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Abstract Trillions of microbes colonize the ungulate gastrointestinal tract, playing a pivotal role in enhancing host nutrient utilization by breaking down cellulose and hemicellulose present in plants. Here, through large-scale metagenomic assembly, we established a catalog of 131,416 metagenome-assembled genomes (MAGs) and 11,175 high-quality species-level genome bins (SGBs) from 17 species of ungulates in China. Our study revealed the convergent evolution of high relative abundances of carbohydrate-active enzymes (CAZymes) in the gut microbiomes of plateau-dwelling ungulates. Notably, two significant factors contribute to this phenotype: structural variations in their gut microbiome genomes, which contain more CAZymes, and the presence of novel gut microbiota species, particularly those in the genus Cryptobacteroides, which are undergoing independent rapid evolution and speciation and have higher gene densities of CAZymes. Furthermore, these enrichment CAZymes in the gut microbiomes are highly enrichment in known metabolic pathways for short-chain fatty acid (SCFA) production. Our findings not only provide a valuable genomic resource for understanding the gut microbiomes of ungulates but also offer fresh insights into the interaction between gut microbiomes and their hosts, as well as the co-adaptation of hosts and their gut microbiomes to their environments.

Aminoglycosides (AGs) are a class of antibiotics with a broad spectrum of activity. However, their use is limited by safety concerns associated with nephrotoxicity and ototoxicity, as well as drug resistance. To address these issues, semi-synthetic approaches for modifying natural AGs have generated new generations of AGs, however, with limited types of modification due to significant challenges in synthesis. This study explores a novel approach that harness the bacterial biosynthetic machinery of gentamicins and kanamycins to create hybrid AGs. This was achieved by glycodiversification of gentamicins via swapping the glycosyltransferase (GT) in their producer with the GT from kanamycins biosynthetic pathway and resulted in the creation of a series of novel AGs, therefore referred to as genkamicins (GKs). The manipulation of the hybrid biosynthetic pathway enabled the targeted accumulation of different GK species and the isolation and characterization of six GK components. These compounds display retained antimicrobial activity against a panel of World Health Organization (WHO) critical priority pathogens, and GK-C2a, in particular, demonstrates low ototoxicity compared to clinical drugs in zebrafish embryos. This study provides a new strategy for diversifying the structure of AGs and a potential avenue for developing less toxic AG drugs to combat infectious diseases.

This paper explores the design of safe coal (rock) pillars and the control effect of water pressure on roof water inrush in the “Code for Coal Pillar Retention and Coal Mining in Buildings, Water Bodies, Railways, and Main Tunnels”. Firstly, by analyzing the header text of Appendix 4–3 of the standard, it is pointed out that the relevant regulations on the thickness of the protective layer only apply to loose aquifers (including surface water bodies), and it is not clear how to determine the thickness of the protective layer for coal mining under bedrock aquifers; Furthermore, taking both mudstone and cohesive soil layers as bridges with water blocking function, it is inferred that coal mining under the bedrock aquifer can be carried out according to the condition that the cumulative thickness of cohesive soil layer under the loose layer is greater than the mining thickness. Following the principle of “high not low”, it is advisable to uniformly take four times the mining thickness as the protective layer under the bedrock aquifer; Since the applicable conditions of the specification are that the thickness of a single layer should not exceed 3.0 m, it is difficult to understand the provision in Appendix 4–3 that “the thickness of the loose layer is less than the thickness of the mining”, and it is recommended to delete it. Secondly, based on the scientific connotation of the term “protection”, the “protective layer” is redefined, which means that the waterproof rock layers between the top interface of the water conducting fracture zone and the bottom interface of the aquifer all have a “protection” function and should be collectively referred to as the protective layer (Hb); Furthermore, the concept of protection factor (Bs) was proposed, which refers to the ratio of the thickness of the protective layer to the thickness of a single layer of mining; The threshold for dividing the protection coefficient under the loose aquifer is Bi=(2, 3, 4, 5, 6, 7), and the threshold for dividing the protection coefficient under the bedrock aquifer is Bi=4. Based on this, the risk of roof water damage is classified into three levels: water inrush zone (Bs≤0), hazardous zone (0

Abstract Base editing (BE) faces protospacer adjacent motif (PAM) constraints and off-target effects in both eukaryotes and prokaryotes. For Streptomyces, renowned as one of the most prolific bacterial producers of antibiotics, the challenges are more pronounced due to its diverse genomic content and high GC content. Here, we develop a base editor named eSCBE3-NG-Hypa, tailored with both high efficiency and -fidelity for Streptomyces. Of note, eSCBE3-NG-Hypa recognizes NG PAM and exhibits high activity at challenging sites with high GC content or GC motifs, while displaying minimal off-target effects. To illustrate its practicability, we employ eSCBE3-NG-Hypa to achieve precise key amino acid conversion of the dehydratase (DH) domains within the modular polyketide synthase (PKS) responsible for the insecticide avermectins biosynthesis, achieving domains inactivation. The resulting DH-inactivated mutants, while ceasing avermectins production, produce a high yield of oligomycin, indicating competitive relationships among multiple biosynthetic gene clusters (BGCs) in Streptomyces avermitilis. Leveraging this insight, we use eSCBE3-NG-Hypa to introduce premature stop codons into competitor gene cluster of ave in an industrial S. avermitilis, with the mutant Δolm exhibiting the highest 4.45-fold increase in avermectin B1a compared to the control. This work provides a potent tool for modifying biosynthetic pathways and advancing metabolic engineering in Streptomyces.

Background: Circular RNAs (circRNAs) have significant roles in tumor progression. The role of circRNA derived from ARP2 actin-related protein 2 homolog (circACTR2) has been reported in various human diseases. However, the functions and regulatory mechanisms of circACTR2 in Bladder Cancer (BCa) remain unknown. Objectives: This study aims to explore the biological role and regulatory mechanism of circACTR2 in BCa. Methods: We analyzed the effects of circACTR2 on BCa through bioinformatics analyses, RT-qPCR, and cell function assays. Results: We observed the upregulation of circACTR2 in BCa tissues and validated its circular structure. Loss-of-function assays demonstrated that silencing circACTR2 suppressed the proliferation, invasion, and migration of BCa cells. Mechanistic investigation revealed that circACTR2 sponges miR-219a-2-3p to elevate the expression of the inhibitor of nuclear factor kappa B kinase subunit beta (IKBKB). This induced upregulation of IKKβ protein promoted the nuclear translocation of p65, thereby activating the NF-κB signaling pathway. Conclusions: Our findings indicate that circACTR2 promotes BCa cell proliferation, migration, and invasion by activating the NF-κB signaling pathway via the miR-219a-2-3p/IKBKB axis, potentially unveiling a new therapeutic target for BCa.

Introduction: Silicon is a major trace element in humans and a prospective supporting biomaterial to bone regeneration. Submicron silicon pillars, as a representative surface topography of silicon-based biomaterials, can regulate macrophage and osteoblastic cell responses. However, the design of submicron silicon pillars for promoting bone regeneration still needs to be optimized. In this study, we proposed a submicron forest-like (Fore) silicon surface (Fore) based on photoetching. The smooth (Smo) silicon surface and photoetched regular (Regu) silicon pillar surface were used for comparison in the bone regeneration evaluation.Methods: Surface parameters were investigated using a field emission scanning electron microscope, atomic force microscope, and contact angle instrument. The regulatory effect of macrophage polarization and succedent osteogenesis was studied using Raw264.7, MC3T3-E1, and rBMSCs. Finally, a mouse calvarial defect model was used for evaluating the promoting effect of bone regeneration on the three surfaces. Results: The results showed that the Fore surface can increase the expression of M2-polarized markers (CD163 and CD206) and decrease the expression of inflammatory cytokines, including interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α). Fore surface can promote the osteogenesis in MC3T3-E1 cells and osteoblastic differentiation of rBMSCs. Furthermore, the volume fraction of new bone and the thickness of trabeculae on the Fore surface were significantly increased, and the expression of RANKL was downregulated. In summary, the upregulation of macrophage M2 polarization on the Fore surface contributed to enhanced osteogenesis in vitro and accelerated bone regeneration in vivo.Discussion: This study strengthens our understanding of the topographic design for developing future silicon-based biomaterials.

Intermodular recognition in polyketide synthase (PKS) is a key prerequisite for catalysis and assembly-line engineering. Here, the authors present a specific domain interaction between modules and an evolution-oriented strategy for PKS engineering derived from the enoylreduction module of azalomycin F.

Pontania dolichura is a leaf-eating pest that mainly damages willow trees and is widely distributed in northern regions. In this study, we sequenced the entire mitochondrial genome of P. dolichura (GenBank accession number: MZ726800). The circular gene was 16,104 bp in length and comprised 38 column elements, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding control region. Most of the PCGs of P. dolichura have typical ATN (Met) start codons and typical TAN stop codons. The A + T contents of the genome, PCGs, transfer RNAs (tRNAs), and ribosomal RNAs (rRNAs) were 80.32%, 78.66%, 81.94%, and 82.59%, respectively. Phylogenetic analysis supported the close genetic relationship between P. dolichura and Mesoneura rufonota indicating that the two species share more recent common ancestor gene. These data will be useful for further molecular identification and population genetics studies.

Streptovaricin C is an antibiotic containing a methylenedioxy bridge (MDB) moiety essential for its activity. Here, the authors show that a P450 monooxygenase StvP2 catalyses MDB formation, report its crystal structure in complex with the substrate, and elucidate mechanistic details of MDB formation.

The African Swine Fever virus (ASFV) causes an infectious viral disease in pigs of all ages. The development of antiviral drugs primarily aimed at inhibition of proteases required for the proteolysis of viral polyproteins. In this study, the conformation of the pS273R protease in physiological states were investigated, virtually screened the multi-protein conformation of pS273R target proteins, combined various molecular docking scoring functions, and identified five potential drugs from the Food and Drug Administration drug library that may inhibit pS273R. Subsequent validation of the dynamic interactions of pS273R with the five putative inhibitors was achieved using molecular dynamics simulations and binding free energy calculations using the molecular mechanics/Poison-Boltzmann (Generalized Born) (MM/PB(GB)SA) surface area. These findings demonstrate that the arm domain and Thr159-Lys167 loop region of pS273R are significantly more flexible compared to the core structural domain, and the Thr159-Lys167 loop region can serve as a “gatekeeper” in the substrate channel. Leucovorin, Carboprost, Protirelin, Flavin Mononucleotide, and Lovastatin Acid all have Gibbs binding free energies with pS273R that were less than −20 Kcal/mol according to the MM/PBSA analyses. In contrast to pS273R in the free energy landscape, the inhibitor and drug complexes of pS273R showed distinct structural group distributions. These five drugs may be used as potential inhibitors of pS273R and may serve as future drug candidates for treating ASFV.

Determining the adaptive mechanisms by which bumblebees adapt to high altitudes can help us to better understand their distribution, providing a basis for the future protection and utilization of bumblebee resources. For this study, the adaptive mechanisms of two dominant bumblebee species in the northeastern Qinghai-Tibet Plateau—Bombus kashmirensis and B. waltoni—were studied through transcriptomics methods. For each species, enrichment analysis of the differentially expressed genes and gene set enrichment analysis were carried out between samples collected at different altitudes (4000 m, 4500 m, and 5000 m). The results indicate that these bumblebees tend to up-regulate energy metabolism-related genes when facing extremely high-altitude environments. Of the enriched pathways up-regulated in higher altitudes, the pentose and glucuronate interconversions pathway presented the most severe up-regulation in multiple comparisons of different altitudes for B. kashmirensis, as well as the AMPK signaling pathway, which was found to be up-regulated in both species. Notably, limited by the extreme hypoxic conditions in this study, oxidative phosphorylation was found to be down-regulated with increasing altitude, which is uncommon in studies on bumblebee adaptation to high altitudes.

Currently, selective laser melting (SLM) has been thriving in implant dentistry for on-demand fabricating dental implants. Based on the coarse microtopography of SLM titanium surfaces, constructing nanostructure to form the hierarchical micro-nano topography is effective in enhancing osseointegration. Given that current nanomodification techniques of SLM implants, such as anodization and hydrothermal treatment, are facing the inadequacy in costly specific apparatus and reagents, there has been no recognized nanomodified SLM dental implants. The present study aimed to construct hierarchical micro-nano topography on self-made SLM dental implants by a simple and safe inorganic chemical oxidation, and to evaluate its contribution on osteoblastic cells bioactivity and osseointegration. The surface chemical and physical parameters were characterized by FE-SEM, EDS, profilometer, AFM, and contact angle meter. The alteration on bioactivity of MG-63 human osteoblastic cells were detected by qRT-PCR. Then the osseointegration was assessed by implanting implants on the femur condyle of New Zealand Rabbits. The hierarchical micro-nano topography was constituted by the microrough surface of SLM implants and nanoneedles (diameter: 20∼50 nm, height: 150∼250 nm), after nanomodifying SLM implants in 30% hydrogen peroxide and 30% hydrochloride acid (volume ratio 1:2.5) at room temperature for 36 h. Low chemical impurities content and high hydrophilicity were observed in the nanomodified group. Cell experiments on the nanomodified group showed higher expression of mitophagy related gene (PINK1, PARKIN, LC3B, and LAMP1) at 5 days and higher expression of osteogenesis related gene (Runx2 and OCN) at 14 days. In the early stage of bone formation, the nanomodified SLM implants demonstrated higher bone-to-implant contact. Intriguingly, the initial bone-to-implant contact of nanomodified SLM implants consisted of more mineralized bone with less immature osteoid. After the cessation of bone formation, the bone-to-implant contact of nanomodified SLM implants was equal to untreated SLM implants and marketable TixOs implants. The overall findings indicated that the inorganic chemical oxidized hierarchical micro-nano topography could enhance the bioactivity of osteoblastic cells, and consequently promote the peri-implant bone formation and mineralization of SLM dental implants. This study sheds some light on improvements in additive manufactured dental implants.

Abstract Coptidis Rhizoma binds to the membrane receptors on hPDLSC/CMC, and the active ingredient Berberine (BER) that can be extracted from it may promote the proliferation and osteogenesis of periodontal ligament stem cells (hPDLSC). The membrane receptor that binds with BER on the cell surface of hPDLSC, the mechanism of direct interaction between BER and hPDLSC, and the related signal pathway are not yet clear. In this research, EGFR was screened as the affinity membrane receptor between BER and hPDLSC, through retention on CMC, competition with BER and by using a molecular docking simulation score. At the same time, the MAPK PCR Array was selected to screen the target genes that changed when hPDLSC was simulated by BER. In conclusion, BER may bind to EGFR on the cell membrane of hPDLSC so the intracellular ERK signalling pathways activate, and nuclear-related genes of FOS change, resulting in the effect of osteogenesis on PDLSC.

Objective: To explore the effects of Ziyu Ointment on granulation tissue, TGF-β and downstream Smad protein in the process of wound healing in rats by constructing a rat model of back trauma. Methods: A rat model of back trauma was constructed, and 100 SD male rats were separated into healthy group, back trauma group, Ziyu Ointment treatment group, petrolatum treatment group, Ziyu Ointment+TGF-β 1 activation group, with 20 per group. Wound formation surgery was performed, and wound healing of rats in each group was recorded at 5th, 10th, and 15th day after operation; the levels of IL-6, IL-1 β and TNF-α in the serum of rats in each group were detected; the granulation tissue formed by wound healing at 15th day was selected for HE and Masson staining, the proportion of blood vessel area and collagen area of granulation tissue of rats in each group were analyzed and calculated; the mRNA expression levels of TGF-β1 and Smad3 in granulation tissues of rats in each group were detected by fluorescence quantitative PCR; the expression levels of TGF-β1, Smad3 and p-Smad3 in granulation tissues of rats in each group were detected by Western blot. Results: The healthy group rats had complete epidermal tissue; the levels of serum IL-6, IL-1 β, TNF-α, the expression of TGF-β1 mRNA and protein in the wound granulation tissue, and the phosphorylation of Smad3 in the back trauma group were obviously higher than the healthy group (P<0.05) ; compared with back trauma group, the wound healing rate, proportion of collagen area, and proportion of blood vessel area in Ziyu Ointment treatment group and petrolatum treatment group were obviously increased, the serum IL-6, IL-1 β, TNF-α contents, TGF-β1 mRNA and protein expression, and Smad3 phosphorylation were obviously decreased (P<0.05) ; compared with Ziyu Ointment treatment group, the petrolatum treatment group, Ziyu Ointment+TGF-β1 activation group had obviously lower wound healing rate, collagen area percentage, and blood vessel area percentage, and obviously lower serum IL-6, IL-1β, TNF-α contents, TGF-β1 mRNA and protein expression and Smad3 phosphorylation (P<0.05). Conclusion: Ziyu Ointment can inhibit the expression of related genes and proteins by regulating the TGF-β/Smad signal pathway, thereby alleviating inflammation and promoting wound healing. [ABSTRACT FROM AUTHOR]

The optimal contraception dosing strategy proposed by Gavina et al. recently is a commendable attempt to model a complex physiological process with potenial to apply to real-life data. However, there is a need to take into account the real challenges that arise when moving from the theory to its practical application, and it is important that lessons learnt from clinical studies be taken into consideration in any theoretical modelling. In this manuscript, we spell out these lessons and elaborate practical challenges facing their model. [ABSTRACT FROM AUTHOR]