Can irisin be developed as the molecular evolutionary clock based on the origin and functions?

Irisin, a myokine identified in 2012, has garnered research interest for its capacity to induce browning of adipocytes and improve metabolic parameters. As such, the potential therapeutic applications of this exercise-induced peptide continue to be explored. Though present across diverse animal species, sequence analysis has revealed subtle variation in the irisin protein. In this review, we consider the effects of irisin on disease states in light of its molecular evolution. We summarize current evidence for irisin's influence on pathologies and discuss how sequence changes may inform development of irisin-based therapies. Furthermore, we propose that the phylogenetic variations in irisin could potentially be leveraged as a molecular clock to elucidate evolutionary relationships.

Learning an Interpretable Stylized Subspace for 3D-aware Animatable Artforms.

Throughout history, static paintings have captivated viewers within display frames, yet the possibility of making these masterpieces vividly interactive remains intriguing. This research paper introduces 3DArtmator, a novel approach that aims to represent artforms in a highly interpretable stylized space, enabling 3D-aware animatable reconstruction and editing. Our rationale is to transfer the interpretability and 3D controllability of the latent space in a 3D-aware GAN to a stylized sub-space of a customized GAN, revitalizing the original artforms. To this end, the proposed two-stage optimization framework of 3DArtmator begins with discovering an anchor in the original latent space that accurately mimics the pose and content of a given art painting. This anchor serves as a reliable indicator of the original latent space local structure, therefore sharing the same editable predefined expression vectors. In the second stage, we train a customized 3D-aware GAN specific to the input artform, while enforcing the preservation of the original latent local structure through a meticulous style-directional difference loss. This approach ensures the creation of a stylized sub-space that remains interpretable and retains 3D control. The effectiveness and versatility of 3DArtmator are validated through extensive experiments across a diverse range of art styles. With the ability to generate 3D reconstruction and editing for artforms while maintaining interpretability, 3DArtmator opens up new possibilities for artistic exploration and engagement.

Panel-Page-Aware Comic Genre Understanding.

Using a sequence of discrete still images to tell a story or introduce a process has become a tradition in the field of digital visual media. With the surge in these media and the requirements in downstream tasks, acquiring their main topics or genres in a very short time is urgently needed. As a representative form of the media, comic enjoys a huge boom as it has gone digital. However, different from natural images, comic images are divided by panels, and the images are not visually consistent from page to page. Therefore, existing works tailored for natural images perform poorly in analyzing comics. Considering the identification of comic genres is tied to the overall story plotting, a long-term understanding that makes full use of the semantic interactions between multi-level comic fragments needs to be fully exploited. In this paper, we propose [Formula: see text]Comic, a Panel-Page-aware Comic genre classification model, which takes page sequences of comics as the input and produces class-wise probabilities. [Formula: see text]Comic utilizes detected panel boxes to extract panel representations and deploys self-attention to construct panel-page understanding, assisted with interdependent classifiers to model label correlation. We develop the first comic dataset for the task of comic genre classification with multi-genre labels. Our approach is proved by experiments to outperform state-of-the-art methods on related tasks. We also validate the extensibility of our network to perform in the multi-modal scenario. Finally, we show the practicability of our approach by giving effective genre prediction results for whole comic books.

Center transfer for supervised domain adaptation.

Domain adaptation (DA) is a popular strategy for pattern recognition and classification tasks. It leverages a large amount of data from the source domain to help train the model applied in the target domain. Supervised domain adaptation (SDA) approaches are desirable when only few labeled samples from the target domain are available. They can be easily adopted in many real-world applications where data collection is expensive. In this study, we propose a new supervision signal, namely center transfer loss (CTL), to efficiently align features under the SDA setting in the deep learning (DL) field. Unlike most previous SDA methods that rely on pairing up training samples, the proposed loss is trainable only using one-stream input based on the mini-batch strategy. The CTL exhibits two main functionalities in training to increase the performance of DL models, i.e., domain alignment and increasing the feature's discriminative power. The hyper-parameter to balance these two functionalities is waived in CTL, which is the second improvement from the previous approaches. Extensive experiments completed on well-known public datasets show that the proposed method performs better than recent state-of-the-art approaches.

Transcriptome analysis of malate-induced Schizochytrium sp. FJU-512 reveals a novel pathway for biosynthesis of docosahexaenoic acid with enhanced expression of genes responsible for acetyl-CoA and NADPH accumulation.

Schizochytrium is one of the few oleaginous microalgae that produce docosahexaenoic acid (DHA)-rich lipids. In this study, global changes in gene expression levels of Schizochytrium sp. FJU-512 cultured with malate in a 15 l-bioreactor was analyzed using comparative transcriptomics. The changes were found mainly in the genes involved in oxidative phosphorylation, ß-oxidation, and pentose phosphate pathways. Consequently, the global changes in genes associated with the pathways could lead to an increase in the influx throughputs of pyruvate, branched-chain amino acids, fatty acids, and vitamin B6. Our transcriptome analysis indicated pyruvate dehydrogenase E2 component and acetolactate synthase I/II/III large subunit as major contributors to acetyl-CoA biosynthesis, whereas glucose-6-phosphate dehydrogenase was indicated as the major contributor to the biosynthesis of NADPH. An increase in DHA titer of up to 22% was achieved with the addition of malate to the fed-batch culture of Schizochytrium sp. FJU-512. This study provides an alternate method to enhance DHA production in Schizochytrium sp. FJU-512 through malate induced upregulation of genes responsible for acetyl-CoA and NADPH biosynthesis.

Mechanosensitive Channels Mediate Hypoionic Shock-Induced Aminoglycoside Potentiation against Bacterial Persisters by Enhancing Antibiotic Uptake.

Improving the efficacy of existing antibiotics is a promising strategy for combating antibiotic-resistant/tolerant bacterial pathogens that have become a severe threat to human health. We previously reported that aminoglycoside antibiotics could be dramatically potentiated against stationary-phase Escherichia coli cells under hypoionic shock conditions (i.e., treatment with ion-free solutions), but the underlying molecular mechanism remains unknown. Here, we show that mechanosensitive (MS) channels, a ubiquitous protein family sensing mechanical forces of cell membrane, mediate such hypoionic shock-induced aminoglycoside potentiation. Two-minute treatment under conditions of hypoionic shock (e.g., in pure water) greatly enhances the bactericidal effects of aminoglycosides against both spontaneous and triggered E. coli persisters, numerous strains of Gram-negative pathogens in vitro, and Pseudomonas aeruginosa in mice. Such potentiation is achieved by hypoionic shock-enhanced bacterial uptake of aminoglycosides and is linked to hypoionic shock-induced destabilization of the cytoplasmic membrane in E. coli. Genetic and biochemical analyses reveal that MscS-family channels directly and redundantly mediate aminoglycoside uptake upon hypoionic shock and thus potentiation, with MscL channel showing reduced effect. Molecular docking and site-directed mutagenesis analyses reveal a putative streptomycin-binding pocket in MscS, critical for streptomycin uptake and potentiation. These results suggest that hypoionic shock treatment destabilizes the cytoplasmic membrane and thus changes the membrane tension, which immediately activates MS channels that are able to effectively transport aminoglycosides into the cytoplasm for downstream killing. Our findings reveal the biological effects of hypoionic shock on bacteria and can help to develop novel adjuvants for aminoglycoside potentiation to combat bacterial pathogens via activating MS channels.

Heterologous Expression of Macrollins from Phytopathogenic Macrophomina phaseolina Revealed a Cytochrome P450 Mono-oxygenase in the Biosynthesis of ß-Hydroxyl Tetramic Acid.

Macrophomina phaseolina (M. phaseolina) is a crucial pathogenic fungus that can cause severe charcoal rot in economic crops and other plants. In this study, four new natural products, macrollins A-D, were discovered from M. phaseolina by the strategy of heterologous expression. To our knowledge, macrollins are the first reported polyketide-amino acid hybrids from the plant pathogen. Heterologous expression and in vitro reactions revealed a cytochrome P450 mono-oxygenase (MacC) catalyzing the hydroxylation at the ß-carbon of tetramic acid molecules, which is different from P450s leading to the ring expansion in the biosynthesis of fungal 2-pyridones. Phylogenetic analysis of P450s involved in the fungal polyketide-amino acid hybrids showed that MacC was not classified in any known clades. The putative oxidative mechanisms of the P450s and the biosynthetic pathway of macrollins were also proposed.

Structural Insights into the Trans-Acting Enoyl Reductase in the Biosynthesis of Long-Chain Polyunsaturated Fatty Acids in Shewanella piezotolerans.

Two long-chain polyunsaturated fatty acids (LC-PUFAs), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), play vital roles in human health. Similarly, two biosynthetic pathways, based on desaturase/elongase and polyketide synthase, have been implicated in the synthesis of microbial LC-PUFA. Up to now, only several microalgae, no bacteria, have been used in the commercial production of oils rich in DHA and/or EPA. Fully understanding the enzymatic mechanism in the biosynthesis of LC-PUFA would contribute significantly to produce EPA and/or DHA by the bacteria. In this study, we report a 1.998 Å-resolution crystal structure of trans-acting enoyl reductase (ER), SpPfaD, from Shewanella piezotolerans. The SpPfaD model consists of one homodimer in the asymmetric unit, and each subunit contains three domains. These include an N-terminal, a central domain forming a classic TIM barrel with a single FMN cofactor molecule bound atop the barrel, and a C-terminal domain with a lid above the TIM barrel. Furthermore, we docked oxidized nicotinamide adenine dinucleotide phosphate (NADP) and an inhibitor 2-(4-(2-((3-(5-(pyridin-2-ylthio)thiazol-2-yl)ureido)methyl)-1H-imidazole-4-yl)phenoxy)acetic acid (TUI) molecule into the active site and analyzed the inhibition and catalytic mechanisms of the enoyl reductase SpPfaD. To the best of our knowledge, this is the first crystal structure of trans-ER in the biosynthesis of bacterial polyketides.

Isolation and characterization of a new cytotoxic polyketide-amino acid hybrid from Thermothelomyces thermophilus ATCC 42464.

Fungi are a rich source of novel anticancer compounds. Bioassay-guided isolation has led to the isolation of four polyketide-amino acid hybrid compounds with trans-fused decalin system from the fungus Thermothelomyces thermophilus ATCC 42464 (=Myceliophthora thermophila ATCC 42464): myceliothermophins A, B, E and F (1-4). The structure of the new compound (myceliothermophin F, compound 4) was clearly determined by a combination of nuclear magnetic resonance (NMR) analysis and high-resolution electrospray ionisation mass spectroscopy (HRESIMS). The new compound exhibited promising cytotoxicity against some cell lines derived from colorectal carcinoma, hepatic carcinoma and gastric carcinoma, indicating that compounds with trans-fused decalin system would be promising in the course of developing novel anticancer drugs.

Perceptual-Aware Sketch Simplification Based on Integrated VGG Layers.

Deep learning has been recently demonstrated as an effective tool for raster-based sketch simplification. Nevertheless, it remains challenging to simplify extremely rough sketches. We found that a simplification network trained with a simple loss, such as pixel loss or discriminator loss, may fail to retain the semantically meaningful details when simplifying a very sketchy and complicated drawing. In this paper, we show that, with a well-designed multi-layer perceptual loss, we are able to obtain aesthetic and neat simplification results preserving semantically important global structures as well as fine details without blurriness and excessive emphasis on local structures. To do so, we design a multi-layer discriminator by fusing all VGG feature layers to differentiate sketches and clean lines. The weights used in layer fusing are automatically learned via an intelligent adjustment mechanism. Furthermore, to evaluate our method, we compare our method to state-of-the-art methods through multiple experiments, including visual comparison and intensive user study.

Insights into the Inhibition of Aeromonas hydrophila d-Alanine-d-Alanine Ligase by Integration of Kinetics and Structural Analysis.

Aeromonas hydrophila, a pathogenic bacterium, is harmful to humans, domestic animals, and fishes and, moreover, of public health concern due to the emergence of multiple drug-resistant strains. The cell wall has been discovered as a novel and efficient drug target against bacteria, and d-alanine-d-alanine ligase (Ddl) is considered as an essential enzyme in bacterial cell wall biosynthesis. Herein, we studied the A. hydrophila HBNUAh01 Ddl (AhDdl) enzyme activity and kinetics and determined the crystal structure of AhDdl/d-Ala complex at 2.7 Å resolution. An enzymatic assay showed that AhDdl exhibited higher affinity to ATP (Km: 54.1 ± 9.1 µM) compared to d-alanine (Km: 1.01 ± 0.19 mM). The kinetic studies indicated a competitive inhibition of AhDdl by d-cycloserine (DCS), with an inhibition constant (Ki) of 120 µM and the 50% inhibitory concentrations (IC50) value of 0.5 mM. Meanwhile, structural analysis indicated that the AhDdl/d-Ala complex structure adopted a semi-closed conformation form, and the active site was extremely conserved. Noteworthy is that the substrate d-Ala occupied the second d-Ala position, not the first d-Ala position. These results provided more insights for understanding the details of the catalytic mechanism and resources for the development of novel drugs against the diseases caused by A. hydrophila.

Genome mining and biosynthesis of the Acyl-CoA:cholesterol acyltransferase inhibitor beauveriolide I and III in Cordyceps militaris.

Ascomycete fungi Cordyceps are widely used in traditional Chinese medicine, and numerous investigations have been carried out to uncover their biological activities. However, primary researches on the physiological effects of Cordyceps were committed using crude extracts. At present, there are only a few compounds which were comprehensively characterized from Cordyceps, partial owing to the low production. In order to scientifically take advantage of Cordyceps, we used the strategy of genome mining to discover bioactive compounds from Cordyceps militaris. We found the putative biosynthetic gene cluster of the acyl-CoA:cholesterol acyltransferase inhibitor beauveriolides in the genome of C. militaris, and produced the compounds by heterologous expression in Aspergillus nidulans. Production of beauveriolide I and III also was detected in both ferment mycelia and fruiting bodies of C. militaris. The possible biosynthetic pathway was proposed. Our studies unveil the active compounds of C. militaris against atherosclerosis and Alzheimer's disease and provide the enzyme resources for the biosynthesis of new cyclodepsipeptide molecules.

Characterization of the Specific Mode of Action of a Chitin Deacetylase and Separation of the Partially Acetylated Chitosan Oligosaccharides.

Partially acetylated chitosan oligosaccharides (COS), which consists of N-acetylglucosamine (GlcNAc) and glucosamine (GlcN) residues, is a structurally complex biopolymer with a variety of biological activities. Therefore, it is challenging to elucidate acetylation patterns and the molecular structure-function relationship of COS. Herein, the detailed deacetylation pattern of chitin deacetylase from Saccharomyces cerevisiae, ScCDA2, was studied. Which solves the randomization of acetylation patterns during COS produced by chemical. ScCDA2 also exhibits about 8% and 20% deacetylation activity on crystalline chitin and colloid chitin, respectively. Besides, a method for separating and detecting partially acetylated chitosan oligosaccharides by high performance liquid chromatography and electrospray ionization mass spectrometry (HPLC-ESI-MS) system has been developed, which is fast and convenient, and can be monitored online. Mass spectrometry sequencing revealed that ScCDA2 produced COS with specific acetylation patterns of DAAA, ADAA, AADA, DDAA, DADA, ADDA and DDDA, respectively. ScCDA2 does not deacetylate the GlcNAc unit that is closest to the reducing end of the oligomer furthermore ScCDA2 has a multiple-attack deacetylation mechanism on chitin oligosaccharides. This specific mode of action significantly enriches the existing limited library of chitin deacetylase deacetylation patterns. This fully defined COS may be used in the study of COS structure and function.

ClyJ Is a Novel Pneumococcal Chimeric Lysin with a Cysteine- and Histidine-Dependent Amidohydrolase/Peptidase Catalytic Domain.

Streptococcus pneumoniae is one of the leading pathogens that cause a variety of mucosal and invasive infections. With the increased emergence of multidrug-resistant S. pneumoniae, new antimicrobials with mechanisms of action different from conventional antibiotics are urgently needed. In this study, we identified a putative lysin (gp20) encoded by the Streptococcus phage SPSL1 using the LytA autolysin as a template. Molecular dissection of gp20 revealed a binding domain (GPB) containing choline-binding repeats (CBRs) that are high specificity for S. pneumoniae By fusing GPB to the CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) catalytic domain of the PlyC lysin, we constructed a novel chimeric lysin, ClyJ, with improved activity to the pneumococcal Cpl-1 lysin. No resistance was observed in S. pneumoniae strains after exposure to incrementally doubling concentrations of ClyJ for 8 continuous days in vitro In a mouse bacteremia model using penicillin G as a control, a single intraperitoneal injection of ClyJ improved the survival rate of lethal S. pneumoniae-infected mice in a dose-dependent manner. Given its high lytic activity and safety profile, ClyJ may represent a promising alternative to combat pneumococcal infections.

Molecular characterization of the hydroxylase HmtN at 1.3 Å resolution.

Himastatin is a novel antibiotic with antitumor and antibacterial activity. In the himastatin biosynthesis pathway, HmtN is responsible for the hydroxylation of the piperazic acid (Pip) motif. Herein, we present the crystal structures of HmtN (1.3 Å), which is the first structure for a cytochrome P450 involved in the hydroxylation of cyclohexadepsipeptide during himastatin biosynthesis. Structure analysis indicated that almost all the surface of HmtN has negative electrostatic potential, only small patches of positive electrostatic potential can be found. It is worth noting that almost the entire active site of HmtT is negatively charged, while HmtN active site is composed of positive and negative charge. This may be relevant to their specific substrate recognition and different catalytic function. In addition, three channels were observed in HmtN crystal structure; channel 3 may be essential for substrate ingress and egress from the active site to the surface, while channel 1 and channel 2 may be the solvent and water pathway, respectively.

Investigation of structure and function of mitochondrial alcohol dehydrogenase isozyme III from Komagataella phaffii GS115.

BACKGROUND: Alcohol dehydrogenases (ADHs) catalyze the reversible oxidation of alcohol using NAD+ or NADP+ as cofactor. Three ADH homologues have been identified in Komagataella phaffii GS115 (also named Pichia pastoris GS115), ADH1, ADH2 and ADH3, among which adh3 is the only gene responsible for consumption of ethanol in Komagataella phaffii GS115. However, the relationship between structure and function of mitochondrial alcohol dehydrogenase isozyme III from Komagataella phaffii GS115 (KpADH3) is still not clear yet. METHODS: KpADH3 was purified, identified and characterized by multiple biophysical techniques (Nano LC-MS/MS, Enzymatic activity assay, X-ray crystallography). RESULTS: The crystal structure of KpADH3, which was the first ADH structure from Komagataella phaffii GS115, was solved at 1.745 Šresolution. Structural analysis indicated that KpADH3 was the sole dimeric ADH structure with face-to-face orientation quaternary structure from yeast. The major structural different conformations located on residues 100-114 (the structural zinc binding loop) and residues 337-344 (the loop between α12 and ß15 which covered the catalytic domain). In addition, three channels were observed in KpADH3 crystal structure, channel 2 and channel 3 may be essential for substrate specific recognition, ingress and egress, channel 1 may be the pass-through for cofactor. CONCLUSIONS: KpADH3 plays an important role in the metabolism of alcohols in Komagataella phaffii GS115, and its crystal structure is the only dimeric medium-chain ADH from yeast described so far. GENERAL SIGNIFICANCE: Knowledge of the relationship between structure and function of KpADH3 is crucial for understanding the role of KpADH3 in Komagataella phaffii GS115 mitochondrial metabolism.

Protein acetylation: an important mechanism in actinobacteria.

This is a commentary on the research article by Lu et al. recently published in Bioscience Reports The GCN5-like acetyltransferases with amino acid-binding (ACT)-GCN5-related N-acetyltransferase (GNAT) domain organization have been identified in actinobacteria by Lu et al. (2017). The ACT domain is fused to the GNAT domain, conferring amino acid-induced allosteric regulation to these protein acetyltransferases (Pat) (amino acid sensing acetyltransferase (AAPatA)). Members of the AAPatA family share similar secondary structure and are divided into two groups based on the allosteric ligands of the ACT domain: the asparagine (Asn)-activated PatA and the cysteine (Cys)-activated PatA. The former are mainly found in Streptomyces; the latter are distributed in other actinobacteria. The authors investigated the effect of Asn and Cys on the acetylation activity of Sven_0867 (SvePatA, from Streptomyces venezuelae DSM 40230) and Amir_5672 (AmiPatA, from Actinosynnema mirum strain DSM 43827), respectively, as well as the relationship between the structure and function of these enzymes. Research history and progress on acetyltransferases and lysine acetylation of proteins were discussed. The activity of PatA and acetylation level of proteins may be closely correlated with intracellular concentrations of Asn and Cys in actinobacteria.

Identification of a Novel Inhibitor against Middle East Respiratory Syndrome Coronavirus.

The Middle East respiratory syndrome coronavirus (MERS-CoV) was first isolated in 2012, and circulated worldwide with high mortality. The continual outbreaks of MERS-CoV highlight the importance of developing antiviral therapeutics. Here, we rationally designed a novel fusion inhibitor named MERS-five-helix bundle (MERS-5HB) derived from the six-helix bundle (MERS-6HB) which was formed by the process of membrane fusion. MERS-5HB consists of three copies of heptad repeat 1 (HR1) and two copies of heptad repeat 2 (HR2) while MERS-6HB includes three copies each of HR1 and HR2. As it lacks one HR2, MERS-5HB was expected to interact with viral HR2 to interrupt the fusion step. What we found was that MERS-5HB could bind to HR2P, a peptide derived from HR2, with a strong affinity value (KD) of up to 0.24 nM. Subsequent assays indicated that MERS-5HB could inhibit pseudotyped MERS-CoV entry effectively with 50% inhibitory concentration (IC50) of about 1 µM. In addition, MERS-5HB significantly inhibited spike (S) glycoprotein-mediated syncytial formation in a dose-dependent manner. Further biophysical characterization showed that MERS-5HB was a thermo-stable α-helical secondary structure. The inhibitory potency of MERS-5HB may provide an attractive basis for identification of a novel inhibitor against MERS-CoV, as a potential antiviral agent.

Structural analysis of SgvP involved in carbon-sulfur bond formation during griseoviridin biosynthesis.

Griseoviridin (GV) is a broad-spectrum antibiotic with antibacterial and antifungal activity. In the GV biosynthetic pathway, SgvP catalyzes formation of the carbon-sulfur bond in GV. Herein, we report the recombinant expression and characterization of SgvP from Streptomyces griseoviridis NRRL2427. We also present the 2.6 Å crystal structure of SgvP, which is the first structure of a cytochrome P450 involved in carbon-sulfur bond formation in GV. Structural analysis indicates that Pro237 in the I-helix of SgvP may play a critical role in dioxygen binding and proton transfer during the catalytic cycle. Of the three channels we observed in SgvP, channel 3 may be essential for substrate ingress and egress from the active site, while channels 1 and 2 may be the solvent and water pathway, respectively. DATABASE: Coordinate and structure factor were deposited in the Protein Data Bank database under the accession number 4MM0.

A novel chimeric lysin with robust antibacterial activity against planktonic and biofilm methicillin-resistant Staphylococcus aureus.

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most threatening pathogens due to its multi-drug resistance (MDR) and strong biofilm-forming capacity. Here, we described the screening of a novel chimeolysin (ClyF) that was active against planktonic and biofilm MRSA. Biochemical tests showed that ClyF was active against all S. aureus clinical isolates tested under planktonic and biofilm conditions. Structure analysis revealed that ClyF has an enhanced thermostability and pH tolerance than its parental lysin Pc by forming a hydrophobic cleft in the catalytic domain and an Ig-like structure in the cell-wall binding domain. A single intraperitoneally or topically administration of ClyF showed good MRSA removing efficacy in mouse models of bacteremia and burn wound infection, respectively. Our data collectively demonstrated that ClyF has good bactericidal activity against planktonic and biofilm MRSA both in vitro and in vivo, and therefore represents a useful antibacterial to combat MDR S. aureus.