BurkHostGEN: a study protocol for evaluating variations in the Burkholderia pseudomallei and host genomes associated with melioidosis infection

Background

Melioidosis is a frequently fatal disease caused by an environmental bacterium Burkholderia pseudomallei. The disease is prevalent in northeast Thailand, particularly among rice field farmers who are at risk of bacterial exposure through contact with contaminated soil and water. However, not all exposure results in disease, and infection can manifest diverse outcomes. We postulate that genetic factors, whether from the bacterium, the host or the combination of both, may influence disease outcomes. To address this hypothesis, we aim to collect, sequence, and analyse genetic data from melioidosis patients and controls, along with isolates of B. pseudomallei obtained from patients. Additionally, we will study the metagenomics of the household water supply for both patients and controls, including the presence of B. pseudomallei.

Methods

BurkHostGEN is an ongoing observational study being conducted at Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand. We are obtaining consent from 600 melioidosis patients and 700 controls, spanning both sexes, to collect 1 mL of blood for host DNA analysis, 3 mL of blood for RNA analysis, as well as 5 L of household water supply for metagenomic analysis. Additionally, we are isolating B. pseudomallei from the melioidosis patients to obtain bacterial DNA. This comprehensive approach will allow us to identify B. pseudomallei and their paired host genetic factors associated with disease acquisition and severity. Ethical approvals have been obtained for BurkHostGEN. Host and bacterial genetic data will be uploaded to European Genome-Phenome Archive (EGA) and European Nucleotide Archive (ENA), respectively.

Conclusions

BurkHostGEN holds the potential to discover bacterial and host genetic factors associated with melioidosis infection and severity of illness. It can also support various study designs, including biomarker validation, disease pathogenesis, and epidemiological analysis not only for melioidosis but also for other infectious diseases.

Extraction and Characterization of Acidolysis Lignin from Turkey Oak (Quercus cerris L.) and Eucalypt (Eucalyptus camaldulensis Dehnh.) Wood from Population Stands in Italy

Acidolysis lignins from the species Quercus cerris L. and Eucalyptus camaldulensis Dehnh. were isolated and characterized using high pressure size exclusion chromatography (HP-SEC), Fourier-transform (FTIR) infrared spectroscopy, analytical pyrolysis-gas chromatography-mass spectrometry (Py-GCMS), and two-dimensional heteronuclear single quantum coherence (2D HSQC) NMR spectroscopy. The acidolysis lignins from the two different species varied in chemical composition and structural characteristics, with Q. cerris L. lignin having a higher S/G ratio and higher molar mass averages with a bimodal molar mass distribution. The different analytical techniques FTIR spectroscopy, Py-GCMS, and 2D NMR spectroscopy provided consistent results regarding the S/G ratio of the lignins from the two wood species. Based on the determined high S/G ratio of both oak and eucalypt lignin, the two wood sources could be promoted as substrates for efficient lignin isolation in modern forest biorefineries in order to develop innovative lignin-based value-added biorefinery products.

Sustainable Elastomers for Actuators: "Green" Synthetic Approaches and Material Properties

Elastomeric materials have great application potential in actuator design and soft robot development. The most common elastomers used for these purposes are polyurethanes, silicones, and acrylic elastomers due to their outstanding physical, mechanical, and electrical properties. Currently, these types of polymers are produced by traditional synthetic methods, which may be harmful to the environment and hazardous to human health. The development of new synthetic routes using green chemistry principles is an important step to reduce the ecological footprint and create more sustainable biocompatible materials. Another promising trend is the synthesis of other types of elastomers from renewable bioresources, such as terpenes, lignin, chitin, various bio-oils, etc. The aim of this review is to address existing approaches to the synthesis of elastomers using "green" chemistry methods, compare the properties of sustainable elastomers with the properties of materials produced by traditional methods, and analyze the feasibility of said sustainable elastomers for the development of actuators. Finally, the advantages and challenges of existing "green" methods of elastomer synthesis will be summarized, along with an estimation of future development prospects.

Plasma Nanoengineering of Bioresource-Derived Graphene Quantum Dots as Ultrasensitive Environmental Nanoprobes

Environmental contamination and energy shortage are among the most critical global issues that require urgent solutions to ensure sustainable ecological balance. Rapid and ultrasensitive monitoring of water quality against pollutant contaminations using a low-cost, easy-to-operate, and environmentally friendly technology is a promising yet not commonly available solution. Here, we demonstrate the effective use of plasma-converted natural bioresources for environmental monitoring. The energy-efficient microplasmas operated at ambient conditions are used to convert diverse bioresources, including fructose, chitosan, citric acid, lignin, cellulose, and starch, into heteroatom-doped graphene quantum dots (GQDs) with controlled structures and functionalities for applications as fluorescence-based environmental nanoprobes. The simple structure of citric acid enables the production of monodispersed 3.6 nm averaged-size GQDs with excitation-independent emissions, while the saccharides including fructose, chitosan, lignin, cellulose, and starch allow the synthesis of GQDs with excitation-dependent emissions due to broader size distribution. Moreover, the presence of heteroatoms such as N and/or S in the chemical structures of chitosan and lignin coupled with the highly reactive species generated by the plasma facilitates the one-step synthesis of N, S-codoped GQDs, which offer selective detection of toxic environmental contaminants with a low limit of detection of 7.4 nM. Our work provides an insight into the rapid and green fabrication of GQDs with tunable emissions from natural resources in a scalable and sustainable manner, which is expected to generate impact in the environmental safety, energy conversion and storage, nanocatalysis, and nanomedicine fields.

The Use of Human Tissues for Research: What Investigators Need to Know

While laboratory animals are necessary for some aspects of the development of scientific and biomedical advances, including those of precision medicine, the use of human tissues is necessary in order to explore the findings and ensure that they are relevant to human systems. Many sources of human tissues exist, but researchers - particularly those making the transition from animal to human systems - may not be aware of how best to find quality sources of human tissues or how best to use them in their research. In this article, we discuss the advantages of using human tissues in research. In addition, we highlight some of the major advances made possible through the use of human tissue, and describe how human tissue is collected for research. We discuss the various types of bioresources that make human tissue available, and advise on how investigators can find and use appropriate bioresources to support their research - with the hope that this information will help facilitate the transition from research on animals to research using human tissues, as rapidly as is practicable.

An Economic Dilemma Between Molecular Weapon Systems May Explain an Arachno-atypical Venom in Wasp Spiders (Argiope bruennichi)

Spiders use venom to subdue their prey, but little is known about the diversity of venoms in different spider families. Given the limited data available for orb-weaver spiders (Araneidae), we selected the wasp spider Argiope bruennichi for detailed analysis. Our strategy combined a transcriptomics pipeline based on multiple assemblies with a dual proteomics workflow involving parallel mass spectrometry techniques and electrophoretic profiling. We found that the remarkably simple venom of A. bruennichi has an atypical composition compared to other spider venoms, prominently featuring members of the cysteine-rich secretory protein, antigen 5 and pathogenesis-related protein 1 (CAP) superfamily and other, mostly high-molecular-weight proteins. We also detected a subset of potentially novel toxins similar to neuropeptides. We discuss the potential function of these proteins in the context of the unique hunting behavior of wasp spiders, which rely mostly on silk to trap their prey. We propose that the simplicity of the venom evolved to solve an economic dilemma between two competing yet metabolically expensive weapon systems. This study emphasizes the importance of cutting-edge methods to encompass the lineages of smaller venomous species that have yet to be characterized in detail, allowing us to understand the biology of their venom systems and to mine this prolific resource for translational research.

Tailoring Surface Chemistry of Sugar-Derived Ordered Mesoporous Carbons Towards Efficient Removal of Diclofenac From Aquatic Environments

Ordered mesoporous carbon (CMK-3), obtained from an abundant natural source, sugar, was thermochemically modified with dicyandiamide and thiourea as well as by classical oxidization with hydrogen peroxide to introduce specific surface groups. Thermochemical modifications resulted in carbon with almost unchanged porosity and altered surface chemistry while porosity of H₂O₂-treated carbon was seriously deteriorated. The obtained carbons were tested as sorbents of diclofenac, considered as one of the emerging water contaminants. Changes in porosity and surface chemistry of modified carbons resulted in significant differences with regard to the uptake of diclofenac. Dicyandiamide-modified carbon showed highest uptake of drugs, reaching 241 mg g⁻¹ that is attributed to its developed microporosity as well as surface chemistry composed of basic groups facilitating electrostatic interactions with diclofenac anions. Desorption study showed that diclofenac is strongly bonded, albeit with a different degree depending on the modification of the CMK-carbon. The obtained results were compared with up-to-date literature regarding sorption of diclofenac by carbon-based sorbents.

Biological, Medical, and Other Tissue Variables Affecting Biospecimen Utilization

Bioresources are critical resources that support biomedical research because of their ability to appropriately collect, process, store, and distribute a wide range of high-quality biospecimens that meet the needs of specific investigators. Of note, some biorepositories are concerned by their growing inventories and their low rates of tissue utilization. This review discusses the technical characteristics of biospecimens that can cause morphological and molecular variability and/or limit the usefulness of biospecimens in research. This article also describes current challenges related to biospecimen characteristics that may affect biospecimen utilization. These include inadequate awareness of investigators about the availability of biospecimens with specific morphologic and molecular features, donor variability, preanalytical variables, technical problems inherent with an investigator's request for biospecimens, limited tissue availability from a biorepository based on requested sizes and/or numbers of available biospecimens, effects of times of warm and cold ischemia, damage of tissues during surgery, and molecular changes during storage. To ensure maximal biospecimen utilization of all types of biospecimens requires continual education of investigators from diverse fields, particularly on factors that cause variability in the morphological and molecular characteristics of tissues. The investigators' requests for biospecimens and associated data should be reviewed carefully, including by a bioresource-associated pathologist. Queries arising from the request/application form should be resolved by bioresource personnel directly with the investigator.