(Pre)Clinical Metabolomics Analysis

Metabolomics is the scientific field with the eager goal to comprehensively analyze the entirety of all small molecules of a biological system, i.e., the metabolome. Over the last few years, metabolomics has matured to become an analytical cornerstone of life science research across diverse fields, from fundamental biochemical applications to preclinical studies, including biomarker discovery and drug development. In this chapter, we provide an introduction to (pre)clinical metabolomics. We define key metabolomics aspects and provide the basis to thoroughly understand the relevance of this field in a biological and clinical context. We present and explain state-of-the-art analytical technologies devoted to metabolomic analysis as well as emerging technologies, discussing both strengths and weaknesses. Given the ever-increasing demand for handling complex datasets, the role of bioinformatics approaches in the context of metabolomic analysis is also illustrated.

Biomarker Discovery via N-Glycoproteomics

Posttranslational modifications (PTMs) of proteins regulate several biological processes, and investigating their diversity is crucial for understanding the mechanisms of cell regulation. Glycosylation is one of the most complex posttranslational modifications that control fundamental cellular processes such as protein folding, protein trafficking, host-pathogen interactions, cell adhesion, and cytokine receptor signaling networks. N-linked glycosylation denotes the attachment of glycans (oligosaccharides) to a nitrogen atom of asparagine (N) residues in the consensus motif Asn-X-Ser/Thr (NXS/T), where X is any amino acid except proline. Therefore, mutations in this posttranslational modification (i.e., N-glycosylation) site cause many human genetic diseases, including cancer. In the past decade, high-throughput quantitative proteome profiling tools have significantly renewed our interest in discovering novel cancer diagnostic or prognostic biomarkers through the simultaneous examination of the enormous amount of high-quality data of thousands of proteins and genes in complex biological systems. In this chapter, we describe how aberrant N-linked glycopeptides could be selectively identified as novel single tumor markers through the use of mass spectrometry (MS)-based proteomics, also known as Solid-phase extraction of N-glycopeptides (SPEG), and reasonable hypotheses that have the potential capacity to revolutionize biomarker discovery and bring those markers to the clinic as early as possible.

Metagenomic perspectives on antibiotic resistance genes in tap water: The environmental characteristic, potential mobility and health threat

As an emerging environmental contaminant, antibiotic resistance genes (ARGs) in tap water have attracted great attention. Although studies have provided ARG profiles in tap water, research on their abundance levels, composition characteristics, and potential threat is still insufficient. Here, 9 household tap water samples were collected from the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) in China. Additionally, 75 sets of environmental sample data (9 types) were downloaded from the public database. Metagenomics was then performed to explore the differences in the abundance and composition of ARGs. 221 ARG subtypes consisting of 17 types were detected in tap water. Although the ARG abundance in tap water was not significantly different from that found in drinking water plants and reservoirs, their composition varied. In tap water samples, the three most abundant classes of resistance genes were multidrug, fosfomycin and MLS (macrolide-lincosamide-streptogramin) ARGs, and their corresponding subtypes ompR, fosX and macB were also the most abundant ARG subtypes. Regarding the potential mobility, vanS had the highest abundance on plasmids and viruses, but the absence of key genes rendered resistance to vancomycin ineffective. Generally, the majority of ARGs present in tap water were those that have not been assessed and are currently not listed as high-threat level ARG families based on the World Health Organization Guideline. Although the current potential threat to human health posed by ARGs in tap water is limited, with persistent transfer and accumulation, especially in pathogens, the potential danger to human health posed by ARGs should not be ignored.

Genome editing in Sub-Saharan Africa: a game-changing strategy for climate change mitigation and sustainable agriculture

Sub-Saharan Africa's agricultural sector faces a multifaceted challenge due to climate change consisting of high temperatures, changing precipitation trends, alongside intensified pest and disease outbreaks. Conventional plant breeding methods have historically contributed to yield gains in Africa, and the intensifying demand for food security outpaces these improvements due to a confluence of factors, including rising urbanization, improved living standards, and population growth. To address escalating food demands amidst urbanization, rising living standards, and population growth, a paradigm shift toward more sustainable and innovative crop improvement strategies is imperative. Genome editing technologies offer a promising avenue for achieving sustained yield increases while bolstering resilience against escalating biotic and abiotic stresses associated with climate change. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein (CRISPR/Cas) is unique due to its ubiquity, efficacy, alongside precision, making it a pivotal tool for Sub-Saharan African crop improvement. This review highlights the challenges and explores the prospect of gene editing to secure the region's future foods.

Lipid Nanovesicle Platforms for Hepatocellular Carcinoma Precision Medicine Therapeutics: Progress and Perspectives

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality globally. HCC is highly heterogenous with diverse etiologies leading to different driver mutations potentiating unique tumor immune microenvironments. Current therapeutic options, including immune checkpoint inhibitors and combinations, have achieved limited objective response rates for the majority of patients. Thus, a precision medicine approach is needed to tailor specific treatment options for molecular subsets of HCC patients. Lipid nanovesicle platforms, either liposome- (synthetic) or extracellular vesicle (natural)-derived present are improved drug delivery vehicles which may be modified to contain specific cargos for targeting specific tumor sites, with a natural affinity for liver with limited toxicity. This mini-review provides updates on the applications of novel lipid nanovesicle-based therapeutics for HCC precision medicine and the challenges associated with translating this therapeutic subclass from preclinical models to the clinic.

Progress in the Application of Organoids-On-A-Chip in Diseases

With the rapid development of the field of life sciences, traditional 2D cell culture and animal models have long been unable to meet the urgent needs of modern biomedical research and new drug development. Establishing a new generation of experimental models and research models is of great significance for deeply understanding human health and disease processes, and developing effective treatment measures. As is well known, long research and development cycles, high risks, and high costs are the "three mountains" facing the development of new drugs today. Organoids and organ-on-chips technology can highly simulate and reproduce the human physiological environment and complex reactions in vitro, greatly improving the accuracy of drug clinical efficacy prediction, reducing drug development costs, and avoiding the defects of drug testing animal models. Therefore, organ-on-chips have enormous potential in medical diagnosis and treatment.

Exosome may be the next generation of promising cell-free vaccines

Traditional vaccines have limits against some persistent infections and pathogens. The development of novel vaccine technologies is particularly critical for the future. Exosomes play an important role in physiological and pathological processes. Exosomes present many advantages, such as inherent capacity being biocompatible, non-toxic, which make them a more desirable candidate for vaccines. However, research on exosomes are in their infancy and the barriers of low yield, low purity, and weak targeting of exosomes limit their applications in vaccines. Accordingly, further exploration is necessary to improve these problems and subsequently facilitate the functional studies of exosomes. In this study, we reviewed the origin, classification, functions, modifications, separation and purification, and characterization methods of exosomes. Meanwhile, we focused on the role and mechanism of exosomes for cancer and COVID-19 vaccines.

Exploring the GMO narrative through labeling: strategies, products, and politics

Labels are influential signals in the marketplace intended to inform and to eliminate buyer confusion. Despite this, food labels continue to be the subject of debate. None more so than non-GMO (genetically modified organisms) labels. This manuscript provides a timeline of the evolution of GMO labels beginning with the early history of the anti-GMO movement to the current National Bioengineered Food Disclosure Standard in the United States. Using media and market intelligence data collected through Buzzsumo™ and Mintel™, public discourse of GMOs is analyzed in relation to sociopolitical events and the number of new food products with anti-GMO labels, respectively. Policy document and publication data is collected with Overton™ to illustrate the policy landscape for the GMO topic and how it has changed over time. Analysis of the collective data illustrates that while social media and policy engagement around the topic of GMOs has diminished over time, the number of new products with a GMO-free designation continues to grow. While discourse peaked at one point, and has since declined, our results suggest that the legacy of an anti-GMO narrative remains firmly embedded in the social psyche, evidenced by the continuing rise of products with GMO-free designation. Campaigns for GMO food labels to satisfy consumers' right to know were successful and the perceived need for this information now appears to be self-sustaining.

In vivo antiviral efficacy of LCTG-002, a pooled, purified human milk secretory IgA product, against SARS-CoV-2 in a murine model of COVID-19

Immunoglobulin A (IgA) is the most abundant antibody (Ab) in human mucosae, with secretory form (sIgA) being dominant and uniquely stable. sIgA is challenging to produce recombinantly but is naturally found in human milk, which could be considered a global resource for this biologic, justifying its development as a mucosal therapeutic. Presently, SARS-CoV-2 was utilized as a model mucosal pathogen, and methods were developed to efficiently extract human milk sIgA from donors who were naïve to SARS-CoV-2 or had recovered from infection that elicited high-titer anti-SARS-CoV-2 Spike sIgA in their milk (pooled to make LCTG-002). Mass spectrometry determined that proteins with a relative abundance of 1% or greater were all associated with sIgA. Western blot demonstrated that all batches consisted predominantly of sIgA. Compared to control IgA, LCTG-002 demonstrated significantly higher Spike binding (mean endpoint of 0.87 versus 5.87). LCTG-002 was capable of blocking the Spike receptor-binding domain - angiotensin-converting enzyme 2 (ACE2) interaction with significantly greater potency compared to control (mean LCTG-002 IC50 154ug/mL versus 50% inhibition not achieved for control), and exhibited significant neutralization activity against Spike-pseudotyped virus infection (mean LCTG-002 IC50 49.8ug/mL versus 114.5ug/mL for control). LCTG-002 was tested for its capacity to reduce viral lung burden in K18+hACE2 transgenic mice inoculated with SARS-CoV-2. LCTG-002 significantly reduced SARS-CoV-2 titers compared to control when administered at 0.25 mg/day or 1 mg/day, with a maximum TCID50 reduction of 4.9 logs. This innovative study demonstrates that LCTG-002 is highly pure and efficacious in vivo, supporting further development of milk-derived, polyclonal sIgA therapeutics.

The recent genetic modification techniques for improve soil conservation, nutrient uptake and utilization

Advances in genetic modification (GM) techniques have generated huge interest in improving nutrient utilization, maximizing nutrient uptake, and conserving soil in the pursuit of sustainable agriculture. Unfortunately, little is still known about the recent advancements in the application of GM tactics to enhance each of these areas. This review explores the latest GM strategies intended to support soil conservation, maximize nutrient uptake, and improve nutrient utilization in farming, highlighting the critical roles that soil health and nutrient management play in sustainable farming. GM strategies such as improving the efficiency of nutrient uptake through enhanced root systems and increased nutrient transport mechanisms are well discussed. This study suggests that addressing potential obstacles, such as ethical and regulatory concerns, is a necessity for long-term sustainability applications of GM technologies to raise agricultural yields.

An assessment of the linkages between GM crop biotechnology and climate change mitigation

This article provides an analysis and evaluation of peer-reviewed evidence on the contribution of crop biotechnology to climate change mitigation and adaption. While there is a range of agricultural technologies and products that contribute to climate change mitigation, this literature landscape analysis focuses on the development of genetically modified traits, their use and adoption in major commodity crops and responsive changes in production techniques. Jointly, these technologies and products are contributing to climate change mitigation, yet the technology, the literature and evidence is still evolving as more sophisticated research methods are used with greater consistency. The literature analysis is undertaken with consideration of the consequential impact that regulatory regimes have on technology development. This assessment utilizes the Maryland Scientific Methods Scale and citation analysis, concluding that GM crops provide benefits that contribute to climate change mitigation.

Biotechnology executive order opens door for regulatory reform and social acceptance of genetically engineered microbes in agriculture

In the United States, regulatory review of genetically engineered microbes for agriculture falls under the Coordinated Framework for the Regulation of Biotechnology (CFRB). However, the lack of a centralized regulatory pathway and multiple oversight authorities can lead to uncertainty in regulatory review. Using three microbial-based technologies for agriculture as illustrative examples, this commentary identifies the weaknesses and challenges associated with the CFRB by assessing the current system and proposed changes to the system under a multi criteria decision analysis framework. In addition, it discusses opportunities for regulatory reform to improve clarity, efficiency, and public acceptance of genetically engineered microbes in agriculture under the CHIPS and Science Act and the 2022 Executive Order on the Bioeconomy.

The high-value and sustainable utilization of grape pomace: A review

A large portion of global grape production has been utilized for wine production, accompanied by tremendous pressure to dispose grape pomace. To achieve circular economy, the high-value recycling of grape pomace must be considered. The social level barriers to circular economy promotion are also important constraints, like the acceptability of upcycled products. The main components of grape pomace and their utilization are summarized, and critical reviews of green extraction methods analyzed the key points of grape pomace recycling process to achieve the goal of sustainability in the production process, culminating in discussions of the factors affecting the acceptability of upcycled products. Grape pomace bioactive substances have higher added value. To realize its green extraction, various emerging technologies need to be made a comprehensive choice. Nevertheless, the acceptability of upcycled products is influenced by personal, context and product factors, optimizing them is essential to remove the constraints of circular economy development.

Use of genomics & proteomics in studying lipase producing microorganisms & its application

In biotechnological applications, lipases are recognized as the most widely utilized and versatile enzymes, pivotal in biocatalytic processes, predominantly produced by various microbial species. Utilizing omics technology, natural sources can be meticulously screened to find microbial flora which are responsible for oil production. Lipases are versatile biocatalysts. They are used in a variety of bioconversion reactions and are receiving a lot of attention because of the quick development of enzyme technology and its usefulness in industrial operations. This article offers recent insights into microbial lipase sources, including fungi, bacteria, and yeast, alongside traditional and modern methods of purification such as precipitation, immunopurification and chromatographic separation. Additionally, it explores innovative methods like the reversed micellar system, aqueous two-phase system (ATPS), and aqueous two-phase flotation (ATPF). The article deals with the use of microbial lipases in a variety of sectors, including the food, textile, leather, cosmetics, paper, detergent, while also critically analyzing lipase-producing microbes. Moreover, it highlights the role of lipases in biosensors, biodiesel production, tea processing, bioremediation, and racemization. This review provides the concept of the use of omics technique in the mechanism of screening of microbial species those are capable of producing lipase and also find the potential applications.

In silico vaccine design for Yersinia enterocolitica: A comprehensive approach to enhanced immunogenicity, efficacy and protection

Yersinia enterocolitica, a foodborne pathogen, has emerged as a significant public health concern due to its increased prevalence and multidrug resistance. This study employed reverse vaccinology to identify novel vaccine candidates against Y. enterocolitica through comprehensive in silico analyses. The core genome's conserved protein translocase subunit SecY was selected as the target, and potential B-cell, MHC class I, and MHC class II epitopes were mapped. 3B-cell epitopes, 3 MHCI and 11 MHCII epitopes were acquired. A multi-epitope vaccine construct was designed by incorporating the identified epitopes, TLR4 Agonist was used as adjuvants to enhance the immunogenic response. EAAAK, CPGPG and AYY linkers were used to form a vaccine construct, followed by extensive computational evaluations. The vaccine exhibited desirable physicochemical properties, stable secondary and tertiary structures as evaluated by PDBSum and trRosetta. Moreover, favorable interactions with the human Toll-like receptor 4 (TLR4) was observed by ClusPro. Population coverage analysis estimated the vaccine's applicability across 99.74 % in diverse populations. In addition, molecular dynamics simulations and normal mode analysis confirmed the vaccine's structural stability and dynamics in a simulated biological environment. Furthermore, codon optimization and in silico cloning facilitated the evaluation of the vaccine's expression potential in E. coli and pET-28a was used a recombinant plasmid. This study provides a promising foundation for the development of an efficacious vaccine against Y. enterocolitica infections.

Isolicoflavonol ameliorates acute liver injury via inhibiting NLRP3 inflammasome activation through boosting Nrf2 signaling in vitro and in vivo

BACKGROUND

NOD like receptor pyrin domain containing 3 (NLRP3) inflammasome is involved in innate immunity, and related to liver injury. However, no inflammasome inhibitors are clinically available until now. Our previous research suggests that isolicoflavonol (ILF), isolated from Macaranga indica, is a potent NLRP3 inflammasome inhibitor, but its mechanism is unclear.

METHODS

Fluorescent imaging and Western blot assay were used to ascertain the effects of ILF on pyroptosis and NLRP3 inflammasome activation in macrophages. Next, Nrf2 signal pathway, its downstream gene transcription and expression were further investigated. ML385, a Nrf2 inhibitor, was used to verify whether ILF targets Nrf2 signaling. A carbon tetrachloride induced liver injury model was introduced to evaluate the liver protection activity of ILF in mice.

RESULTS

This work revealed that ILF inhibited macrophage LDH release and IL-1β secretion in a dose-dependent manner. ILF had no significant cytotoxic effect on macrophage, it reduced pyroptosis and Gasdermin D N-terminal fragment formation. Moreover, ILF inhibited IL-1β maturation and Caspase-1 cleavage, but did not affect NLRP3, pro-Caspase-1, pro-IL-1β and ASC expression. ILF decreased ASC speck rate and reduced ASC oligomer formation. ILF decreased aggregated JC-1 formation restoring mitochondria membrane potential. In addition, ILF increased Nrf2 expression, extended Nrf2 lifespan and upregulated Nrf2 signaling pathway in macrophages whether the NLRP3 inflammasome was activated or not. Besides, ILF increased Nrf2 nuclear translocation, maintained a high proportion of Nrf2 in the nucleus, and upregulated ARE-related gene transcription and expression. Furthermore, Nrf2 signal inhibition attenuated compound ILF-mediated inhibition of pyroptosis, inflammasome activation and upregulation of Nrf2 signaling. ILF in a liver injury mouse model inhibited NLRP3 inflammasome activation and enhanced Nrf2 signaling.

CONCLUSION

Our study verified that ILF ameliorates liver injury via inhibiting NLRP3 inflammasome activation through boosting Nrf2 signaling, and highlighted that ILF is a potent anti-inflammatory drug for inflammasome-related liver diseases.

A high-strength collagen-based antimicrobial film grafted with ε-polylysine fabrication by riboflavin-mediated ultraviolet irradiation for pork preservation

In this study, a UV-cured collagen-based film (C-P-H film) with high mechanical strength and antimicrobial properties was developed by riboflavin-mediated ultraviolet irradiation of collagen solution containing histidine-modified ε-polylysine. Fourier transform infrared analysis indicated that covalent cross-linking was formed between the collagen molecule and the histidine-grafted ε-polylysine. Compared with the pure collagen film, the C-P-H film containing 5 wt% histidine-modified ε-polylysine showed higher tensile strength (145.98 MPa), higher thermal denaturation temperature (76.5 °C), lower water vapor permeability (5.54 × 10-11 g m-1 s-1 Pa) and excellent antimicrobial activities against Escherichia coli and Staphylococcus aureus. In addition, the wrapping of the C-P-H film effectively inhibited bacterial growth of pork during storage time, successfully prolonging the shelf-life of pork by approximately 4 days compared to that of plastic wrap. These results suggested that collagen-based film grafted with histidine-modified ε-polylysine via riboflavin-mediated ultraviolet irradiation process had a great potential for pork preservation.

Evolution of multi-scale structure and microbiota metabolism of lentil resistant starch during the dynamic fermentation in vitro

This study investigated the structural changes of resistant starch (RS) derived from autoclaved lentil starch (ALRS) and untreated lentil starch (ULRS) during in vitro colonic fermentation, as well as their regulatory effects on the composition of the intestinal microbiota. Following in vitro fermentation, both RS samples exhibited a progressive decrease in molecular weight and a gradual increase in double helix/order. Bifidobacterium was more abundant in ULRS during the initial period of fermentation, while ALRS showed higher abundance in the later stage. ALRS demonstrated greater production of short-chain fatty acids (SCFAs) compared to ULRS, likely attributed to its higher structural order and faster fermentation pattern. The distinct surface morphologies of ULRS and ALRS played a crucial role in determining the accessibility of RS substrates for microbial fermentation. These different structural patterns also influenced the shifts in microbial composition in fecal cultures, leading to variations in SCFAs production through anaerobic fermentation.

D-π-A type fluorescent dyes: Effect of π-bridge units on optical and G4 DNA binding properties

Fluorescent solvatochromic dyes that are sensitive to the nature of local microenvironmental, have been explored as probes in applications ranging from the imaging biomolecules to understanding of basic biomolecule functions. To expand the scope of fluorescent solvatochromic dyes for G-quadruplex (G4) DNA structures, and to illustrate the relationship between structure and properties, three newly designed D-π-A type fluorescent dyes were synthesized by introducing diarylimidazole to carbazole skeleton linked to benzene, furan or thiophene π-conjugated bridge and connected with pyridinium acceptor, respectively. Their structural characteristics, optical properties, and G4 DNA binding properties were discussed in detail. In general, the incorporation of furan and thiophene as π-conjugated bridges leads the better conjugation and molecular coplanarity with more efficient intramolecular charge transfer (ICT) effect compared with benzene bridge. The fluorescence intensities induced upon interaction were found that TP-6 with thiophene π-conjugated bridge had the strongest response toward G4 DNAs. In addition, the application of this dye as a fluorescent agent for living cell imaging was also demonstrated.

Electric-field assisted cascade reactions to create alginate/carboxymethyl chitosan composite hydrogels with gradient architecture and reconfigurable mechanical properties

Rational designs of polysaccharide-based hydrogels with organ-like three-dimensional architecture provide a great possibility for addressing the shortages of allograft tissues and organs. However, spatial-temporal control over structure in bulk hydrogel and acquire satisfied mechanical properties remain an intrinsic challenge to achieve. Here, we show how electric-field assisted molecular self-assembly can be coupled to a directional reaction-diffusion (RD) process to produce macroscopic hydrogel in a controllable manner. The electrical energy input was not only to generate complex molecule gradients and initiate the molecular self-assembly, but also to guide/facilitate the RD processes for the gel rapid growth via a cascade construction interaction. The hydrogel mechanical properties can be tuned and enhanced by using an interpenetrating biopolymer network and multiple ionic crosslinkers, leading to a wide-range of mechanical modulus to match with biological organs or tissues. We demonstrate diverse 3D macroscopic hydrogels can be easily prepared via field-assisted directional reaction-diffusion and specific joint interactions. The humility-triggered dissipation of functional gradients and antibacterial performance confirm that the hydrogels can serve as an optically variable soft device for wound management. Therefore, this work provides a general approach toward the rational fabrication of soft hydrogels with controlled architectures and functionality for advanced biomedical systems.

Identification of a novel neutralization epitope in rhesus AAVs

Adeno-associated viruses (AAVs) are popular gene therapy delivery vectors, but their application can be limited by anti-vector immunity. Both preexisting neutralizing antibodies (NAbs) and post-administration NAbs can limit transgene expression and reduce the clinical utility of AAVs. The development of novel AAVs will advance our understanding of AAV immunity and may also have practical applications. In this study, we identified five novel AAV capsids from rhesus macaques. RhAAV4282 exhibited 91.4% capsid sequence similarity with AAV7 and showed similar tissue tropism with slightly diminished overall signal. Despite this sequence homology, RhAAV4282 and AAV7 showed limited cross-neutralization. We determined a cryo-EM structure of the RhAAV4282 capsid at 2.57 Å resolution and identified a small segment within the hypervariable region IV, involving seven amino acids that formed a shortened external loop in RhAAV4282 compared with AAV7. We generated RhAAV4282 and AAV7 mutants that involved swaps of this region and showed that this region partially determined neutralization phenotype. We termed this region the hypervariable region IV neutralizing epitope (HRNE). Our data suggests that modification of the HRNE can lead to AAVs with altered neutralization profiles.

Quality by design for mRNA platform purification based on continuous oligo-dT chromatography

Oligo-deoxythymidine (oligo-dT) ligand-based affinity chromatography is a robust method for purifying mRNA drug substances within the manufacturing process of mRNA-based products, including vaccines and therapeutics. However, the conventional batch mode of operation for oligo-dT chromatography has certain drawbacks that reduce the productivity of this process. Here, we report a new continuous oligo-dT chromatography process for the purification of in vitro transcribed mRNA, which reduces losses, improves the efficiency of oligo-dT resin use, and intensifies the chromatography process. Furthermore, the quality by design (QbD) framework was used to establish a design space for the newly developed method. The optimization of process parameters (PPs), including salt type, salt concentration, load flow rate and mRNA load concentration both in batch and the continuous mode, achieved a greater than 90% yield (mRNA recovery) along with greater than 95% mRNA integrity and greater than 99% purity. The productivity of continuous chromatography was estimated to be 5.75-fold higher, and the operating cost was estimated 15% lower, when compared with batch chromatography. Moreover, the QbD framework was further used to map the relationship between critical quality attributes and key performance indicators as a function of critical process parameters and critical material attributes.

Highly efficient nucleic acid encapsulation method for targeted gene therapy using antibody conjugation system

Gene therapy has surfaced as a promising avenue for treating cancers, offering the advantage of deliberate adjustment of targeted genes. Nonetheless, the swift degradation of nucleic acids in the bloodstream necessitates an effective and secure delivery system. The widespread utilization of poly(lactic-co-glycolic acid) (PLGA) nanoparticles as drug delivery systems has highlighted challenges in controlling particle size and release properties. Moreover, the encapsulation of nucleic acids exacerbates these difficulties due to the negatively charged surface of PLGA nanoparticles. In this study, we aimed to improve the encapsulation efficiency of nucleic acids by employing negatively charged microbeads and optimizing the timing of the specific formulation steps. Furthermore, by conjugating PSMA-617, a ligand for the prostate-specific membrane antigen (PSMA), with PLGA nanoparticles, we assessed the antitumor effects and the efficacy of a nucleic acid delivery system on a prostate cancer model. The employed technique within the nucleic acid encapsulation system represents a novel approach that could be adapted to encapsulate various kinds of nucleic acids. Moreover, it enables the attachment of targeting moieties to different cell membrane proteins, thereby unveiling new prospects for precise therapeutics in cancer therapy.

Application of artificial intelligence combined with near infrared spectroscopy in the continuous counter-current extraction process of Angelica dahurica formula granules

The establishment of near infrared (NIR) spectroscopy model mostly relies on chemometrics, and spectral analysis combined with artificial intelligence (AI) provides a new way of thinking for pharmaceutical quality inspection, new algorithms such as back propagation artificial neural networks (BP-ANN) and swarm intelligence optimization algorithms such as sparrow search algorithm (SSA) provide core technical support. In order to explore the application of AI in the pharmaceutical field, in this study, Angelica dahurica formula granules with a relatively complex system were selected as the research object. Quantitative analysis models were established by using partial least squares regression (PLSR) with a micro-NIR spectrometer, and BP-ANN modeling results were compared. For the best PLSR models of six characteristic components in the continuous counter-current extract of Angelica dahurica, R2v of imperatorin was lower than 0.90, and the RPD values of imperatorin, phellopterin, and isoimperatorin were even lower than 1. When the prediction model established by SSA-BP-ANN was used for quantitative analysis, R2v of six components were all higher than 0.92, and the RPD values all higher than 1.5, which proved that the BP-ANN method was better than PLSR. This study confirmed that in the continuous counter-current extraction progress of Angelica dahurica formula granules, the use of micro-NIR spectrometer combined with AI could realize the rapid prediction of the contents of six characteristic components. The comparison results provided a scientific reference for the process analysis and on-line monitoring in the production process of traditional Chinese medicine by micro-NIR spectrometer combined with AI.

An insight into G-quadruplexes: Identification and potential therapeutic targets in livestock viruses

G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that involve in the regulation of some key biological processes, such as replication, transcription, and translation. G4s have been extensively described in the genomes of human and related diseases. In recent years, G4s were identified in several livestock viruses, including those of the emerging epidemics, like Nipah virus (NiV). Since their discovery, G4s have been developed as the potential antiviral targets, and the employment of G4 ligands or interacting proteins has helped to expound the viral infectivity and pathogenesis through G4-mediated mechanisms, and highlight the potential as therapeutic approaches. However, the comprehensively studies of G4s in livestock viruses have not been summarized. This review delves into the reported literatures of G4s in livestock viruses, particular focus on the presence, biophysical identification, and possible function of G4s in viral genome, summarizing the G4 ligands, interacted proteins and aptamers on antiviral applications. The strengths and the challenges of G4 targeting in this field are also discussed. Therefore, this review will shed new light on the future development of highly potent and targeting antiviral therapy.

Endogenous retroviruses modulate the susceptibility of mice to Staphylococcus aureus-induced mastitis by activating cGAS-STING signaling

Recently studies showed that cow mastitis seriously affected the economic benefit of dairy industry and pathogen infection including S. aureus is the main cause of mastitis. However, there is still a lack of safe and effective treatment for S. aureus-induced mastitis due to its complex pathogenesis. Endogenous retroviruses (ERVs) have long been symbiotic with mammals, and most ERVs still have the ability to produces complementary DNA (cDNA) by reverse transcription, whose induction by commensal or pathogens can regulate host immunity and inflammatory responses through the cGAS-STING pathway. However, whether and how ERVs participate in the pathogenesis of S. aureus-induced mastitis still unclear. In this study, we found that S. aureus treatment increased the levels of ERVs and IFN-β. Inhibition the transcription of ERVs by emtricitabine alleviated S. aureus-induced mammary injury, reduced mammary bacterial burden, and inhibited the production of mammary proinflammatory factors including TNF-α, IL-1β and MPO activity. Moreover, inhibition of ERVs restored the function of blood-milk barrier caused by S. aureus. Next, we showed that S. aureus infection activated mammary cGAS-STING signaling pathway, which was mediated by ERVs, as evidenced by emtricitabine inhibited S. aureus-induced activation of the cGAS-STING pathway. Interestingly, inhibition of cGAS-STING by Ru.521 and H151 respectively, significantly alleviated S. aureus-induced mammary injury and inflammatory responses, which was associated with the inhibition of NF-κB and NLRP3 signaling pathways. In conclusion, our study revealed that ERVs regulate the development of S. aureus-induced mastitis in mice through NF-κB- and NLRP3-mediated inflammatory responses via the activation of cGAS-STING pathway, suggesting that targeting ERVs-cGAS-STING axis may be a potential approach for the treatment of S. aureus-induced mastitis.

Discovery of membrane-targeting amphiphilic honokiol derivatives containing an oxazolethione moiety to combat methicillin-resistant Staphylococcus aureus (MRSA) infections

Methicillin-resistant Staphylococcus aureus (MRSA) has emerged as a major pathogen causing infections in hospitals and the community, and there is an urgent need for the development of novel antibacterials to combat MRSA infections. Herein, a series of amphiphilic honokiol derivatives containing an oxazolethione moiety were prepared and evaluated for their in vitro antibacterial and hemolytic activities. The screened optimal derivative, I3, exhibited potent in vitro antibacterial activity against S. aureus and clinical MRSA isolates with MIC values of 2-4 μg/mL, which was superior to vancomycin in terms of its rapid bactericidal properties and was less susceptible to the development of resistance. The SARs analysis indicated that amphiphilic honokiol derivatives with fluorine substituents had better antibacterial activity than those with chlorine and bromine substituents. In vitro and in vivo toxicity studies revealed that I3 has relatively low toxicity. In a MRSA-infected mouse skin abscess model, I3 (5 mg/kg) effectively killed MRSA at the infected site and attenuated the inflammation effects, comparable to vancomycin. In a MRSA-infected mouse sepsis model, I3 (12 mg/kg) was found to significantly reduce the bacterial load in infected mice and increase survival of infected mice. Mechanistic studies indicated that I3 has membrane targeting properties and can interact with phosphatidylglycerol (PG) and cardiolipin (CL) of MRSA cell membranes, thereby disrupting MRSA cell membranes, further inducing the increase of reactive oxygen species (ROS), protein and DNA leakage to achieve rapid bactericidal effects. Finally, we hope that I3 is a potential candidate molecule for the development of antibiotics to conquer superbacteria-related infections.

Fuzi lizhong pills alter microbial community compositions and metabolite profiles in ulcerative colitis rat with spleen-kidney yang deficiency syndrome

ETHNOPHARMACOLOGICAL RELEVANCE

Ulcerative colitis (UC) is a chronic inflammatory bowel condition that is frequently related with Spleen-Kidney Yang Deficiency Syndrome (SKYD) in Chinese medicine. Fuzi Lizhong Pill (FLZP), a traditional medicine for SKYD, has been utilized in China for generations, although the exact mechanism by which it treats UC is unknown.

AIM OF THE STUDY

The goal of this study is to further understand FLZP's therapeutic mechanism in SKYD-associated UC.

MATERIALS AND METHODS

To investigate the impact of FLZP on SKYD-associated UC, we used a comprehensive method that included serum metabolomics and gut microbiota profiling. The chemical composition of FLZP was determined using mass spectrometry. UC rats with SKYD were induced and treated with FLZP. Serum metabolomics and 16S rRNA microbial community analysis were used to evaluate FLZP's effects on endogenous metabolites and gut microbiota, respectively. Correlation analysis investigated the association between metabolites and intestinal flora. A metabolic pathway analysis was undertaken to discover putative FLZP action mechanisms.

RESULTS

FLZP contains 109 components, including liquiritin (584.8176 μg/g), benzoylaconine (16.3087 μg/g), benzoylhypaconine (31.9583), and hypaconitine (8.1160 μg/g). FLZP predominantly regulated seven metabolites and eight metabolic pathways involved in amino acid and nucleotide metabolism, with an emphasis on energy metabolism and gastrointestinal digestion. FLZP also influenced intestinal flora variety, increasing probiotic abundance while decreasing pathogenic bacteria prevalence. An integrated investigation identified associations between changes in certain gut flora and energy metabolism, specifically the tricarboxylic acid (TCA) cycle.

CONCLUSIONS

FLZP successfully cures UC in SKYD rats by regulating amino acid and energy metabolism. Its positive effects may include altering microbiota composition and metabolite profiles in UC rats with SKYD. These findings shed light on FLZP's mode of action and its implications for UC management.

Trimethylamine N-oxide promotes PERK-mediated endothelial-mesenchymal transition and apoptosis thereby aggravates atherosclerosis

The endothelial-mesenchymal transition (EndMT) is involved in the development of atherosclerosis (AS) and is a key process in vascular endothelial injury. Oxidative stress, inflammation, and apoptosis are common causes of EndMT, and EndMT progression can further accelerate the development of AS. The metabolite trimethylamine N-oxide (TMAO) is produced by the gut microbiome and is implicated in the development of several diseases, including diabetes and chronic kidney disease. However, the impact of TMAO on transforming growth factor β1(TGF-β1)-induced EndMT remains unclear. We hypothesize that TMAO exacerbates plaque formation and cardiac function impairment by promoting EndMT. Herein, we showed that high serum TMAO levels caused plaque formation, cardiac function damage and haemodynamic changes in ApoE-/- mice. In vitro, TMAO upregulated mesenchymal markers and downregulated endothelial markers in HAECs. Furthermore, TMAO increased the migratory capacity of EndMT cells. Mechanistically, we found that PERK downregulation could alleviate TMAO-induced oxidative stress, EndMT, plaque formation and cardiac function damage. Further study showed that activated transcription factor 3 (ATF3), the downstream molecule of protein kinase RNA-like endoplasmic reticulum kinase (PERK), could bind with TGF-β1/2 and affect EndMT. Overall, TMAO promotes EndMT, possibly through the PERK-eIF2α-ATF4-CHOP or the PERk-eIF2α-ATF3-TGF-β signalling pathways.

A bacteriocin-based coating strategy to prevent vancomycin-resistant Enterococcus faecium biofilm formation on materials of interest for indwelling medical devices

The ever-increasing use of exogenous materials as indwelling medical devices in modern medicine offers to pathogens new ways to gain access to human body and begin, in some cases, life threatening infections. Biofouling of such materials with bacteria or fungi is a major concern during surgeries, since this is often associated with biofilm formation and difficult to treat, recalcitrant infections. Intense research efforts have therefore developed several strategies to shield the medical devices' surface from colonization by pathogenic microorganisms. Here, we used dopamine as a coupling agent to coat four different materials of medical interest (plastic polyetheretherketone (PEEK), stainless steel, titanium and silicone catheter) with the bacteriocins, enterocin EJ97-short and the thiopeptide micrococcin P1. Water contact angle measurements and x-ray photoelectron spectroscopy were used to verify the effective coating of the materials. The effect of bacteriocins coated on these materials on the biofilm formation by a vancomycin resistant Enterococcus faecium (VRE) strain was studied by biofilm-oriented antimicrobial test (BOAT) and electron scanning microscopy. The in vitro biocompatibility of bacteriocin-modified biomaterials was tested on cultured human cells. The results demonstrated that the binding of the bacteriocins to the implant surfaces is achieved, and the two bacteriocins in combination could inhibit biofilm formation by E. faecium on all four materials. The modified implant showed no cytotoxicity to the human cells tested. Therefore, surface modification with the two bacteriocins may offer a novel and effective way to prevent biofilm formation on a wide range of implant materials.

Emerging trends and recent advances in MXene/MXene-based nanocomposites toward electrochemiluminescence sensing and biosensing

Electrochemiluminescence (ECL) sensing systems have surged in popularity in recent years, making significant strides in sensing and biosensing applications. The realization of high-throughput ECL sensors hinges on the implementation of novel signal amplification strategies, propelling the field toward a new era of ultrasensitive analysis. A key strategy for developing advanced ECL sensors and biosensors involves utilizing novel structures with remarkable properties. The past few years have witnessed the emergence of MXenes as a captivating class of 2D materials, with their unique properties leading to exploitation in diverse applications. This review provides a comprehensive summary of the latest advancements in MXene-modified materials specifically engineered for ECL sensing and biosensing applications. We thoroughly analyze the structure, surface functionalization, and intrinsic properties of MXenes that render them exceptionally suitable candidates for the development of highly sensitive ECL sensors and biosensors. Furthermore, this study explores the broad spectrum of applications of MXenes in ECL sensing, detailing their multifaceted roles in enhancing the performance and sensitivity of ECL (bio)sensors. By providing a comprehensive overview, this review is expected to promote progress in related areas.

Production of (R)-citramalate by engineered Saccharomyces cerevisiae

The budding yeast, Saccharomyces cerevisiae, has a high tolerance to organic acids and alcohols, and thus grows well under toxic concentrations of various compounds in the culture medium, potentially allowing for highly efficient compound production. (R)-citramalate is a raw material for methyl methacrylate and can be used as a metabolic intermediate in the biosynthesis of higher alcohols. (R)-citramalate is synthesized from pyruvate and acetyl-CoA. Unlike Escherichia coli, S. cerevisiae has organelles, and its intracellular metabolites are compartmentalized, preventing full use of intracellular acetyl-CoA. Therefore, in this study, to increase the amount of cytosolic acetyl-CoA for highly efficient production of (R)-citramalate, we inhibited the transport of cytosolic acetyl-CoA and pyruvate to the mitochondria. We also constructed a heterologous pathway to supply cytosolic acetyl-CoA. Additionally, we attempted to export (R)-citramalate from cells by expressing a heterologous dicarboxylate transporter gene. We evaluated the effects of these approaches on (R)-citramalate production and constructed a final strain by combining these positive approaches. The resulting strain produced 16.5 mM (R)-citramalate in batch culture flasks. This is the first report of (R)-citramalate production by recombinant S. cerevisiae, and the (R)-citramalate production by recombinant yeast achieved in this study was the highest reported to date.

High-throughput single-cell screening of viable hybridomas and patient-derived antibody-secreting cells using punchable microwells

Monoclonal antibodies (mAbs) hold significant potential as therapeutic agents and are invaluable tools in biomedical research. However, the lack of efficient high-throughput screening methods for single antibody-secreting cells (ASCs) has limited the diversity of available antibodies. Here, we introduce a novel, integrated workflow employing self-seeding microwells and an automated microscope-puncher system for the swift, high-throughput screening and isolation of single ASCs. The system allows for the individual screening and isolation of up to 6,400 cells within approximately one day, with the opportunity for parallelization and efficient upscaling. We successfully applied this workflow to both hybridomas and human patient-derived B cells, enabling subsequent clonal expansion or antibody sequence analysis through an optimized, single-cell nested reverse transcription-polymerase chain reaction (RT-PCR) procedure. By providing a time-efficient and more streamlined single ASC screening and isolation process, our workflow holds promise for driving forward progress in mAb development.

Efficient expression of OUC-Sb-lip2 in Yarrowia lipolytica and its comprehensive utilization in the enrichment of DHA and EPA from fish oil

Lipases are widely used in the modification of functional lipids, particularly in the enrichment of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). In this study, a lipase named OUC-Sb-lip2 was expressed in Yarrowia lipolytica, achieving a promising enzyme activity of 472.6 U/mL by optimizing the culture medium, notably through olive oil supplementation. A significant proportion (58.8%) of the lipase activity was located in the cells, whereas 41.2% was secreted into the supernatant. Both whole-cell and immobilized OUC-Sb-lip2 were used to enrich DHA and EPA from fish oil. The whole-cell approach increased the DHA and EPA contents to 2.59 and 2.55 times that of the original oil, respectively. Similarly, the immobilized OUC-Sb-lip2 resulted in a 2.00-fold increase in DHA and an 1.99-fold increase in EPA after a 6-h hydrolysis period. Whole cell and the immobilized OUC-Sb-lip2 retained 48.7% and 52.7% of their activity after six cycles of reuse, respectively.

Combined release of LL37 peptide and zinc ion from a mussel-inspired coating on porous titanium for infected bone defect repairing

Implant-associated infections impose great burden on patient health and public healthcare. Antimicrobial peptides and metal ions are generally incorporated onto implant surface to deter bacteria colonization. However, it is still challenging to efficiently prevent postoperative infections at non-cytotoxic dosages. Herein, a scaffold based on porous titanium coated with a mussel-inspired dual-diameter TiO2 nanotubes is developed for loading dual drugs of LL37 peptide and Zn2+ with different sizes and characteristics. Benefiting from in-situ formed polydopamine layer and dual-diameter nanotubular structure, the scaffold provides an efficient platform for controllable drugs elution: accelerated release under acidic condition and sustained release for up to 28 days under neutral/alkalescent circumstances. Such combination of dual drugs simultaneously enhanced antibacterial efficacy and osteogenesis. In antibacterial test, LL37 peptide serving as bacteria membrane puncture agent, and Zn2+ acting as ROS generator, cooperatively destroyed bacterial membrane integrity and subsequently damaged bacterial DNA, endowing dual-drug loaded scaffold with remarkable bactericidal efficiency of > 92 % in vitro and > 99 % in vivo. Noteworthily, dual-drug loaded scaffold promoted bone-implant osteointegration under infectious microenvironment, overmatching single-drug load ones. It provides a promising strategy on surface modification of implant for infected bone defect repairing.

Fe/GMP functional nanomaterial enhancing the denitrification efficiency by bi-signal regulation: Electron transfer and microbial community

A novel functional nanomaterial composed of guanosine monophosphate (GMP) and Fe enhanced denitrification efficiency by regulating electron transfer and microbial community. Fe/GMP enhanced nitrate (NO3-) degradation rates by 3.00-fold in serum vial batch experiments, with a rate constant of 17.39 mg/(L·h) in sequencing batch reactor. Fe/GMP-mediated interface promoted the secretion of redox-active substances in the extracellular polymeric substances to enhance the extracellular electron transfer. Specifically, Fe/GMP regulated electron transfer and metabolism activity by dynamic conversion of Fe3+/Fe2+ redox signal. Additionally, enzyme activity assays verified the optimized electron distribution function of Fe/GMP and thus enhanced intracellular electron transfer. High-throughput sequencing confirmed Fe/GMP selectively enriched microorganisms (especially Thauera 50.70 %). The tetraethylammonium stress experiment demonstrated Fe/GMP as an exogenous signaling molecule to restore microbial communication for microbial community regulation. The study proposes a multifaceted synergistic mechanism based on the repeater function of Fe/GMP in denitrification and offers insights for practical applications.

Optimization of bacteriophage propagation in high-yield continuous culture (cellstat) meeting the constraints of industrial manufacturing processes

The growing use of bacteriophages in the fields of agriculture, agri-food, veterinary treatments, and medicine involves the quantitative production of these bacteriophages. In this study, we propose a bacteriophage production protocol that can easily be transposed to industry. We used a cellstat production system because the latest studies have shown that it is the most suitable process for the production of phages due to volumetric productivity, safety (limitation of co-evolution), and flexibility (choice of growth rate criteria). Sizing of the assembly used makes it possible to extrapolate the results to industrial production. The production conditions are indicated precisely, which would allow manufacturers to adapt the protocol to their own equipment. We propose experimental conditions in order to obtain a stable Escherichia coli population, qualitatively and over time, and production of high-titer T7 bacteriophages. The optimized production conditions (yield, cost and simplicity of the process) are: a buffered peptone water medium concentration of 11 g L-1 and a dilution rate of 1.6 h-1. Under these conditions, we obtained a production of 7.35×1016 plaque-forming units (PFU) L-1 day-1 with a concentration of 9.8×1012 PFU mL-1. The strength of this work lies in its focus on industrial applicability.

Systematic data analysis pipeline for quantitative morphological cell phenotyping

Quantitative morphological phenotyping (QMP) is an image-based method used to capture morphological features at both the cellular and population level. Its interdisciplinary nature, spanning from data collection to result analysis and interpretation, can lead to uncertainties, particularly among those new to this actively growing field. High analytical specificity for a typical QMP is achieved through sophisticated approaches that can leverage subtle cellular morphological changes. Here, we outline a systematic workflow to refine the QMP methodology. For a practical review, we describe the main steps of a typical QMP; in each step, we discuss the available methods, their applications, advantages, and disadvantages, along with the R functions and packages for easy implementation. This review does not cover theoretical backgrounds, but provides several references for interested researchers. It aims to broaden the horizons for future phenome studies and demonstrate how to exploit years of endeavors to achieve more with less.

A systematic discussion and comparison of the construction methods of synthetic microbial community

Synthetic microbial community has widely concerned in the fields of agriculture, food and environment over the past few years. However, there is little consensus on the method to synthetic microbial community from construction to functional verification. Here, we review the concept, characteristics, history and applications of synthetic microbial community, summarizing several methods for synthetic microbial community construction, such as isolation culture, core microbiome mining, automated design, and gene editing. In addition, we also systematically summarized the design concepts, technological thresholds, and applicable scenarios of various construction methods, and highlighted their advantages and limitations. Ultimately, this review provides four efficient, detailed, easy-to-understand and -follow steps for synthetic microbial community construction, with major implications for agricultural practices, food production, and environmental governance.

Screening optimal DC-targeting peptide to enhance the immune efficacy of recombinant Lactobacillus expressing RHDV VP60

Dendritic cells (DCs) present an ideal target for delivering immunogenic cargo due to their potent antigen-presenting capabilities. This targeting approach holds promise in vaccine development by enhancing the efficiency of antigen recognition and capture by DCs. To identify a high-affinity targeting peptide binding to rabbit DCs, rabbit monocyte-derived DCs (raMoDCs) were isolated and cultured, and a novel peptide, HS (HSLRHDYGYPGH), was identified using a phage-displayed peptide library. Alongside HS, two other DC-targeting peptides, KC1 and MY, previously validated in our laboratory, were employed to construct recombinant Lactgobacillus reuteri fusion-expressed rabbit hemorrhagic disease virus (RHDV) capsid protein VP60. These recombinant Lactobacillus strains were named HS-VP60/L. reuteri, KC1-VP60/L. reuteri, and MY-VP60/L. reuteri. The ability of these recombinant Lactobacillus to bind rabbit DCs was evaluated both in vivo and in vitro. Results demonstrated that the DC-targeting peptide KC1 significantly enhanced the capture efficiency of recombinant Lactobacillus by raMoDCs, promoted DC maturation, and increased cytokine secretion. Furthermore, oral administration of KC1-VP60/L. reuteri effectively induced SIgA and IgG production in rabbits, prolonged rabbit survival post-challenge, and reduced RHDV copies in organs. In summary, the DC-targeting peptide KC1 exhibited robust binding to raMoDCs, and recombinant Lactobacillus expressing KC1-VP60 protein antigens efficiently induced systemic and mucosal immune responses in rabbits, conferring protective efficacy against RHDV. This study offers valuable insights for the development of novel RHDV vaccines.

Recent findings in methanotrophs: genetics, molecular ecology, and biopotential

The potential consequences for mankind could be disastrous due to global warming, which arises from an increase in the average temperature on Earth. The elevation in temperature primarily stems from the escalation in the concentration of greenhouse gases (GHG) such as CO2, CH4, and N2O within the atmosphere. Among these gases, methane (CH4) is particularly significant in driving alterations to the worldwide climate. Methanotrophic bacteria possess the distinctive ability to employ methane as both as source of carbon and energy. These bacteria show great potential as exceptional biocatalysts in advancing C1 bioconversion technology. The present review describes recent findings in methanotrophs including aerobic and anaerobic methanotroph bacteria, phenotypic characteristics, biotechnological potential, their physiology, ecology, and native multi-carbon utilizing pathways, and their molecular biology. The existing understanding of methanogenesis and methanotrophy in soil, as well as anaerobic methane oxidation and methanotrophy in temperate and extreme environments, is also covered in this discussion. New types of methanogens and communities of methanotrophic bacteria have been identified from various ecosystems and thoroughly examined for a range of biotechnological uses. Grasping the processes of methanogenesis and methanotrophy holds significant importance in the development of innovative agricultural techniques and industrial procedures that contribute to a more favorable equilibrium of GHG. This current review centers on the diversity of emerging methanogen and methanotroph species and their effects on the environment. By amalgamating advanced genetic analysis with ecological insights, this study pioneers a holistic approach to unraveling the biopotential of methanotrophs, offering unprecedented avenues for biotechnological applications. KEY POINTS: • The physiology of methanotrophic bacteria is fundamentally determined. • Native multi-carbon utilizing pathways in methanotrophic bacteria are summarized. • The genes responsible for encoding methane monooxygenase are discussed.

Microbial bacterioruberin: The new C50 carotenoid player in food industries

The demand for natural products has significantly increased, driving interest in carotenoids as bioactive compounds for both human and animal consumption. Carotenoids, natural pigments with several biological properties, like antioxidant and antimicrobial, are increasingly preferred over synthetic colorants by the consumers (chemophobia). The global carotenoid market is projected to reach US$ 2.45 billion by 2034, driven by consumer preferences for natural ingredients and regulatory restrictions on synthetic products. Among carotenoids, bacterioruberin (BR), a C50 carotenoid naturally found in microbial hyperhalophilic archaea and in moderate halophilic archaea, stands out for its exceptional antioxidant capabilities, surpassing even well-known carotenoids like astaxanthin. BR's and its derivatives unique structure, with 13 conjugated double bonds and four -OH groups, contributes to its potent antioxidant activity and potential applications in food, feed, supplements, pharmaceuticals, and cosmeceuticals. This review explores BR's chemical and biological properties, upstream and downstream technologies, analytical techniques, market applications, and prospects in the colorants industry. While BR is not intended to replace existing carotenoids, its inclusion enriches the range of natural products available to meet the rising demand for natural alternatives. Furthermore, BR's promising antioxidant capacity positions it as a key player in the future carotenoid market, offering diverse industries a natural and potent alternative for several applications.

Extraction of polyphenols and essential oils from herbs with green extraction methods - An insightful review

The demand for polyphenols and essential oils (EOs) on the food market is high and grows every year. Its partially the result of the fact that these compounds can be used in formulation of clean label foods, a fast growing food sector. A significant share of polyphenols and EOs are extracted from herbs. The quality of the extracts is determined mainly by the extraction method. Conventional extraction techniques of phytochemicals are time-consuming, operate at high temperatures, and require usage of organic solvents and energy in large quantities. According to the United Nations Sustainability Development Plan, chemical processes should be replaced by green alternatives that would reduce the use of solvents and energy. Ultrasound-Assisted Extraction (UAE), Microwave-Assisted Extraction (MAE) and Cold Plasma-Assisted Extraction (CPAE) meets these criteria. The review shows that each of these techniques seems to be a great alternative for conventional extraction methods ensuring higher yields of bioactive compounds.

Engineering lipase TLL to improve its acid tolerance and its biosynthesis in Trichoderma reesei for biodiesel production from acidified oil

Lipases catalyze the synthesis of biodiesel, which is an important renewable alternative energy source. Cost-efficient conversion of waste acidified oil to biodiesel entails acid-tolerant lipases which have not been extensively studied. This study showed that the commonly used Thermomyces lanuginosus lipase TLL displayed a weak acid tolerance and an unsatisfactory performance in biodiesel production from acidified oil. Directed evolution of TLL identified one TLL-T3 variant with three residue substitutions (A69S/V150P/N222G). TLL-T3 displayed significantly enhanced acid tolerance, and its application in acidified oil treatment led to a biodiesel yield up to 90 % (w/w). A scaled-up production of TLL-T3 in Trichoderma reesei was further achieved and the highest extracellular lipase activity reached 16,123 U/mL after fermentation optimization. These results provide new insights into structural adaptation to acid tolerance by lipases and show that TLL-T3 holds great potential in commercial biodiesel production from waste acidified oil.

3D digital light process bioprinting: Cutting-edge platforms for resolution of organ fabrication

Research in the field of regenerative medicine, which replaces or restores the function of human damaged organs is advancing rapidly. These advances are fostering important innovations in the development of artificial organs. In recent years, three-dimensional (3D) bioprinting has emerged as a promising technology for regenerative medicine applications. Among various techniques, digital light process (DLP) 3D bioprinting stands out for its ability to precisely create high-resolution, structurally complex artificial organs. This review explores the types and usage trends of DLP printing equipment, bioinks, and photoinitiators. Building on this foundation, the applications of DLP bioprinting for creating precise microstructures of human organs and for regenerating tissue and organ models in regenerative medicine are examined. Finally, challenges and future perspectives regarding DLP-based bioprinting, particularly for precision printing applications in regenerative medicine, are discussed.

Optimization of donor cell production for somatic cell nuclear transfer in the critically endangered Vietnamese Ỉ pig

We aimed to establish efficient donor cells to produce piglets by somatic cell nuclear transfer (SCNT) of the endangered Vietnamese Ỉ pig. In Experiment 1, we assessed the effects of cell passages on the in vitro development of SCNT embryos. Cells with five and six passages showed significantly cleaved and blastocyst formation rates (86.72 and 86.64; 35.68 and 35.51, respectively, P < 0.05). The highest average total cell number per blastocyst was observed in groups of cells with five and six passages (50.45 and 50.18, respectively). Experiment 2 was performed to assess the sex of donor cells on the subsequent development of SCNT embryos. There was no significant difference in the cleaved and blastocyst formation rates, and the average total cell between female and male groups (86.51 % vs 86.94 % and 35.31 % vs 35.08 %, 50.29 % vs 50.67 %, respectively, P > 0.05). Experiment 3 was performed to assess the effect of cell lines on the development of SCNT embryos. Our results showed no significant difference in the success rate of fibroblast nuclear transfer into recipient oocytes, the cleaved and blastocyst formation rates, and the average total cell number per blastocyst among the cell lines 6004, 9154, 9155, 9156 and 9157 (P > 0.05). Experiment 4 was performed to assess the ability of SCNT embryos to induce pregnancy and to develop term. SCNT embryos were produced from Ỉ fibroblast cells established based on the results of Experiments 1, 2 and 3. Transfer of blastocyst stage embryos into 19 recipients (100-120 embryos in each) resulted in 14 pregnancies, in which 8 pregnant females terminated on Day 22-42 and 6 others produced 20 cloned piglets from donor cells of a female pig but 5 piglets died before birth and 15 healthy cloned piglets. However, 3 out of 15 healthy piglets died of unknown causes within 24h of birth and 3 out of 15 healthy piglets died at 3-5 days of age due to diarrhoea, 9 out of 15 healthy piglets are now 3 months of age. Finally, we established a protocol for the donor cell production which enabled the production of the endangered Ỉ pig embryos by SCNT and maximized blastocyst production rate by more than 35 % and pregnant rate after the transfer of cloned Ỉ pig embryos to recipients at 73.68 % for the first time in Vietnam.

Piezo1 facilitates the initiation and progression of renal fibrosis by mediating cell apoptosis and mitochondrial dysfunction

Renal fibrosis is the major pathological changes of Chronic kidney disease (CKD). Piezo1, a mechanical sensitive ion channel, is implicated in organ fibrosis. However, the precise role of Piezo1 in CKD fibrosis is unknown. The aims of this study were to identify that the role of Piezo1 in CKD fibrosis and its potential involvement of mitochondrial dysfunction. We performed the study with the Piezo1 agonist Yoda1, Bax inhibitor BAI1, Piezo1 inhibitor GsMTx4 and detected the injury, fibrosis, apoptosis markers and mitochondrial dysfunction. The results showed that the levels of apoptosis, mitochondrial dysfunction, injury and fibrosis increased in TCMK-1 cells after treatment with Yoda1. However, these changes that induced by Yoda1 were relieved by BAI1. Similarly, inhibition Piezo1 with GsMTx4 also partly relieved the renal injury, renal fibrosis, apoptosis and mitochondrial dysfunction in vivo and vitro. In conclusion, we found Piezo1 promoted the initiation and development of renal fibrosis and inhibiting Piezo1 improved the fibrosis.

Thin layer chromatography assay to detect laccase inhibitors

Thin-layer chromatography (TLC) hyphenated to bioassays is a modern tool used for discovery of biologically active compounds from complex mixtures. The first bioautographic assay for detecting laccase inhibitors on a TLC plate was developed in this study. The on-plate reaction of laccase with colourless ABTS that renders the blue ABTS∙+ radical was optimised. Combination of the enzymatic TLC-assay with a control TLC-assay, wherein ABTS∙+ radical is chemically generated and then applied on the TLC, allowed to differentiate between the pure laccase inhibitor sodium azide and radical scavengers such as gallic and kojic acids. The limit of detection and quantification for the method were 54.9 and 166 ng of sodium azide respectively. The methodology was applied successfully to a recently discovered laccase inhibitor chemotype: hydrazones. A model hydrazone was compared with several hydrazones synthesized for this study. For the first time, laccase inhibitors separated on a TLC plate can be detected individually.

ECM-mimicking composite hydrogel for accelerated vascularized bone regeneration

Bioactive hydrogel materials have great potential for applications in bone tissue engineering. However, fabrication of functional hydrogels that mimic the natural bone extracellular matrix (ECM) remains a challenge, because they need to provide mechanical support and embody physiological cues for angiogenesis and osteogenesis. Inspired by the features of ECM, we constructed a dual-component composite hydrogel comprising interpenetrating polymer networks of gelatin methacryloyl (GelMA) and deoxyribonucleic acid (DNA). Within the composite hydrogel, the GelMA network serves as the backbone for mechanical and biological stability, whereas the DNA network realizes dynamic capabilities (e.g., stress relaxation), thereby promoting cell proliferation and osteogenic differentiation. Furthermore, functional aptamers (Apt19S and AptV) are readily attached to the DNA network to recruit bone marrow mesenchymal stem cells (BMSCs) and achieve sustained release of loaded vascular endothelial growth factor towards angiogenesis. Our results showed that the composite hydrogel could facilitate the adhesion of BMSCs, promote osteogenic differentiation by activating focal adhesion kinase (FAK)/phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt)/β-Catenin signaling pathway, and eventually enhance vascularized bone regeneration. This study shows that the multifunctional composite hydrogel of GelMA and DNA can successfully simulate the biological functions of natural bone ECM and has great potential for repairing bone defects.