Elucidating the molecular docking and binding dynamics of aptamers with spike proteins across SARS-CoV-2 variants of concern.

DNA aptamers with high binding affinity against SARS-CoV-2 spike proteins have been selected and analyzed. To better understand the binding affinities between DNA aptamers and spike proteins (S-proteins) of relevant variants of concerns (VOCs), and characterization are excellent approaches to implement. Here, we identified and generated DNA aptamer sequences targeting the S-protein of SARS-CoV-2 VOCs through systematic evolution of ligands by exponential enrichment (SELEX).

Endothelial PPARδ Ablation Exacerbates Vascular Hyperpermeability via STAT1/CXCL10 Signaling in Acute Lung Injury.

Background: Vascular hyperpermeability is one of the hallmarks of acute lung injury, contributing to excessive inflammation and respiratory failure. The PPARδ (peroxisome proliferator-activated receptor delta) is an anti-inflammatory transcription factor, although its role in endothelial barrier function remains unclear. Here, we studied the essential role of PPARδ in maintaining vascular endothelial barrier integrity during lung inflammation and investigated the underlying mechanisms.

Principles of visual cortex excitatory microcircuit organization.

Synapse-specific connectivity and dynamics determine microcircuit function but are challenging to explore with classic paired recordings due to their low throughput. We therefore implemented optomapping, a ∼100-fold faster two-photon optogenetic method. In mouse primary visual cortex (V1), we optomapped 30,454 candidate inputs to reveal 1,790 excitatory inputs to pyramidal, basket, and Martinotti cells.

Retinal Degeneration Associated With Biallelic RDH12 Variants: Longitudinal Evaluation of Retinal Structure and Visual Function in Pediatric Patients.

Purpose: The purpose of this study was to determine the natural history of the photoreceptor disease in a large group of pediatric patients with RHD12-associated Leber congenital amaurosis (RDH12-LCA), to estimate the changes expected over the duration of a clinical trial, and to define the relationship between the photoreceptor loss and visual dysfunction.

Methods: Forty-six patients representing 36 families were included. The great majority of patients were under the age of 18 years.

Erratum: Safety and improved efficacy signals following gene therapy in childhood blindness caused by mutations.

[This corrects the article DOI: 10.1016/j.isci.

Chlorine dioxide is a broad-spectrum disinfectant against Shiga toxin-producing and in agricultural water.

Agricultural water is commonly treated with chlorine-based disinfectants, which are impacted by water quality. Understanding how water quality influences disinfectants such as chlorine dioxide (ClO) against pathogenic bacteria is important for creating efficacious sanitation regimens. In this study, the minimum inhibitory concentration (MIC) of ClO needed to achieve a 3-Log reduction against Shiga toxin-producing (STEC) and was compared across agricultural water samples.

Pretreatment Quality of Life and Substance Use Among Patients Diagnosed With Head and Neck Cancer.

Background: There is a paucity of research on the effects of commonly used substances, such as cannabis and other drugs, on quality of life as a contributor to head and neck cancer (HNC) prognosis. We examined associations between non-alcohol or tobacco substance use (cannabis and other illicit drug) and self-reported quality of life in patients with HNC prior to starting treatment.

Methods: This was a cross-sectional study of patients who presented for routine psych-oncologevaluation prior to treatment between 11/2015 and 9/2022.

DeepPL: A deep-learning-based tool for the prediction of bacteriophage lifecycle.

Bacteriophages (phages) are viruses that infect bacteria and can be classified into two different lifecycles. Virulent phages (or lytic phages) have a lytic cycle that can lyse the bacteria host after their infection. Temperate phages (or lysogenic phages) can integrate their phage genomes into bacterial chromosomes and replicate with bacterial hosts via the lysogenic cycle.

Safety and efficacy of ATSN-101 in patients with Leber congenital amaurosis caused by biallelic mutations in GUCY2D: a phase 1/2, multicentre, open-label, unilateral dose escalation study.

Background: Leber congenital amaurosis 1 (LCA1), caused by mutations in GUCY2D, is a rare inherited retinal disease that typically causes blindness in early childhood. The aim of this study was to evaluate the safety and preliminary efficacy of ascending doses of ATSN-101, a subretinal AAV5 gene therapy for LCA1.

Methods: 15 patients with genetically confirmed biallelic mutations in GUCY2D were included in this phase 1/2 study.

Comprehensive immune profiling of SARS-CoV-2 infected kidney transplant patients.

Introduction: The immune responses of kidney transplant recipients against SARS-CoV-2 remains under studied.

Methods: In this prospective pilot study, we performed comprehensive immune profiling using cellular, proteomic, and serologic assays on a cohort of 9 kidney transplant recipients and 12 non-transplant individuals diagnosed with COVID-19.

Results: Our data show that in addition to having reduced SARS-CoV-2 specific antibody levels, kidney transplant recipients exhibited significant cellular differences including a decrease in naïve-but increase in effector T cells, a high number of CD28+ CD4 effector memory T cells, and increased CD8 T memory stem cells compared with non-transplant patients.

Characterization of two novel Salmonella phages having biocontrol potential against Salmonella spp. in gastrointestinal conditions.

Salmonella is a primary enteric pathogen related to the contamination of poultry and other food products in numerous foodborne outbreaks. The continuous emergence of multidrug-resistant bacteria has become a serious issue due to the overuse of antibiotics. Hence, lytic phages are considered alternative biocontrol agents against these bacterial superbugs.

Retinal response to light exposure in BEST1-mutant dogs evaluated with ultra-high resolution OCT.

Mutations in BEST1 cause an autosomal recessive disease in dogs where the earliest changes localize to the photoreceptor-RPE interface and show a retina-wide micro-detachment that is modulated by light exposure. The purpose of this study was to define the spatial and temporal details of the outer retina and its response to light with ultra-high resolution OCT across a range of ages and with different BEST1 mutations. Three retinal regions were selected in each eye: near the fovea-like area, near the optic nerve, both in the tapetal area, and inferior to the optic nerve in the non-tapetal area.

A new Rogue-like phage UDF157lw to control O157:H7.

Introduction: Shiga toxin-producing (STEC) O157:H7 is one of the notorious foodborne pathogens causing high mortality through the consumption of contaminated food items. The food safety risk from STEC pathogens could escalate when a group of bacterial cells aggregates to form a biofilm. Bacterial biofilm can diminish the effects of various antimicrobial interventions and enhance the pathogenicity of the pathogens.

Benefits of isochoric freezing for carrot juice preservation.

Isochoric freezing (IF) at -5°C/77 and -10°C/100 MPa was used to preserve carrot juice for 12 weeks. The juice qualities were compared to those using heat treatment (HT) at 95°C for 15 s followed by cold storage at 4°C. The native population of total aerobic bacteria, yeasts, and molds in isochoric frozen juice remained below the detection limit for 12 weeks.

Inherited Retinal Degeneration Caused by Dehydrodolichyl Diphosphate Synthase Mutation-Effect of an Modifier Variant.

Modern advances in disease genetics have uncovered numerous modifier genes that play a role in the severity of disease expression. One such class of genetic conditions is known as inherited retinal degenerations (IRDs), a collection of retinal degenerative disorders caused by mutations in over 300 genes. A single missense mutation (K42E) in the gene encoding the enzyme dehydrodolichyl diphosphate synthase (DHDDS), which is required for protein N-glycosylation in all cells and tissues, causes -IRD (retinitis pigmentosa type 59 (RP59; OMIM #613861)).

Role of Argininosuccinate Synthase 1 -Dependent L-Arginine Biosynthesis in the Protective Effect of Endothelial Sirtuin 3 Against Atherosclerosis.

Atherosclerosis is initiated with endothelial cell (EC) dysfunction and vascular inflammation under hyperlipidemia. Sirtuin 3 (SIRT3) is a mitochondrial deacetylase. However, the specific role of endothelial SIRT3 during atherosclerosis remains poorly understood.

Gut Phageome-An Insight into the Role and Impact of Gut Microbiome and Their Correlation with Mammal Health and Diseases.

The gut microbiota, including bacteria, archaea, fungi, and viruses, compose a diverse mammalian gut environment and are highly associated with host health. Bacteriophages, the viruses that infect bacteria, are the primary members of the gastrointestinal virome, known as the phageome. However, our knowledge regarding the gut phageome remains poorly understood.

Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem.

Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes.

Long-Term Safety of Bone Regeneration Using Autologous Stromal Vascular Fraction and Calcium Phosphate Ceramics: A 10-Year Prospective Cohort Study.

This prospective cohort study aimed to assess long-term safety, dental implant survival, and clinical and radiological outcomes after maxillary sinus floor elevation (MSFE; lateral window technique) using freshly isolated autologous stromal vascular fraction (SVF) combined with calcium phosphate ceramics. All 10 patients previously participating in a phase I trial were included in a 10-year follow-up. They received either β-tricalcium phosphate (β-TCP; n = 5) or biphasic calcium phosphate (BCP; n = 5) with SVF-supplementation on one side (study).

Durable vision improvement after a single intravitreal treatment with antisense oligonucleotide in 90-LCA: Replication in two eyes.

Purpose: An intravitreally injected antisense oligonucleotide, sepofarsen, was designed to modulate splicing within retinas of patients with severe vision loss due to deep intronic c.2991 + 1655A > G variant in the gene. A previous report showed vision improvements following a single injection in one eye with unexpected durability lasting at least 15 months.

AxonQuantifier: A semi-automated program for quantifying axonal density from whole-mounted optic nerves.

Background: Here, we present a semi-automated method for quantifying retinal ganglion cell (RGC) axon density at different distances from the optic nerve crush site using longitudinal, confocal microscopy images taken from whole-mounted optic nerves. This method employs the algorithm AxonQuantifier which operates on the freely available program, ImageJ.

New Method: To validate this method, seven adult male Long Evans rats underwent optic nerve crush injury followed by in vivo treatment with electric fields of varying strengths for 30 days to produce optic nerves with a wide range of axon densities distal to the optic nerve crush site.