Transcriptomics using lung resection material to advance our understanding of COPD and idiopathic pulmonary fibrosis pathogenesis.

https://bit.ly/3JoW73H.

Establishment of a 3D organoid culture model for the investigation of adult slow-cycling putative intestinal stem cells.

The study of intestinal stem cells is a prerequisite for the development of therapies aimed at regenerating the gut. To enable investigation of adult slow-cycling H2B-GFP-retaining putative small intestinal (SI) stem cells in vitro, we have developed a three-dimensional (3D) SI organoid culture model based on the Tet-Op histone 2 B (H2B)-green fluorescent protein (GFP) fusion protein (Tet-Op-H2B-GFP) transgenic mouse. SI crypts were isolated from 6- to 12-week-old Tet-Op-H2B-GFP transgenic mice and cultured with appropriate growth factors and an animal-derived matrix (Matrigel).

RNA-Seq Analysis of Mammalian Prion Disease.

A protein, which can attain a prion state, differs from standard proteins in terms of structural conformation and aggregation propensity. High-throughput sequencing technology provides an opportunity to gain insight into the prion disease condition when coupled with single-cell RNA-Seq analysis to reveal transcriptional changes during prion-based pathogenicity. In this chapter, we present a protocol for RNA-Seq analysis of mammalian prion disease using a single-cell RNA sequencing dataset procured from the NCBI GEO database.

Cotton Meristem Transcriptomes: Constructing an RNA-Seq Pipeline to Explore Crop Architecture Regulation.

Plants stem cells, known as meristems, specify all patterns of growth and organ size. Differences in meristem activities contribute to diverse shoot architectures. As many architectural traits, such as branching patterns, flowering time, and fruit size, are yield determinants, meristem regulation is of fundamental importance to crop productivity.

Efficient and Powerful Integration of Targeted Metabolomics and Transcriptomics for Analyzing the Metabolism Behind Desirable Traits in Plants.

Through current mass spectrometry methods and multiple RNA-Seq technologies, large metabolomics and transcriptomics datasets are readily obtainable, which provide a powerful and global perspective on metabolism. Indeed, one "omics" method is often not enough to draw strong conclusions about metabolism. Combining and interpreting multiple "omics" datasets remains a challenging task that requires careful statistical considerations and pre-planning.

An RNA-Seq Data Analysis Pipeline.

In this chapter, we present an established pipeline for analyzing RNA-Seq data, which involves a step-by-step flow starting from raw data obtained from a sequencer and culminating in the identification of differentially expressed genes with their functional characterization. The pipeline is divided into three sections, each addressing crucial stages of the analysis process. The first section covers the initial steps of the pipeline, including downloading of the data of interest and performing quality control assessment.

Colistin Induces Oxidative Stress and Apoptotic Cell Death through the Activation of the AhR/CYP1A1 Pathway in PC12 Cells.

Colistin is commonly regarded as the "last-resort" antibiotic for combating life-threatening infections caused by multidrug-resistant (MDR) gram-negative bacteria. Neurotoxicity is a potential adverse event associated with colistin application in clinical settings, yet the exact molecular mechanisms remain unclear. This study examined the detrimental impact of colistin exposure on PC12 cells and the associated molecular mechanisms.

The impact of imposter syndrome on self-esteem and intention to quit among respiratory therapy (RT) students in Saudi Arabia.

Introduction: Imposter syndrome is common among health disciplinary students, leading to serious consequences. However, the impact of imposter syndrome on self-esteem and quitting intention among respiratory therapy students has not been well researched.

Objective: To report on the prevalence of imposter syndrome and assess its impacts on self-esteem and quitting intention among respiratory therapy students in Saudi Arabia.

Enabling Lignin Valorization Through Integrated Advances in Plant Biology and Biorefining.

Despite lignin having long been viewed as an impediment to the processing of biomass for the production of paper, biofuels, and high-value chemicals, the valorization of lignin to fuels, chemicals, and materials is now clearly recognized as a critical element for the lignocellulosic bioeconomy. However, the intended application for lignin will likely require a preferred lignin composition and form. To that end, effective lignin valorization will require the integration of plant biology, providing optimal feedstocks, with chemical process engineering, providing efficient lignin transformations.

Epitranscriptomic mechanisms of androgen signalling and prostate cancer.

Prostate cancer (PCa) is the second most common cancer diagnosed in men. While radical prostatectomy and radiotherapy are often successful in treating localised disease, post-treatment recurrence is common. As the androgen receptor (AR) and androgen hormones play an essential role in prostate carcinogenesis and progression, androgen deprivation therapy (ADT) is often used to deprive PCa cells of the pro-proliferative effect of androgens.

Advantages of automated immunostain analyses for complex membranous immunostains: An exemplar investigating loss of E-cadherin expression in colorectal cancer.

As pathology moves towards digitisation, biomarker profiling through automated image analysis provides potentially objective and time-efficient means of assessment. This study set out to determine how a complex membranous immunostain, E-cadherin, assessed using an automated digital platform fares in comparison to manual evaluation in terms of clinical correlations and prognostication. Tissue microarrays containing 1000 colorectal cancer samples, stained with clinical E-cadherin antibodies were assessed through both manual scoring and automated image analysis.

A novel and selective fluorescent ligand for the study of adenosine A receptors.

Fluorescent ligands have proved to be powerful tools in the study of G protein-coupled receptors in living cells. Here we have characterized a new fluorescent ligand PSB603-BY630 that has high selectivity for the human adenosine A receptor (AR). The AR appears to play an important role in regulating immune responses in the tumor microenvironment.

Strategies for producing high value small molecules in microalgae.

Eukaryotic microalgae are a diverse group of organisms that can be used for the sustainable production of a wide range of high value compounds, including lipids, flavours and dyes, bioplastics, and cosmetics. Optimising total biomass production often does not lead to optimal product yield and more sophisticated biphasic growth strategies are needed, introducing specific stresses to induce product synthesis. Genetic tools have been used to increase yields of natural products or to introduce new pathways to algae, and wider deployment of these tools offers promising routes for commercial production of high value compounds utilising minimal inputs.

Radiogenomics as an Integrated Approach to Glioblastoma Precision Medicine.

Purpose Of Review: Isocitrate dehydrogenase wild-type glioblastoma is the most aggressive primary brain tumour in adults. Its infiltrative nature and heterogeneity confer a dismal prognosis, despite multimodal treatment. Precision medicine is increasingly advocated to improve survival rates in glioblastoma management; however, conventional neuroimaging techniques are insufficient in providing the detail required for accurate diagnosis of this complex condition.

Ligand-Directed Labeling of the Adenosine A Receptor in Living Cells.

The study of protein function and dynamics in their native cellular environment is essential for progressing fundamental science. To overcome the requirement of genetic modification of the protein or the limitations of dissociable fluorescent ligands, ligand-directed (LD) chemistry has most recently emerged as a complementary, bioorthogonal approach for labeling native proteins. Here, we describe the rational design, development, and application of the first ligand-directed chemistry approach for labeling the AAR in living cells.

β-glycerophosphate, not low magnitude fluid shear stress, increases osteocytogenesis in the osteoblast-to-osteocyte cell line IDG-SW3.

Aim: As osteoblasts deposit a mineralized collagen network, a subpopulation of these cells differentiates into osteocytes. Biochemical and mechanical stimuli, particularly fluid shear stress (FSS), are thought to regulate this, but their relative influence remains unclear. Here, we assess both biochemical and mechanical stimuli on long-term bone formation and osteocytogenesis using the osteoblast-osteocyte cell line IDG-SW3.

Stromal lymphocytes are associated with upgrade of B3 breast lesions.

Various histopathological, clinical and imaging parameters have been evaluated to identify a subset of women diagnosed with lesions with uncertain malignant potential (B3 or BIRADS 3/4A lesions) who could safely be observed rather than being treated with surgical excision, with little impact on clinical practice. The primary reason for surgery is to rule out an upgrade to either ductal carcinoma in situ or invasive breast cancer, which occurs in up to 30% of patients. We hypothesised that the stromal immune microenvironment could indicate the presence of carcinoma associated with a ductal B3 lesion and that this could be detected in biopsies by counting lymphocytes as a predictive biomarker for upgrade.

Evaluation of secretome biomarkers in glioblastoma cancer stem cells: A bioinformatics analysis.

Background: Glioblastoma (GBM) is a malignant brain tumor that frequently occurs alongside other central nervous system (CNS) conditions. The secretome of GBM cells contains a diverse array of proteins released into the extracellular space, influencing the tumor microenvironment. These proteins can serve as potential biomarkers for GBM due to their involvement in key biological processes, exploring the secretome biomarkers in GBM research represents a cutting-edge strategy with significant potential for advancing diagnostic precision, treatment monitoring, and ultimately improving outcomes for patients with this challenging brain cancer.

Pilot Evaluation of S-(3-[F]Fluoropropyl)-D-Homocysteine and O-(2-[F]Fluoroethyl)-D-Tyrosine as Bacteria-Specific Radiotracers for PET Imaging of Infection.

Purpose: There is currently no ideal radiotracer for imaging bacterial infections. Radiolabelled D-amino acids are promising candidates because they are actively incorporated into the peptidoglycan of the bacterial cell wall, a structural feature which is absent in human cells. This work describes fluorine-18 labelled analogues of D-tyrosine and D-methionine, O-(2-[F]fluoroethyl)-D-tyrosine (D-[F]FET) and S-(3-[F]fluoropropyl)-D-homocysteine (D-[F]FPHCys), and their pilot evaluation studies as potential radiotracers for imaging bacterial infection.

TA-RNN: an attention-based time-aware recurrent neural network architecture for electronic health records.

Motivation: Electronic health records (EHRs) represent a comprehensive resource of a patient's medical history. EHRs are essential for utilizing advanced technologies such as deep learning (DL), enabling healthcare providers to analyze extensive data, extract valuable insights, and make precise and data-driven clinical decisions. DL methods such as recurrent neural networks (RNN) have been utilized to analyze EHR to model disease progression and predict diagnosis.

Peptide macrocyclisation intramolecular interception of visible-light-mediated desulfurisation.

Synthetic methods that enable the macrocyclisation of peptides facilitate the development of effective therapeutic and diagnostic tools. Herein we report a peptide cyclisation strategy based on intramolecular interception of visible-light-mediated cysteine desulfurisation. This method allows cyclisation of unprotected peptides in an aqueous solution the installation of a hydrocarbon linkage.

Clinical application of biomaterials in orbital implants: a systematic review.

Purpose: Various materials have been proposed for reconstructing orbital fractures. The materials used must meet certain criteria to ensure their suitability for restoring the structure and function of the organ. These criteria include biocompatibility, ease of application, non-toxicity, hypo-allergenicity, and non-carcinogenicity.