Rational strategies for enhancing mAb binding to SARS-CoV-2 variants through CDR diversification and antibody-escape prediction

Since the emergence of SARS-CoV-2, dozens of variants of interest and half a dozen variants of concern (VOCs) have been documented by the World Health Organization. The emergence of these VOCs due to the continuous evolution of the virus is a major concern for COVID-19 therapeutic antibodies and vaccines because they are designed to target prototype/previous strains and lose effectiveness against new VOCs. Therefore, there is a need for time- and cost-effective strategies to estimate the immune escape and redirect therapeutic antibodies against newly emerging variants. Here, we computationally predicted the neutralization escape of the SARS-CoV-2 Delta and Omicron variants against the mutational space of RBD-mAbs interfaces. Leveraging knowledge of the existing RBD-mAb interfaces and mutational space, we fine-tuned and redirected CT-p59 (Regdanvimab) and Etesevimab against the escaped variants through complementarity-determining regions (CDRs) diversification. We identified antibodies against the Omicron lineage BA.1 and BA.2 and Delta variants with comparable or better binding affinities to that of prototype Spike. This suggests that CDRs diversification by hotspot grafting, given an existing insight into the Ag-Abs interface, is an exquisite strategy to redirect antibodies against preselected epitopes and combat the neutralization escape of emerging SARS-CoV-2 variants

Strategic Asset Allocation Of Credit Guarantors

How to manage the portfolio of credit guarantors is important in practice and public policy, but has not been investigated well in the prior literature. We empirically compare four different approaches in managing credit guarantor portfolios. The four approaches are equal weighted, minimum variance, mean variance optimization and equal risk contribution methods. In terms of risk return ratio, the mean variance optimization model performs best in out-of-sample test. This result contrasts with previous findings against mean variance optimization. Our results are robust. The results do not change as the characteristics of guarantee portfolio vary

Generalized Lymphangiomatosis: Radiologic Findings in Three Pediatric Patients

Generalized lymphangiomatosis is a rare disease that is characterized by widespread bony and soft tissue involvement of lymphangioma. Radiological evaluation is crucial because the site and extent of the lymphangioma are important prognostic factors. We reported here on three cases of generalized lymphangiomatosis and all three cases showed similar radiologic findings, but a different clinical course. The CT, US and MR images showed sharply defined, non-enhanced cystic lesions involving the mediastinum, bones, spleen, lung and lower neck. The whole body MR imaging with the short tau inversion recovery (STIR) sequence showed good capability for evaluating the extent of disease

State-of-the-Art CT Imaging Techniques for Congenital Heart Disease

CT is increasingly being used for evaluating the cardiovascular structures and airways in the patients with congenital heart disease. Multi-slice CT has traditionally been used for the evaluation of the extracardiac vascular and airway abnormalities because of its inherent high spatial resolution and excellent air-tissue contrast. Recent developments in CT technology primarily by reducing the cardiac motion and the radiation dose usage in congenital heart disease evaluation have helped expand the indications for CT usage. Tracheobronchomalacia associated with congenital heart disease can be evaluated with cine CT. Intravenous contrast injection should be tailored to unequivocally demonstrate cardiovascular abnormalities. Knowledge of the state-of-the-art CT imaging techniques that are used for evaluating congenital heart disease is helpful not only for planning and performing CT examinations, but also for interpreting and presenting the CT image findings that consequently guide the proper medical and surgical management

GS2PATH: A web-based integrated analysis tool for finding functional relationships using gene ontology and biochemical pathway data

GS2PATH is a Web-based pipeline tool to permit functional enrichment of a given gene set from prior knowledge databases, including gene ontology (GO) database and biological pathway databases. The tool also provides an estimation of gene set enrichment, in GO terms, from the databases of the KEGG and BioCarta pathways, which may allow users to compute and compare functional over-representations. This is especially useful in the perspective of biological pathways such as metabolic, signal transduction, genetic information processing, environmental information processing, cellular process, disease, and drug development. It provides relevant images of biochemical pathways with highlighting of the gene set by customized colors, which can directly assist in the visualization of functional alteration

Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome

<p>Abstract</p> <p>Background</p> <p>There is no dedicated database available for Expressed Sequence Tags (EST) of the chili pepper (<it>Capsicum annuum</it>), although the interest in a chili pepper EST database is increasing internationally due to the nutritional, economic, and pharmaceutical value of the plant. Recent advances in high-throughput sequencing of the ESTs of chili pepper cv. Bukang have produced hundreds of thousands of complementary DNA (cDNA) sequences. Therefore, a chili pepper EST database was designed and constructed to enable comprehensive analysis of chili pepper gene expression in response to biotic and abiotic stresses.</p> <p>Results</p> <p>We built the Pepper EST database to mine the complexity of chili pepper ESTs. The database was built on 122,582 sequenced ESTs and 116,412 refined ESTs from 21 pepper EST libraries. The ESTs were clustered and assembled into virtual consensus cDNAs and the cDNAs were assigned to metabolic pathway, Gene Ontology (GO), and MIPS Functional Catalogue (FunCat). The Pepper EST database is designed to provide a workbench for (i) identifying unigenes in pepper plants, (ii) analyzing expression patterns in different developmental tissues and under conditions of stress, and (iii) comparing the ESTs with those of other members of the <it>Solanaceae </it>family. The Pepper EST database is freely available at <url>http://genepool.kribb.re.kr/pepper/</url>.</p> <p>Conclusion</p> <p>The Pepper EST database is expected to provide a high-quality resource, which will contribute to gaining a systemic understanding of plant diseases and facilitate genetics-based population studies. The database is also expected to contribute to analysis of gene synteny as part of the chili pepper sequencing project by mapping ESTs to the genome.</p

Immature Gastric Teratoma in an Infant: A Case Report

Gastric teratomas are extremely rare neoplasms and almost exclusively benign. They occur predominantly in males and generally present as a palpable abdominal mass. To our knowledge, only one adult case has been described in the Korean literature. We report a case in which an immature gastric teratoma in a 3-month-old boy was revealed by CT and US

PDZ-based adaptor proteins in epithelial anion transport and VIP receptor regulation

Polarized protein deposition at the apical and basolateral membranes of epithelial cells is critical for the asymmetrical transport of ions and fluids across the epithelia. PDZ-based modular adaptor proteins are expressed in the junctional areas in epithelial cells and are generally part of a molecular scaffold that determines the localization and activity of ion channels, receptors, and other signaling molecules to their correct spatial arrangement for proper response to diverse stimuli. Hence, understanding the regulatory mechanisms of channels and receptors via PDZ-based adaptors will provide valuable insights into the physiology of epithelial cells as well as pathophysiology of many human diseases including cystic fibrosis

Acute Necrotizing Encephalopathy: Diffusion MR Imaging and Localized Proton MR Spectroscopic Findings in Two Infants

In this report, we describe the findings of diffusion MR imaging and proton MR spectroscopy in two infants with acute necrotizing encephalopathy in which there was characteristic symmetrical involvement of the thalami. Diffusion MR images of the lesions showed that the observed apparent diffusion coefficient (ADC) decrease was more prominent in the first patient, who had more severe brain damage and a poorer clinical outcome, than in the second. Proton MR spectroscopy detected an increase in the glutamate/glutamine complex and mobile lipids in the first case but only a small increase of lactate in the second. Diffusion MR imaging and proton MR spectroscopy may provide useful information not only for diagnosis but also for estimating the severity and clinical outcome of acute necrotizing encephalopathy