high throughput

The advancement of mRNA-based immunotherapies for cancer is highly dependent on the effective delivery of RNA payloads using ionizable lipid nanoparticles (LNPs). However, the clinical application of these therapies is hindered by variable mRNA expression among different cancer types and the risk of systemic toxicity. The transient expression profile of mRNA further complicates this issue, necessitating frequent dosing and thus increasing the potential for adverse effects. Addressing these challenges, we utilized a high-throughput combinatorial method to synthesize and screen LNPs that efficiently deliver circular RNA (circRNA) to lung tumors...

Chemotherapeutics, radiation, targeted therapeutics and immunotherapeutics each demonstrate clinical benefits for a small subset of patients with solid malignancies. Immune cells infiltrating the tumor and the surrounding stroma play a critical role in shaping cancer progression and modulating therapy response. They do this by interacting with the other cellular and molecular components of the tumor microenvironment (TME). Spatial multi-OMICs technologies are rapidly evolving. Currently, such technologies allow high-throughput RNA and protein profiling and retain geographical information about the TME cellular architecture and the functional phenotype of tumor, immune and stromal cells...

Cytotoxic enzymes often exist as zymogens containing prodomains to keep them in an inactive state. Protein-glutaminase (PG), which can enhance various functional characteristics of food proteins, is an enzyme containing pro-PG and mature-PG (mPG). However, poor activity and stability limit its application while tedious purification and activation steps limit its high-throughput engineering. Here, based on structural analysis, we replaced the linker sequence between pro-PG and mPG with the HRV3C protease recognition sequence and then coexpressed it with HRV3C protease in Escherichia coli to develop an efficient one-step purification and activation method for PG...

Increased cellular senescence burden contributes in part to age-related organ dysfunction and pathologies. In our study, using mouse models of natural aging, we observed structural and functional decline in the aged retina, which was accompanied by the accumulation of senescent cells and senescence-associated secretory phenotype factors. We further validated the senolytic and senomorphic properties of procyanidin C1 (PCC1) both in vitro and in vivo, the long-term treatment of which ameliorated age-related retinal impairment...

Crohn's disease (CD) entails intricate interactions with gut microbiome diversity, richness, and composition. The relationship between CD and gut microbiome is not clearly understood and has not been previously characterized in Saudi Arabia. We performed statistical analysis about various factors influencing CD activity and microbiota dysbiosis, including diagnosis, treatment, and its impact on their quality of life as well as high-throughput metagenomic V3-V4 16S rRNA encoding gene hypervariable region of a total of eighty patients with CD, both in its active and inactive state with healthy controls...

Immunoassays serve as powerful diagnostic tools for early disease screening, process monitoring, and precision treatment. However, the current methods are limited by high costs, prolonged processing times (>2 h), and operational complexities that hinder their widespread application in point-of-care testing. Here, we propose a novel centrifugo- p neumatic r eciprocating flowing coupled with spatial c onfinement strategy, termed PRCM , for ultrafast multiplexed immunoassay of pathogens on a centrifugal m icrofluidic platform...

PacBio long-read sequencing is a third-generation technology that generates long reads up to 20 kilobases (kb), unlike short-read sequencing instruments that produce up to 600 bases. Long-read sequencing is particularly advantageous in higher organisms, such as humans and plants, where repetitive regions in the genome are more abundant. The PacBio long-read sequencing uses a single molecule, real-time approach where the SMRT cells contain several zero-mode waveguides (ZMWs). Each ZMW contains a single DNA molecule bound by a DNA polymerase...

Induced mutations have been an important tool for plant breeding and functional genomics for more than 80 years. Novel mutations can be induced by treating seed or other plant cells with chemical mutagens or ionizing radiation. The majority of released mutant crop varieties were developed using ionizing radiation. This has been shown to create a variety of different DNA lesions including large (e.g., >=10,000 bps) copy number variations (CNV). Detection of induced DNA lesions from whole genome sequence data is useful for choosing a mutagen dosage prior to committing resources to develop a large mutant population for forward or reverse-genetic screening...

Treatment of plants with chemical mutagens results primarily in the production of novel single nucleotide variants. Mutagenesis is a mostly random process and as such plants derived from mutagenesis of different seeds or in vitro material are expected to accumulate different mutations. An important step in the creation of a mutant population for forward or reverse genetics is the choice of treatment conditions (e.g., dosage) such that sufficient mutations accumulate while not adversely affecting propagation of the plant...

Genetic diversity refers to the variety of genetic traits within a population or a species. It is an essential aspect of both plant ecology and plant breeding because it contributes to the adaptability, survival, and resilience of populations in changing environments. This chapter outlines a pipeline for estimating genetic diversity statistics from reduced representation or whole genome sequencing data. The pipeline involves obtaining DNA sequence reads, mapping the corresponding reads to a reference genome, calling variants from the alignments, and generating an unbiased estimation of nucleotide diversity and divergence between populations...

This chapter presents the application of Plantarray, a high-throughput platform commercially available for noninvasive monitoring of plant functional physiology phenotyping (FPP). The platform continuously measures water flux in the soil-plant-atmosphere for each plant in dynamic environments. To better interpret the massive phenotypic data acquired with FPP, several quantitative analysis methods were demonstrated for various types of data. Simple mathematical models were utilized to fit characteristic parameters of plant transpiration response to drought stress...

The study of natural variations in photosynthesis in the Brassicaceae family offers the possibility of identifying mechanisms to enhance photosynthetic efficiency in crop plants. Indeed, this family, and particularly its tribe Brassiceae, has been shown to harbor species that have a higher-than-expected photosynthetic efficiency, possibly as a result of a complex evolutionary history. Over the past two decades, methods have been developed to measure photosynthetic efficiency based on chlorophyll fluorescence...

In this chapter, we explore the application of high-throughput crop phenotyping facilities for phenotype data acquisition and the extraction of significant information from the collected data through image processing and data mining methods. Additionally, the construction and outlook of crop phenotype databases are introduced and the need for global cooperation and data sharing is emphasized. High-throughput crop phenotyping significantly improves accuracy and efficiency compared to traditional measurements, making significant contributions to overcoming bottlenecks in the phenotyping field and advancing crop genetics...

When chemical pollutants enter the environment, they can undergo diverse transformation processes, forming a wide range of transformation products (TPs), some of them benign and others more harmful than their precursors. To date, the majority of TPs remain largely unrecognized and unregulated, particularly as TPs are generally not part of routine chemical risk or hazard assessment. Since many TPs formed from oxidative processes are more polar than their precursors, they may be especially relevant in the context of persistent, mobile, and toxic (PMT) and very persistent and very mobile (vPvM) substances, which are two new hazard classes that have recently been established on a European level...

Neuroactive steroids are a group of steroid molecules that are involved in the regulation of functions of the nervous system. The nervous system is not only the site of their action, but their biosynthesis can also occur there. Neuroactive steroid levels depend not only on the physiological state of an individual (person's sex, age, diurnal variation, etc.), but they are also affected by various pathological processes in the nervous system (some neurological and psychiatric diseases or injuries), and new knowledge can be gained by monitoring these processes...

Controlling the enantiomeric purity of chiral drugs is of paramount importance in pharmaceutical chemistry. Isotropic 1 H NMR spectroscopy involving chiral agents is a widely used method for discriminating enantiomers and quantifying their relative proportions. However, the relatively weak spectral separation of enantiomers (1 H Δ δ iso ( R , S )) in frequency units at low and moderate magnetic fields, as well as the lack of versatility of a majority of those agents with respect to different chemical functions, may limit the general use of this approach...

Ex vivo genetically-modified cellular immunotherapies, such as chimeric antigen receptor T cell (CAR-T) therapies, have generated significant clinical and commercial outcomes due to their unparalleled response rates against relapsed and refractory blood cancers. However, the development and scalable manufacture of these novel therapies remains challenging and further process understanding and optimisation is required to improve product quality and yield. In this study, we employ a quality-by-design (QbD) approach to systematically investigate the impact of critical process parameters (CPPs) during the expansion step on the critical quality attributes (CQAs) of CAR-T cells...

BACKGROUND: Cystic echinococcosis, caused by the larval stage of Echinococcus granulosus , remains a global health challenge. Mesenchymal stem cells (MSCs) are renowned for their regenerative and immunomodulatory properties. Given the parasite's mode of establishment, we postulate that MSCs likely play a pivotal role in the interaction between the parasite and the host. This study aims to explore the response of MSCs to antigens derived from Echinococcus granulosus , the etiological agent of hydatid disease, with the hypothesis that exposure to these antigens may alter MSC function and impact the host's immune response to the parasite...

Nanoimprint lithography (NIL) has been utilized to address the manufacturing challenges of high cost and low throughput for optical metasurfaces. To overcome the limitations inherent in conventional imprint resins characterized by a low refractive index ( n ), high- n nanocomposites have been introduced to directly serve as meta-atoms. However, comprehensive research on these nanocomposites is notably lacking. In this study, we focus on the composition of high- n zirconium dioxide (ZrO2 ) nanoparticle (NP) concentration and solvents used to produce ultraviolet (UV) metaholograms and quantify the transfer fidelity by the measured conversion efficiency...

In 2022, a series of human monkeypox cases in multiple countries led to the largest and most widespread outbreak outside the known endemic areas. Setup of proper genomic surveillance is of utmost importance to control such outbreaks. To this end, we performed Nanopore (PromethION P24) and Illumina (NextSeq. 2000) Whole Genome Sequencing (WGS) of a monkeypox sample. Adaptive sampling was applied for in silico depletion of the human host genome, allowing for the enrichment of low abundance viral DNA without a priori knowledge of sample composition...