61 research outputs found
COVID-19: An update with future urgent priorities and a case study of repurposing drug design
SARS-CoV-2 is highly transmissible and pathogenic, with nearly 6.5 million infected people dying worldwide. A severe acute respiratory syndrome is one of the primary COVID-19 outcomes, often related to bacterial co-infections. In addition, infective variants of SARS-CoV-2 have constantly emerged in different countries, causing recurrent waves of infection. These variants increase the chances of vaccine failure, even in countries with accelerated vaccination programs, such as Israel and the USA. In this brief review, the subjects addressed include aspects of the SARS-CoV-2 variants, vaccines, drug therapy, and new alternative therapies. Finally, this review also discussed articles that addressed the repositioning of drugs against the SarsCov2 MPro enzyme using in silico approaches. In addition, we discussed the repositioning of drugs in silico, which can be a valuable strategy to guide and optimize the selection of elective compounds already approved for human use. Bearing in mind that few drugs, such as nirmatrelvir, ritonavir (Paxlovid), molnupiravir, and some monoclonal antibodies, have received authorization throughout the COVID-19 pandemic, according to Food and Drug Administration guidelines
Flippase Inhibitors as Antimicrobial Agents
Drug resistant microbes are a considerable challenge for modern medicine to overcome. The research described in this dissertation involved development of lipid flippase inhibitors and investigating their potential as antimicrobial agents against various drug resistant microbes. The microbes primarily investigated were methicillin resistant Staphylococcus aureus (MRSA) & Cryptococcus neoformans. Chapter 1 reviews the historical perspective and summarizes the current state of the field of research. In Chapter 2, the design space of an antimicrobial peptide known as humimycin was explored and the effects of modifications on its structure were observed against MRSA. Several key observations resulted. Most notably, the nanoparticles formed by the drug in solution are a likely contributor to the ability for various versions of the peptide to work synergistically when mixed in checkerboard assays. Chapter 3 details the investigation of a P4 type ATPase flippase inhibitor as an antimicrobial agent against C. neoformans and to potentiate the effects of Caspofungin. Efficacy of the peptide was observed in vitro against the wild type strain. Annexin assays and confocal microscopy provide evidence towards the underlying mechanism of activity, relating to phosphatidylserine distribution in the membrane. Flippase inhibitors are drugs ripe for investigation due to their antimicrobial potential against drug resistant microbes
Mathematical Models of Infection Prevention Programs in Hospital Settings
Hospitals play a vital role in providing for the healthcare needs of a community. Patients can develop hospital-acquired infections (HAIs) during their hospitalization due to exposure to foreign bacteria, viruses, and fungi. Infection prevention programs target and reduce HAIs, but implementing the infection prevention programs often comes with a cost. The goal of my research is to use mathematical models to quantify the impact of infection prevention programs on cases of HAIs and total healthcare costs. First, I use a Markov chain model to quantify how one infection prevention program reduces general HAIs in the hospital. Then, I calculate the impact of resistance by healthcare leaders to implement two infection prevention techniques on two HAIs in the hospital. I used ordinary differential equations to quantify the timing of initiation and termination of two infection prevention programs within a region divided into two components to understand how a community intervention and a localized intervention affect the peak number of infections in an epidemic. Finally, I used an agent-based model to quantify the impact of one specific infection prevention program on one HAI in one ward within the hospital. Overall, my research supports implementing the specific infection prevention programs examined to reduce the burden on healthcare systems and improve patient outcomes
Characterization of the salivary microbiome in COVID-19 infection and development of a cpn60 classifier
The human microbiome is thought to play an important role in many diseases. Recently, many studies have been done on the human microbiome and COVID19, caused by SARS-CoV-2, however only a few have been focused on the salivary microbiome, or oral microbiome in general, even though several oral symptoms of COVID19 are widely reported. In this study, we explored whether there is a difference in the taxonomic composition of the salivary microbiomes of people who are SARS-CoV-2 positive and people who are SARS-CoV-2 negative. We collected saliva samples from 138 volunteers (78 SARS-CoV-2 negative and 60 positive) and identified the salivary microbiota by chaperonin-60 (cpn60) amplicon sequencing. Taxonomic identification of the resulting sequencing was done by alignment to our cpn60 reference database using wateredBLAST. We found that the SARS-CoV-2 positive groups and the SARS-CoV-2 negative groups are different in their salivary microbiome composition on a population scale, however, the two groups are not significantly different in species diversity. Hierarchical clustering resulted in the identification of six clusters. Clusters dominated by Porphyromonas sp. or Prevotella melaninogenica contained significantly more SARS-CoV-2 positive samples than negatives, while clusters dominated by Streptococcus sanguinis or Megasphaera micronuciformis contained more SARS-CoV-2 negative samples. The results of the salivary microbiome study offered an opportunity to explore use of a Naïve-Bayesian classifier an alternative method for identification of cpn60 sequences that would overcome some of the limitations of the wateredBLAST alignment method. We trained the RDP classifier on a curated set of cpn60 barcode sequences, and tested its performance on cpn60 data from three human microbiomes: saliva, vagina, and stool. We found that 62%, 74% and 69% of salivary, vaginal and stool sequence variants were classified to the species level with confidence score >0.8, respectively. These confidently classified sequences accounted for 79%, 86% and 92% of the salivary, vaginal and stool microbiomes, respectively. Identification with the classifier also took significantly less time than wateredBLAST alignment. The results of the studies described in this thesis provide a foundation for future studies aimed at understanding the relationship of oral microbiota to SARS-CoV-2 infection and demonstrate that use of a Naïve-Bayesian classifier is a robust method for taxonomic identification of cpn60 sequences generated in these studies and studies of other microbiomes
Reactogenicity, safety and antibody response, after one and two doses of mRNA-1273 in seronegative and seropositive healthcare workers
SCOPUS: le.jinfo:eu-repo/semantics/publishe
Characterization of new virucidal and antiviral compounds against coronaviruses and herpesviruses. Study of viral entry by Clathrin
Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de Lectura: 01-07-202
Clinical and Cellular Response to Abatacept Therapy and Haematopoietic Stem Cell Transplantation in LRBA Deficiency
The lipopolysaccharide-responsive beige-like anchor (LRBA) gene comprises 58 exons, is located at chromosome 4q31, and encodes one of nine human BEACH proteins that participate in intracellular protein trafficking. Although ubiquitously expressed, LRBA is particularly vital to the function of regulatory T cells where it traffics CTLA4 to the cell surface, and prevents its lysosomal degradation. CTLA4 is an inhibitory receptor that competes with CD28 to bind CD80/CD86 on antigen presenting cells, thus preventing T cell activation. By interaction with CTLA4, LRBA plays an important role in maintaining immune homeostasis. Biallelic deleterious mutations throughout LRBA abolish expression of LRBA protein in almost all described cases, and cause a rare clinical syndrome characterised by cytopenia, inflammatory bowel disease, lymphadenopathy, and recurrent sinopulmonary disease. For reasons that are not completely understood, the spectrum of disease severity and manifestations is broad, ranging from asymptomatic individuals through to patients requiring profound immune suppression. Targeted therapy with the CTLA4-IgG fusion protein Abatacept has shown promise in some patients but cure is only possible through haematopoietic stem cell transplantation, a high-risk procedure with mixed early outcomes in LRBA deficiency.
This thesis follows a cohort of 16 LRBA-deficient patients from diagnosis through to the introduction of Abatacept therapy, and finally bone marrow transplantation with reduced intensity conditioning. In-depth immune system interrogation was performed to characterise the impact of LRBA deficiency on T- and B-lymphocytes, as well as the innate immune system, which had not previously been studied in this disease. This study found that Abatacept therapy successfully modulates disease activity, both clinically and immunologically, but does not halt disease progression. Transplantation with reduced intensity conditioning can lead to complete disease remission with full donor chimerism, and correction of most immunological defects. A range of biological markers of disease activity were identified across the immune system, which can aid the monitoring of response to therapeutic interventions
The effect of green extraction method, subcritical, water extraction, on selected biological activities of Chaga mushroom
Inonotus obliquus, or Chaga, is a medicinal mushroom with a long history of folk medicinal use and growing popularity worldwide. It cannot be cultivated so novel, greener extraction methods are needed to satisfy the market and obtain high-quality supplements. In this study, we evaluated the biological activity (antimicrobial and antioxidant) of Mongolian (IM) and Serbian (IS) Chaga extracts obtained by subcritical water extraction. They were also screened for general chemical composition. Both IM and IS, have high phenolic content. HPLC analysis revealed that extracts are especially rich in chlorogenic acid, followed by catechins, p-coumaric and cinnamic acids. ABTS assay confirmed the remarkable scavenging ability of extracts, reaching 98% when a concentration of 2 mg/mL was tested. The antimicrobial potential was examined by microdilution method using Gram-positive and (Enterococcus faecalis and Staphylococcus aureus), Gram-negative bacteria (Escherichia coli and Actinetobacteria baumannii). According to the obtained minimal inhibitory concentration (MIC) for E. faecalis S. aureus (MIC -1.25 mg / mL), E. coli, and A. baumannii (MIC -2.5 mg / mL) both extracts were shown to have the same effect on the tested bacteria. Hereby, we demonstrated the high biological potential of extracts obtained by subcritical water extraction
Interaktion von eosinophilen Granulozyten und Aspergillus fumigatus im Kontext der allergischen bronchopulmonalen Aspergillose (ABPA)
Ein nicht unwesentlicher Teil der Patienten, die unter zystischer Fibrose oder schwerem Asthma leiden, erkranken ab dem jungen Erwachsenenalter an der allergischen bronchopulmonalen Aspergillose. Dieses Krankheitsbild ist durch eine starke, durch A. fumigatus induzierte, Th2-polarisierte allergische Entzündung der Lunge gekennzeichnet. Ein wichtiges Kriterium dieser nicht-invasiven Erkrankung ist zudem der Einstrom von eosinophilen Granulozyten in die Lunge.
In dieser Arbeit stand die Untersuchung der Interaktion zwischen Eosinophilen als immunologische Effektorzellen und dem Pilzerreger im Focus. Es konnte gezeigt werden, dass Eosinophile über die Fähigkeit verfügen, in Pilzzellen apoptoseähnliche Prozesse zu induzieren und diese damit abzutöten. Auch wurde beobachtet, dass unter speziellen Bedingungen eine Phagozytose von A. fumigatus-Konidien durch Eosinophile möglich ist, die allerdings als Ursache für den in vitro beobachteten antifungalen Effekt ausgeschlossen werden kann. Für diesen antimikrobiellen Mechanismus scheint ein direkter Zell-Zell-Kontakt notwendig zu sein, der schließlich auch die Sekretion von Zytokinen auslöst, wie beispielsweise IL-4 oder MIP1α, aber auch in geringerem Umfang IL-13. Dieser zellulären Antwort liegen ausgeprägte Änderungen im Transkriptom der Eosinophilen zugrunde. Aber auch A. fumigatus reagiert auf die Anwesenheit der Effektorzellen mit transkriptionellen Veränderungen. Da der direkte Kontakt zwischen beiden Zellarten für die Interaktion eine wichtige Grundlage darstellt, liegt es nahe, dass vor allem auf der Pilzzellwand relevante Determinanten exponiert werden. Das Adhärenzmolekül Galactosaminogalactan scheint eine wesentliche Komponente für die Adhärenz von Hyphen und Eosinophilen darzustellen. Ursächlich hierfür ist anscheinend allerdings nicht eine direkte Bindung des Heteropolymers, sondern vielmehr eine elektrostatische Wechselwirkung. Über diese werden beide Zelltypen zusammengeführt, sodass eine Bindung von Erkennungsrezeptoren an Pilzstrukturen und eine anschließende Granulozytenaktivierung ermöglicht wird. Das Oberflächensaccharid Galactofuranose wird hingegen sehr wahrscheinlich direkt gebunden und trägt darüber hinaus zur Widerstandsfähigkeit des Pilzes gegenüber der antifungalen Wirkung von Eosinophilen bei. Ein Molekül, das nur bei Konidien vorliegt, ist das Hydrophobin RodA. Dieses Protein hat ebenfalls eine protektive Wirkung für den Pilz. Es verhindert die Erkennung von inhalierten Sporen in der frühen Phase einer Infektion bzw. Exposition. Dieser molekulare Schutzschild geht jedoch bei der Auskeimung der Konidien verloren. Neben diesen Oberflächenstrukturen sind auch sekretierte A. fumigatus-Proteasen in der Lage Eosinophile über den protease activated receptor 2 zu aktivieren. Auch können von Eosinophilen sekretierte Zytokine, wie IL-4, durch diese proteolytisch aktiven Enzyme degradiert werden und es kann ein Eingriff in die Immunantwort erfolgen. Neben der Charakterisierung dieser etablierten Pilzvirulenzdeterminanten wurde auch ein Screening nach Transkriptionsfaktoren durchgeführt, die einen Einfluss auf die Interaktion haben können. Hierbei konnten 53 potenzielle Kandidatengene identifiziert werden, bei denen entweder eine Beeinflussung der Sensitivität des Pilzes gegenüber Eosinophilen beobachtet wurde oder ein Einfluss auf die Eosinophilenaktivierung.
Die in dieser Arbeit gewonnen Erkenntnisse hinsichtlich der Interaktion von Eosinophilen und A. fumigatus zeigen die Vielfältigkeit der molekularen Strukturen des Pilzes, über die dieser mit den Effektorzellen des Immunsystems wechselwirken kann. Komplexe Glycanstrukturen spielen dabei ebenso eine wichtige Rolle wie sezernierte Proteasen oder zellwanddekorierende Proteine. Die dargestellten Ergebnisse bilden jedoch lediglich eine erste Grundlage im Verständnis der Wirt-Pathogen-Interaktion im Kontext von ABPA und werfen an einigen Stellen sogar neue Fragestellungen auf, die in weiterführenden Versuchen näher beleuchtet werden müssen
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