Screening and identification of linear B-cell epitopes on structural proteins of African Swine Fever Virus.

This study aims to screen and identify linear B-cell epitopes on the structural proteins of African Swine Fever Virus (ASFV) to assist in the development of peptide-based vaccines. In experiments, 66 peptides of 12 structural proteins of ASFV were predicted as potential linear B-cell epitopes using bioinformatics tools and were designed; the potential epitope proteins carried the GST tag were expressed, purified, and subjected to antigenicity analysis with porcine antiserum against ASFV, and further identified based on their immunogenicity in mice. A total of 22 potential linear B-cell epitopes showed immunoreactivity and immunogenicity. Of these epitopes, 13 epitopes were firstly identified including 4 epitopes located in p72 (352-363, 416-434, 424-439, 496-530 aa), 3 epitopes located in pE248R (121-136, 138-169, 158-185 aa), and only one epitope of each protein of pH108R (33-46 aa), p17 (63-86 aa), pE120R (65-117 aa), pE199L (175-189 aa), p12 (36-56 aa) as well as pB438L (211-230 aa). Notably, the immunoreactivity of the epitopes from the 63-86 aa of p17 and the 65-117 aa of pE120R were the highest amongst identified epitopes, while the immunogenicity of epitopes from the 36-56 aa of p12, the 211-230 aa of pB438L, the 352-363 aa of p72 and the 63-86 aa of p17 were the best strong. The other 9 epitopes are partly overlapped with previous researches. These epitopes identified here will further enrich the database of ASFV epitope, as well as help to develop safe, effective epitope-based ASF vaccines and ASF diagnostic reagents.

Spatio-temporal microbial regulation of aggregate-associated priming effects under contrasting tillage practices.

Tillage intensity significantly influences the heterogeneous distribution and dynamic changes of soil microorganisms, consequently shaping spatio-temporal patterns of SOC decomposition. However, little is known about the microbial mechanisms by which tillage intensity regulates the priming effect (PE) dynamics in heterogeneous spatial environments such as aggregates. Herein, a microcosm experiment was established by adding 13C-labeled straw residue to three distinct aggregate-size classes (i.e., mega-, macro-, and micro-aggregates) from two long-term contrasting tillage histories (no-till [NT] and conventional plow tillage [CT]) for 160 days to observe the spatio-temporal variations in PE. Metagenomic sequencing and Fourier transform mid-infrared techniques were used to assess the relative importance of C-degrading functional genes, microbial community succession, and SOC chemical composition in the aggregate-associated PE dynamics during straw decomposition. Spatially, straw addition induced a positive PE for all aggregates, with stronger PE occurring in larger aggregates, especially in CT soil compared to NT soil. Larger aggregates have more unique microbial communities enriched in genes for simple C degradation (e.g., E5.1.3.6, E2.4.1.7, pmm-pgm, and KduD in Nitrosospeera and Burkholderia), contributing to the higher short-term PE; however, CT soils harbored more genes for complex C degradation (e.g., TSTA3, fcl, pmm-pgm, and K06871 in Gammaproteobacteria and Phycicoccus), supporting a stronger long-term PE. Temporally, soil aggregates played a significant role in the early-stage PEs (i.e., < 59 days after residue addition) through co-metabolism and nitrogen (N) mining, as evidenced by the increased microbial biomass C and dissolved organic C (DOC) and reduced inorganic N with increasing aggregate-size class. At a later stage, however, the legacy effect of tillage histories controlled the PEs via microbial stoichiometry decomposition, as suggested by the higher DOC-to-inorganic N and DOC-to-available P stoichiometries in CT than NT. Our study underscores the importance of incorporating both spatial and temporal microbial dynamics for a comprehensive understanding of the mechanisms underlying SOC priming, especially in the context of long-term contrasting tillage practices.

In Silico Investigation of Palladium-Catalyzed Chemoselective Monoalkoxycarbonylation of 1,3-diynes for Conjugated Enynes Synthesis.

The palladium-catalyzed monoalkoxycarbonylation of 1,3-diynes provides a chemoselective method for the construction of synthetically useful conjugated enynes. Here, in silico unraveling the detailed mechanism of this reaction and the origin of chemoselectivity were conducted. It is shown that the alkoxycarbonylation reaction preferably proceeds by a NH-Pd pathway, which including three substeps: hydropalladation, CO migratory insertion and methanolysis. The effectiveness of the NH-Pd catalytic system is attributed to the alkynyl-palladium π-back-bonding interaction, C-H⋅⋅⋅π interaction in reactant moiety and d-pπ conjugation between the Pd center and alkenyl group. The hydropalladation step was identified as the rate- and chemoselectivity-determining step, and the first alkoxycarbonylation requires a much lower energy barrier in comparison with the second alkoxycarbonylation, in line with the experimental outcomes that the monoalkoxycarbonylation product was obtained in high yield. Distortion-interaction analysis indicates the more favorable monoalkoxycarbonylation (compared to double alkoxycarbonylation) is caused by steric effect.

Quantitative and modularized CRISPR/dCas9-dCpf1 dual function system in Saccharomyces cerevisiae.

Introduction: Both CRISPR/dCas9 and CRISPR/dCpf1 genome editing systems have shown exciting promises in modulating yeast cell metabolic pathways. However, each system has its deficiencies to overcome. In this study, to achieve a compensatory effect, we successfully constructed a dual functional CRISPR activation/inhibition (CRISPRa/i) system based on Sp-dCas9 and Fn-dCpf1 proteins, along with their corresponding complementary RNAs. Methods: We validated the high orthogonality and precise quantity targeting of selected yeast promoters. Various activating effector proteins (VP64, p65, Rta, and VP64-p65-Rta) and inhibiting effector proteins (KRAB, MeCP2, and KRAB-MeCP2), along with RNA scaffolds of MS2, PP7 and crRNA arrays were implemented in different combinations to investigate quantitative promoter strength. In the CRISPR/dCas9 system, the regulation rate ranged from 81.9% suppression to 627% activation in the mCherry gene reporter system. Studies on crRNA point mutations and crRNA arrays were conducted in the CRISPR/dCpf1 system, with the highest transcriptional inhibitory rate reaching up to 530% higher than the control. Furthermore, the orthogonal CRISPR/dCas9-dCpf1 inhibition system displayed distinct dual functions, simultaneously regulating the mCherry gene by dCas9/gRNA (54.6% efficiency) and eGFP gene by dCpf1/crRNA (62.4% efficiency) without signal crosstalk. Results and discussion: Finally, we established an engineered yeast cell factory for ß-carotene production using the CRISPR/dCas9-dCpf1 bifunctional system to achieve targeted modulation of both heterologous and endogenous metabolic pathways in Saccharomyces cerevisiae. The system includes an activation module of CRISPRa/dCas9 corresponding to a gRNA-protein complex library of 136 plasmids, and an inhibition module of CRISPRi/dCpf1 corresponding to a small crRNA array library. Results show that this CRISPR/dCas9-dCpf1 bifunctional orthogonal system is more quantitatively effective and expandable for simultaneous CRISPRa/i network control compared to single-guide edition, demonstrating higher potential of future application in yeast biotechnology.

Transcriptome analysis used to identify and characterize odorant binding proteins in Agasicles hygrophila (Coleoptera: Chryspmelidae).

The transcriptomes of Agasicles hygrophila eggs and first instar larvae were analyzed to explore the olfactory mechanism of larval behavior. The analysis resulted in 135,359 unigenes and the identification of 38 odorant-binding proteins (OBPs), including 23 Minus-C OBPs, 8 Plus-C OBPs, and 7 Classic OBPs. Further analysis of differentially expressed genes (DEGs) revealed 10 DEG OBPs, with 5 (AhygOBP5, AhygOBP9, AhygOBP12, AhygOBP15 and AhygOBP36) up-regulated in first instar larvae. Verification of expression patterns of these 5 AhygOBPs using qPCR showed that AhygOBP9 and AhygOBP36 were mainly expressed in the adult stage with gradually increasing expression in the larval stage. AhygOBP5, AhygOBP12, and AhygOBP15 were not expressed in eggs and pupae, and their expression in larvae and adults showed no clear pattern. These 5 AhygOBPs may play an olfactory role in larval behavior, providing a basis for further investigation of their specific functions and clarifying the olfactory mechanism of A. hygrophila.

Semiconducting Polymer Nanospherical Nucleic Acid Probe for Transcriptomic Imaging of Cancer Chemo-Immunotherapy.

Real-time in vivo imaging of RNA can enhance the understanding of physio-pathological processes. However, most nucleic acid-based sensors have poor resistance to nucleases and limited photophysical properties, making them suboptimal for this purpose. To address this, a semiconducting polymer nanospherical nucleic acid probe (SENSE) for transcriptomic imaging of cancer immunity in living mice is developed. SENSE comprises a semiconducting polymer (SP) backbone covalently linked with recognition DNA strands, which are complemented by dye-labeled signal DNA strands. Upon detection of targeted T lymphocyte transcript (Gzmb: granzyme B), the signal strands are released, leading to a fluorescence enhancement correlated to transcript levels with superb sensitivity. The always-on fluorescence of the SP core also serves as an internal reference for tracking SENSE uptake in tumors. Thus, SENSE has the dual-signal channel that enables ratiometric imaging of Gzmb transcripts in the tumor of living mice for evaluating chemo-immunotherapy; moreover, it has demonstrated sensitivity and specificity comparable to flow cytometry and quantitative polymerase chain reaction,  yet offering a faster and simpler means of T cell detection in resected tumors. Therefore, SENSE represents a promising tool for in vivo RNA imaging.

Physicochemical changes in microplastics and formation of DBPs under ozonation.

Microplastics (MPs) are substances that pose a risk to both human life and the environment. Their types and production are increasing year on year, and their potential to cause environmental pollution is a worldwide concern. Conventional water treatment processes, particularly coagulation and sedimentation, are not effective at removing all MPs. It is therefore important to assess the morphological changes in the MPs, i.e., the thermoplastic polyurethane (TPU) and polyethylene (PE), during ozonation and the dissolved organic carbon leaching as well as chloroform formation in the subsequent chlorination. The results show that the appearance and surface chemistry of the MPs changed during the ozonation process, most notably for TPU. The trichloromethane (CHCl3) generation during chlorination was 0.168 and 0.152 µmol/L for TPU and PE, respectively, and the ozone pretreatment significantly increased the CHCl3 yield of TPU, while it had a weak effect on PE. Additional disinfection byproducts (DBPs), including CHCl2Br, CHClBr2, and CHBr3, were produced in the presence of bromide ions in the water column, and the total amount of DBPs produced by PE, PE-O, TPU, and TPU-O was significantly increased to 0.787, 0.814, 0.931, and 1.391 µmol/L, respectively. The study provides useful information for the environmental risk assessment of two representative MPs, i.e., TPU and MPs, in disinfection procedures for drinking water.

The impact of chlorination on the tetracycline sorption behavior of microplastics in aqueous solution.

Considering the large volumes of treated water and incomplete elimination of pollutants, wastewater treatment plants (WWTPs) remain a considerable source of microplastics (MPs). Chlorine, the most frequently used disinfectant in WWTPs, has a strong oxidizing impact on MPs. However, little is documented, to date, about the impact of chlorination on the transformation of MPs and the subsequent environmental behaviors of the chlorinated MPs when released into the aquatic environment. This study explored the response of the physicochemical properties of specific thermoplastics, namely polyurethane (TPU) MPs and polystyrene (PS) MPs, to chlorination and their emerging pollutant [tetracycline (TC)] adsorption behavior in aqueous solution. The results indicated that the O/C ratio of the MP surface did not significantly change, and that there were increases in the O-containing functional groups of the TPU and PS MPs, after chlorination. The surface area of the chlorinated TPU MPs increased by 45 %, and that of the chlorinated PS increased by 21 %, compared with the pristine ones, which contributed to the TC adsorption. The adsorption isotherm fitting parameters suggested that the chlorinated TPU fitted the multilayer adsorption, and the chlorinated PS was inclined to the monolayer adsorption. The relative abundance of the O-containing functional groups, on the TPU surface, led to the release of CHCl3 molecules, and the clear surface irregularities and fissures occurred after chlorine treatment. No fissures were found on the surface of the chlorinated PS MPs. The hydrophobicity and electrostatic adsorption were proved to be the major impacts on the TC adsorption of the chlorinated MPs, and the subsequently formed hydrogen bonds led to the stronger adsorption capacity of the chlorinated TPU than the chlorinated PS MPs.

Autonomous Bionanorobots via a Cage-Shaped Silsesquioxane Vehicle for In Vivo Heavy Metal Detoxification.

Nanorobots hold great promise for integrated drug delivery systems that are responsive to molecular triggers. Herein, we successfully developed an automatic smart bionanorobot that has transport capability and recognizes and removes zinc ions from poisoned cells based on nanoscale polyhedral oligomeric silsesquioxane molecules. This intelligent bionanorobot can easily move inside and outside the cell and find zinc ions owing to its highly selective recognition to zinc ions and high cell permeability, especially the well-combined high penetration and strong binding energy. More importantly, it was also found that this intelligent bionanorobot can restore round HeLa cells to a normal fusiform cell morphology following high-concentration zinc treatment and does not interfere with cell proliferation and division. It was also shown by in vivo experiments that the bionanorobot can inhibit persistent enlargement of the liver caused by zinc ion poisoning.

Monitoring Wound Healing with Topically Applied Optical NanoFlare mRNA Nanosensors.

An effective wound management strategy needs accurate assessment of wound status throughout the whole healing process. This can be achieved by examining molecular biomarkers including proteins, DNAs, and RNAs. However, existing methods for quantifying these biomarkers such as immunohistochemistry and quantitative polymerase chain reaction are usually laborious, resource-intensive, and disruptive. This article reports the development and utilization of mRNA nanosensors (i.e., NanoFlare) that are topically applied on cutaneous wounds to reveal the healing status through targeted and semi-quantitative examination of the mRNA biomarkers in skin cells. In 2D and 3D in vitro models, the efficacy and efficiency of these nanosensors are demonstrated in revealing the dynamic changes of mRNA biomarkers for different stages of wound development. In mouse models, this platform permits the tracking and identification of wound healing stages and a normal and diabetic wound healing process by wound healing index in real time.