High Sensitivity of Ammonia Sensor through 2D Black Phosphorus/Polyaniline Nanocomposite

Recently, as a two-dimensional (2D) material, black phosphorous (BP) has attracted more and more attention. However, few efforts have been made to investigate the BP/polyaniline (PANI) nanocomposite for ammonia (NH3) gas sensors. In this work, the BP/PANI nanocomposite as a novel sensing material for NH3 detection, has been synthesized via in situ chemical oxidative polymerization, which is then fabricated onto the interdigitated transducer (IDTs). The electrical properties of the BP/PANI thin film are studied in a large detection range from 1 to 4000 ppm, such as conduction mechanism, response, reproducibility, and selectivity. The experimental result indicates that the BP/PANI sensor shows higher sensitivity and larger detection range than that of PANI. The BP added into PANI, that may enlarge the specific surface area, obtain the special trough structure for gas channels, and form the p–π conjugation system and p–p isotype heterojunctions, which are beneficial to increase the response of BP/PANI to NH3 sensing. Meanwhile, in order to support the discussion result, the structure and morphology of the BP/PANI are respectively measured by Fourier transform infrared spectroscopy (FTIR), ultraviolet-visible spectroscopy (UV−vis), transmission electron microscopy (TEM), and field emissions scanning electron microscopy (SEM). Moreover, the sensor shows good reproducibility, and fast response and recovery behavior, on NH3 sensing. In addition, this route may offer the advantages of an NH3 sensor, which are of simple structure, low cost, easy to assemble, and operate at room temperature.

AMBRA1 Negatively Regulates the Function of ALDH1B1, a Cancer Stem Cell Marker, by Controlling Its Ubiquitination

Activating molecule in Beclin-1-regulated autophagy (AMBRA1), a negative regulator of tumorigenesis, is a substrate receptor of the ubiquitin conjugation system. ALDH1B1, an aldehyde dehydrogenase, is a cancer stem cell (CSC) marker that is required for carcinogenesis via upregulation of the β-catenin pathway. Although accumulating evidence suggests a role for ubiquitination in the regulation of CSC markers, the ubiquitination-mediated regulation of ALDH1B1 has not been unraveled. While proteome analysis has suggested that AMBRA1 and ALDH1B1 can interact, their interaction has not been validated. Here, we show that AMBRA1 is a negative regulator of ALDH1B1. The expression of ALDH1B1-regulated genes, including PTEN, CTNNB1 (β-catenin), and CSC-related β-catenin target genes, is inversely regulated by AMBRA1, suggesting a negative regulatory role of AMBRA1 in the expression of ALDH1B1-regulated genes. We found that the K27- and K33-linked ubiquitination of ALDH1B1 is mediated via the cooperation of AMBRA1 with other E3 ligases, such as TRAF6. Importantly, ubiquitination site mapping revealed that K506, K511, and K515 are important for the K27-linked ubiquitination of ALDH1B1, while K33-linked ubiquitination occurs at K506. A ubiquitination-defective mutant of ALDH1B1 increased the self-association ability of ALDH1B1, suggesting a negative correlation between the ubiquitination and self-association of ALDH1B1. Together, our findings indicate that ALDH1B1 is negatively regulated by AMBRA1-mediated noncanonical ubiquitination.

Signaling from the RNA sensor RIG-I is regulated by ufmylation

The RNA binding protein RIG-I is a key initiator of the antiviral innate immune response. The signaling that mediates the antiviral response downstream of RIG-I is transduced through the adaptor protein MAVS and results in the induction of type I and III interferons (IFN). This signal transduction occurs at endoplasmic reticulum (ER)-mitochondrial contact sites, to which RIG-I and other signaling proteins are recruited following their activation. RIG-I signaling is highly regulated to prevent aberrant activation of this pathway and dysregulated induction of IFN. Previously, we identified UFL1, the E3 ligase of the ubiquitin-like modifier conjugation system called ufmylation, UFL1, as one of the proteins recruited to membranes at ER-mitochondrial contact sites in response to RIG-I activation. Here, we show that UFL1, as well as the process of ufmylation, promote IFN induction in response to RIG-I activation. We find that following RNA virus infection, UFL1 is recruited to the membrane targeting protein 14-3-3ε, and that this complex is then recruited to activated RIG-I to promote downstream innate immune signaling. Importantly, loss of ufmylation prevents 14-3-3ε interaction with RIG-I, which abrogates the interaction of RIG-I with MAVS and thus downstream signal transduction that induces IFN. Our results define ufmylation as an integral regulatory component of the RIG-I signaling pathway and as a post-translational control for IFN induction.

Synthesis, Characterization, and Application of Chalcone Derivatives as Chemosensors for Cyanide Anions

Research Background: The extreme toxicity of cyanide ions to living organisms encourages the researcher to develop new chemosensors for their sensitive and selective detection. Among various classes of chemosensors, chalcones are believed to be a promising candidate for designing new chemosensors for anions due to easy modification in its skeleton and conjugation system. Research Gap and Problem Statement: Despite having various medical applications and properties, the recognition ability of chalcone derivatives is not widely explored. The traditional methods known for the sensing of cyanide ions are ion chromatography or cyanide selective electrodes. However, these methods need skilled operators and are found to be expensive and time-consuming. Also, the available methods for detection of cyanide ions are not suitable for on-site monitoring and show interference from other competitive anions such as fluoride, acetate, and hydroxide ions. Hence, this encouraged us to explore the chalcone derivatives as chemical sensors that are capable of detecting the cyanide ions in presence of competitive anions such as fluoride, acetate, and hydroxide ions. Objectives of the study: The development of new chalcone analogs (1E,4E)-1,5-bis(4-chlorophenyl)penta-1,4-dien-3-one (3) and (E)-3-phenyl-1-(pyridin-2-yl)prop-2-en-1-one (6), which are particularly important for the future development of chemosensors for the detection of cyanide ions in presence of various interfering ions such as fluoride, acetate, and hydroxide ions. Methods: The sensing behavior of chalcone derivatives (1E,4E)-1,5-bis(4-chlorophenyl)penta-1,4-dien-3-one (3) and (E)-3-phenyl-1-(pyridin-2-yl)prop-2-en-1-one (6) have been investigated toward various anions (CN-, F-, Cl-, Br-, NO3-, SO42-, PO42-, OH-, OAc-) using UV-vis spectroscopy. Interestingly, among various anions tested, derivatives (1E,4E)-1,5-bis(4-chlorophenyl)penta-1,4-dien-3-one (3) and (E)-3-phenyl-1-(pyridin-2-yl)prop-2-en-1-one (6) function as highly selective chemosensors for the detection of cyanide ions. Results: We have synthesized two chalcone based derivatives (1E,4E)-1,5-bis(4-chlorophenyl)penta-1,4-dien-3-one (3) and (E)-3-phenyl-1-(pyridin-2-yl)prop-2-en-1-one (6) with simple condensation reaction for the detection of cyanide ions. The various results indicated the quick response of (1E,4E)-1,5-bis(4-chlorophenyl)penta-1,4-dien-3-one (3) and (E)-3-phenyl-1-(pyridin-2-yl)prop-2-en-1-one (6) toward cyanide anions. These two chalcone derivatives (1E,4E)-1,5-bis(4-chlorophenyl)penta-1,4-dien-3-one (3) and (E)-3-phenyl-1-(pyridin-2-yl)prop-2-en-1-one (6) showed not only spectral change with selectivity but also showed sensitivity for the detection of cyanide anions. The developed chalcone derivatives (1E,4E)-1,5-bis(4-chlorophenyl)penta-1,4-dien-3-one (3) and (E)-3-phenyl-1-(pyridin-2-yl)prop-2-en-1-one (6) detect cyanide ions in presence of various interfering ions such as fluoride, acetate, and hydroxide ions. The chemosensors (1E,4E)-1,5-bis(4-chlorophenyl)penta-1,4-dien-3-one (3) and (E)-3-phenyl-1-(pyridin-2-yl)prop-2-en-1-one (6) for the detection of cyanide ions are particularly smart due to their real-time analysis, simplicity, and low cost in comparison to other closely related processes such as fluorescence. Conclusion: The sensitivity studies show the high reactivity of derivative 1,5-bis(4-chlorophenyl)penta-1,4-dien-3-one (3) as compared to (E)-3-phenyl-1-(pyridin-2-yl)prop-2-en-1-one (6). The detection limit for derivatives (1E,4E)-1,5-bis(4-chlorophenyl)penta-1,4-dien-3-one (3) and (E)-3-phenyl-1-(pyridin-2-yl)prop-2-en-1-one (6) was 1.2 µM and 300 µM, respectively. The results of (1E,4E)-1,5-bis(4-chlorophenyl)penta-1,4-dien-3-one (3) and (E)-3-phenyl-1-(pyridin-2-yl)prop-2-en-1-one (6) for cyanide detection were satisfying and suggesting their potential application for cyanide detection. Future direction: Further research of this field is to develop water soluble chalcone based probes, which show emission in the Near Infra-Red (NIR) region to provide favorable conditions for biological applications.

Ufbp1, a Key Player of Ufm1 Conjugation System, Protects Against Ketosis-Induced Liver Injury via Suppressing Smad3 Activation

The dairy cattle suffer from severe liver dysfunction during the pathogenesis of ketosis. The Ufm1 conjugation system is crucial for liver development and homeostasis. Ufm1 binding protein (Ufbp1) is a putative Ufm1 target and an integral component, but its role in ketosis-induced liver injury is unclear so far. The purpose of this study is to explore the key role of Ufbp1 in liver fibrosis caused by ketosis in vivo and in vitro. Liver tissues were collected from ketotic cows and Ufbp1 conditional knockout (CKO) mice in vivo. However, Ufbp1–/– mouse embryonic fibroblast cells and Hela cells were used for in vitro validation. Subsequently, various assays were performed to reveal the underlying molecular mechanisms of the Ufbp1 protective effect. In this study, hepatic fibrosis, endoplasmic reticulum (ER) stress, and apoptosis were reported in the liver of ketotic cows, fibrotic markers (alpha-smooth muscle actin, Collagen1) and ER stress markers (glucose-regulated protein 78, CEBP homologous protein) were upregulated remarkably, and the apoptosis-related genes (Bcl2, Bax) were in line with expectations. Interestingly, Ufbp1 expression was almost disappeared, and Smad2/Smad3 protein was largely phosphorylated in the liver of ketotic cows, but Ufbp1 deletion caused Smad3 phosphorylation apparently, rather than Smad2, and elevated ER stress was observed in the CKO mice model. At the cellular level, Ufbp1 deficiency led to serious fibrotic and ER stress response, Smad3 was activated by phosphorylation significantly and then was translocated into the nucleus, whereas p-Smad2 was largely unaffected in embryonic fibroblast cells. Ufbp1 overexpression obviously suppressed Smad3 phosphorylation in Hela cells. Ufbp1 was found to be in full combination with Smad3 using endogenous immunoprecipitation. Taken together, our findings suggest that downregulation or ablation of Ufbp1 leads to Smad3 activation, elevated ER stress, and hepatocyte apoptosis, which in turn causes liver fibrosis. Ufbp1 plays a protective role in ketosis-induced liver injury.

Binding Features and Functions of ATG3

Autophagy is an evolutionarily conserved catabolic process that is essential for maintaining cellular, tissue, and organismal homeostasis. Autophagy-related (ATG) genes are indispensable for autophagosome formation. ATG3 is one of the key genes involved in autophagy, and its homologs are common in eukaryotes. During autophagy, ATG3 acts as an E2 ubiquitin-like conjugating enzyme in the ATG8 conjugation system, contributing to phagophore elongation. ATG3 has also been found to participate in many physiological and pathological processes in an autophagy-dependent manner, such as tumor occurrence and progression, ischemia–reperfusion injury, clearance of pathogens, and maintenance of organelle homeostasis. Intriguingly, a few studies have recently discovered the autophagy-independent functions of ATG3, including cell differentiation and mitosis. Here, we summarize the current knowledge of ATG3 in autophagosome formation, highlight its binding partners and binding sites, review its autophagy-dependent functions, and provide a brief introduction into its autophagy-independent functions.

Genetic Dissection of a Prevalent Plasmid-Encoded Conjugation System in Lactococcus lactis

Plasmid pNP40, which was first identified nearly 40 years ago in Lactococcus lactis subsp. lactis biovar diacetylactis DRC3, encodes functions such as heavy metal-, bacteriophage-, and nisin-resistance, as well as plasmid transfer ability by conjugation. Here, we report an optimized conjugation protocol for this plasmid, yielding a transfer frequency that is approximately 4,000-fold higher than those previously reported in literature, while we also observed high-frequency plasmid co-mobilization. Individual mutations in 18 genes that encompass the presumed conjugation cluster of pNP40 were generated using ssDNA recombineering to evaluate the role of each gene in the conjugation process. A possible transcriptional repressor of this conjugation cluster, the product of the traR gene, was identified in this manner. This mutational analysis, paired with bioinformatic predictions as based on sequence and structural similarities, allowed us to generate a preliminary model of the pNP40 conjugation machinery.

Head-to-Head Comparison of Modular Vaccines Developed Using Different Capsid Virus-Like Particle Backbones and Antigen Conjugation Systems

Capsid virus-like particles (cVLPs) are used as molecular scaffolds to increase the immunogenicity of displayed antigens. Modular platforms have been developed whereby antigens are attached to the surface of pre-assembled cVLPs. However, it remains unknown to what extent the employed cVLP backbone and conjugation system may influence the immune response elicited against the displayed antigen. Here, we performed a head-to-head comparison of antigen-specific IgG responses elicited by modular cVLP-vaccines differing by their employed cVLP backbone or conjugation system, respectively. Covalent antigen conjugation (i.e., employing the SpyTag/SpyCatcher system) resulted in significantly higher antigen-specific IgG titers compared to when using affinity-based conjugation (i.e., using biotin/streptavidin). The cVLP backbone also influenced the antigen-specific IgG response. Specifically, vaccines based on the bacteriophage AP205 cVLP elicited significantly higher antigen-specific IgG compared to corresponding vaccines using the human papillomavirus major capsid protein (HPV L1) cVLP. In addition, the AP205 cVLP platform mediated induction of antigen-specific IgG with a different subclass profile (i.e., higher IgG2a and IgG2b) compared to HPV L1 cVLP. These results demonstrate that the cVLP backbone and conjugation system can individually affect the IgG response elicited against a displayed antigen. These data will aid the understanding and process of tailoring modular cVLP vaccines to achieve improved immune responses.

pCTX-M3—Structure, Function, and Evolution of a Multi-Resistance Conjugative Plasmid of a Broad Recipient Range

pCTX-M3 is the archetypic member of the IncM incompatibility group of conjugative plasmids (recently referred to as IncM2). It is responsible for the worldwide dissemination of numerous antibiotic resistance genes, including those coding for extended-spectrum β-lactamases and conferring resistance to aminoglycosides. The IncM plasmids acquired during evolution diverse mobile genetic elements found in one or two multiple resistance regions, MRR(s), grouping antibiotic resistance genes as well as mobile genetic elements or their remnants. The IncM plasmids can be found in bacteria inhabiting various environments. The information on the structure and biology of pCTX-M3 is integrated in this review. It focuses on the functional modules of pCTX-M3 responsible for its replication, stable maintenance, and conjugative transfer, indicating that the host range of the pCTX-M3 replicon is limited to representatives of the family Enterobacteriaceae (Enterobacterales ord. nov.), while the range of recipients of its conjugation system is wide, comprising Alpha-, Beta-, and Gammaproteobacteria, and also Firmicutes.