POSEIDON: Peptidic Objects SEquence-based Interaction with cellular DOmaiNs: a new database and predictor

Cell-penetrating peptides (CPPs) are short chains of amino acids that have shown remarkable potential to cross the cell membrane and deliver coupled therapeutic cargoes into cells. Designing and testing different CPPs to target specific cells or tissues is crucial to ensure high delivery efficiency and reduced toxicity. However, in vivo/in vitro testing of various CPPs can be both time-consuming and costly, which has led to interest in computational methodologies, such as Machine Learning (ML) approaches, as faster and cheaper methods for CPP design and uptake prediction. However, most ML models developed to date focus on classification rather than regression techniques, because of the lack of informative quantitative uptake values. To address these challenges, we developed POSEIDON, an open-access and up-to-date curated database that provides experimental quantitative uptake values for over 2,300 entries and physicochemical properties of 1,315 peptides. POSEIDON also offers physicochemical properties, such as cell line, cargo, and sequence, among others. By leveraging this database along with cell line genomic features, we processed a dataset of over 1,200 entries to develop an ML regression CPP uptake predictor. Our results demonstrated that POSEIDON accurately predicted peptide cell line uptake, achieving a Pearson correlation of 0.87, Spearman correlation of 0.88, and r2 score of 0.76, on an independent test set. With its comprehensive and novel dataset, along with its potent predictive capabilities, the POSEIDON database and its associated ML predictor signify a significant leap forward in CPP research and development. The POSEIDON database and ML Predictor are available for free and with a user-friendly interface at https://moreiralab.com/resources/poseidon/ , making them valuable resources for advancing research on CPP-related topics. Scientific Contribution Statement: Our research addresses the critical need for more efficient and cost-effective methodologies in Cell-Penetrating Peptide (CPP) research. We introduced POSEIDON, a comprehensive and freely accessible database that delivers quantitative uptake values for over 2,300 entries, along with detailed physicochemical profiles for 1,315 peptides. Recognizing the limitations of current Machine Learning (ML) models for CPP design, our work leveraged the rich dataset provided by POSEIDON to develop a highly accurate ML regression model for predicting CPP uptake.

Performance evaluation of commercially available swabs for environmental monitoring: Uptake and release efficiency

Safety and the quality of products rely on proper cleanliness procedures and good manufacturing practices in the production environment. The use of swabs for the collection of samples from surfaces has been a common practice in industries, medicine and forensic studies. To accommodate these different purposes, many varieties of swabs have been introduced into the market, and it is important to assess the performance of these swabs before incorporating into an environmental monitoring procedure. The overall effectiveness of a swab is determined by two factors: the number of bacteria that a swab can uptake from a surface and the number of picked-up bacteria the swab can elute into a releasing buffer. This study evaluated the uptake efficiency and release efficiency of four different commercially available swabs: CleanFoam (Texwipes, USA), FLOQSwabs (Copan diagnostic Inc., USA), Hydraflock swabs (Puritan medical products, USA), and Cotton swabs. Cotton swabs showed the highest uptake efficiency (96.5 ± 1.9%), whereas CleanFoam swabs (57.9 ± 20.3%) showed the least. Both flocked (FLOQSwabs and Hydraflock) swabs showed over 80% uptake efficiency. Releasing efficiency of swabs was tested with eight different releasing buffers. Cotton swabs displayed the lowest release efficiency with most of the tested releasing buffers. When employed with Tris HEPES, Tris MOPS, Tris TAPS, FLOQSwabs, and Hydraflock swabs exhibited releasing efficiency of over 75%. The overall efficiency of the swabs was determined using TAPS as the releasing buffer and the values obtained were 80.4 ± 9.8%, 54.7 ± 16.9%, 35.0 ± 12.7% and 25.2 ± 6.9% for Hydraflock swabs, FLOQSwabs, Cotton swabs and Cleanfoam swabs, respectively.

Effect of phosphorus limitation on Se uptake efficiency in the microalga Nannochloropsis oceanica

Microalgae are considered an efficient accumulator and promising source of Se for feed additive purposes. This study aimed at investigating, for the first time, the effect of phosphorus limitation on Se accumulation and uptake efficiency in N.oceanica. A range of phosphorus concentrations (0-2470 µM) were tested in either the presence or absence of sodium selenite (0, 5, 30 µM). Se accumulation was increased up to 16-fold and Se uptake efficiency was increased up to 3.6-fold under phosphorus growth-limiting concentrations. N.oceanica was then cultivated in a 1.8L flat-panel photobioreactor in batch operation under two phosphorus growth-limiting concentrations (250 and 750 µM) where the accumulation of Se in the microalgal biomass, as well as its presence in the spent medium were analysed. This study is the first to investigate the effect of phosphorus limitation for increasing Se accumulation in microalgae, and to prevent the release of Se in wastewater.

Interaction of silicon and manganese in nutritional and physiological aspects of energy cane with high fiber content

BACKGROUND

Silicon (Si) is a multiple stress attenuator element in plants, however more research is needed to elucidate the actions in the plants defense system with low nutrition of manganese (Mn) for a prolonged period, and the attenuation mechanisms involved in the effects of Mn deficiency on energy cane with high fiber content. Thus, the objective of this study was to evaluate whether Si reduces the oxidative stress of the energy cane grown in low Mn in nutrient solution, to mitigate the effects of Mn deficiency, improving enzymatic and non-enzymatic defense, uptake of Mn the plant growth.

METHODS

An experiment was carried out with pre-sprouted seedlings of Saccharum spontaneum L. in a 2 × 2 factorial scheme in five replications in which the plants were grown under sufficiency (20.5 μmol L^-1) and deficiency (0.1 μmol L^-1) of Mn combined with the absence and presence of Si (2.0 mmol L^-1) for 160 days from the application of the treatments. The following parameters were evaluated: accumulation of Mn and Si, H₂O_2, MDA, activity of SOD and GPOX, total phenol content, pigments, and quantum efficiency of PSII.

RESULTS

Mn deficiency induced the oxidative stress for increase the H₂O₂ and MDA content in leaves of plants and reduce the activity of antioxidant enzymes and total phenols causing damage to quantum efficiency of photosystem II and pigment content. Si attenuated the effects of Mn deficiency even for a longer period of stress by reducing H₂O₂ (18%) and MDA (32%) content, and increased the Mn uptake efficiency (53%), SOD activity (23%), GPOX (76%), phenol contents, thus improving growth.

CONCLUSIONS

The supply of Si promoted great nutritional and physiological improvements in energy cane with high fiber content in Mn deficiency. The results of this study propose the supply of Si via fertirrigation as a new sustainable strategy for energy cane cultivation in low Mn environments.

Phytoremediation potential of Ulva ohnoi (Chlorophyta): Influence of temperature and salinity on the uptake efficiency and toxicity of cadmium

Ulva ohnoi is a green macroalga with fast growth and high rates of nitrogen and phosphorus absorption. Recently, this species has been recorded in several places with record green tide formation in some of them. Using molecular tools, we herein report the first occurrence of this species in Brazil and demonstrate its potential for phytoremediation in typical environmental concentrations of Cd (0.625-15 µg L^-1). Similarly, the effects of physicochemical parameters (salinity and temperature) on the toxicity and uptake efficiency of this species were evaluated. Molecular analysis of two sequences (1141 bp) obtained corroborates another 34 sequences for U. ohnoi obtained from GenBank. The addition of Cd in the medium affected photosynthetic parameters and reduced growth rate. U. ohnoi showed resistance to Cd when cultivated at 18 °C, S15 and 18-25 °C, S35, at concentrations between 0.625 and 2.5 μg. L^-1 of Cd; yet, positive growth rate was maintained. Dose-dependent accumulation was observed in all combinations of factors used with a maximum value of 4.20 μg Cd per gram of dry seaweed at 15 μg. L^-1 of Cd at 18 °C and S35. Maximum value of the concentration factor was 81.3 ± 1.1% of Cd added at the concentration of 0.625 μg. L^-1 to S15 and 18 °C. Our results demonstrate the potential of using U. ohnoi in the phytoremediation of Cd in saltwater or brackish water.

Uptake Characterization of Tumor Cell-derived Exosomes by Natural Killer Cells

BACKGROUND

Cancer is the leading cause of death in human disease and is a major public health problem around the world. Exosomes are a promising cancer biomarker and therapy target. Recent evidence demonstrate that tumor cells could inhibit natural killer (NK) cells' immune surveillance function by releasing exosomes into tumor microenvironment. The intercelluar uptake of tumor cell-derived exosomes by NK cells is vital for using these exosomes in tumor diagnose and therapy. We aimed to investigate the efficiency of NK cell uptake of tumor exosomes.

METHODS

Exosomes derived from different tumor cells, RAW264.7 cells and NK cells were labeled by fluorescent dye and co-cultured with NK cells. The uptake rates of NK cells were observed by fluorescence microscope and analyzed by flow cytometry.

RESULTS

NK cells could take up more exosomes from themselves and cell lines originating from bone marrow. Epithelial cell lines can take up more exosomes from epithelial cells. There was no significant difference in uptake efficiency between Jurkat cells and RAW264.7 cells by NK cells, indicating that maybe the origin other than species affects the efficiency of recipient cell uptake of exosomes. Different tumor cells derived exosomes had different uptake efficiency by NK cells.

CONCLUSION

There is certain pattern of NK cells uptake tumor exosomes, which provide important insights on how tumors affect NK cells and develop appropriate countermeasures. In addition, it can be also helpful to select and design proper exosomes as a drug carrier in future.