Helix matrix-enhanced transformer model for high-accuracy Raman identification of biological products

Rapid quantification of polysorbates in complex in-process formulation buffers using variable pathlength UV spectrometry with a slope-intercept strategy

• Stress alters pigment production and composition in Talaromyces purpureogenus • EtOH and H 2 O 2 addition increases red pigment productivity • T. purpureogenus pigments exhibit anti-glycation activity • Fungal pigments show potential as sustainable, functional food dyes Biological pigment production has become increasingly important because of adverse health effects associated with chemical dyes. The fungus Talaromyces purpureogenus has been used to produce extracellular water-soluble red pigments similar to those produced by Monascus . Several studies have investigated Monascus pigment production under certain stress conditions; however, few have examined extracellular pigment production in Talaromyces . Furthermore, little research has been conducted on the use of fungal pigments as functional food dyes. Therefore, we evaluated the ability of T. purpureogenus to withstand abiotic stress in cultivation media and the effects of stress on pigment productivity. Abiotic stress was induced via the addition of sodium chloride (NaCl), sea salts, ethanol (EtOH), and hydrogen peroxide (H 2 O 2 ). Stressful conditions altered pigment production and composition. An increase in yellow-to-red pigment production ratio was observed under saline stress with both NaCl and sea salts. The yield of yellow pigment increased 1.44-fold in the presence of 1% (w/v) NaCl, while the yellow-to-red pigment ratio rose from 1.59 to 3.88 in the presence of 2% (w/v) sea salts. Addition of 1% (v/v) EtOH and 0.5% v/v H 2 O 2 (30% w/w) increased red pigment production by 2.59- and 1.67-fold, respectively. Differences in colourant properties were highlighted using UV-Vis and fluorescence spectroscopic measurements. Partially purified pigments inhibited bovine serum albumin glycation in the presence of ᴅ-ribose, demonstrating their potential to prevent the formation of advanced glycation end products. Overall, these findings demonstrated that stress conditions can improve pigment productivity in T. purpureogenus and highlight the possibility of producing functional food dyes.

Biological and biogenic carbon production in Southwestern Atlantic coralline algal beds.

Oceans exhibit complex dynamics influenced by climate change, anthropogenic activities, and natural phenomena. Understanding these dynamics is critical for ensuring the sustainability of marine environments and their optimal utilization. This research aims to study and monitor upwelling phenomena in the South Sea of Java. Upwelling, the exchange of nutrient-rich, cold water from deeper layers to the surface, enhances marine biological productivity; Sea Surface Temperature (SST) serves as a key indicator for its detection. To achieve these objectives, this study employs both ConvLSTM and 3D-CNN. ConvLSTM, a deep learning architecture that integrates convolutional structures within LSTM units, effectively captures spatiotemporal dependencies in sequential data. 3D-CNN, a deep learning model extending traditional 2D convolutional neural networks, processes volumetric data, enabling the extraction of spatial features across three dimensions. Analysis reveals that ConvLSTM outperforms 3D-CNN in modeling upwelling data in the South Sea of Java. This is evidenced by lower Root Mean Square Error (RMSE) and Mean Absolute Error (MAE). The ConvLSTM method was then used for forecasting, and the results were validated with data obtained from local fishermen regarding their fishing expeditions. Visual analysis confirms that the ConvLSTM method accurately models upwelling data in the South Sea of Java with fishermen's schedules. ConvLSTM and 3D-CNN methods were comparatively evaluated for modeling Sea Surface Temperature (SST) data, considering wind speed, sea surface salinity, and the El Niño-Southern Oscillation (ENSO) phase as influential factors. Based on Root Mean Square Error (RMSE) and Mean Absolute Error (MAE) values, the ConvLSTM method exhibited lower values, indicating superior performance compared to the 3D-CNN approach. Specifically, RMSE and MAE values for ConvLSTM were 0.4161 and 0.3017, respectively, while for 3D-CNN, the corresponding values were 0.6095 and 0.4259. Upwelling data forecasting results were validated against local fishermen's schedules, with data collected in July 2022. Visual inspection confirmed alignment between the forecasted upwelling patterns and the fishermen's activity.

MSC secretomes as a cell-free therapeutic platform: molecular heterogeneity, disease-specific bioactivity, delivery strategies, and regulatory translation across six major disease areas.

Prostate cancer (PCa) is in the top three most common cancers among the world's male population, and its incidence has been increasing over the years. However, the primary screening and diagnostic tools still rely on serum prostate-specific antigen (PSA) and digital rectal examination (DRE), both of which have been inconclusive. Raised serum PSA and abnormal DRE findings require an invasive prostate biopsy, which has inherent surgical risk. This review aims to provide a comprehensive understanding of the biological production and properties of extracellular vesicles (EVs), which are released by all cell types, including cancer cells, and carry proteins and other biomolecules from their parent cells. EVs are becoming increasingly popular as possible biomarker candidates to improve the accuracy of diagnosing many diseases. Growing data suggest that EVs are crucial for cellular communication and tumour progression via multiple signalling pathways, including epithelial-to-mesenchymal transition (EMT), migration, and invasion, making them suitable for tracking PCa growth and metastasis. Furthermore, choosing the appropriate EV isolation method is essential to ensure accurate diagnosis. More clinically relevant, this review also identifies potential EV protein biomarkers derived from urine, serum, and tissue samples from PCa patients.

Prepectoral direct-to-implant (DTI) breast reconstruction is commonly performed with adjunct implant support products to optimize surgical outcomes. While products that provide breast implants with positional support are utilized with increasing frequency, a dearth of rigorous studies comparing synthetic to biologic products remains. We sought to compare outcomes of two implant support strategies: acellular dermal matrix (ADM) alone for total anterior implant coverage versus ADM and resorbable mesh (GalaFLEX™) for complete implant coverage. A retrospective cohort design was utilized to compare the surgical costs and complications (primary clinical outcome of interest - implant malposition) among patients undergoing immediate prepectoral DTI breast reconstruction with either ADM alone or ADM + GalaFLEX™ between 2019 and 2024. All patients received smooth, round, silicone implants. Outcomes at 6 months postoperatively were analyzed. 170 breasts underwent DTI reconstruction with ADM alone and 168 breasts with ADM + GalaFLEX™. Patients with ADM + GalaFLEX™ had significantly lower rates of implant malposition (1.8% vs 7.1%, p=0.031). On survival analysis, the chance of malposition with ADM alone was found to be 7.7 times higher than with ADM + GalaFLEX™. Despite these findings, revision surgery frequency was no different between groups. When comparing ADM + GalaFLEX™ to ADM alone, index operating room costs were significantly less in the ADM + GalaFLEX™ cohort. Utilizing ADM + GalaFLEX™ for complete implant coverage in immediate prepectoral DTI breast reconstruction is associated with lower cost and a decreased incidence of implant malposition compared to total anterior coverage with ADM alone.

Conventional sulfuric acid production is tied heavily to the fossil fuel industry, where it is typically obtained from the desulfurization of fuels. Here, the biological production of sulfuric acid by Acidithiobacillus thiooxidans in a reactor setup was optimized using design of experiments methodology. The effects of initial sulfur dosage, phosphate (PO43-) concentration, and inoculum size were evaluated with respect to sulfate (SO42-) concentration, optical density, and pH. A significant effect was observed for sulfur dosage; the highest sulfur supplementation, 35 g L-1, yielded the highest SO42- concentration and lowest pH after 14 days of cultivation. A mean sulfur-to-SO42- conversion rate of 81 ± 9% was determined across all trials conducted with35gL-1 of sulfur. Among all trials, a maximum SO42- molarity of 1.08 M was achieved, with a corresponding pH of 0.18. No significanteffects were determined for PO43- and inoculum volume. The feasibility of using an industrial by-product as a sulfur source was demonstrated, in addition to establishing a strong correlation between the measured SO42- concentration and conductivity of the biological lixiviant. KEY POINTS: • Sulfur dosage correlated positively with SO42- concentration. • DoE revealed no significant effect for PO43- concentration and inoculum size. • Strong correlation between SO42- concentration and conductivity was established.

Bispecific antibodies are a growing class of therapeutics that simultaneously engage two targets. However, their complex molecular structures pose challenges for production in Chinese hamster ovary cells, the current industry standard for biologics manufacturing. Here we present a case study of three IgG-scFv format bsAbs expressed in CHO cells, in which one candidate exhibited markedly lower titers despite high sequence homology to the other two. Using multi-omics analysis (RNA sequencing, splicing prediction, codon optimization assessment, and motif screening) to investigate potential causes, we identified several likely mechanisms for poor expression, including aberrant splicing motifs, ribosome pausing sites, and suboptimal codon usage. Through targeted protein and DNA sequence engineering, we generated a revised variant with an 11-fold increase in stable expression titers. This work demonstrates that integrating sequence-level bioinformatic and synthetic biology diagnostics can directly improve manufacturability, providing a generalizable framework for resolving hidden expression liabilities in complex biologics.

Mannose constitutes a principal component in numerous biomass hemicelluloses; however, its utilization by the cellulose-producing bacterium Komagataeibacter xylinus is inefficient. Consequently, during biorefinery and the transformation of biomass rich in mannose for the production of the high-value biological product, bacterial cellulose (BC), the biomass components cannot be fully utilized, leading to resource wastage. Moreover, inappropriate discharge of the fermentation effluent may also result in environmental pollution. This study addressed the underutilization of mannose in spent coffee grounds (SCGs) by introducing a fusion vector expressing mannokinase and phosphomannose isomerase into K. xylinus ATCC 23770, thereby enhancing mannose utilization in this strain model. SCG was pretreated with concentrated sulfuric acid to disrupt crystalline structures, followed by enzymatic hydrolysis to extract saccharides. When culturing in SCG hydrolysate, BC pellicle-derived inoculum achieved 1.2-fold higher BC yield than broth inoculum, attributed to BC matrix protection. The engineered strain K. xylinus CGMCC 31806 demonstrated superior mannose assimilation, yielding 1.5-fold more BC than wild type in simulated SCG medium. In authentic SCG medium without extra nitrogen addition, BC production reached 3.80 g/L, a 1.2- to 2.5-fold increase. The obtained BC exhibited enhanced mechanical properties with 40-84% higher tensile strength and 20-75% increased Young's modulus. This study validates a dual strategy combining agro-waste valorization and targeted strain modification, establishing a collaborative optimization framework linking biomass feedstocks, microbial engineering, and bioprocessing for cost-effective BC production. Future research would utilize existing commercial high-yield strains to replicate the expression strategy of this fusion protein, in order to achieve truly efficient industrial production.IMPORTANCEThe inefficient utilization of mannose, a major hemicellulose component prevalent in biomass by Komagataeibacter xylinus represents a significant bottleneck in the sustainable, cost-effective bioproduction of bacterial cellulose (BC). This underutilization would lead to wasted resources and potential environmental pollution from fermentation effluents. The study directly addresses this critical challenge by pioneering a synergistic "Feedstock-Strain-Process" integration strategy in advancing BC industrialization. We demonstrate the significant impact of engineering K. xylinus for enhanced mannose assimilation coupled with optimized biorefinery of agro-industrial waste, taking mannose-rich spent coffee grounds, as the representative raw material. This integrated approach not only valorizes abundant agricultural waste streams significantly boosting BC yields under nutrient-limited conditions but also generates BC with superior mechanical properties. The study establishes an actionable blueprint for advancing BC industrialization through collaborative optimization of biomass feedstocks, targeted microbial engineering, and process innovation, aligning with the goals of the circular bioeconomy and sustainable material production.

Biological CO2-capture technologies, such as biogas upgrading, constitute essential tools toward decarbonization of the chemical and energy industries. Biological succinic acid production is one such process that naturally fixes CO2 while producing an important platform chemical for the chemical and food industries. However, the high costs associated with biosuccinic acid production render it economically uncompetitive compared to petrochemically produced succinic acid. Here, we propose an integrated platform combining fermentation for succinic acid production from industrial waste streams with the successful upgrade of raw biogas from anaerobic digestion, which repurposes the process into a multi-product platform for increasing its economic viability. To reduce downstream separation costs, the fermentation process is also coupled with an in situ separation module that increases the performance of both the succinic acid fermentation and the biogas upgrade, reaching a CH4 percentage of 93% in the final biogas and triggering a 32.5% increase in succinic acid production. Moreover, the use of the electrochemical module aids in the separation of succinic acid from the fermentation broth, resulting in 94.80% recovery of the succinic acid produced. All experiments were performed at semi-pilot scale.

Abstract. The Levantine Basin is an ultra-oligotrophic region and the formation site of Levantine Intermediate Water. A high-resolution 3D coupled hydrodynamic-biogeochemical model (SYMPHONIE-Eco3MS) was used to investigate the seasonal and interannual variability of dissolved oxygen (O2) in the Levantine Basin and to estimate its basin-wide budget over the period 2013–2020. The model results show a pronounced seasonal cycle of air–sea exchanges. During winter, cooling and vertical mixing induce an undersaturation in oxygen of the surface layer by up to 2 % across the entire basin, leading to atmospheric oxygen absorption. In contrast, during the stratified period, primary production and warming induce a slight oversaturation and subsequent oxygen release to the atmosphere. The annual budget over the 7-year period shows that the basin acts as a net sink for atmospheric oxygen. The oxygen budget analyses further indicate that the surface layer (0–150 m) acts as a source of dissolved oxygen for intermediate depths through winter vertical export, whose amplitude is significantly governed by the magnitude of heat fluxes. At the basin and annual scale, we estimate a net lateral oxygen input into the basin from the Ionian Sea and a net export towards the Aegean Sea, with this lateral export at both surface and intermediate layers enhanced when winter heat loss is intense. Biogeochemically, the Levantine Basin alternates between autotrophic and heterotrophic states on an annual basis, depending on the intensity of winter surface heat loss. Spatially, the Rhodes Gyre, a quasi-permanent cyclonic structure and major site of intermediate water formation, emerges as a significant oxygen pump in winter, with annual uptake rates twice as high as the rest of the Levantine Basin, and shows enhanced biological production during the productive season, contributing to 41 % of the net annual oxygen production in the surface layer in the basin. This study highlights the need for further modeling studies on pluri-annual and multi-decadal scales to explore interannual variability and evolution of the annual oxygen budget across the entire Eastern Basin, particularly in the context of climate change.

Chinese hamster ovary (CHO) cells serve as the backbone of modern large-scale manufacturing of monoclonal antibodies. Central to this process are fed-batch cultures, where cells are grown from low to high cell densities and go through a mAb production phase. Despite CHO cells' widespread usage and vital role in the production of biologics, the cellular states during fed-batch coinciding with high specific productivity and apoptosis are poorly understood. Crucial to this understanding is a clear depiction of the various subpopulations of cells that exist in a fed-batch culture over time. In this work, an Ovizio iLine F PRO was used to image the cells in benchtop bioreactors and gather morphological and optical information for several CHO cell lines. A cluster analysis was applied to the Ovizio iLine F PRO raw data, revealing a diverse set of cellular sub-populations within each culture. Raw data from the Ovizio were then transformed into tank-level data and applied to offline measurements for viability and apoptosis in regression analysis. We used the results from the cluster analysis and feature averaging to set up regressions for offline measurements. Our regression analysis illustrates the power of in-line imaging of CHO cells as a rich process analytical tool.

Freezing and thawing of biologics in bottles and downscale modelling evaluation.

Evaluation of DMSO extraction efficiency compared to other solvents on representative polymeric materials used in biologics production.

Previously, we reported that netoglitazone, a thiadolidinedione, enhanced both adipogenesis and osteoblastogenesis, and that fatty acid synthase knockdown could selectively repress the adipogenic effect. Here, molecular evidence further demonstrated that pioglitazone enhanced osteoblastic differentiation at least through the protein kinase A/glycogen synthase kinase 3β signaling. (-)-Epigallocatechin gallate (EGCG), a fatty acid synthase inhibitor, selectively retained pioglitazone's pro-osteoblastic effect. Cultures of aged human bone marrow mesenchymal stem cells (bmMSCs) in alginate scaffolds revealed that pioglitazone and EGCG cooperatively enhanced osteoblastic differentiation, biological apatite production, and bone-like tissue maturation. These findings demonstrate that the combination of pioglitazone and EGCG is a promising strategy to enhance osteogenic performance in aged bmMSCs for the development of advanced bone graft materials.

High concentration subcutaneous biological drug products: challenges and advancements.

Unraveling spatiotemporal dynamics of dissolved organic phosphorus in an urban lake using FT-ICR MS and fluorescence spectroscopy.

Leveraging analytical and bioprocess platforms for biological product development and commercialization - A meeting report.