Search Results (148)

RNA, like DNA and proteins, can undergo modifications. To date, over 170 RNA modifications have been identified, leading to the emergence of a new research area known as epitranscriptomics. RNA editing is the most frequent RNA modification in mammalian transcriptomes, and two types have been identified: (1) the most frequent, adenosine to inosine (A-to-I); and (2) the less frequent, cysteine to uracil (C-to-U) RNA editing. Unlike other epitranscriptomic marks, RNA editing can be readily detected from RNA sequencing (RNA-seq) data without any chemical conversions of RNA before sequencing library preparation. Furthermore, analyzing RNA editing patterns from transcriptomic data provides an additional layer of information about the epitranscriptome. As the significance of epitranscriptomics, particularly RNA editing, gains recognition in various fields of biology and medicine, there is a growing interest in detecting RNA editing sites (RES) by analyzing RNA-seq data. To cope with this increased interest, several bioinformatic tools are available. However, each tool has its advantages and disadvantages, which makes the choice of the most appropriate tool for bench scientists and clinicians difficult. Here, we have benchmarked bioinformatic tools to detect RES from RNA-seq data. We provide a comprehensive view of each tool and its performance using previously published RNA-seq data to suggest recommendations on the most appropriate for utilization in future studies. Full article

The paper proposed a new porous material for wound healing based on chitosan and C-phycocyanin (C-PC). In this work, C-PC was extracted from the cyanobacteria Arthrospira platensis biomass and purified through ammonium sulfate precipitation. The obtained C-PC with a purity index (PI) of 3.36 ± 0.24 was loaded into a chitosan sponge from aqueous solutions of various concentrations (250, 500, and 1000 mg/L). According to the FTIR study, chitosan did not form new bonds with C-PC, but acted as a carrier. The encapsulation efficiency value exceeded 90%, and the maximum loading capacity was 172.67 ± 0.47 mg/g. The release of C-PC from the polymer matrix into the saline medium was estimated, and it was found 50% of C-PC was released in the first hour and the maximum concentration was reached in 5–7 h after the sponge immersion. The PI of the released C-PC was 3.79 and 4.43 depending on the concentration of the initial solution. Full article

Nontyphoidal Salmonella (NTS) is a leading cause of morbidity and mortality caused by enteric pathogens worldwide in both children and adults, and vaccines are not yet available. The measurement of antigen-specific antibodies in the sera of vaccinated or convalescent individuals is crucial to understand the incidence of disease and the immunogenicity of vaccine candidates. A solid and standardized assay used to determine the level of specific anti-antigens IgG is therefore of paramount importance. In this work, we presented the characterization of a customized enzyme-linked immunosorbent assay (ELISA) with continuous readouts and a standardized definition of EU/mL. We assessed various performance parameters: standard curve accuracy, dilutional linearity, intermediate precision, specificity, limits of blanks, and quantification. The simplicity of the assay, its high sensitivity and specificity coupled with its low cost and the use of basic consumables and instruments without the need of high automation makes it suitable for transfer and application to different laboratories, including resource-limiting settings where the disease is endemic. This ELISA is, therefore, fit for purpose to be used for quantification of antibodies against Salmonella Typhimurium and Salmonella Enteritidis O-antigens in human samples, both for vaccine clinical trials and large sero-epidemiological studies. Full article

Incorporating a variety of microalgae into wastewater treatment is considered an economically viable and environmentally sound strategy. The present work assessed the growth characteristics of Chlorella sorokiniana during cultivation in balanced synthetic media and domestic wastewater. Increasing the NH₄⁺–N concentration to 360 mg L⁻¹ and adding extra PO₄³⁻–P and SO₄²⁻–S (up to 80 and 36 mg L⁻¹, respectively) contributed to an increase in the total biomass levels (5.7–5.9 g L⁻¹) during the cultivation of C. sorokiniana in synthetic media. Under these conditions, the maximum concentrations of chlorophylls and carotenoids were 180 ± 7.5 and 26 ± 1.4 mg L⁻¹, respectively. Furthermore, when studying three types of domestic wastewaters, it was noted that only one wastewater contributed to the productive growth of C. sorokiniana, but all wastewaters stimulated an increased accumulation of protein. Finally, the alga, when growing in optimal unsterilized wastewater, showed a maximum specific growth rate of 0.73 day⁻¹, a biomass productivity of 0.21 g L⁻¹ day⁻¹, and 100% NH₄⁺–N removal. These results demonstrate that the tested alga actively adapts to changes in the composition of the growth medium and accumulates high levels of protein in systems with poor-quality water. Full article

Categorical data analysis becomes challenging when high-dimensional sparse covariates are involved, which is often the case for omics data. We introduce a statistical procedure based on multinomial logistic regression analysis for such scenarios, including variable screening, model selection, order selection for response categories, and variable selection. We perform our procedure on high-dimensional gene expression data with 801 patients, 2426 genes, and five types of cancerous tumors. As a result, we recommend three finalized models: one with 74 genes achieves extremely low cross-entropy loss and zero predictive error rate based on a five-fold cross-validation; and two other models with 31 and 4 genes, respectively, are recommended for prognostic multi-gene signatures. Full article

This article extends an exploration into renewed ethico-legal perspectives of genome editing technologies, examined from an evolved conceptualization of eugenics in contemporary human reproduction. Whilst the ethico-legal conundrums presented by genome-editing technologies in various aspects of modern medicine have thus far inspired a comprehensive trove of academic scholarship—and notwithstanding the World Health Organization’s (WHO) publication of guidelines on human genome editing in 2021—the legislative landscape for these technologies remain relatively unchanged. Accordingly, this paper presents the unresolved problematic questions that still require significant reflection. First, the paper highlights these questions, which primarily center around the tension between reproductive autonomy and the legal governance of reproductive/genome editing technologies by a democratic state. Secondly, the paper interrogates the evolved conceptualization of eugenics, exercised on the part of prospective parents as part of reproductive autonomy. By this, the paper predicates that it indirectly reinforces societal and systemic problems of discrimination and “othering”, increasing reproductive inequalities in excluded communities. Thirdly, the paper attempts to offer narratives of intersectionality as a facilitating tool in a continuing dialogue to build belonging, foster a healthy and balanced exercise of reproductive autonomy, and increase reproductive equalities. Full article

In this study, we elaborated new chitosan-based films reinforced by iron(III)-containing chitosan nanoparticles Fe(III)-CS-NPs at different concentrations. We found that the optimum concentration of Fe(III)-CS-NPs for the improvement of antibacterial and mechanical properties of the films was 10% (σ_b = ca. 8.8 N/mm², ε_b = ca. 41%, inhibition zone for S. aureus = ca. 16.8 mm and for E. coli = ca. 11.2 mm). Also, using the click-chemistry approach (thiol–ene reaction), we have synthesized a novel water-soluble cationic derivative of chitin. The addition of this derivative of chitin to the chitosan polymer matrix of the elaborated film significantly improved its mechanical (σ_b = ca. 11.6 N/mm², ε_b = ca. 75%) and antimicrobial (inhibition zone for S. aureus = ca. 19.6 mm and for E. coli = ca. 14.2 mm) properties. The key mechanism of the antibacterial action of the obtained films is the disruption of the membranes of bacterial cells. The elaborated antibacterial films are of interest for potential biomedical and food applications. Full article

Microalgae can treat waste streams containing elevated levels of organic carbon and nitrogen. This process can be economically attractive if high value products are created simultaneously from the relatively low-cost waste stream. Co-production of two high value microalgal products, phycocyanin and polyhydroxybutyrate (PHB), was investigated using non-axenic Arthrospira platensis MUR126 and supplemental organic carbon (acetate, oxalate, glycerol and combinations). All supplemented cultures had higher biomass yield (g/L) than photoautotrophic control. All cultures produced PHB (3.6–7.8% w/w), except the control and those fed oxalate. Supplemented cultures showed a two to three-fold increase in phycocyanin content over the eight-day cultivation. Results indicate co-production of phycocyanin and PHB is possible in A. platensis, using mixed-waste organic carbon. However, supplementation resulted in growth of extremophile bacteria, particularly in cultures fed glycerol, and this had a negative impact on culture health. Refinement of the carbon dosing rate is required to minimise impacts of native bacterial contamination. Full article

The ocular surface is a complex structure that includes cornea, conjunctiva, limbus, and tear film, and is critical for maintaining visual function. When the ocular-surface integrity is altered by a disease, conventional therapies usually rely on topical drops or tissue replacement with more invasive procedures, such as corneal transplants. However, in the last years, regeneration therapies have emerged as a promising approach to repair the damaged ocular surface by stimulating cell proliferation and restoring the eye homeostasis and function. This article reviews the different strategies employed in ocular-surface regeneration, including cell-based therapies, growth-factor-based therapies, and tissue-engineering approaches. Dry eye and neurotrophic keratopathy diseases can be treated with nerve-growth factors to stimulate the limbal stem-cell proliferation and the corneal nerve regeneration, whereas conjunctival autograft or amniotic membrane are used in subjects with corneal limbus dysfunction, such as limbal stem-cell deficiency or pterygium. Further, new therapies are available for patients with corneal endothelium diseases to promote the expansion and migration of cells without the need of corneal keratoplasty. Finally, gene therapy is a promising new frontier of regeneration medicine that can modify the gene expression and, potentially, restore the corneal transparency by reducing fibrosis and neovascularization, as well as by stimulating stem-cell proliferation and tissue regeneration. Full article

The Bioethics Act in the Republic of Korea has undergone great fluctuations akin to the pendulum of a clock. Since Professor Hwang’s research ethics issue, domestic embryonic stem cell research has lost its vitality. This study argues that the Republic of Korea needs a reference point that does not waiver. This study examined the characteristics of life science- and ethics-related systems in the Republic of Korea and Japan. It also examined the pendulum-like policy changes in the Republic of Korea. It then compared the strengths and weaknesses between the Republic of Korea and Japan. Finally, we proposed a system improvement strategy for the development of bioethics research in Asian countries. In particular, this study argues that the advantages of Japan’s slow but stable system should be introduced. Full article

The COVID-19 disease is a major problem affecting human health all over the world. Consequently, researchers have been trying to find solutions to treat this pandemic-scale disease. Even if there are vaccines and approved drugs that could decrease the spread of this pandemic, multidisciplinary approaches are still needed to identify new small molecules as alternatives to combat COVID-19, especially those from nature. In this study, we employed computational approaches by screening 17 natural compounds from the tropical brown seaweed Sargassum polycystum known to have anti-viral properties that benefit human health. This study assessed some seaweed natural products that are bound to the PLpro of SARS-CoV-2. By employing pharmacophore and molecular docking, these natural compounds from S. polycystum showed remarkable scores for protein targets with competitive scores compared to X-ray crystallography ligands and well-known antiviral compounds. This study provides insightful information for advanced study and further in vitro examination and clinical investigation for drug development prospects of abundant yet underexploited tropical seaweeds. Full article

Genetic risk information has relevance for patients’ blood relatives. However, cascade testing uptake in at-risk families is <50%. International research supports direct notification of at-risk relatives by health professionals (HPs), with patient consent. However, HPs express concerns about the privacy implications of this practice. Our privacy analysis, grounded in a clinically relevant hypothetical scenario, considers the types of personal information involved in direct notification of at-risk relatives and the application of Australian privacy regulations. It finds that collecting relatives’ contact details, and using those details (with patient consent) to notify relatives of possible genetic risk, does not breach Australian privacy law, providing that HPs adhere to regulatory requirements. It finds the purported “right to know” does not prevent disclosure of genetic information to at-risk relatives. Finally, the analysis confirms that the discretion available to HPs does not equate to a positive duty to warn at-risk relatives. Thus, direct notification of a patient’s at-risk relatives regarding medically actionable genetic information, with patient consent, is not a breach of Australian privacy regulations, providing it is conducted in accordance with the applicable principles set out. Clinical services should consider offering this service to patients where appropriate. National guidelines would assist with the clarification of the discretion for HPs. Full article

The demand for data storage is growing at an unprecedented rate, and current methods are not sufficient to accommodate such rapid growth due to their cost, space requirements, and energy consumption. Therefore, there is a need for a new, long-lasting data storage medium with high capacity, high data density, and high durability against extreme conditions. DNA is one of the most promising next-generation data carriers, with a storage density of 10¹⁹ bits of data per cubic centimeter, and its three-dimensional structure makes it about eight orders of magnitude denser than other storage media. DNA amplification during PCR or replication during cell proliferation enables the quick and inexpensive copying of vast amounts of data. In addition, DNA can possibly endure millions of years if stored in optimal conditions and dehydrated, making it useful for data storage. Numerous space experiments on microorganisms have also proven their extraordinary durability in extreme conditions, which suggests that DNA could be a durable storage medium for data. Despite some remaining challenges, such as the need to refine methods for the fast and error-free synthesis of oligonucleotides, DNA is a promising candidate for future data storage. Full article

The ability of hydrogen sulfide (H₂S) to protect bacteria from bactericidal antibiotics has previously been described. The main source of H₂S is the desulfurization of cysteine, which is either synthesized by cells from sulfate or transported from the medium, depending on its composition. Applying electrochemical sensors and a complex of biochemical and microbiological methods, changes in growth, respiration, membrane potential, SOS response, H₂S production and bacterial survival under the action of bactericidal ciprofloxacin and bacteriostatic chloramphenicol in commonly used media were studied. Chloramphenicol caused a sharp inhibition of metabolism in all studied media. The physiological response of bacteria to ciprofloxacin strongly depended on its dose. In rich LB medium, cells retained metabolic activity at higher concentrations of ciprofloxacin than in minimal M9 medium. This decreased number of surviving cells (CFU) by 2–3 orders of magnitude in LB compared to M9 medium, and shifted optimal bactericidal concentration (OBC) from 0.3 µg/mL in M9 to 3 µg/mL in LB. Both drugs induced transient production of H₂S in M9 medium. In media containing cystine, H₂S was produced independently of antibiotics. Thus, medium composition significantly modifies physiological response of E. coli to bactericidal antibiotic, which should be taken into account when interpreting data and developing drugs. Full article

Hydroponics is a promising method for growing agricultural plants and is especially relevant in the context of global climate change. Microscopic algae, including Chlorella vulgaris, have great potential for use in hydroponic systems as natural growth stimulators. The effect of the suspension of an authentic strain of Chlorella vulgaris Beijerinck on the length of cucumber shoots and roots, as well as its dry biomass, was studied. During cultivation in a Knop medium with the addition of Chlorella suspension, the length of the shoots was shortened from 11.30 to 8.15 cm, while the length of the roots also decreased from 16.41 to 10.59 cm. At the same time, the biomass of the roots increased from 0.04 to 0.05 g. The data obtained indicate the positive effect of the suspension of the Chlorella vulgaris authentic strain on the dry biomass of cucumber plants in hydroponic conditions and make it possible to recommend this strain for use when growing plants in hydroponic systems. Full article