyanobacterial H2 production

Antimicrobial Cyanopeptide Action on Bacterial Cells Observed with Atomic Force Microscopy

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Cyanobacteria produce oligopeptides that are predominantly synthesized by the non-ribosomal pathway. Among these are the aeruginosin and cyanopeptolin protease inhibitors, which act against enzymes known to cause several human health problems. Atomic force microscopy (AFM) was used to study the effect of cyanopeptides produced by Microcystis aeruginosa NPCD-1 on pathogenic bacterial cell surfaces. The selected strain was characterized based on the 16S rRNA gene sequence and the intergenic spacer region of the phycocyanin operon. PCR amplification was employed to investigate the presence of genes encoding for aeruginosin and cyanopeptolin. Purified extract from M. aeruginosa NPCD-1 cells was screened for bioactive compounds. The effect of purified extract containing protease inhibitors produced by the NPCD-1 strain on bacterial cells was observed using AFM. Aeruginosin and cyanopeptolin genes were confirmed by both PCR amplification and gene sequencing. Mass spectrometry analysis confirmed the production of aeruginosin. The interaction of Bacillus cereus, Escherichia coli and Staphylococcus aureus with cyanopeptides was characterized by examining the loss of surface stiffness and the formation of micelles, most likely originating from the membrane disruption. The AFM results demonstrate the ability of cyanobacterial extract to alter the cellular membrane of bacterial pathogens.91141148Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)FAPESP [FAPESP - 2003/12529-4, 2009/05474-5]CNPq [CNPq 559720/2009-2]CNPq [308299/2009-4, 151931/2010-0]FAPESP [2010/09867-9, 2008/53627-2, 2006/01671-2

CYP1A1, GSTM1 and GSTT1 polymorphisms, tobacco and alcohol status and risk of head and neck squamous cell carcinoma

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)We examined the influence of the CYP1A1 A4889G and T6235C, GSTM1 and GSTT1 polymorphisms, involved in carcinogen metabolism, on the head and neck (HN) squamous cell carcinoma (SCC) risk. DNA from 142 HNSCC patients and 142 controls was analysed by polymerase chain reaction (PCR)-restriction fragment length polymorphism or multiplex-PCR for the polymorphisms analyses. Excesses of the CYP1A1 4889AG+GG and 4889AG+GG plus GSTT1 null genotype were seen in patients with heavy tobacco habit compared with controls (41.9% versus 26.8%, P=0.03; 26.2% versus 10.3%, P=0.04, respectively). Carriers of the referred genotypes and heavy tobacco consumption were under a 2.0-fold and 2.8-fold increased risks for HNSCC than others, respectively. The CYP1A1 6235TC+CC plus GSTM1 and GSTT1 null genotypes were more common in pharyngeal SCC patients than in controls (5.3% versus 0.7%, P=0.04). Carriers of the combined genotype had 16.0-fold increased risk for the disease than others. The frequency of one null genotype of the GSTM1 or GSTT1 gene was higher in patients with pharyngeal SCC and heavy smoking status than in controls (76.3% versus 57.7%, P=0.04). Carriers of the referred genotype and heavy tobacco status had a 2.4-fold increased risk for pharyngeal SCC than others. In contrast, the CYP1A1 6235TC+CC genotype was more common in controls than in laryngeal SCC patients (35.9% versus 21.6%, P=0.01). Carriers of the genotype had a 0.2-fold decreased risk for the disease than others. Our data present preliminary evidence that inherited combined CYP1A1 A4889G and T6235C abnormalities and GSTM1 and GSTT1 pathways are important determinants of HNSCC, particularly pharyngeal SCC in heavy smoking individuals from southeastern Brazil.32612091215Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Financiadora de Estudos e Projetos do Ministerio da Ciencia e Tecnologia do Brasil (FINEP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Risk factors for conjunctival and retinal vessel alterations in sickle cell disease

Purpose: The aim of this study was to clarify whether the clinical, laboratory and genetic aspects of sickle cell disease (SCD) influence the occurrence of vessel alterations in the conjunctiva and retina. Methods: A total of 102 SCD patients underwent biomicroscopical and retinal examination, in addition to evaluations of haemoglobin (Hb) and haematocrit (Ht) levels, fetal haemoglobin (HbF) estimations, serum creatinine and albuminuria levels, glomerular filtration rate (GFR) values, phenotypes, beta-globin gene haplotypes and alpha-thalassaemia. The relationship between ocular vessel alterations and clinical, laboratory and genetic features were evaluated using chi-squared or Fisher tests and logistic regression analysis. In 13 patients on enalapril treatment, a second ophthalmological evaluation was performed after a 12-month period to evaluate the longitudinal effect of the drug on ocular vessels. Results: Conjunctival vessel alteration (CVA) was not influenced by age, gender, HbF estimation, serum creatinine and albuminuria levels, GFR values, beta-globin gene haplotypes or alpha-thalassaemia. However, increased frequencies of CVA were found in patients with Hb <= 9.0 g/dl, Ht <= 26.7% and sickle cell anaemia (SS) phenotype. Retinal vessel alteration (RVA) was identified only in patients aged 17 years or older. Enalapril did not demonstrate ocular vessel amelioration after 12-months of daily use. Conclusion: The results indicate that lower Hb and Ht levels and SS phenotype are risk factors for CVA, and age over 17 years may be risk factors for RVA in SCD patients.84223424

Review on the effect of moisture and contamination on the interfacial properties of adhesive joints

Adhesives play an important role in many key industrial sectors, such as the automotive industry, enabling the construction of lightweight, multi-material structures, combining polymers, composites and metals. However, adhesives are usually polymeric materials, which can be affected by environmental and working conditions, such as moisture and contamination. Although moisture and contamination degrade the adhesive, the failure of a bonded joint is often ultimately interfacial. Therefore, a literature review on the influence of those factors on the interfacial properties of adhesive joints is performed to understand the phenomena that take part in the degradation on adhesive joints when subjected to humid and contaminated environments, which can oftentimes be the case in factory conditions, especially for parts from third-party suppliers. The mechanisms and effects of moisture aging and contamination are presented, as well as experimental testing methods and practical case studies. It is concluded that both moisture and other contaminants may lead to a reduction in joint strength and catastrophic adhesive failure. Moisture absorption can occur through the adhesive, but in an adhesive joint, it can additionally occur through the substrate, the interface between the adhesive and the substrate or in the cracks and pores of the adhesive. After water ingresses into the adhesive, it decreases its mechanical properties and plasticizes it. However, in an adhesive joint, the water diffusion occurs much faster than in bulk adhesive due to the complementary diffusion paths, which typically leads to adhesive failure at the adhesive/substrate interface. Additionally, in an adhesive joint, water may induce the hydrolysis of the substrates or have other chemical interactions with them. Contaminants can diffuse through the joint or remain at the adhesive/ substrate interface. When they diffuse through the joint, they have consequences similar to those of water sorption. However, when they remain at the interface, they can produce locally debonded areas, which may lead to joint failure. </jats:p

Inherited pericentric inversion of chromosome 16 in chronic phase of chronic myeloid leukaemia

The simultaneous occurrence of two specific acquired chromosomal abnormalities in chronic or acute leukaemias is rare. Inherited chromosomal abnormalities are also rare events in the general population. In chronic myeloid leukaemia (CML), characterised by the t(9;22)(q34;q11), the inv(16)(p13q22) has been described associated with the acceleration of disease or onset of blast crisis. We report on a patient with chronic phase of CML and both acquired t(9;22)(q34;q11) and inherited inv(16)(p13q22), who obtained a complete remission of the disease after bone marrow transplant. Therefore, it is worth to comment that an additional chromosomal abnormality in disease does not obligatory mean transformation of the disease to a more aggressive form, since chromosomal abnormalities are also seen in normal individuals. (c) 2005 Elsevier Ltd. All rights reserved.30111511