Proteome-wide prediction and analysis of the Cryptosporidium parvum protein-protein interaction network through integrative methods.

As one of the most studied Apicomplexan parasite Cryptosporidium, Cryptosporidium parvum (C. parvum) causes worldwide serious diarrhea disease cryptosporidiosis, which can be deadly to immunodeficiency individuals, newly born children, and animals. Proteome-wide identification of protein-protein interactions (PPIs) has proven valuable in the systematic understanding of the genome-phenome relationship. However, the PPIs of C. parvum are largely unknown because of the limited experimental studies carried out. Therefore, we took full advantage of three bioinformatics methods, i.e., interolog mapping (IM), domain-domain interaction (DDI)-based inference, and machine learning (ML) method, to jointly predict PPIs of C. parvum. Due to the lack of experimental PPIs of C. parvum, we used the PPI data of Plasmodium falciparum (P. falciparum), which owned the largest number of PPIs in Apicomplexa, to train an ML model to infer C. parvum PPIs. We utilized consistent results of these three methods as the predicted high-confidence PPI network, which contains 4,578 PPIs covering 554 proteins. To further explore the biological significance of the constructed PPI network, we also conducted essential network and protein functional analysis, mainly focusing on hub proteins and functional modules. We anticipate the constructed PPI network can become an important data resource to accelerate the functional genomics studies of C. parvum as well as offer new hints to the target discovery in developing drugs/vaccines.

Deep Learning-Powered Prediction of Human-Virus Protein-Protein Interactions.

Identifying human-virus protein-protein interactions (PPIs) is an essential step for understanding viral infection mechanisms and antiviral response of the human host. Recent advances in high-throughput experimental techniques enable the significant accumulation of human-virus PPI data, which have further fueled the development of machine learning-based human-virus PPI prediction methods. Emerging as a very promising method to predict human-virus PPIs, deep learning shows the powerful ability to integrate large-scale datasets, learn complex sequence-structure relationships of proteins and convert the learned patterns into final prediction models with high accuracy. Focusing on the recent progresses of deep learning-powered human-virus PPI predictions, we review technical details of these newly developed methods, including dataset preparation, deep learning architectures, feature engineering, and performance assessment. Moreover, we discuss the current challenges and potential solutions and provide future perspectives of human-virus PPI prediction in the coming post-AlphaFold2 era.

Artificially Increasing Cortical Tension Improves Mouse Oocytes Development by Attenuating Meiotic Defects During Vitrification.

Oocyte cryopreservation demonstrates great benefits in the conservation of animal germplasm resources and assisted reproductive technology. However, vitrification causes damages in oocytes, which would lead to the decrease of oocyte quality, and embryonic development post fertilization. Cytoskeleton plays an important role in regulating cell shape, organelle migration, cell division and mechanical signal transduction. Cortical tension is a reflection of the physiological state and contractile ability of cortical cytoskeleton. Appropriate cortical tension is prerequesite for normal oocyte meiosis. In the present study, oocyte cortical tension was examined by evaluating the levels of cortical tension-related protein pERM (Phospho-Ezrin/Radixin/Moesin) and pMRLC (Phospho-Myosin Light Chain 2). We found that the cortical tension of vitrified oocytes was decreased. Increasing cortical tension of vitrified oocytes by adding 10 µg/ml ConA during in vitro culture could significantly improve the polar body extrusion rate and embryo development. Furthermore, increasing the cortical tension could improve spindle positioning, maintain kinetochore-microtubule (KT-MT) attachment, strengthen spindle assembly checkpoint (SAC) activity, and reduce the aneuploidy rate in vitrified oocytes. In conclusion, vitrification induced a remarkable decrease in cortical tension, and increasing the cortical tension could rescue the meiosis defect and improve oocyte quality.

Transcriptomic comparison of ovarian granulosa cells between adult sheep and prepubertal lambs.

BACKGROUND: The oocyte development ability of prepubertal animals is significantly lower than that of adult animals. Granulosa cells (GCs) have an important function on regulation of follicular and oocyte development. Therefore, analysis of GC characteristics can be used to explore the developmental mechanism of follicles and oocytes. RESULTS: In order to understand the possible reasons for the differences in follicle and oocyte development between lambs and adult sheep, we utilized high-throughput sequencing technique to analyze the transcriptome of GCs from follicle-stimulating hormone (FSH) superstimulated adult ewes and prepubertal lambs. Adult ewes were treated with FSH for 3 days (group A) and lambs were FSH-treated for 2 days (group B) or 3 days (group C). Transcriptome analysis of GCs showed that there were 405 and 159 differentially expressed genes from A vs. B and A vs. C, respectively. The results indicated that prolonging the FSH-treatment of lambs made the GC state of lambs more similar to the adult ewes, but there were still a large number of differentially expressed genes between adult ewes and lambs. Further analysis showed that many differently expressed genes were implicated in cell proliferation and apoptosis, oocyte development and follicular ovulation. Cellular examination demonstrated that fatty acid binding protein 4 (FABP4), which was highly expressed in lamb GCs, had a potential of promoting cell apoptosis. Cytoplasmic phospholipase A2 (PLA2G4A), which was expressed lowly in lamb GCs, may be responsible for reduced synthesis of prostaglandins in cells and impaired follicle/oocyte development. In contrast, glutathione S-transferase ß-1 (GSTT2B) and forkhead boxO6 (FOXO6) had no apparent effect on the proliferation and apoptosis of GCs. CONCLUSIONS: Our study found dramatic transcriptomic differences in GCs between lambs and adult sheep, which may explain the possible reasons for the defects of follicle and oocyte development in lambs compared to adult sheep. Our data provides important information for further understanding the mechanism of follicular development in prepubertal animals and improving their oocyte developmental competence.

Simultaneous Efficient Decontamination of Bacteria and Heavy Metals via Capacitive Deionization Using Polydopamine/Polyhexamethylene Guanidine Co-deposited Activated Carbon Electrodes.

The contamination of pathogenic micro-organisms and heavy metals in drinking water sources poses a serious threat to human health, which raises the demand for efficient water treatments. Herein, multi-functional capacitive deionization (CDI) electrodes were developed for the simultaneous decontamination of bacteria and heavy metal contaminants. Polyhexamethylene guanidine (PHMG), an antibacterial polymer, was deposited on the surface of the activated carbon (AC) electrode with the assistance of mussel-inspired polydopamine (PDA) chemistry. The main characterization results proved successful co-deposition of PDA and PHMG on the AC electrode, forming a hydrophilic coating layer in one step. Electrochemical analyses indicated that the AC-PDA/PHMG electrodes presented satisfactory capacitive behaviors, with outstanding salt adsorption capacity and cycling stability. The modified electrodes also exhibit excellent disinfection performance and heavy metal adsorption performance. The bacterial elimination rate of co-deposited electrodes grew along with the increase in the PHMG content. Particularly, AC-PDA/PHMG2 electrodes successfully removed and deactivated 99.11% Escherichia coli and 98.67% Pseudomonas aeruginosa (104 CFU mL-1) in water within 60 min. Furthermore, three flow cells made by AC-PDA/PHMG2 electrodes connected in series achieved efficient removal of salt, heavy metals such as lead and cadmium, and bacteria simultaneously, which indicated that the adsorption performance is significantly improved compared with pristine AC electrodes. These results denote the enormous potential of this one-step prepared multi-functional electrodes for facile and effective water purification using CDI technology.

General One-Pot Method for Preparing Highly Water-Soluble and Biocompatible Photoinitiators for Digital Light Processing-Based 3D Printing of Hydrogels.

We report a facile but general method to prepare highly water-soluble and biocompatible photoinitiators for digital light processing (DLP)-based 3D printing of high-resolution hydrogel structures. Through a simple and straightforward one-pot procedure, we can synthesize a metal-phenyl(2,4,6-trimethylbenzoyl)phosphinates (M-TMPP)-based photoinitiator with excellent water solubility (up to ∼50 g/L), which is much higher than that of previously reported water-soluble photoinitiators. The M-TMPP aqueous solutions show excellent biocompatibility, which meets the prerequisite for biomedical applications. Moreover, we used M-TMPP to prepare visible light (405 nm)-curable hydrogel precursor solutions for 3D printing hydrogel structures with a high water content (80 wt %), high resolution (∼7 µm), high deformability (more than 80% compression), and complex geometry. The printed hydrogel structures demonstrate great potential in flexible electronic sensors due to the fast mechanical response and high stability under cyclic loadings.

The pollination ecology of Paraboea rufescens (Gesneriaceae): a buzz-pollinated tropical herb with mirror-image flowers.

BACKGROUND AND AIMS: Gesneriaceae is a pantropical plant family with over 3000 species. A great variety of pollination mechanisms have been reported for the neotropical members of the family, but the details of buzz-pollination and enantiostyly for the family have not been described. We investigated the floral biology and pollination ecology of Paraboea rufescens in Xishuangbanna, south-west China, considering three aspects: (1) the type of enantiostyly exhibited; (2) whether the species is self-compatible; and (3) whether pollinator behaviour could enhance the precision of pollen transfer between flowers of contrasting stylar orientation. METHODS: Flowering phenology was monitored once a month during vegetative growth, and once a week during flowering both in the field and under cultivation. Pollination manipulations and pollinator observation in the field were conducted. KEY RESULTS: Anthesis occurred early during the morning, and flowers remained open for 1-5 d, depending on weather conditions. Controlled pollinations revealed that P. rufescens is self-compatible, and exhibited inbreeding depression in seed set. Plants were pollinator limited in natural populations. The similar stylar deflection among flowers within a plant limits autonomous self-pollination as well as pollination between flowers. Two species of bumble bees (Bombus spp.), Amegila malaccensis and Nomia sp. effectively pollinated P. rufescens. These pollinators visited flowers in search of pollen with almost the same frequency. None of the pollinators appeared to discriminate between left- or right-handed flowers. CONCLUSIONS: Paraboea rufescens exhibits monomorphic enantiostylous flowers and a buzz-pollination syndrome. Floral morphology in P. rufescens and pollinator foraging behaviour seems likely to reduce self-pollination and pollinations between flowers of the same stylar deflection.

The floral biology of Curcumorpha longiflora (Zingiberaceae): a ginger with two-day flowers.

Curcumorpha longiflora is a perennial chasmophyte (rock fissure plant) ginger that usually grows in crevices of calcareous rocks and forms patches on the understory of limestone monsoon rainforests. The pollination ecology of C. longiflora was studied by monitoring phenology and flowering behavior, observing pollinator activity (frequency and behavior of visitors), and the quantity and quality of pollination services. We also investigated the germination of pollen grains and growth of pollen tubes after different pollination treatments to detect its breeding system. Based on the results: (1) for the first time in Zingiberaceae a new protandrous mechanism was found with a two-day flowering to avoid autogamy in this species; (2) under field conditions, all individuals of C. longiflora usually produced only one flower every other day to keep geitonogamy to a minimum; (3) germination of pollen grains and growth rates of pollen tubes under different pollination treatments were the same 4 h later after pollination, suggesting that C. longiflora is completely self-compatible; (4) among the limited visitors, Bombus sp. and Apis florae were effective pollinators, but they were active at different times and at different stages of the flower, probably receiving different rewards.