AutoMolDesigner for Antibiotic Discovery: An AI-Based Open-Source Software for Automated Design of Small-Molecule Antibiotics.

Discovery of small-molecule antibiotics with novel chemotypes serves as one of the essential strategies to address antibiotic resistance. Although a considerable number of computational tools committed to molecular design have been reported, there is a deficit in holistic and efficient tools specifically developed for small-molecule antibiotic discovery. To address this issue, we report AutoMolDesigner, a computational modeling software dedicated to small-molecule antibiotic design. It is a generalized framework comprising two functional modules, i.e., generative-deep-learning-enabled molecular generation and automated machine-learning-based antibacterial activity/property prediction, wherein individually trained models and curated datasets are out-of-the-box for whole-cell-based antibiotic screening and design. It is open-source, thus allowing for the incorporation of new features for flexible use. Unlike most software programs based on Linux and command lines, this application equipped with a Qt-based graphical user interface can be run on personal computers with multiple operating systems, making it much easier to use for experimental scientists. The software and related materials are freely available at GitHub (https://github.com/taoshen99/AutoMolDesigner) and Zenodo (https://zenodo.org/record/10097899).

CO2-Sensitive Porous Magnet: Antiferromagnet Creation from a Paramagnetic Charge-Transfer Layered Metal-Organic Framework.

Porous magnets that undergo a magnetic phase transition in response to gaseous adsorbates are desirable for the development of sustainable sensing and memory devices. Familiar gases such as O2 and CO2 are one class of target adsorbates because of their close association with life sciences and environmental issues; however, it is not easy to develop magnetic devices that respond to these ubiquitous gases. To date, only three examples of gas-responsive magnetic phase transitions have been demonstrated: (i) from a ferrimagnet to an antiferromagnet, (ii) its vice versa (i.e., change of magnetic phase), and (iii) from a ferrimagnet to a paramagnet (i.e., erasure of the magnetic phase). However, the creation of a magnet, meaning the change from a nonmagnet to a magnet by O2 or CO2 gas adsorption and magnetic switching by this phenomenon have not yet been explored. Herein, we report a CO2-induced antiferromagnet modified from a paramagnetic charge-flexible layered compound, [{Ru2(2,4-F2PhCO2)4}2TCNQ(OEt)2] (1; 2,4-F2PhCO2- = 2,4-difluorobenzoate; TCNQ(OEt)2 = 2,5-diethoxy-7,7,8,8-tetracyanoquinodimethane), where three molar equivalents of CO2 was accommodated at a CO2 pressure of 100 kPa. The magnetic change originates from charge fluctuation due to the transfer of electrons moving from the electron-donor to the electron-acceptor unit or vice versa, resulting in a change in the electron distribution induced by CO2 adsorption/desorption in the donor-acceptor-type charge transfer framework. Owing to the reversible electronic state change upon CO2 adsorption/desorption, these magnetic phases are switched, accompanied by modification of the electrical conductivity, which is boosted by the CO2 accommodation. This is the first example of the creation of a CO2-responsive magnet, which is promising for novel molecular multifunctional devices.

Identification of the cuticle protein AccCPR2 gene in Apis cerana cerana and its response to environmental stress.

Cuticular proteins (CPs) are known to play important roles in insect development and defence responses. The loss of CP genes can lead to changes in insect morphology and sensitivity to the external environment. In this study, we identified the AccCPR2 gene, which belongs to the CPR family (including the R&R consensus motif) of CPs, and explored its function in the response of Apis cerana cerana to adverse external stresses. Our results demonstrated that AccCPR2 was highly expressed in the late pupal stage and epidermis, and the expression of AccCPR2 may be induced or inhibited under different stressors. RNA interference experiments showed that knockdown of AccCPR2 reduced the activity of antioxidant enzymes, led to the accumulation of oxidative damage and suppressed the expression of several antioxidant genes. In addition, knockdown of AccCPR2 also reduced the pesticide resistance of A. cerana cerana. The overexpression of AccCPR2 in a prokaryotic system further confirmed its role in resistance to various stresses. In summary, AccCPR2 may play pivotal roles in the normal development and environmental stress response of A. cerana cerana. This study also enriched the theoretical knowledge of the resistance biology of bees.

FGF2 positively regulates osteoclastogenesis via activating the ERK-CREB pathway.

Fibroblast growth factor 2 (FGF2) plays crucial roles in the growth and development of several tissues. However, its function in bone homeostasis remains controversial. Here, we found that exogenous FGF2 supplementation inhibited the mineralization of bone marrow stromal cells (BMSCs), at least partially, via up-regulating the gene expression of osteoclastogenesis. The FGF receptor (FGFR) allosteric antagonist SSR128129E modestly, whereas the FGFR tyrosine kinase inhibitor AZD4547 significantly antagonized the effects of FGF2. Mechanistically, FGF2 stimulated ERK phosphorylation, and the ERK signaling inhibitor PD325901 strongly blocked FGF2 enhancement of osteoclastogenesis. Moreover, the phosphorylation of CREB was also activated in response to FGF2, thereby potentiating the interaction of p-CREB with the promoter region of Rankl gene. Notably, FGF2-deficient BMSCs exhibited higher mineralization capability and lower osteoclastogenic gene expression. Correspondingly, FGF2-knockout mice showed increased bone mass and attenuated expression of osteoclast-related markers, which were associated with moderate inhibition of the ERK signaling. In conclusion, FGF2 positively regulates osteoclastogenesis via stimulating the ERK-CREB pathway. These findings establish the importance of FGF2 in bone homeostasis, hinting the potential use of FGF2/ERK/CREB specific inhibitors to fight against bone-related disorders, such as osteoporosis.

Characterization and genomic analysis of a Demerecviridae phage SP76 with lytic multiple-serotypes of Salmonella.

With the increase in antimicrobial resistance of Salmonella, phages have been paid more attention to as an alternative to antibiotics. In this study, a phage designated as SP76 was isolated from sewage. It can lyse several serotypes of Salmonella, including S. typhimurium (21/33), S. enteritidis (7/7), S. dublin (4/4), S. pullorum (2/2) and S. choleraesuis (1/2). SP76 showed a latent time of about 10 min, and maintained good lytic activity at a pH range of 3-10 and temperatures between 4 and 37 °C. Moreover, its optimal multiplicity of infection (MOI) was 0.0001. Based on the results of genomic sequence and analysis, SP76 was found to have a genome of 111,639 bp that encoded 166 predicted ORFs and belong to the Demerecviridae family, order Caudovirales. No virulence or lysogen formation gene clusters were identified in the SP76 genome. A pan-genome analysis based on 100 phages within the subfamily Markadamsvirinae indicated that SP76 had 23 core genes and 1199 accessory genes. We grouped the subfamily Markadamsvirinae and found that the main difference was in group III. In vitro bacteriostasis, experiments showed that the phage SP76 reduced planktonic bacteria by 1.52 log10 CFU/mL, and biofilms (24 h old) by 0.372 log10 CFU/mL, respectively. Thus, we isolated a safe and efficient phage that might be a good antibacterial agent.

Distinct molecular impact patterns of abamectin on Apis mellifera ligustica and Apis cerana cerana.

The effects of insecticides on bee health are a topic of intensive research. Although abamectin is toxic to bees, the molecular impact of abamectin needs to be clarified. Here, we found that Apis cerana cerana exhibited a higher mortality rate when exposed to abamectin than Apis mellifera ligustica. In addition, A. cerana cerana had markedly higher numbers of differentially expressed genes (DEGs), differentially expressed proteins (DEPs) and differentially expressed metabolites (DEMs) than A. mellifera ligustica during exposure to abamectin. These results indicate that abamectin exposure exerts stronger effects on A. cerana cerana than on A. mellifera ligustica. In addition, six DEGs, two DEPs and two DEMs overlapped between the two bee species under abamectin exposure; however, some genes or proteins from the zinc finger protein, superoxide dismutase and peroxiredoxin families and the energy metabolism pathway were only unregulated in A. cerana cerana, which indicates a significant difference in the impact of abamectin on the two bee species. Despite these differences, several of the same gene families, such as heat shock proteins, cytochrome P450, odorant-binding proteins and cuticle proteins, and pathways, including the carbohydrate metabolism, immune system, lipid metabolism, amino acid metabolism, sensory system, locomotion and development pathways, were influenced by abamectin exposure in both A. cerana cerana and A. mellifera ligustica. Together, our results indicate that abamectin causes adverse effects on bees and thus poses a risk to bee populations and that abamectin exposure affects A. cerana cerana more strongly than A. mellifera ligustica. These findings improve our understanding of the behavioural and physiological effects of abamectin on bees.

Identification and antioxidant capacity of 4-hydroxyphenylpyruvate dioxygenase (HPPD), a new favored herbicide target, in Apis cerana cerana.

4-Hydroxyphenylpyruvate dioxygenase (HPPD), a nonheme oxygenase, catalyzes the second step of the tyrosine catabolic pathway, which is shared by almost all aerobic life forms. This demonstrates its importance in aerobic biology. We isolated an HPPD homolog from Apis cerana cerana and named it AccHPPD. AccHPPD has an open reading frame (ORF) length of 900 bp and encodes a 299 amino acid protein that has a predicted molecular weight of 34.67 kDa and an isoelectric point of 6.27. Amino acid analysis showed that AccHPPD contained three conserved metal ion active sites, H-101, H-184 and E-267. Real-time fluorescence quantitative PCR (RT-qPCR) analysis showed that AccHPPD mainly existed in specific tissue sites, mainly high in the legs and in the thorax and epidermis, and in specific developmental stages, mainly adults. Under temperature, pesticide, heavy metal and ultraviolet (UV) radiation treatments, the expression level was downregulated, but under H2O2 treatment, the expression level was upregulated. Exogenous expression of the recombinant AccHPPD plasmid in E. coli enhanced the resistance to HgCl2 and H2O2. Inhibition of AccHPPD activity was demonstrated by the upregulation of the tyrosine content after feeding with the inhibitor 2-(2-nitro-4-trifluoromethyl benzoyl)-1,3-cyclohexanedione (NTBC). After silencing of AccHPPD, the activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) decreased, and the expression levels of AccBax- and AccCaspase8-related genes were upregulated. The antioxidant genes AccCAT, AccGSTZ1, AccGSTD, AccSOD2, AccTpx3, AccCYP4G11, AccGDTS4, AccGSTO2 and AccMSRA were all upregulated. These results suggest that AccHPPD may serve an integral function in the response of A. cerana cerana to oxidative stress.

The effects of Anisodamine-Tirofiban Combined Therapy in acute myocardial infarction treated with Percutaneous Coronary Intervention (PCI).

Objectives: To study the effects of anisodamine-tirofiban combined therapy on cardiac function and serological expression of serum NGF and ESM-1 in patients with acute myocardial infarction treated with percutaneous coronary intervention (PCI). Methods: Eighty patients with myocardial infarction treated in Cangzhou Medical College, Hebei, China from February 2015 to April 2017 were selected and divided into the control group and the research group according to the principle of random draw, 40 patients per group. The patients in the control group received symptomatic routine treatment, while the patients in the research group received anisodamine-tirofiban combined therapy on the top of symptomatic routine treatment. Differences between the two groups in TIMI flow grades, cardiac function, levels of NGF and ESM-1 and adverse response were observed. Results: The recovery of cardiac function in the research group was statistically significant with P value (p<0.05) and better than the control group in TIMI flow grades, myocardial perfusion capacity and cardiac function. The serological indicators in the research group had a higher level of NGF and a lower level of ESM-1 than the control group, and the differences were statistically significant (p<0.05). In terms of safety, neither group showed significant hepatorenal disorders. Conclusion: The combined treatment of anisodamine-tirofiban in patients with acute myocardial infarction after percutaneous coronary intervention (PCI) can recover NGF and ESM-1 related proteins, improve postoperative myocardial perfusion, and accelerate the recovery of cardiac function. It is worth promoting in clinic.

Identification of an MGST2 gene and analysis of its function in antioxidant processes in Apis cerana cerana.

MGST2 is a member of the MAPEG superfamily, which participates in LTC4 synthesis and plays important roles in the regulation of the oxidative stress pathway and some diseases. Here, we isolated a previously uncharacterized gene in Apis cerana cerana named AccMGST2 by reverse transcription-polymerase chain reaction. The biological characteristics of AccMGST2 were analyzed by bioinformatics. The amino acid sequence similarity between AccMGST2 and AmMGST2 of Apis mellifera reached 96.08%. The expression characteristics of AccMGST2 were explored in several tissues. The quantitative real-time polymerase chain reaction results showed that the AccMGST2 gene was highly expressed in the head and muscle and that AccMGST2 expression responded to oxidative stress caused by different abiotic stresses. AccMGST2 was silenced using RNA interference, which decreased the expression levels of some MAPK and antioxidant genes. Therefore, we conclude that AccMGST2 is involved in the regulation of oxidative stress in A. cerana cerana.

Correction: CSN6-TRIM21 axis instigates cancer stemness during tumorigenesis.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

CSN6-TRIM21 axis instigates cancer stemness during tumorigenesis.

BACKGROUND: Cancer stem cells (CSCs) are responsible for tumour initiation, metastasis and recurrence. However, the mechanism of CSC formation, maintenance and expansion in colorectal cancer (CRC) remains poorly characterised. METHODS: The role of COP9 signalosome subunit 6 (CSN6) in regulating cancer stemness was evaluated by organoid formation and limited dilution analysis. The role of CSN6-TRIM21-OCT1-ALDH1A1 axis in CSC formation was evaluated in vitro and in vivo. The association of CSN6, TRIM21 and ALDH1A1 expression was validated by a tissue microarray with 267 CRC patients. RESULTS: The results showed that CSN6 is critical for sphere formation and maintaining the growth of patient-derived organoids (PDOs). We characterised the role of CSN6 in regulating cancer stemness, which involves the TRIM21 E3 ubiquitin ligase, transcription factor POU class 2 homeobox 1 (OCT1) and cancer stem cell marker aldehyde dehydrogenase 1 A1 (ALDH1A1). Our data showed that CSN6 facilitates ubiquitin-mediated degradation of TRIM21, which in turn decreases TRIM21-mediated OCT1 ubiquitination and subsequently stabilises OCT1. Consequently, OCT1 stabilisation leads to ALDH1A1expression and promotes cancer stemness. We further showed that the protein expression levels of CSN6, TRIM21 and ALDH1A1 can serve as prognostic markers for human CRC. CONCLUSIONS: In conclusion, we validate a pathway for cancer stemness regulation involving ALDH1A1 levels through the CSN6-TRIM21 axis, which may be utilised as CRC molecular markers and be targeted for therapeutic intervention in cancers.

An ultrasensitive and simple assay for the Hepatitis C virus using a reduced graphene oxide-assisted hybridization chain reaction.

Hepatitis C virus (HCV) is a major cause of chronic liver disease, which affects 2-3% of the world population. Until now, the early detection of HCV has been a great challenge, especially for those who live in developing countries. In this study, we developed a novel and ultrasensitive assay for the detection of HCV RNA based on the reduced graphene oxide nanosheets (rGONS) and hybridization chain reaction (HCR) amplification technique. This detection system contains a pair of single fluorophore-labeled hairpin probes that can freely exist in the solution in the absence of target RNA. The introduction of target RNA can robustly trigger a HCR with the two probes and produce long nanowires containing a double-stranded structure. The weak adsorption to rGONS makes the long nanowires emit a strong fluorescence. Using this enzyme-free amplification strategy, we developed a new method for the HCV RNA assay with a detection limit of 10 fM, which is far more sensitive than the common GO-based fluorescence method. Furthermore, the new method exhibits high selectivity for the discrimination of perfectly complementary and mismatched sequences. Finally, the new method was successfully used as a HCV RNA assay in biological samples with a strong anti-interference capability in complicated environments. In summary, these remarkable characteristics of the new method highlight its potential use in a clinical sample primary screening.

The transcriptional factor Apt regulates neuroblast differentiation through activating CycE expression.

In Drosophila, the thoracic neuroblast 6-4 (NB6-4T) divides asymmetrically into a glial precursor and a neuronal precursor, while the abdominal neuroblast 6-4 (NB6-4A) divides symmetrically to produce two glial cells. The underlying mechanism by which NB6-4T and NB6-4A undergo distinct differentiation is still elusive. Here, we find that the transcription factor Apontic (Apt) exclusively expresses in NB6-4T cells and is involved in regulating NB6-4T differentiation. Loss of Apt results in neuronal precursor loss. Epistasis analysis shows that Apt controls NB6-4T differentiation through activating CycE expression. On the other hand, Gcm suppresses Apt expression in the NB6-4A cell, thus inhibiting CycE expression. Taken together, our findings reveal a Gcm-Apt-CycE axis that regulates neuroblast and glia cell differentiation.

Treatment of Hepatocellular Carcinoma with Tumor Thrombus with the Use of Iodine-125 Seed Strand Implantation and Transarterial Chemoembolization: A Propensity-Score Analysis.

PURPOSE: To evaluate the safety and efficacy of iodine-125 (125I) seed strand implantation in combination with transarterial chemoembolization for the treatment of hepatitis B-related unresectable hepatocellular carcinoma (HCC) with portal vein invasion. MATERIALS AND METHODS: From January 2013 to June 2016, 76 HCC patients with type II tumor thrombus were included in this single-center retrospective study. Twenty patients underwent 125I seed strand implantation combined with transarterial chemoembolization (group A; n = 20), while 56 patients underwent transarterial chemoembolization alone (group B; n = 56). The procedure-related and radiation complications were assessed. Overall survivals were compared by propensity-score analysis. RESULTS: The technique was successfully performed in all patients. The mean intended dose (r = 10 mm; z = 0; 240 days) was 62.6 ± 1.8 Gy. No grade 3 or 4 adverse events related to the procedure occurred in either group. After propensity-score-matching analysis, 19 patients were selected into each group, respectively. In the propensity-matching cohort, the median overall survival time was significantly longer in group A than in the group B (19 pairs; 28.0 ± 2.4 vs 8.7 ± 0.4 mo; P = .001). Treatment strategy, arterioportal shunt, and number of transarterial chemoembolization sessions were significant predictors of favorable overall survival time. CONCLUSIONS: 125I seed strand implantation combined with transarterial chemoembolization is a safe and effective treatment for HCC patients with portal vein invasion.

Evolutionarily conserved transcription factor Apontic controls the G1/S progression by inducing cyclin E during eye development.

During Drosophila eye development, differentiation initiates in the posterior region of the eye disk and progresses anteriorly as a wave marked by the morphogenetic furrow (MF), which demarcates the boundary between anterior undifferentiated cells and posterior differentiated photoreceptors. However, the mechanism underlying the regulation of gene expression immediately before the onset of differentiation remains unclear. Here, we show that Apontic (Apt), which is an evolutionarily conserved transcription factor, is expressed in the differentiating cells posterior to the MF. Moreover, it directly induces the expression of cyclin E and is also required for the G1-to-S phase transition, which is known to be essential for the initiation of cell differentiation at the MF. These observations identify a pathway crucial for eye development, governed by a mechanism in which Cyclin E promotes the G1-to-S phase transition when regulated by Apt.

Midline governs axon pathfinding by coordinating expression of two major guidance systems.

Formation of the neural network requires concerted action of multiple axon guidance systems. How neurons orchestrate expression of multiple guidance genes is poorly understood. Here, we show that Drosophila T-box protein Midline controls expression of genes encoding components of two major guidance systems: Frazzled, ROBO, and Slit. In midline mutant, expression of all these molecules are reduced, resulting in severe axon guidance defects, whereas misexpression of Midline induces their expression. Midline is present on the promoter regions of these genes, indicating that Midline controls transcription directly. We propose that Midline controls axon pathfinding through coordinating the two guidance systems.

Isolation, Structure Elucidation, and Absolute Configuration of Highly Oxygenated Germacranolides from Carpesium cernuum.

The new highly oxygenated germacranolides cernuumolides A-J (1-10) and the known compounds 11-20 were isolated from Carpesium cernuum. Among these compounds, 1-4 are 11-methoxymethylgermacranolides and 5-7 as well as 11-17 are 2,9-hemiacetal-linked germacranolides. Their structures were elucidated using NMR and HRESIMS analyses, and X-ray diffraction studies were used to confirm the absolute configurations of 1, 2, 5, 6, 8, and 9. Cernuumolides A-J were evaluated for their in vitro cytotoxicity against the A549, HCT116, MDA-MB-231, and BEL7404 cell lines, and 8 exhibited moderate cytotoxicity with IC50 values in the 0.87-2.02 µM range.

Gene coexpression networks reveal key drivers of phenotypic divergence in porcine muscle.

BACKGROUND: Domestication of the wild pig has led to obese and lean phenotype breeds, and evolutionary genome research has sought to identify the regulatory mechanisms underlying this phenotypic diversity. However, revealing the molecular mechanisms underlying muscle phenotype variation based on differentially expressed genes has proved to be difficult. To characterize the mechanisms regulating muscle phenotype variation under artificial selection, we aimed to provide an integrated view of genome organization by weighted gene coexpression network analysis. RESULTS: Our analysis was based on 20 publicly available next-generation sequencing datasets of lean and obese pig muscle generated from 10 developmental stages. The evolution of the constructed coexpression modules was examined using the genome resequencing data of 37 domestic pigs and 11 wild boars. Our results showed the regulation of muscle development might be more complex than had been previously acknowledged, and is regulated by the coordinated action of muscle, nerve and immunity related genes. Breed-specific modules that regulated muscle phenotype divergence were identified, and hundreds of hub genes with major roles in muscle development were determined to be responsible for key functional distinctions between breeds. Our evolutionary analysis showed that the role of changes in the coding sequence under positive selection in muscle phenotype divergence was minor. CONCLUSIONS: Muscle phenotype divergence was found to be regulated by the divergence of coexpression network modules under artificial selection, and not by changes in the coding sequence of genes. Our results present multiple lines of evidence suggesting links between modules and muscle phenotypes, and provide insights into the molecular bases of genome organization in muscle development and phenotype variation.

Metabolomic analysis reveals the potential metabolites and pathogenesis involved in mulberry yellow dwarf disease.

To analyse the molecular mechanisms of phytoplasma pathogenicity, the comprehensive metabolomic changes of mulberry leaf and phloem sap in response to phytoplasma infection were examined using gas chromatography-mass spectrometry. The metabolic profiles obtained revealed that the metabolite compositions of leaf and phloem sap were different, and phytoplasma infection has a greater impact on the metabolome of phloem sap than of leaf. Phytoplasma infection brought about the content changes in various metabolites, such as carbohydrates, amino acids, organic acids, etc. Meanwhile, the results of biochemical analysis showed that the degradation of starch was repressed, and the starch content was increased in the infected leaves. In addition, we found that phytoplasma infection changed the levels of abscisic acid and cytokinin and break phytohormone balance. Interestingly, our data showed that the contents of H2O2 and superoxide were increased in the infected leaves, but not in the phloem saps. Based on the results, the expression levels of the genes involved in the metabolism of some changed metabolites were examined, and the potential molecular mechanisms of these changes were discussed. It can be concluded that both the leaf and phloem saps have a complicated metabolic response to phytoplasma infection, but their response mechanisms were different.

[Current progress in functions of axon guidance molecule Robo and underlying molecular mechanism].

The axon guidance molecule Robo is a transmembrane protein which is conserved during evolution. Robo and its ligand, Slit, have been implicated in regulating many developmental processes, such as axon guidance, neuronal migration, tumor metastasis, angiogenesis, lung morphogenesis, kidney morphogenesis, heart morphogenesis, ovary development and gonad development. Robo function mainly depends on the binding of its Ig1 domain to the LRR-2 domain of Slit ligand. Meanwhile, Robo function is also mediated by binding to some signaling molecules, including the heparan sulfate proteoglycans (HSPGs), GTPase-activating proteins (GAPs) and tyrosine kinase Abelson. Several transcription factors, including Hox, Midline and Nkx2.9, were shown to regulate robo expression. In addition, alternative splicing and transport regulation also affect Robo function. In this review, we summarized the studies on the molecular structure, functions and molecular mechanism of Robo, which would propose a novel strategy for the research of neural development, as well as prevention and treatment of nervous system diseases and cancers.