Structural and functional analysis of Cyanovirin-N homologs: Carbohydrate binding affinities and antiviral potential of cyanobacterial peptides

Cyanobacteria, a group of photosynthetic prokaryotes, can sinthesize several substances due to their secondary metabolism, with notable properties, such as Cyanovirin-N(CVN), a carbohydrate-binding lectin, that exhibits antiviral activity against several pathogens, due to its ability to bind viral surface carbohydrates such as mannose, thus interfering with the viral entry on the cell. CVN has been described in several cyanobacterial strains and shows biotechnological potential for the development of drugs of pharmaceutical interest. This study focuses on the genomic exploration and characterization of Cyanovirin-N homologs to assess the conservation of carbohydrate-binding affinity within the group. The analysis of their antiviral properties was carried out using bioinformatics tools to study protein models through an in silico pipeline, following the steps of genomic prospection on public databases, homology modeling, docking, molecular dynamics and energetic analysis. Mannose served as the reference ligand, and the lectins' binding affinity with mannose was assessed across Cyanovirin-N homologs. Genomic mining identified 33 cyanobacterial lectin sequences, which underwent structural and functional characterization. The results obtained from this work indicate strong carbohydrate affinity on several homologs, pointing to the conservation of antiviral properties alongside the group. However, this affinity was not uniformly distributed among sequences, exhibiting significant heterogeneity in binding site residues, suggesting potential multi-ligand binding capabilities on the Cyanovirin-N homologs group. Studies focused on the properties involved in these molecules and the investigation of the genetic diversity of Cyanovirin-N homologs could provide valuable insights into the discovery of new drug candidates, harvesting the potential of bioinformatics for large-scale functional and structural analysis.

Hypoxia stimulates CTC-platelet cluster formation to promote breast cancer metastasis

Circulating tumor cell clusters/micro-emboli (CTM) possess greater metastatic capacity and survival advantage compared to individual circulating tumor cell (CTC). However, the formation of CTM subtypes and their role in tumor metastasis remain unclear. In this study, we used a microfluidic Cluster-Chip with easy operation and high efficiency to isolate CTM from peripheral blood, which confirmed their correlation with clinicopathological features and identified the critical role of CTC-platelet clusters in breast cancer metastasis. The correlation between platelets and CTM function was further confirmed in a mouse model and RNA sequencing of CTM identified high-expressed genes related to hypoxia stimulation and platelet activation which possibly suggested the correlation of hypoxia and CTC-platelet cluster formation. In conclusion, we successfully developed the Cluster-Chip platform to realize the clinical capture of CTMs and analyze the biological properties of CTC-platelet clusters, which could benefit the design of potential treatment regimens to prevent CTM-mediated metastasis and tumor malignant progression.

RGD targeted magnetic ferrite nanoparticles enhance antitumor immunotherapeutic efficacy by activating STING signaling pathway

Manganese has been used in tumor imaging for their ability to provide T1-weighted MRI signal. Recent research find Mn2+ can induce activation of the stimulator of interferon gene (STING) pathway to create an active and favorable tumor immune microenvironment. However, the direct injection of Mn2+ often results in toxicity. In this study, we developed an RGD targeted magnetic ferrite nanoparticle (RGD-MnFe2O4) to facilitate tumor targeted imaging and improve tumor immunotherapy. Magnetic resonance imaging and fluorescence molecular imaging were performed to monitor its in vivo biodistribution. We found that RGD-MnFe2O4 showed active tumor targeting and longer accumulation at tumor sites. Moreover, RGD-MnFe2O4 can activate STING pathway with low toxicity to enhance the PD-L1 expression. Furthermore, combining RGD-MnFe2O4 and anti-PD-L1 antibody (aPD-L1) can treat several types of immunogenic tumors through promoting the accumulation of tumor-infiltrating cytotoxic T cells. In general, our study provides a promising new strategy for the targeted and multifunctional theranostic nanoparticle for the improvement of tumor immunotherapy.

Turbo autoencoders for the DNA data storage channel with Autoturbo-DNA

DNA, with its high storage density and long-term stability, is a potential candidate for a next-generation storage device. The DNA data storage channel, composed of synthesis, amplification, storage, and sequencing, exhibits error probabilities and error profiles specific to the components of the channel. Here, we present Autoturbo-DNA, a PyTorch framework for training error-correcting, overcomplete autoencoders specifically tailored for the DNA data storage channel. It allows training different architecture combinations and using a wide variety of channel component models for noise generation during training. It further supports training the encoder to generate DNA sequences that adhere to user-defined constraints. Autoturbo-DNA exhibits error-correction capabilities close to non-neural-network state-of-the-art error correction and constrained codes for DNA data storage. Our results indicate that neural-network-based codes can be a viable alternative to traditionally designed codes for the DNA data storage channel.

Insights into membrane interactions and their therapeutic potential

Recent research into membrane interactions has uncovered a diverse range of therapeutic opportunities through the bioengineering of human and non-human macromolecules. Although the majority of this research is focussed on fundamental developments, emerging studies are showcasing promising new technologies to combat conditions such as cancer, Alzheimer's and inflammatory and immune-based disease, utilising the alteration of bacteriophage, adenovirus, bacterial toxins, type 6 secretion systems, annexins, mitochondrial antiviral signalling proteins and bacterial nano-syringes. To advance the field further, each of these opportunities need to be better understood, and the therapeutic models need to be further optimised. Here, we summarise the knowledge and insights into several membrane interactions and detail their current and potential uses therapeutically.

Biosurfactants production by marine yeasts isolated from zoanthids and characterization of an emulsifier produced by Yarrowia lipolytica LMS 24B

The present study investigates the potential for biosurfactant production of 19 marine yeast species obtained from zoanthids. Using the emulsification index test to screen the samples produced by the marine yeasts, we verified that five isolates exhibited an emulsification index ≥50%. Additional tests were performed on such isolates, including oil displacement, drop collapse, Parafilm M assay, and surface tension measurement. The tolerance of produced biosurfactants for environmental conditions was also analyzed, especially considering the media's temperature, pH, and salinity. Moreover, the surfactant's ability to emulsify different hydrocarbon sources and to metabolize kerosene as the sole carbon source was evaluated in vitro. Our results demonstrate that yeast biosurfactants can emulsify hydrocarbon sources under different physicochemical conditions and metabolize kerosene as a carbon source. Considering the Yarrowia lipolytica LMS 24B as the yeast model for biosurfactant production from the cell's wall biomass, emulsification indexes of 61.2% were obtained, even at a high temperature of 120 °C. Furthermore, the Fourier-transform middle infrared spectroscopy (FTIR) analysis of the biosurfactant's chemical composition revealed the presence of distinct functional groups assigned to a glycoprotein complex. Considering the status of developing new bioproducts and bioprocesses nowadays, our findings bring a new perspective to biosurfactant production by marine yeasts, especially Y. lipolytica LMS 24B. In particular, the presented results validate the relevance of marine environments as valuable sources of genetic resources, i.e., yeast strains capable of metabolizing and emulsifying petroleum derivatives.

Nisin variants: what makes them different and unique?

Nisin A is a lantibiotic bacteriocin typically produced by strains of Lactococcus lactis. This bacteriocin has been approved as a natural food preservative since the late 1980s and shows antimicrobial activity against a range of food-borne spoilage and pathogenic microorganisms. The therapeutic potential of nisin A has also been explored increasingly both in human and veterinary medicine. Nisin has been shown to be effective in treating bovine mastitis, dental caries, cancer, and skin infections. Recently, it was demonstrated that nisin has an affinity for the same receptor used by SARS-CoV-2 to enter human cells and was proposed as a blocker of the viral infection. Several nisin variants produced by distinct bacterial strains or modified by bioengineering have been described since the discovery of nisin A. These variants present modifications in the peptide structure, biosynthesis, mode of action, and spectrum of activity. Given the importance of nisin for industrial and therapeutic applications, the objective of this study was to describe the characteristics of the nisin variants, highlighting the main differences between these molecules and their potential applications. This review will be useful to researchers interested in studying the specifics of nisin A and its variants.

Harnessing iron‑sulfur enzymes for synthetic biology

Reactions catalysed by iron-sulfur (Fe-S) enzymes appear in a variety of biosynthetic pathways that produce valuable natural products. Harnessing these biosynthetic pathways by expression in microbial cell factories grown on an industrial scale would yield enormous economic and environmental benefits. However, Fe-S enzymes often become bottlenecks that limits the productivity of engineered pathways. As a consequence, achieving the production metrics required for industrial application remains a distant goal for Fe-S enzyme-dependent pathways. Here, we identify and review three core challenges in harnessing Fe-S enzyme activity, which all stem from the properties of Fe-S clusters: 1) limited Fe-S cluster supply within the host cell, 2) Fe-S cluster instability, and 3) lack of specialized reducing cofactor proteins often required for Fe-S enzyme activity, such as enzyme-specific flavodoxins and ferredoxins. We highlight successful methods developed for a variety of Fe-S enzymes and electron carriers for overcoming these difficulties. We use heterologous nitrogenase expression as a grand case study demonstrating how each of these challenges can be addressed. We predict that recent breakthroughs in protein structure prediction and design will prove well-suited to addressing each of these challenges. A reliable toolkit for harnessing Fe-S enzymes in engineered metabolic pathways will accelerate the development of industry-ready Fe-S enzyme-dependent biosynthesis pathways.

Association of a Skin Dressing Made With the Organic Part of Marine Sponges and Photobiomodulation on the Wound Healing in an Animal Model

The present study aims to characterize and to evaluate the biological effects of a skin dressing manufactured with the organic part of the Chondrilla caribensis marine sponge (called spongin-like collagen (SC)) associated or not to photobiomodulation (PBM) on the skin wound healing of rats. Skin dressings were manufactured with SC and it was characterized using scanning electron microscopy (SEM) and a tensile assay. In order to evaluate its biological effects, an experimental model of cutaneous wounds was surgically performed. Eighteen rats were randomly distributed into three experimental groups: control group (CG): animals with skin wounds but without any treatment; marine collagen dressing group (DG): animals with skin wounds treated with marine collagen dressing; and the marine collagen dressing + PBM group (DPG): animals with skin wounds treated with marine collagen dressing and PBM. Histopathological, histomorphometric, and immunohistochemical evaluations (qualitative and semiquantitative) of COX2, TGFβ, FGF, and VEGF were done. SEM demonstrates that the marine collagen dressing presented pores and interconnected fibers and adequate mechanical strength. Furthermore, in the microscopic analysis, an incomplete reepithelialization and the presence of granulation tissue with inflammatory infiltrate were observed in all experimental groups. In addition, foreign body was identified in the DG and DPG. COX2, TGFβ, FGF, and VEGF immunostaining was observed predominantly in the wound area of all experimental groups, with a statistically significant difference for FGF immunostaining score of DPG in relation to CG. The marine collagen dressing presented adequate physical characteristics and its association with PBM presented favorable biological effects to the skin repair process.

Sustainable Bombyx mori's silk fibroin for biomedical applications as a molecular biotechnology challenge: A review

Silk is a natural engineering material with a unique set of properties. The major constituent of silk is fibroin, a protein widely used in the biomedical field because of its mechanical strength, toughness and elasticity, as well as its biocompatibility and biodegradability. The domestication of silkworms allows large amounts of fibroin to be extracted inexpensively from silk cocoons. However, the industrial extraction process has drawbacks in terms of sustainability and the quality of the final medical product. The heterologous production of fibroin using recombinant DNA technology is a promising approach to address these issues, but the production of such recombinant proteins is challenging and further optimization is required due to the large size and repetitive structure of fibroin's DNA and amino acid sequence. In this review, we describe the structure-function relationship of fibroin, the current extraction process, and some insights into the sustainability of silk production for biomedical applications. We focus on recent advances in molecular biotechnology underpinning the production of recombinant fibroin, working toward a standardized, successful and sustainable process.

Nature as blueprint: Global phenotype engineering of CHO production cells based on a multi-omics comparison with plasma cells

Especially for the production of artificial, difficult to express molecules a further development of the CHO production cell line is required to keep pace with the continuously increasing demands. However, the identification of novel targets for cell line engineering to improve CHO cells is a time and cost intensive process. Since plasma cells are evolutionary optimized for a high antibody expression in mammals, we performed a comprehensive multi-omics comparison between CHO and plasma cells to exploit optimized cellular production traits. Comparing the transcriptome, proteome, miRNome, surfaceome and secretome of both cell lines identified key differences including 392 potential overexpression targets for CHO cell engineering categorized in 15 functional classes like transcription factors, protein processing or secretory pathway. In addition, 3 protein classes including 209 potential knock-down/out targets for CHO engineering were determined likely to affect aggregation or proteolysis. For production phenotype engineering, several of these novel targets were successfully applied to transient and transposase mediated overexpression or knock-down strategies to efficiently improve productivity of CHO cells. Thus, substantial improvement of CHO productivity was achieved by taking nature as a blueprint for cell line engineering.

Development of a hybrid bio-purification process of lactic acid solutions employing an engineered E. coli strain in a membrane bioreactor

BACKGROUND

A potential alternative to lactic acid production through sugar fermentation is its recovery from grass silage leachate. The separation and purification of lactic acid from fermentation broths remain a key issue, as it amounts to up to 80% of its industrial production cost. In this study, a genetically engineered E. coli strain (A1:ldhA), that cannot catabolize lactic acid, has been used to selectively remove impurities from a synthetic medium comprising typical components (i.e., glucose and acetic acid) of green grass silage leachate. A systematic approach has been followed to provide a proof-of-concept for a bio-purification process of lactic acid solutions in a membrane bioreactor operating in semi-continuous mode.

RESULTS

The synthetic medium composition was initially optimized in shake-flasks experiments, followed by scale-up in bench-scale bioreactor. Complete (i.e., 100%) and 60.4% removal for glucose and acetic acid, respectively, has been achieved in batch bioreactor experiments with a synthetic medium comprising 0.5 g/L glucose and 0.5 g/L acetic acid as carbon sources, and 10 g/L lactic acid; no lactic acid catabolism was observed in all batch fermentation tests. Afterwards, a hybrid biotechnological process combining semi-continuous bioreactor fermentation and ultrafiltration membrane separation (membrane bioreactor) was applied to in-situ separate purified medium from the active cells. The process was assessed under different semi-continuous operating conditions, resulting in a bacteria-free effluent and 100% glucose and acetic acid depletion, with no lactic acid catabolism, thus increasing the purity of the synthetic lactic acid solution.

CONCLUSIONS

The study clearly demonstrated that a bio-purification process for lactic acid employing the engineered E. coli strain cultivated in a membrane bioreactor is a technically feasible concept, paving the way for further technological advancement.

Antarctic marine sediment as a source of filamentous fungi-derived antimicrobial and antitumor compounds of pharmaceutical interest

Antarctica harbors a microbial diversity still poorly explored and of inestimable biotechnological value. Cold-adapted microorganisms can produce a diverse range of metabolites stable at low temperatures, making these compounds industrially interesting for biotechnological use. The present work investigated the biotechnological potential for antimicrobial and antitumor activity of filamentous fungi and bacteria isolated from marine sediment samples collected at Deception Island, Antarctica. A total of 89 microbial isolates were recovered from marine sediments and submitted to an initial screening for L-glutaminase with antitumoral activity and for antimicrobial metabolites. The isolates Pseudogymnoascus sp. FDG01, Pseudogymnoascus sp. FDG02, and Penicillium sp. FAD33 showed potential antiproliferative action against human pancreatic carcinoma cells while showing no toxic effect on non-tumor cells. The microbial extracts from unidentified three bacteria and four filamentous fungi showed antibacterial activity against at least one tested pathogenic bacterial strain. The isolate FDG01 inhibited four bacterial species, while the isolate FDG01 was active against Micrococcus luteus in the minimal inhibitory concentration of 0.015625 μg mL -1. The results pave the way for further optimization of enzyme production and characterization of enzymes and metabolites found and reaffirm Antarctic marine environments as a wealthy source of compounds potentially applicable in the healthcare and pharmaceutical industry.

Inteins: A Swiss army knife for synthetic biology

Inteins are proteins found in nature that execute protein splicing. Among them, split inteins stand out for their versatility and adaptability, presenting creative solutions for addressing intricate challenges in various biological applications. Their exquisite attributes, including compactness, reliability, orthogonality, low toxicity, and irreversibility, make them of interest to various fields including synthetic biology, biotechnology and biomedicine. In this review, we delve into the inherent challenges of using inteins, present approaches for overcoming these challenges, and detail their reliable use for specific cellular tasks. We will discuss the use of conditional inteins in areas like cancer therapy, drug screening, patterning, infection treatment, diagnostics and biocontainment. Additionally, we will underscore the potential of inteins in executing basic logical operations with practical implications. We conclude by showcasing their potential in crafting complex genetic circuits for performing computations and feedback control that achieves robust perfect adaptation.

Display of FliC131 on the Surface of Lactococcus lactis as a Strategy to Increase its Adjuvanticity for Mucosal Immunization

Research on innovative mucosal adjuvants is essential to develop new vaccines for safe mucosal application. In this work, we propose the development of a Lactococcus lactis that expresses a variant of flagellin on its surface (FliC131*), to increase the adjuvanticity of the living cell and cell wall-derived particles (CWDP). We optimized the expression of FliC131*, and confirmed its identity and localization by Western blot and flow cytometry. We also generated CWDP containing FliC131* (CDWP-FliC131*) and evaluated their storage stability. Lastly, we measured the human TLR5 stimulating activity in vitro and assessed the adjuvanticity in vivo using ovalbumin (OVA) as a model antigen. As a result, we generated L. lactis/pCWA-FliC131*, that expresses and displays FliC131* on its surface, obtained the corresponding CWDP-FliC131*, and showed that both activated hTLR5 in vitro in a dose-dependent manner. Furthermore, CWDP-FliC131* retained this biological activity after being lyophilized and stored for a year. Finally, intranasal immunization of mice with OVA plus live L. lactis/pCWA-FliC131* or CWDP-FliC131* induced OVA-specific IgG and IgA in serum, intestinal lavages, and bronchoalveolar lavages. Our work demonstrates the potential of this recombinant L. lactis with an enhanced adjuvant effect, prompting its further evaluation for the design of novel mucosal vaccines.

Effective control of sclerotinia stem rot in canola plants through application of exogenous hairpin RNA of multiple S. sclerotiorum genes

Sclerotinia stem rot (SSR) is a globally destructive plant disease caused by Sclerotinia sclerotiorum. Current management of SSR primarily relies on chemical fungicides and crop rotation, raising environmental concerns. In this study, we developed an eco-friendly RNA bio-fungicide targeting S. sclerotiorum. Six S. sclerotiorum genes were selected for dsRNA synthesis. Four genes, including a Chitin binding domain (CBD), Mitogen-activated protein kinase (MAPK), oxaloacetate acetylhydrolase (OA), and Abhydrolase-3 (Abh), were combined to express hairpin RNA in E. coli HT115. Application of total RNA extracted from E. coli HT115 expressing hairpin RNA on disease progressive and necrosis lesion was evaluated. Gene expression analysis using real-time PCR showed silencing of the target genes using 50 ng/µl of dsRNA in a fungal liquid culture. Detached leaf assay and greenhouse application of dsRNA on canola stem and leaves showed variation in the reduction of necrosis symptoms by dsRNA of different genes, with Abhydrolase-3 being the most effective. The dsRNA from a combination of four genes reduced disease severity significantly (P = 0.01). Plants sprayed with hpRNA from four genes had lesions that were almost 30% smaller than that of plants treated with Abh alone, in lab and greenhouse assays. Results of this study highlight the potential of RNAi to manage diseases caused by S. sclerotiorum; however, it also shows that additional research is necessary to optimize its efficacy.

Noninvasive total counting of cultured cells using a home-use scanner with a pattern sheet

The inherent variability in cell culture techniques hinders their reproducibility. To address this issue, we introduce a comprehensive cell observation device. This new approach enhances the features of existing home-use scanners by implementing a pattern sheet. Compared with fluorescent staining, our method over- or underestimated the cell count by a mere 5%. The proposed technique showcased a strong correlation with conventional methodologies, displaying R2 values of 0.91 and 0.99 compared with the standard chamber and fluorescence methods, respectively. Simulations of microscopic observations indicated the potential to estimate accurately the total cell count using just 20 fields of view. Our proposed cell-counting device offers a straightforward, noninvasive means of measuring the number of cultured cells. By harnessing the power of deep learning, this device ensures data integrity, thereby making it an attractive option for future cell culture research.

Uptake, translocation, and nutrient efficiency of nano-bonechar as a plant growth regulator in hydroponics and soil systems

The use of nanotechnology in terms of nanoparticles, carbon nanotubes, and quantum dots, when exposed to the plants, helps increase their productivity. It is worth the effort to comprehend the fate of these nanoparticles in plants. Bonechar derived from bones is a rich source of C, P, Ca2+, and Mg2+ nutrients, which can significantly contribute to the growth of the plants. This study focused on the uptake of nano-bonechar (NBC) in the Syngonium podophyllum plant, and its effects on plant growth under hydroponics and soil systems. The compound microscopy and SEM-EDX results confirmed the presence of NBC in the leaves and roots of the plants in hydroponics and soil systems. The FTIR spectra reflected the presence of functional groups of the NBC in the leaves of the Syngonium podophyllum plant. The plant's growth parameters showed an increase in fresh weight, dry weight, shoot length, chlorophyll content, leaf count, total Ca2+, total PO43-, and total organic carbon of plants in both systems. The NBC not just improved plant physiochemical parameters but also built up the soil quality in terms of bioavailable Ca2+, PO43-, water holding capacity, and soil organic matter. It is concluded that the production of carbon-based NBC not only helps manage bone waste but also their efficient uptake in plants significantly improving plant productivity.

Breaking down barriers: comprehensive functional analysis of the Aspergillus niger chitin synthase repertoire

BACKGROUND

Members of the fungal kingdom are heterotrophic eukaryotes encased in a chitin containing cell wall. This polymer is vital for cell wall stiffness and, ultimately, cell shape. Most fungal genomes contain numerous putative chitin synthase encoding genes. However, systematic functional analysis of the full chitin synthase catalogue in a given species is rare. This greatly limits fundamental understanding and potential applications of manipulating chitin synthesis across the fungal kingdom.

RESULTS

In this study, we conducted in silico profiling and subsequently deleted all predicted chitin synthase encoding genes in the multipurpose cell factory Aspergillus niger. Phylogenetic analysis suggested nine chitin synthases evolved as three distinct groups. Transcript profiling and co-expression network construction revealed remarkably independent expression, strongly supporting specific role(s) for the respective chitin synthases. Deletion mutants confirmed all genes were dispensable for germination, yet impacted colony spore titres, chitin content at hyphal septa, and internal architecture of submerged fungal pellets. We were also able to assign specific roles to individual chitin synthases, including those impacting colony radial growth rates (ChsE, ChsF), lateral cell wall chitin content (CsmA), chemical genetic interactions with a secreted antifungal protein (CsmA, CsmB, ChsE, ChsF), resistance to therapeutics (ChsE), and those that modulated pellet diameter in liquid culture (ChsA, ChsB). From an applied perspective, we show chsF deletion increases total protein in culture supernatant over threefold compared to the control strain, indicating engineering filamentous fungal chitin content is a high priority yet underexplored strategy for strain optimization.

CONCLUSION

This study has conducted extensive analysis for the full chitin synthase encoding gene repertoire of A. niger. For the first time we reveal both redundant and non-redundant functional roles of chitin synthases in this fungus. Our data shed light on the complex, multifaceted, and dynamic role of chitin in fungal growth, morphology, survival, and secretion, thus improving fundamental understanding and opening new avenues for biotechnological applications in fungi.

A global analysis of bioeconomy visions in governmental bioeconomy strategies

Against the background of climate change and scarce non-renewable resources, transforming the fossil-based toward a bio-based economy is considered crucial for sustainable development. Numerous countries have released governmental strategies outlining their bioeconomy visions. This study examines the bioeconomy visions presented in 78 policy documents from 50 countries worldwide, building on earlier vision typologies. Through qualitative content analysis, 227 distinct policy goals were identified and analyzed. Descriptive statistics were used to determine the salience of specific goals, overarching goal categories, and distinct bioeconomy visions: bioresource, biotechnology, and bioecology visions. The results reveal that goals and visions prioritize economic growth, while environmental considerations are less salient. The bioresource vision emerges as the globally dominant perspective, while the bioecology and biotechnology visions have lower salience. These findings deepen our comprehension of current bioeconomy policies and emphasize the need for critical research on bioeconomy visions and their implications for public policy.

Machine Learning and Gene Editing at the Helm of a Societal Evolution

The integration of artificial intelligence (AI) and biotechnology, whilst in its infancy, presents significant opportunities and risks, and proactive policy is needed to manage these emerging technologies. Whilst AI continues to have significant and broad impact, its relevance and complexity magnify when integrated with other emerging technologies. The confluence of Machine Learning (ML), a subset of AI, with gene editing (GE) in particular can foster substantial benefits as well as daunting risks that range from ethics to national security. These complex technologies have implications for multiple sectors, ranging from agriculture and medicine to economic competition and national security. Consideration of technology advancements and policies in different geographic regions, and involvement of multiple organisations further confound this complexity. As the impact of ML and GE expands, forward looking policy is needed to mitigate risks and leverage opportunities. Thus, this study explores the technological and policy implications of the intersection of ML and GE, with a focus on the United States (US), the United Kingdom (UK), China, and the European Union (EU). Analysis of technical and policy developments over time and an assessment of their current state have informed policy recommendations that can help manage beneficial use of technology advancements and their convergence, which can be applied to other sectors. This study is intended for policymakers to prompt reflection on how to best approach the convergence of the two technologies. Technical practitioners may also find it valuable as a resource to consider the type of information and policy stakeholders engage with.

PHA is not just a bioplastic!

Polyhydroxyalkanoates (PHA) have evolved into versatile biopolymers, transcending their origins as mere bioplastics. This extensive review delves into the multifaceted landscape of PHA applications, shedding light on the diverse industries that have harnessed their potential. PHA has proven to be an invaluable eco-conscious option for packaging materials, finding use in films foams, paper coatings and even straws. In the textile industry, PHA offers a sustainable alternative, while its application as a carbon source for denitrification in wastewater treatment showcases its versatility in environmental remediation. In addition, PHA has made notable contributions to the medical and consumer sectors, with various roles ranging from 3D printing, tissue engineering implants, and cell growth matrices to drug delivery carriers, and cosmetic products. Through metabolic engineering efforts, PHA can be fine-tuned to align with the specific requirements of each industry, enabling the customization of material properties such as ductility, elasticity, thermal conductivity, and transparency. To unleash PHA's full potential, bridging the gap between research and commercial viability is paramount. Successful PHA production scale-up hinges on establishing direct supply chains to specific application domains, including packaging, food and beverage materials, medical devices, and agriculture. This review underscores that PHA's future rests on ongoing exploration across these industries and more, paving the way for PHA to supplant conventional plastics and foster a circular economy.

Identification and characterization of integrated prophages and CRISPR-Cas system in Bacillus subtilis RS10 genome

Bacteriophages have been extensively investigated due to their prominent role in the virulence and resistance of pathogenic bacteria. However, little attention has been given to the non-pathogenic Bacillus phages, and their role in the ecological bacteria genome is overlooked. In the present study, we characterized two Bacillus phages with a linear DNA genome of 33.6 kb with 44.83% GC contents and 129.3 kb with 34.70% GC contents. A total of 46 and 175 putative coding DNA sequences (CDS) were identified in prophage 1 (P1) and prophage 2 (P2), respectively, with no tRNA genes. Comparative genome sequence analysis revealed that P1 shares eight CDS with phage Jimmer 2 (NC-041976), and phage Osiris (NC-028969), and six with phage phi CT9441A (NC-029022). On the other hand, P2 showed high similarity with Bacill_SPbeta_NC_001884 and Bacillus phage phi 105. Further, genome analysis indicates several horizontal gene transfer events in both phages during the evolution process. In addition, we detected two CRISPR-Cas systems for the first time in B. subtilis. The identified CRISPR system consists of 24 and 25 direct repeats and integrase coding genes, while the cas gene which encodes Cas protein involved in the cleavage of a target sequence is missing. These findings will expand the current knowledge of soil phages as well as help to develop a new perspective for investigating more ecological phages to understand their role in bacterial communities and diversity.

Advances in chitosan and chitosan derivatives for biomedical applications in tissue engineering: An updated review

In recent years, chitosan (CS) has received much attention as a functional biopolymer for various applications, especially in the biomedical field. It is a natural polysaccharide created by the chemical deacetylation of chitin (CT) that is nontoxic, biocompatible, and biodegradable. This natural polymer is difficult to process; however, chemical modification of the CS backbone allows improved use of functional derivatives. CS and its derivatives are used to prepare hydrogels, membranes, scaffolds, fibers, foams, and sponges, primarily for regenerative medicine. Tissue engineering (TE), currently one of the fastest-growing fields in the life sciences, primarily aims to restore or replace lost or damaged organs and tissues using supports that, combined with cells and biomolecules, generate new tissue. In this sense, the growing interest in the application of biomaterials based on CS and some of its derivatives is justifiable. This review aims to summarize the most important recent advances in developing biomaterials based on CS and its derivatives and to study their synthesis, characterization, and applications in the biomedical field, especially in the TE area.

No country for old methods: New tools for studying microproteins

Microproteins encoded by small open reading frames (sORFs) have emerged as a fascinating frontier in genomics. Traditionally overlooked due to their small size, recent technological advancements such as ribosome profiling, mass spectrometry-based strategies and advanced computational approaches have led to the annotation of more than 7000 sORFs in the human genome. Despite the vast progress, only a tiny portion of these microproteins have been characterized and an important challenge in the field lies in identifying functionally relevant microproteins and understanding their role in different cellular contexts. In this review, we explore the recent advancements in sORF research, focusing on the new methodologies and computational approaches that have facilitated their identification and functional characterization. Leveraging these new tools hold great promise for dissecting the diverse cellular roles of microproteins and will ultimately pave the way for understanding their role in the pathogenesis of diseases and identifying new therapeutic targets.

Ultrasound-targeted microbubble technology facilitates SAHH gene delivery to treat diabetic cardiomyopathy by activating AMPK pathway

Diabetic cardiomyopathy (DCM) is a cardiovascular complication with no known cure. In this study, we evaluated the combination of ultrasound-targeted microbubble destruction (UTMD) and cationic microbubbles (CMBs) for cardiac S-adenosyl homocysteine hydrolase (SAHH) gene transfection as potential DCM therapy. Models of high glucose/fat (HG/HF)-induced H9C2 cells and streptozotocin-induced DCM rats were established. Ultrasound-mediated SAHH delivery using CMBs was a safe and noninvasive approach for spatially localized drug administration both in vitro and in vivo. Notably, SAHH overexpression increased cell viability and antioxidative stress and inhibited apoptosis of HG/HF-induced H9C2 cells. Likewise, UTMD-mediated SAHH delivery attenuated apoptosis, oxidative stress, cardiac fibrosis, and myocardial dysfunction in DCM rats. Activation of the AMPK/FOXO3/SIRT3 signaling pathway may be a key mechanism mediating the role of SAHH in regulating myocardial injury. Thus, UTMD-mediated SAHH transfection may be an important advancement in cardiac gene therapy for restoring ventricular function after DCM.

Toward understanding and utilizing crop heterosis in the age of biotechnology

Heterosis, a universal phenomenon in nature, mainly reflected in the superior productivity, quality, and fitness of F1 hybrids compared with their inbred parents, has been exploited in agriculture and greatly benefited human society in terms of food security. However, the flexible and efficient utilization of heterosis has remained a challenge in hybrid breeding systems because of the limitations of "three-line" and "two-line" methods. In the past two decades, rapidly developed biotechnologies have provided unprecedented conveniences for both understanding and utilizing heterosis. Notably, "third-generation" (3G) hybrid breeding technology together with high-throughput sequencing and gene editing greatly promoted the efficiency of hybrid breeding. Here, we review emerging ideas about the genetic or molecular mechanisms of heterosis and the development of 3G hybrid breeding system in the age of biotechnology. In addition, we summarized opportunities and challenges for optimal heterosis utilization in the future.

Effective wound healing on diabetic mice by adhesive antibacterial GNPs-lysine composited hydrogel

Current trends in wound care research focus on creating dressings for diverse wound types, aiming to effectively control the wound healing process. We proposed a wound dressing composed of oxidized hyaluronic acid and amine gelatin with embedded lysine-modified gelatin nanoparticles (HGel-GNPs-lysine). This dressing improves mechanical properties and reduces degradation rates. The storage modulus for HGel-GNPs-lysine was 3,800 Pa, exceeding that of HGel (1,750 Pa). The positively charged surface of GNPs-lysine effectively eliminated Escherichia coli and Staphylococcus aureus. In a diabetic mice model (C57BL/6), HGel-GNPs-lysine immobilized with basic-fibroblast growth factor promoted granulation tissue thickness and collagen density. Gene expression analysis indicated that HGel-GNPs-lysine reduced inflammation and enhanced angiogenesis. This study highlights that HGel-GNPs-lysine could offer alternative treatment strategies for regulating the inflammatory response at the injury site in wound dressing applications.

Human induced pluripotent stem cell-derived closed-loop cardiac tissue for drug assessment

Human iPSC-derived cardiomyocytes (hiPSC-CMs) exhibit functional immaturity, potentially impacting their suitability for assessing drug proarrhythmic potential. We previously devised a traveling wave (TW) system to promote maturation in 3D cardiac tissue. To align with current drug assessment paradigms (CiPA and JiCSA), necessitating a 2D monolayer cardiac tissue, we integrated the TW system with a multi-electrode array. This gave rise to a hiPSC-derived closed-loop cardiac tissue (iCT), enabling spontaneous TW initiation and swift pacing of cardiomyocytes from various cell lines. The TW-paced cardiomyocytes demonstrated heightened sarcomeric and functional maturation, exhibiting enhanced response to isoproterenol. Moreover, these cells showcased diminished sensitivity to verapamil and maintained low arrhythmia rates with ranolazine-two drugs associated with a low risk of torsades de pointes (TdP). Notably, the TW group displayed increased arrhythmia rates with high and intermediate risk TdP drugs (quinidine and pimozide), underscoring the potential utility of this system in drug assessment applications.

Characterization of membrane protein interactions by peptidisc-mediated mass photometry

Membrane proteins perform numerous critical functions in the cell, making many of them primary drug targets. However, their preference for a lipid environment makes them challenging to study using established solution-based methods. Here, we show that peptidiscs, a recently developed membrane mimetic, provide an ideal platform to study membrane proteins and their interactions with mass photometry (MP) in detergent-free conditions. The mass resolution for membrane protein complexes is similar to that achievable with soluble proteins owing to the low carrier heterogeneity. Using the ABC transporter BtuCD, we show that MP can quantify interactions between peptidisc-reconstituted membrane protein receptors and their soluble protein binding partners. Using the BAM complex, we further show that MP reveals interactions between a membrane protein receptor and a bactericidal antibody. Our results highlight the utility of peptidiscs for membrane protein characterization in detergent-free solution and provide a rapid and powerful platform for quantifying membrane protein interactions.

Investigation of synergic effects of nanogroove topography and polyaniline-chitosan nanocomposites on PC12 cell differentiation and axonogenesis

Axonal damage is the main characteristic of neurodegenerative diseases. This research was focused on remodeling cell morphology and developing a semi-tissue nanoenvironment via mechanobiological stimuli. The combination of nanogroove topography and polyaniline-chitosan enabled the manipulation of the cells by changing the morphology of PC12 cells to spindle shape and inducing the early stage of signal transduction, which is vital for differentiation. The nanosubstarte embedded with nanogooves induced PC12 cells to elongate their morphology and increase their size by 51% as compared with controls. In addition, the use of an electroconductive nanocomposite alongside nanogrooves resulted in the differentiation of PC12 cells into neurons with an average length of 193 ± 7 μm for each axon and an average number of seven axons for each neurite. Our results represent a combined tool to initiate a promising future for cell reprogramming by inducing cell differentiation and specific cellular morphology in many cases, including neurodegenerative diseases.

Exploring the substrate stereoselectivity and catalytic mechanism of nonribosomal peptide macrocyclization in surugamides biosynthesis

SurE, the first reported penicillin-binding protein-like thioesterase (PBP-like TE), is known as a new off-loading cyclase, which catalyzes heterochiral coupling in nonribosomal peptides (NRPs). However, the structural rationale for substrate stereoselectivity and enzymatic mechanism remains mysterious. Here, computational models, integrating MD simulations and QM/MM methods, unveiled SurE's substrate recognition and catalytic process. An oxyanion hole stabilized the C-terminal D-residue during recognition. Residue R446 anchored the substrate for macrocyclization. A vital hydrogen-bonding network (Y154, K66, N156), verified by mutation results, was responsible for the recognition of N-terminal L-residue and involvement in catalytic process with a calculated 19.4 kcal/mol energy barrier. Four novel-designed peptide precursors were effectively cyclized into cyclopeptides by SurE based on computational analysis. Our results provide a comprehensive understanding of SurE's catalytic mechanism and guiding design of versatile PBP-like TEs for novel macrocyclic NRPs.

Enhancing the functionality of plant-based Yogurt: Integration of lycopene through dual-stage fermentation of soymilk

Well-defined compositional assemblies of plant-based yogurt are of fast-growing awareness for world population concerning environmental sustainability, economic burdens and health risks. Soybean is an attractive candidate for plant yogurt, suffering from poor flavor, limited nutrition, and undesired allergens to offer healthy-functional segments. Herein, we deciphered a novel lycopene-soy yogurt by efficient two-stage fermentation of engineered B. subtilis and LAB. The fortified sogurt was ensured with redundant lycopene of 22.67 ± 2.95 mg/g DCW by engineered B. subtilis and enriched soy isoflavone from synergistic effects of engineered B. subtilis and LAB, possessing strong antioxidant capacity for upgrading functionality. Moreover, the desired pH, accelerated protein hydrolysis, enhanced amino acid availability, and expected sensory attributes cooperatively conferred lycopene-soy yogurt as healthy functional food. High potential is firstly ascribed to sequential dual culture of engineered B. subtilis and LAB in lycopene-soy yogurt, in which flavorful, hypoallergenic and antioxidative ingredients enabled functionalities for plant-based yogurt.

Adeno-associated virus-mediated gene therapy for cardiac tachyarrhythmia: A systematic review and meta-analysis

Cardiac tachyarrhythmia presents a significant health care challenge, causing notable morbidity and mortality. Conventional treatments have limitations and potential risks, resulting in an elevated disease burden. Adeno-associated virus (AAV)-mediated gene therapy holds promise as a potential future treatment option. Therefore, we aimed to provide a measured overview of the latest developments in this rapidly growing field. PubMed and Embase databases were searched up to January 2024. Studies that employed AAV as a vector for delivery of therapeutic agents to treat cardiac tachyarrhythmia were included. Of the 26 studies included, 20 published in the last 5 years. There were 22 novel molecular targets identified. More than 80% of the included studies employed small-animal models or used AAV9. In atrial fibrillation preclinical studies, AAV-mediated gene therapy reduced atrial fibrillation inducibility by 81% (odds ratio, 0.19 [0.08-0.45]; P < .01). Similarly, for acquired and inherited ventricular arrhythmia, animal models receiving gene therapy had less inducible ventricular arrhythmia (odds ratio, 0.06 [0.03-0.11]; P < .01). This review highlights the rapid progress of AAV-mediated gene therapy for cardiac tachyarrhythmia. Although these investigations are currently in the early stages of clinical application, they present promising prospects for gene therapy. (PROSPERO registry: CRD42023479448).

Filling Unit Operation for Biological Drug Products: Challenges and Considerations

One of the key unit operations during the aseptic fill-finish process of parenteral products, such as biologics, is the filling process of the formulated, sterile filtered drug substance into primary packaging containers. The applied filling technology as well as the process performance majorly impacts final drug product quality. The present review provides an overview of commonly used filling technologies during fill-finish operations of biologics including positive displacement pump systems such as radial peristaltic pump, rotary piston pump, rolling diaphragm pump, or innovative systems such as the linear peristaltic pump, as well as time-over-pressure filling technology. The article describes the operating principle of each pump system and reviews advantages and drawbacks. We highlight specific considerations for individual systems, such as the risk of protein particle formation and particle shedding from wear and tear of tubing, and discuss current literature about general challenges associated with the filling process, such as hydrogen peroxide uptake, adsorption phenomena to tubing material, and needle clogging. We suggest process development and process characterization studies to assess the impact of the filling process on product quality, and lastly provide an outlook about the use of disposable equipment during filling operations related to sustainability considerations.

Self-assembling peptides: Perspectives regarding biotechnological applications and vaccine development

Self-assembly involves a set of molecules spontaneously interacting in a highly coordinated and dynamic manner to form a specific supramolecular structure having new and clearly defined properties. Many examples of this occur in nature and many more came from research laboratories, with their number increasing every day via ongoing research concerning complex biomolecules and the possibility of harnessing it when developing new applications. As a phenomenon, self-assembly has been described on very different types of molecules (biomolecules including), so this review focuses on what is known about peptide self-assembly, its origins, the forces behind it, how the properties of the resulting material can be tuned in relation to experimental considerations, some biotechnological applications (in which the main protagonists are peptide sequences capable of self-assembly) and what is yet to be tuned regarding their research and development.

Genome-wide identification and in-silico analysis of papain-family cysteine protease encoding genes in Tetrahymena thermophila

Tetrahymena thermophila is a promising host for recombinant protein production, but its utilization in biotechnology is mostly limited due to the presence of intracellular and extracellular papain-family cysteine proteases (PFCPs). In this study, we employed bioinformatics approaches to investigate the T. thermophila PFCP genes and their encoded proteases (TtPFCPs), the most prominent protease family in the genome. Results from the multiple sequence alignment, protein modeling, and conserved motif analyses revealed that all TtPFCPs showed considerably high homology with mammalian cysteine cathepsins and contained conserved amino acid motifs. The total of 121 TtPFCP-encoding genes, 14 of which were classified as non-peptidase homologs, were found. Remaining 107 true TtPFCPs were divided into four distinct subgroups depending on their homology with mammalian lysosomal cathepsins: cathepsin L-like (TtCATLs), cathepsin B-like (TtCATBs), cathepsin C-like (TtCATCs), and cathepsin X-like (TtCATXs) PFCPs. The majority of true TtPFCPs (96 out of the total) were in TtCATL-like peptidase subgroup. Both phylogenetic and chromosomal localization analyses of TtPFCPs supported the hypothesis that TtPFCPs likely evolved through tandem gene duplication events and predominantly accumulated on micronuclear chromosome 5. Additionally, more than half of the identified TtPFCP genes are expressed in considerably low quantities compared to the rest of the TtPFCP genes, which are expressed at a higher level. However, their expression patterns fluctuate based on the stage of the life cycle. In conclusion, this study provides the first comprehensive in-silico analysis of TtPFCP genes and encoded proteases. The results would help designing an effective strategy for protease knockout mutant cell lines to discover biological function and to improve the recombinant protein production in T. thermophila.

Hurdles in translating science from lab to market in delivery systems for Cosmetics: An industrial perspective

In recent decades, a sweeping technological wave has reshaped the global economic landscape. Fueled by the unceasing forces of digital innovation and venture capital investment, this transformative machine has left a significant mark across numerous economic sectors. More recently, the emergence of 'deep tech' start-ups, focusing on areas such as artificial intelligence, nanotechnology, and biotechnology, has infused a fresh wave of innovation into various sectors, including the pharmaceutical and cosmetic industry. This review explores the significance of innovation within the cosmetics sector, with a particular emphasis on delivery systems. It assesses the crucial process of bridging the gap between research and the market, particularly in the translation of nanotechnology into tangible real-world applications. With the rise of nanotechnology-based beauty ingredients, we can anticipate groundbreaking advancements that promise to surpass consumer expectations, ushering in a new era of unparalleled innovation in beauty products.

Sorting Technology for Mesenchymal Stem Cells from a Single Tissue Source

Mesenchymal stem cells (MSCs) are adult stem cells that can be obtained, enriched and proliferated in vitro. They owned enormous potential in fields like regenerative medicine, tissue engineering and immunomodulation. However, though isolated from the same origin, MSCs are still essentially heterogeneous cell populations with different phenotypes and functions. This heterogeneity of MSCs significantly affects their therapeutic efficacy and brings obstacles to scientific research. Thus, reliable sorting technology which can isolate or purify MSC subpopulations with various potential and differentiation pathways is urgently needed. This review summarized principles, application status and clinical implications for these sorting methods, aiming at improving the understanding of MSC heterogeneity as well as providing fresh perspectives for subsequent clinical applications.

Lysozyme aggregation and unfolding in ionic liquid solvents: Insights from small angle X-ray scattering and high throughput screening

Understanding protein behaviour is crucial for developing functional solvent systems. Ionic liquids (ILs) are designer salts with versatile ion combinations, where some suppress unfavourable protein behaviour. This work utilizes small angle X-ray scattering (SAXS) to investigate the size and shape changes of model protein hen egg white lysozyme (HEWL) in 137 IL and salt solutions. Guinier, Kratky, and pair distance distribution analysis were used to evaluate the protein size, shape, and aggregation changes in these solvents. At low IL and salt concentration (1 mol%), HEWL remained monodispersed and globular. Most ILs increased HEWL size compared to buffer, while the nitrate and mesylate anions induced the most significant size increases. IL cation branching, hydroxyl groups, and longer alkyl chains counteracted this size increase. Common salts exhibited specific ion effects, while the IL effect varied with concentration due to complex ion-pairing. Protein aggregation and unfolding occurred at 10 mol% IL, altering the protein shape, especially for ILs with multiple alkyl chains on the cation, or with a mesylate/nitrate anion. This study highlights the usefulness of adopting a high-throughput SAXS strategy for understanding IL effects on protein behaviour and provides insights on controlling protein aggregation and unfolding with ILs.