Biotechnology Industry Research Articles

Exploring quorum sensing for inducing bioactives overproduction in the dinoflagellate microalga Amphidinium carterae

The dinoflagellate Amphidinium carterae is a promising source of unique bioactive compounds with potential applications in diverse industries. Abiotic strategies for increasing bioactive cell quota have been preferred for cost-effectiveness, controllability, and existing knowledge. The supernatants of Heterosigma akashiwo and Pavlova sp. enhanced haemolytic activity of A. carterae by 2.3 times and improved its final biomass by 10 % when added to the growth medium. Prymnesium parvum supernatant increased the total lipid content of A. carterae by 50 %, while Pleurochrysis roscoffensis supernatant boosted its total carotenoid content by 40 %. This study demonstrated a rapid screening strategy for evaluating growth responses and highlights the potential of using allelopathic strategies to enhance bioactive metabolite production. Utilizing supernatants for the formulation of growth media fosters a circular economy by repurposing resources, minimizing waste, and promoting sustainability in the microalgal biotechnological industry.

Continuous biomanufacturing for sustainable bioeconomy applications

The bioeconomy provides an alternative to non-renewable or fossil-based products. Biomanufacturing is emerging as a sustainable platform for the production of a wide range of value-added products, including chemicals and biodegradable materials. At present, the biotechnology industry is dominated by batch and fed-batch processes and there is increasing interest in continuous biomanufacturing (CBM) as an alternative to reduce capital and operating costs. However, CBM faces adoption challenges due to perceived operational complexities. This review critically evaluates the state-of-the-art in CBM, examining its benefits, limitations, and successful industrial applications across key sectors. Transitioning from batch to continuous processes can enhance productivity and reduce environmental impacts, making CBM a cornerstone technology for a sustainable bioeconomy.

Production of Cellulolytic Enzymes by Paecilomyces TP08 Using Grape Stalk and Wheat Bran as Substrates in Solid State Culture

Objective: The objective of this study is to investigate the use of grape stems and wheat bran as substrates in solid state fermentation, for the production of cellulolytic enzymes using the fungus Paecilomyces TP08 sp. Theoretical Framework: In grape production, driven by increased consumption and exports, by-products represent 30% of the total volume of grapes processed for wine, requiring efficient management to ensure sustainability. Method: The methodology adopted for this research involves solid-state cultivation, with a substrate made up of 50% grape stems and 50% wheat bran, with samples taken every 24 hours. Each sample taken went through a filtration process, followed by enzyme activity analysis using the DNS method. Results and Discussion: The results obtained showed that the cultivation with the association of wheat bran and grape stalks presented good total cellulase activity during the process, value of 0.846 U/g in 144h, followed by the activity of 0.663U/g observed in 24h. Research Implications: The practical and theoretical implications of this research are discussed, providing insights into how the results can be applied or influence practices in the field of industrial biotechnology. These implications could cover the food, textile and pharmaceutical industries. Originality/Value: This study contributes to the literature by associating grape stalks with wheat bran for the production of fungal enzymes. The relevance and value of this research are evidenced by the use of an innovative substrate (grape stalks) associated with a conventional substrate (wheat bran) for induction of the microorganism little used in the literature for enzyme production.

Patent Clearinghouse and Technology Diffusion: What is the Contribution of Arbitration Agreements?

Abstract One of the acknowledged advantages of patent clearinghouses is that they favor the diffusion of technology. In traditional clearinghouses, patents are usually bundled in pools and sold at a pre-set price. Recently, in the biotechnology industry a new form of clearinghouse has been observed, where patent tariffs are instead bargained over by the clearinghouse members. Exchange is then guaranteed by arbitration agreements to which the negotiating parties are bound, should their bargaining reach a dead end. This paper assesses the effect on technology diffusion of this new type of clearinghouse. We show that such arbitration agreements, through their effect on the outside options, may reduce the incentives of a member of the clearinghouse to license to non-members. This result highlights the role of such arbitration agreements in the diffusion of technology outside the clearinghouse.

Engineered Halomonas for production of gamma-aminobutyric acid and 2-pyrrolidone

Gamma-Aminobutyric acid (GABA) is a derivative of L-glutamate, also a precursor for the synthesis of 2-pyrrolidone, which is a monomer of nylon-4. This study achieved a one-step biosynthesis of GABA and 2-pyrrolidone by Halomonas bluephagenesis overexpressing key genes involved in GABA and 2-pyrrolidone synthesis and deleting GABA degradation genes combined with reducing the degradation of 2-pyrrolidone precursor. The resulting H. bluephagenesis strain WLp07 was employed in whole-cell catalysis, producing 357 g/L of GABA and 72 wt% of PHA. Furthermore, a self-flocculating H. bluephagenesis allowed rapid, convenient recycling of the cells, achieving 880 g/L of GABA over three cycles. Shake flask studies showed that engineered H. bluephagenesis harboring β-alanine CoA transferase was able to synthesized 2-pyrrolidone from GABA. H. bluephagenesis as a chassis of next generation industrial biotechnology (NGIB), demonstrated its diverse ability to produce GABA and 2-pyrrolidone in addition to intracellular PHA.

Exploring Fungal Diversity in Seagrass Ecosystems for Pharmaceutical and Ecological Insights.

Marine ecosystems are important in discovering novel fungi with interesting metabolites that have shown great potential in pharmaceutical and biotechnological industries. Seagrasses, the sole submerged marine angiosperm, host diverse fungal taxa with mostly unknown metabolic capabilities. They are considered to be one of the least studied marine fungal habitats in the world. This review gathers and analyzes data from studies related to seagrasses-associated fungi, including taxonomy and biogeography, and highlights existing research gaps. The significance of the seagrass-fungal associations remains largely unknown, and current understanding of fungal diversity is limited to specific geographical regions such as the Tropical Atlantic, Mediterranean, and Indo-Pacific. Our survey yielded 29 culture-dependent studies on seagrass-associated endophytic and epiphytic fungi, and 13 miscellaneous studies, as well as 11 meta-studies, with no pathogenic true fungi described. There is a significant opportunity to expand existing studies and conduct multidisciplinary research into novel species and their potential applications, especially from understudied geographical locations. Future research should prioritize high-throughput sequencing and mycobiome studies, utilizing both culture-dependent and -independent approaches to effectively identify novel seagrass-associated fungal taxa.

CNN-FL for Biotechnology Industry Empowered by Internet-of-BioNano Things and Digital Twins

CNN-FL for Biotechnology Industry Empowered by Internet-of-BioNano Things and Digital Twins

Enhanced degradation of insoluble chitin: Engineering high-efficiency chitinase fusion enzymes for sustainable applications

N-acetyl-D-glucosamine and its dimer are degradation products of chitin waste with great potential in therapeutic and agricultural applications. However, the hydrolysis of insoluble chitin by chitinases remains a major bottleneck. This study investigated the biochemical properties and catalytic mechanisms of PoChi chitinase obtained from Penicillium oxalicum with a focus on enhancing its efficiency during the degradation of insoluble chitin. Recombinant plasmids were engineered to incorporate chitin-binding (ChBD) and/or fibronectin III (FnIII) domains. Notably, PoChi-FnIII-ChBD exhibited the highest substrate affinity (Km = 2.7 mg/mL) and a specific activity of 15.4 U/mg, which surpasses those of previously reported chitinases. These findings highlight the potential of engineered chitinases in advancing industrial biotechnology applications and offer a promising approach to more sustainable chitin waste management.

Surface-enhanced Raman spectroscopy for the characterization of xylanases enzyme

Xylanases are essential hydrolytic enzymes which break down the plant cell wall polysaccharide, xylan composed of D-xylose monomers. Surface-enhanced Raman Spectroscopy (SERS) was utilized for the characterization of interaction of xylanases with xylan at varying concentrations. The study focuses on the application of SERS for the characterization of enzymatic activity of xylanases causing hydrolysis of Xylan substrate with increase in its concentration which is substrate for this enzyme in the range of 0.2% to 1.0%. SERS differentiating features are identified which can be associated with xylanases treated with different concentrations of xylan. SERS measurements were performed using silver nanoparticles as SERS substrate to amplify Raman signal intensity for the characterization of xylan treated with xylanases. Principal Component Analysis (PCA) and Partial Least Square Discriminant Analysis (PLS-DA) were applied to analyze the spectral data to analyze differentiation between the SERS spectra of different samples. Mean SERS spectra revealed significant differences in spectral features particularly related to carbohydrate skeletal mode and O-C-O and C–C–C ring deformations. PCA scatter plot effectively differentiates data sets, demonstrating SERS ability to distinguish treated xylanases samples and the PC-loadings plot highlights the variables responsible for differentiation. PLS-DA was employed as a quantitative classification model for treated xylanase enzymes with increasing concentrations of xylan. The values of sensitivity, specificity, and accuracy were found to be 0.98%, 0.99%, and 100% respectively. Moreover, the AUC value was found to be 0.9947 which signifies the excellent performance of PLS-DA model. SERS combined with multivariate techniques, effectively characterized and differentiated xylanase samples as a result of interaction with different concentrations of the Xylan substrate. The identified SERS features can help to characterize xylanases treated with various concentrations of xylan with promising applications in the bio-processing and biotechnology industries.

Harnessing native-cryptic plasmids for stable overexpression of heterologous genes in Clostridium butyricum DSM 10702 for industrial and medical applications

Clostridium butyricum has emerged as a promising candidate for both industrial and medical biotechnologies, underscoring the key pursuit of stable gene overexpression in engineering C. butyricum. Unlike antibiotic-selective vectors, native-cryptic plasmids can be utilized for antibiotic-free expression systems in bacteria but have not been effectively exploited in C. butyricum to date. This study focuses on leveraging these plasmids, pCB101 and pCB102, in C. butyricum DSM10702 for stable gene overexpression without antibiotic selection via efficient gene integration using the SacB-based allelic exchange method. Integration of reporter IFP2.0 and glucuronidase generated sustained near-infrared fluorescence and robust enzyme activity across successive subcultures. Furthermore, successful secretion of a cellulase, Cel9M, and the human interleukin 10 from pCB102 highlights native-cryptic plasmids’ potential in conferring stable gene products for industrial and medical applications in C. butyricum. This work appears to be the first study to harness the Clostridium native-cryptic plasmid for stable gene overexpression without antibiotics, thereby advancing the biotechnological prospects of C. butyricum.

As published in the 2024 European Congress on Biotechnology abstracts: Exploring yeast diversity for ethanol-fueled industrial biotechnology

As published in the 2024 European Congress on Biotechnology abstracts: Exploring yeast diversity for ethanol-fueled industrial biotechnology

The improved purification technique for isolation of the novel CGTase from the alkaliphilc strain Caldalkalibacillus mannanilyticus IB-OR17-B1

Cyclodextrin-glucanotransferase (CGTase, EC 2.4.1.19) is a multifunctional enzyme that catalyzes many enzymatic reactions including cyclization, binding, disproportionation and hydrolysis reactions, playing an important role in the enzymatic synthesis of compounds that are widely used in agriculture, pharmaceuticals, food, chemical and biotechnology industries. The present research is aimed to optimize the purification protocol for the extracellular CGTase of alkaliphilc bacterial strain Caldalkalibacillus mannanilyticus IB-OR17-B1 guaranteeing the enzyme homogeneity and its high yield. The improved combination of ultrafiltration and corn-starch (5% w/v) affinity sorption techniques resulted to mild and rapid isolation of electrophoritically homogenic enzyme at 18 × increase of its specific activity and yield 56%. The developed two-step procedure instead the practiced tree-step one using commonly ion-exchange chromatography as final purification technique highly contributes in advance of cost-effectiveness for industrial production and isolation of valuable CGTases.

Selected Developments in Biotechnology Law and the Biotechnology Industry

Selected Developments in Biotechnology Law and the Biotechnology Industry

Advances in Aureobasidium research: Paving the path to industrial utilization.

We here explore the potential of the fungal genus Aureobasidium as a prototype for a microbial chassis for industrial biotechnology in the context of a developing circular bioeconomy. The study emphasizes the physiological advantages of Aureobasidium, including its polyextremotolerance, broad substrate spectrum, and diverse product range, making it a promising candidate for cost-effective and sustainable industrial processes. In the second part, recent advances in genetic tool development, as well as approaches for up-scaled fermentation, are described. This review adds to the growing body of scientific literature on this remarkable fungus and reveals its potential for future use in the biotechnological industry.

A Comparative Study on Transgenic Animal Breeding and Patentability Analysis in India: Reference to Animal Husbandry in Biotechnology Industries

A Comparative Study on Transgenic Animal Breeding and Patentability Analysis in India: Reference to Animal Husbandry in Biotechnology Industries

Establishment of a semi-continuous scale-down clone screening model for intensified perfusion culture.

Perfusion cultures have been extensively used in the biotechnology industry to achieve high yields of recombinant products, especially those with stability issue. The WuXiUP™ platform represents a novel intensified perfusion that can achieve ultra-high productivity. This study describes a representative scale-down 24-deep well plate (24-DWP) cell culture model for intensified perfusion clone screening. Clonal cell lines were expanded and evaluated in 24-DWP semi-continuous culture. Cell were sampled and counted daily with the aid of an automated liquid handler and high-throughput cell counter. To mimic perfusion culture, 24-DWP plates were spun down and resuspended with fresh medium daily. Top clones were ranked based on growth profiles and productivities. The best performing clones were evaluated on bioreactors. The selected clones achieved volumetric productivity (Pv) up to 5g/L/day when expressing a monoclonal antibody, with the accumulative harvest Pv exceeding 60g/L in a 21-day cell culture. Product quality attributes of clones cultured in 24-DWP were comparable with those from bioreactors. A high seeding strategy further shortened the clone screening timeline. In this study, a 24-DWP semi-continuous scale-down model was successfully developed to screen for cell lines suitable for intensified perfusion culture.

GloEC: a hierarchical-aware global model for predicting enzyme function.

The annotation of enzyme function is a fundamental challenge in industrial biotechnology and pathologies. Numerous computational methods have been proposed to predict enzyme function by annotating enzyme labels with Enzyme Commission number. However, the existing methods face difficulties in modelling the hierarchical structure of enzyme label in a global view. Moreover, they haven't gone entirely to leverage the mutual interactions between different levels of enzyme label. In this paper, we formulate the hierarchy of enzyme label as a directed enzyme graph and propose a hierarchy-GCN (Graph Convolutional Network) encoder to globally model enzyme label dependency on the enzyme graph. Based on the enzyme hierarchy encoder, we develop an end-to-end hierarchical-aware global model named GloEC to predict enzyme function. GloEC learns hierarchical-aware enzyme label embeddings via the hierarchy-GCN encoder and conducts deductive fusion of label-aware enzyme features to predict enzyme labels. Meanwhile, our hierarchy-GCN encoder is designed to bidirectionally compute to investigate the enzyme label correlation information in both bottom-up and top-down manners, which has not been explored in enzyme function prediction. Comparative experiments on three benchmark datasets show that GloEC achieves better predictive performance as compared to the existing methods. The case studies also demonstrate that GloEC is capable of effectively predicting the function of isoenzyme. GloEC is available at: https://github.com/hyr0771/GloEC.

Stability Oracle: a structure-based graph-transformer framework for identifying stabilizing mutations

Engineering stabilized proteins is a fundamental challenge in the development of industrial and pharmaceutical biotechnologies. We present Stability Oracle: a structure-based graph-transformer framework that achieves SOTA performance on accurately identifying thermodynamically stabilizing mutations. Our framework introduces several innovations to overcome well-known challenges in data scarcity and bias, generalization, and computation time, such as: Thermodynamic Permutations for data augmentation, structural amino acid embeddings to model a mutation with a single structure, a protein structure-specific attention-bias mechanism that makes transformers a viable alternative to graph neural networks. We provide training/test splits that mitigate data leakage and ensure proper model evaluation. Furthermore, to examine our data engineering contributions, we fine-tune ESM2 representations (Prostata-IFML) and achieve SOTA for sequence-based models. Notably, Stability Oracle outperforms Prostata-IFML even though it was pretrained on 2000X less proteins and has 548X less parameters. Our framework establishes a path for fine-tuning structure-based transformers to virtually any phenotype, a necessary task for accelerating the development of protein-based biotechnologies.

Genomic Analysis of Aspergillus Section Terrei Reveals a High Potential in Secondary Metabolite Production and Plant Biomass Degradation.

Aspergillus terreus has attracted interest due to its application in industrial biotechnology, particularly for the production of itaconic acid and bioactive secondary metabolites. As related species also seem to possess a prosperous secondary metabolism, they are of high interest for genome mining and exploitation. Here, we present draft genome sequences for six species from Aspergillus section Terrei and one species from Aspergillus section Nidulantes. Whole-genome phylogeny confirmed that section Terrei is monophyletic. Genome analyses identified between 70 and 108 key secondary metabolism genes in each of the genomes of section Terrei, the highest rate found in the genus Aspergillus so far. The respective enzymes fall into 167 distinct families with most of them corresponding to potentially unique compounds or compound families. Moreover, 53% of the families were only found in a single species, which supports the suitability of species from section Terrei for further genome mining. Intriguingly, this analysis, combined with heterologous gene expression and metabolite identification, suggested that species from section Terrei use a strategy for UV protection different to other species from the genus Aspergillus. Section Terrei contains a complete plant polysaccharide degrading potential and an even higher cellulolytic potential than other Aspergilli, possibly facilitating additional applications for these species in biotechnology.

Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

The biotechnological industry faces a crucial demand for novel bioactive compounds, particularly antimicrobial agents, to address the rising challenge of bacterial resistance to current available antibiotics. Traditional strategies for cultivating naturally occurring microorganisms often limit the discovery of novel antimicrobial producers. This study presents a protocol for targeted selection of bacterial strains using the supernatant of Paenibacillus elgii, which produces abundant signal molecules and antimicrobial peptides. Soil samples were inoculated in these enriched culture media to selectively cultivate bacteria resistant to the supernatant, indicating their potential to produce similar compounds. The bacterial strains isolated through this method were assessed for their antibacterial activity. In addition, the functional annotation of the genome of one of these strains revealed several gene clusters of biotechnological interest. This study highlights the effectiveness of using this approach for selective cultivation of microorganisms with potential for biotechnological applications.