Pathway Annotation Research Articles

Chemical Informatics Combined with Kendrick Mass Analysis to Enhance Annotation and Identify Pathways in Soybean Metabolomics

Background: Among abiotic stresses to agricultural crops, drought stress is the most prolific and has worldwide detrimental impacts. The soybean (Glycine max) is one of the most important sources of nutrition to both livestock and humans. Different plant introductions (PI) of soybeans have been identified to have different drought tolerance levels. Objectives: Here, two soybean lines, Pana (drought sensitive) and PI 567731 (drought tolerant) were selected to identify chemical compounds and pathways which could be targets for metabolomic analysis induced by abiotic stress. Methods: Extracts from the two lines are analyzed by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. The high mass resolution and accuracy of the method allows for identification of ions from hundreds of different compounds in each cultivar. The exact m/z of these species were filtered through SoyCyc and the Human Metabolome Database to identify possible molecular formulas of the ions. Next, the exact m/z values were converted into Kendrick masses and their Kendrick mass defects (KMD) computed, which were then sorted from high to low KMD. This latter process assists in identifying many additional molecular formulas, and is noted to be particularly useful in identifying formulas whose mass difference corresponds to two hydrogen atoms. Results: In this study, more than 460 ionic formulas were identified in Pana, and more than 340 ionic formulas were identified in PI 567731, with many of these formulas reported from soybean for the first time. Conclusions: Using the SoyCyc matches, the metabolic pathways from each cultivar were compared, providing lists of molecular targets available to profile effects of abiotic stress on these soybean cultivars. Key metabolites include chlorophylls, pheophytins, mono- and diacylglycerols, cycloeucalenone, squalene, and plastoquinones and involve pathways which include the anabolism and catabolism of chlorophyll, glycolipid desaturation, and biosynthesis of phytosterols, plant sterols, and carotenoids.

P0121 Molecular features of extracellular matrix activity persist in patients who achieve mucosal healing with ustekinumab induction

Abstract Background Phase 3 trials demonstrate rates of secondary loss of response of up to 40% for many advanced therapies in ulcerative colitis (UC). At a molecular level, this may be explained by persistence of inflammatory mediators in the mucosa despite successful treatment induction, and transcripts involved in leukocyte infiltration persist in patients responding to infliximab and vedolizumab compared to non-IBD controls [1]. We considered if any disease-relevant transcripts persisted in ustekinumab induction responders and if these differed depending on symptom resolution. Methods We interrogated data from the UNIFI trial, where baseline mucosal biopsies from patients treated with ustekinumab for moderate-to-severe UC underwent RNA profiling (Gene Expression Omnibus, GSE206285). Patients who achieved combined histo-endoscopic (mucosal) healing either with (disease clearance, “DC”) or without (mucosal healing, “MH only”) clinical remission at week 8 were included in subsequent analyses, along with non-IBD controls from this cohort (n=18). We compared gene expression and the enrichment of functional pathways using limma and GSEA (gene set enrichment analysis), respectively, between the two groups of responders and controls in R (v 4.2.3, Vienna). The Reactome database of pathway annotations was used. Gene signature enrichment was calculated by gene set variation analysis. Results Of the 54 patients who responded to ustekinumab, 15 experienced MH only and 39 had DC. Principal component analysis showed that these responders were distinct from controls but overlapped with each other (figure 1). For MH only compared to controls, there were 8375 differentially expressed genes (DEGs), of which 4936 were upregulated. There were 8778 DEGs between DC and controls, with 5331 upregulated. GSEA revealed that the DEGs in each comparison mainly represented pathways relating to the extracellular matrix (ECM), such as ECM degradation and collagen formation. There were no DEGs between MH only and DC but GSEA suggested that interleukin signalling and ECM organisation were upregulated in MH only. Interestingly, there was large heterogeneity in enrichment of the DEGs amongst all the responders. Similarly, there was wide variation in the enrichment of genes relating to the ECM. Conclusion Despite resolution of histo-endoscopic disease activity at week 8 in ustekinumab-treated UC patients, there was persistence of molecular inflammation, particularly ECM-related genes. However, the extent of this varied between patients; future work will examine if this explains why some eventually lose response whilst others maintain long-term remission. Ongoing inflammatory mechanisms may explain symptom persistence despite mucosal healing.

Genomic and biochemical investigations in the biomineralizing potential of an isolated marine ureolytic Bacillus sp. N₉.

Microbially Induced Calcium Carbonate Precipitation (MICP) plays a significant role in coastal soil stabilization and erosion prevention. In the present study, the biomineralizing potential of a newly isolated Bacillus sp. N₉ was investigated through MICP. The isolated Bacillus sp. N₉ induced calcium carbonate (CaCO3) precipitation in broth, agar, and real beach rock was evaluated by X-ray Fluorescence, Scanning Electron Microscopy, and X-ray Diffraction. The visual appearance of calcites as white crystals on the rock and the sealing of cracks in the beach sand cubes confirmed the CaCO3 precipitation by the isolated strain. The pH changes, soluble calcium (Ca2+) concentration levels and urease activity during the growth of the isolated Bacillus sp. N₉ were studied. High urease activity was observed, resulting in an increased production of carbonate (CO32-) ions, which in turn promoted a higher rate of CaCO₃ precipitation. Further, the assembly of the 3.27Mb genome of the isolated Bacillus sp. N₉ was evaluated using Nanopore sequencing technology, and various extracellular proteins, including urease, were identified. The gene annotation through PROKKA and RAST predicted 6700 and 7317 protein-coding sequences. The pathway annotation analysis through gene ontology, KEGG, and COG inferred the presence of genes in proteolytic characteristics, carbohydrate metabolism, and amino acid derivatives. The present study provides valuable insights into the isolated native Bacillus sp. N₉, demonstrating its potential to produce high urease activity and calcite precipitation through combined genomics and in vitro techniques.

Enzymatic browning of button mushrooms during postharvest cold chain circulation

This study aimed to investigate the molecular mechanism of browning of postharvest button mushrooms during cold chain circulation. Transcriptomic techniques based on RNA-seq sequencing data were used on the basis of sensory evaluation and determination of physiological and biochemical indexes. The differentially expressed genes (DEGs) related to quality deterioration and enzymatic browning of mushrooms in different stages of the postharvest precooling, cold chain shipping, and simulated cold shelf life were identified by GO functional annotation and KEGG pathway metabolic pathway analysis. These were subsequently verified by quantitative real-time polymerase chain reaction (RT-PCR). The results indicated that the quality changes were not significant during precooling and cold chain shipping (4–8 h) but were pronounced during the simulated cold shelf life (12°C ± 1°C) due to accelerated primary metabolic pathways involving glycolysis and organic acid utilization, leading to noticeable quality degradation. The analysis of selected DEGs through GO and KEGG pathway annotations revealed that the main genes related to browning included polyphenol oxidase (AGABI2DRAFT_194055), tyrosinase (AGABI2DRAFT_191532), peroxidases (AGABI2DRAFT_115586, AGABI2DRAFT_239410586, and AGABI2DRAFT_200291), and superoxide dismutase (AGABI2DRAFT_194955 and AGABI2DRAFT_207393), all of which were either significantly upregulated or downregulated. The validation by RT-PCR confirmed that these findings were consistent with the transcriptomic data. The combination of sensory scores, changes in physiological and biochemical indicators, and bioinformatics analysis revealed the effect of the modulation of energy metabolism and related enzymatic activities on the quality degradation and enzymatic browning of button mushrooms during the postharvest cold chain circulation.

Genomic insights into the probiotic potential and genes linked to gallic acid metabolism in Pediococcus pentosaceus MBBL6 isolated from healthy cow milk.

Pediococcus pentosaceus is well known for its probiotic properties, including roles in improving health, antimicrobial production, and enhancing fermented food quality. This study aimed to comprehensively analyze the whole genome of P. pentosaceus MBBL6, isolated from healthy cow milk, to assess its probiotic and antimicrobial potentials. P. pentosaceus MBBL6, isolated from a healthy cow milk at BSMRAU dairy farm, Gazipur, Bangladesh, underwent comprehensive genomic analysis, including whole genome sequencing, assembly, annotation, phylogenetic comparison, and assessment of metabolic pathways and secondary metabolites. Antimicrobial efficacy was evaluated through in-vitro and in-vivo studies, alongside in-silico exploration for potential mastitis therapy. We predicted 1,906 genes and 204 SEED sub-systems involved in carbohydrate metabolism and vitamin B complex biosynthesis, with a focus on lactose metabolism in MMBL6. Notably, 43 putative carbohydrate-active enzyme genes, including lysozymes, suggest the ability of MBBL6 for carbohydrate biotransformation and antimicrobial activity. The genome also revealed primary metabolic pathways for arginine and gallic acid metabolism and secondary metabolite gene clusters, including T3PKS and RiPP-like regions. Importantly, two bacteriocin biosynthesis gene clusters namely bovicin_255_variant and penocin_A, were identified in MBBL6. The safety assessment of MBBL6 genome revealed no virulence genes and a low pathogenicity score (0.196 out of 1.0). Several genes related to survival in gastrointestinal tract and colonization were also identified. Furthermore, MBBL6 exhibited susceptibility to a wide range of antibiotics in-vitro, and effectively suppressed mastitis pathogens in an in-vivo mouse mastitis model trial. The observed bacteriocin, particularly bovicin, demonstrated the ability to disrupt the function of an essential protein, Rho factor of mastitis pathogens by blocking transcription termination process. Taken together, our in-depth genomic analysis underscores the metabolic versatility, safety profile, and antimicrobial potential of P. pentosaceus MBBL6, suggesting its promise for applications in therapeutics, bioremediation, and biopreservation.

Towards the Albino Mutant Gene in Malus × Domestica Borkh.

Albino mutation is among the most common phenomena that often causes a water imbalance and disturbs physiological functions in higher species of trees. Albinism frequently occurs in hybridized apples, but almost all seedlings die shortly after germination. In this study, a spontaneous albino mutant on Fuji apple trees was obtained. After bud grafting, new albino shoots with greenish-white leaves grew, although they were slender, small, and died easily. Resequencing analysis indicated that a total of 49.37 Gbp clean data of the albino mutant samples was obtained; its Q30 reached 91.43%, the average rate mapped was 93.69%, and genome coverage was 96.47% (at least one base cover). Comparisons of the sequences for the albino mutants revealed 4,817,412 single-nucleotide polymorphisms (SNPs), 721,688 insertion/deletion markers (InDels), and 43,072 structural variations (SVs). The genes with non-synonymous SNPs, InDels, and SVs in CDS were compared with KEGG, GO, COG, NR, and SwissProt databases, and a total of 5700 variant genes were identified. A total of 1377 mutant genes had the GO annotation information. Among these, 1520 mutant genes had the pathway annotation and took part in 123 pathways. A total of 1935 variant genes were functionally classified into 25 COG categories. Further research on these variants could help understand the molecular regulatory mechanism of the apple albino mutant. Similarly, variations in the homologous MdAPG1 (Albino or pale-green mutant 1) gene, which was located on Chromosome 11 and belonged to the S-adenosyl-L-methionine-dependent methyltransferases superfamily, may have led to the generation of this apple albino mutant.

Influence of different diet categories on gut bacterial diversity in Frankliniella occidentalis.

The microbial composition of insect guts is typically influenced by the type of food consumed, and conversely, these microbes influence the food habits of insects. Western flower thrips (WFT; Frankliniella occidentalis) is an invasive pest with a wide range of hosts, including vegetables and horticultural crops. To elucidate variations in gut bacteria among WFT feeding on rose (Rosa rugosa) flowers (FF), kidney bean (Phaseolus vulgaris) pods (PF), and kidney bean leaves (LF), we collected adult guts and extracted DNA for 16S ribosomal RNA gene sequencing of microbial communities. The results revealed that the FF population had the highest number of annotations. Alpha diversity analysis revealed that the Chao and Ace indexes were the greatest in the PF population, indicating a higher abundance of gut bacteria. Moreover, the Simpson index was the highest in the FF population, indicating that gut bacterial diversity was the highest in the FF population. Comparison of species composition demonstrated that Proteobacteria dominated all 3 populations at the phylum level, with Actinobacteria being the subdominant phylum. At the genus level, Stenotrophomonas was the dominant bacteria in the PF and LF populations, whereas Rosenbergiella was dominant in the FF population. KEGG pathway annotation predicted that the gut bacteria of adult WFT were mainly involved in carbohydrate and amino acid metabolism. Our results revealed that the diversity and composition of WFT gut microbiota are influenced by diet, offering evidence for future studies on the ecological adaptability of WFT and the mechanisms underlying the interaction between gut microbiota and host.

NMI, POLR3G and APIP are the key molecules connecting glaucoma with high intraocular pressure: a clue for early diagnostic biomarker candidates.

To understand the molecular connectivity between the intraocular pressure (IOP) and glaucoma which will provide possible clues for biomarker candidates. The current study uncovers the important genes connecting IOP with the core functional modules of glaucoma. An integrated analysis was performed using glaucoma and IOP microarray datasets to screen for differentially expressed genes (DEGs) in both conditions. To the selected DEGs, the protein interaction network was constructed and dissected to determine the core functional clusters of glaucoma. For the clusters, the connectivity of IOP DEGs was determined. Further, enrichment analyses were performed to assess the functional annotation and potential pathways of the crucial clusters. The gene expression analysis of glaucoma and IOP with normal control showed that 408 DEGs (277 glaucoma and 131 IOP genes) were discovered from two GEO datasets. The 290 DEGs of glaucoma were extended to form a network containing 1495 proteins with 9462 edges. Using ClusterONE, the network was dissected to have 12 clusters. Among them, three clusters were linked with three IOP DEGs [N-Myc and STAT Interactor (NMI), POLR3G (RNA Polymerase III Subunit G), and APAF1-interacting protein (APIP)]. In the clusters, ontology analysis revealed that RNA processing and transport, p53 class mediators resulting in cell cycle arrest, cellular response to cytokine stimulus, regulation of phosphorylation, regulation of type I interferon production, DNA deamination, and cellular response to hypoxia were significantly enriched to be implicated in the development of glaucoma. Finally, NMI, POLR3G, and APIP may have roles that were noticed altered in glaucoma and IOP conditions. Our findings could help to discover new potential biomarkers, elucidate the underlying pathophysiology, and identify new therapeutic targets for glaucoma.

Time-course RNA sequencing reveals high similarity in mRNAome between hepatic stellate cells activated by agalactosyl IgG and TGF-β1.

Previous studies have demonstrated the clinical relevance of aberrant serum immunoglobulin G (IgG) N-glycomic profiles in liver fibrosis and the pathogenic effects of agalactosyl IgG on activating hepatic stellate cells (HSCs). However, the dynamics of gene expression changes during HSC activation by agalactosyl IgG remain poorly understood. We performed RNA sequencing to analyze the mRNAome of human LX-2 HSCs at multiple time points after treatment with agalactosyl IgG and then compared these results with those obtained after normal IgG and transforming growth factor (TGF)-β1 treatments. Gene expression changes were significantly pronounced on day 5 and subsided by day 11 after HSC activation. A high degree of similarity in gene expression patterns between HSCs treated with agalactosyl IgG and TGF-β1 was observed, of which 1796 and 1785 differentially expressed genes (DEGs) were identified, respectively. Disease ontology analyses revealed that 114 and 105 DEGs in activated HSCs following agalactosyl IgG and TGF-β1 treatments, respectively, were linked to liver cirrhosis, hepatitis, fatty liver disease, hepatitis B, and alcoholic hepatitis, with CCL5 and FAS being the most commonly affected genes. DEGs associated with liver fibrosis or aforementioned liver diseases involved in gene annotation, physiological functions, and signaling pathways regarding secretion of cytokines and chemokines, expression of fibrosis-related growth factors and their receptors, modification of extracellular matrices, and regulation of cell viability in activated HSCs. In conclusion, this study characterized the dynamics of mRNAome and gene networks and identified the liver fibrosis-related DEGs during HSC activation by agalactosyl IgG and TGF-β1.

The miR-665/SOST Axis Regulates the Phenotypes of Bone Marrow Mesenchymal Stem Cells and Osteoporotic Symptoms in Female Mice

Osteoporosis is a common degenerative skeletal disease among older people, especially postmenopausal women. Bone marrow mesenchymal stem cells (BMSCs), the progenitors of osteoblasts, are essential to the pathophysiology of osteoporosis. Herein, targeting miRNAs with differential expression in dysfunctional BMSCs was accomplished by bioinformatics analysis based on public databases. Target mRNAs were predicted and applied for signaling pathway and function enrichment annotations. Invitro and invivo effects of selected miRNA on BMSC proliferation and osteogenesis were investigated, the putative binding between selected miRNA and predicted target mRNA was verified, and the co-effects of the miRNA/mRNA axis on BMSCs were determined. miRNA 665 (miR-665) was down-regulated in osteoporotic BMSCs compared with normal BMSCs and elevated in BMSCs experiencing osteogenic differentiation. In BMSCs, miR-665 overexpression promoted cell proliferation and osteogenic differentiation. miR-665 targeted the Wnt signaling inhibitor sclerostin (SOST) and inhibited SOST mRNA and protein expression. SOST overexpression inhibited BMSC cell proliferation and osteogenic differentiation. When co-transduced to BMSCs, SOST knockdown significantly reversed the effects of miR-665 on BMSCs. In ovariectomy (OVX)-induced osteoporosis model mice, OVX remarkably decreased bone mass, whereas miR-665 overexpression partially improved OVX-induced bone mass loss. miR-665 was down-regulated in osteoporotic BMSCs and up-regulated in osteogenically differentiated BMSCs. In conclusion, the miR-665/SOST axis modulates BMSC proliferation, osteogenic differentiation, and OVX-induced osteoporosis in mice, possibly through Wnt signaling.

Predicting the Pathway Involvement of All Pathway and Associated Compound Entries Defined in the Kyoto Encyclopedia of Genes and Genomes.

Background/Objectives: Predicting the biochemical pathway involvement of a compound could facilitate the interpretation of biological and biomedical research. Prior prediction approaches have largely focused on metabolism, training machine learning models to solely predict based on metabolic pathways. However, there are many other types of pathways in cells and organisms that are of interest to biologists. Methods: While several publications have made use of the metabolites and metabolic pathways available in the Kyoto Encyclopedia of Genes and Genomes (KEGG), we downloaded all the compound entries with pathway annotations available in the KEGG. From these data, we constructed a dataset where each entry contained features representing compounds combined with features representing pathways, followed by a binary label indicating whether the given compound is associated with the given pathway. We trained multi-layer perceptron binary classifiers on variations of this dataset. Results: The models trained on 6485 KEGG compounds and 502 pathways scored an overall mean Matthews correlation coefficient (MCC) performance of 0.847, a median MCC of 0.848, and a standard deviation of 0.0098. Conclusions: This performance on all 502 KEGG pathways represents a roughly 6% improvement over the performance of models trained on only the 184 KEGG metabolic pathways, which had a mean MCC of 0.800 and a standard deviation of 0.021. These results demonstrate the capability to effectively predict biochemical pathways in general, in addition to those specifically related to metabolism. Moreover, the improvement in the performance demonstrates additional transfer learning with the inclusion of non-metabolic pathways.

Comparative metabolomics reveals the mechanism for the high GA4 production in Gibberella fujikuroi CGMCC 17793

With unique advantages, gibberellin GA4 has broad application prospects. To explore the regulatory mechanism for the biosynthesis of GA4, we combined liquid chromatography-mass spectrometry (LC-MS)-based metabolomics with principal component analysis (principal component analysis, PCA) and partial least squares-discriminant analysis (PLS-DA) to screen and identify the differential metabolites between the GA4-producing strains S (industrial high-yield strain CGMCC 17793) and wild-type strain Y (NRRL 13620) of Gibberella fujikuroi fermented for the same time and the differential metabolites of strain S fermented for different time periods. KEGG and MBROLE 2.0 were used to analyze the metabolic pathways involving the differential metabolites. The results showed that compared with strain Y, strain S significantly upregulated and downregulated 107 and 66, 136 and 47, and 94 and 65 metabolites on days 3, 6, and 9, respectively. Compared with that on day 3 of fermentation, strain S upregulated 29 metabolites and downregulated 40 metabolites on day 6 and upregulated 52 metabolites and downregulated 67 metabolites on day 9. The differential metabolites between strain S and strain Y after fermentation for the same time were mainly enriched in amino acid metabolism, tricarboxylic acid (TCA) cycle, and terpenoid biosynthesis. The differential metabolites of strain S after fermentation for different time periods were mainly enriched in amino acid and sugar metabolism pathways. Pathway annotation results indicated that strain S increased the production of acetyl-CoA by promoting amino acid and sugar metabolism and TCA cycle, thereby enhancing the mevalonic acid pathway and increasing the content of isopentenyl pyrophosphate (IPP), a precursor for the synthesis of terpenoids, which ultimately led to increased GA4 production. This study explored the metabolic rules of Gibberella fujikuroi GA4, providing a theoretical basis for regulating Gibberella fujikuroi to improve GA4 production.

Multifaceted natural drought response mechanisms in three elite date palm cultivars uncovered by expressed sequence tags analysis.

This study extends our prior research on drought responses in three date palm cultivars (Khalas, Reziz, and Sheshi) under controlled conditions. Here, we investigated their drought stress adaptive strategies under ambient environment. Under natural field drought conditions, three date palm cultivars experienced significantly (p ≤ 0.05) varying regulations in their physiological attributes. Specifically, chlorophyll content, leaf RWC, photosynthesis, stomatal conductance, and transpiration reduced significantly, while intercellular CO2 concentration and water use efficiency increased. Through suppression subtraction hybridization (SSH), a rich repertoire (1026) of drought-responsive expressed sequence tags (ESTs) were identified: 300 in Khalas, 343 in Reziz, and 383 in Sheshi. Functional analysis of ESTs, including gene annotation and KEGG pathways elucidation, unveiled that these cultivars withstand drought by leveraging indigenous and multifaceted pathways. While some pathways aligned with previously reported drought resilience mechanism observed under controlled conditions, several new indigenous pathways were noted, pinpointing cultivar-specific adaptations. ESTs identified in three date palm cultivars were enriched through GSEA analysis. Khalas exhibited enrichment in cellular and metabolic processes, catalytic activity, and metal ion binding. Reziz showed enrichment in biological regulation, metabolic processes, signaling, and nuclear functions. Conversely, Sheshi displayed enrichment in organelle, photosynthetic, and ribosomal components. Notably, ca. 50% of the ESTs were unique and novel, underlining the complexity of their adaptive genetic toolkit. Overall, Khalas displayed superior drought tolerance, followed by Reziz and Sheshi, highlighting cultivar-specific variability in adaptation. Conclusively, date palm cultivars exhibited diverse genetic and physiological strategies to cope with drought, demonstrating greater complexity in their resilience compared to controlled settings.

Systems Biology Methods via Genome-Wide RNA Sequences to Investigate Pathogenic Mechanisms for Identifying Biomarkers and Constructing a DNN-Based Drug–Target Interaction Model to Predict Potential Molecular Drugs for Treating Atopic Dermatitis

This study aimed to construct genome-wide genetic and epigenetic networks (GWGENs) of atopic dermatitis (AD) and healthy controls through systems biology methods based on genome-wide microarray data. Subsequently, the core GWGENs of AD and healthy controls were extracted from their real GWGENs by the principal network projection (PNP) method for Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation. Then, we identified the abnormal signaling pathways by comparing the core signaling pathways of AD and healthy controls to investigate the pathogenesis of AD. Then, IL-1β, GATA3, Akt, and NF-κB were selected as biomarkers for their important roles in the abnormal regulation of downstream genes, leading to cellular dysfunctions in AD patients. Next, a deep neural network (DNN)-based drug–target interaction (DTI) model was pre-trained on DTI databases to predict molecular drugs that interact with these biomarkers. Finally, we screened the candidate molecular drugs based on drug toxicity, sensitivity, and regulatory ability as drug design specifications to select potential molecular drugs for these biomarkers to treat AD, including metformin, allantoin, and U-0126, which have shown potential for therapeutic treatment by regulating abnormal immune responses and restoring the pathogenic signaling pathways of AD.

Main active components and mechanism of Sanmiao Pills in treating rheumatoid arthritis

UPLC-Q-TOF-MS was employed to analyze the chemical components of Sanmiao Pills(SMP) and network pharmacology and animal experiments were employed to investigate the mechanism of SMP in treating rheumatoid arthritis(RA). DisGeNET and SwissTargetPrediction were used to identify the overlapping targets between RA and SMP. Subsequently, a protein-protein interaction(PPI) network was built based on the key targets. The identified targets were further subjected to Gene Ontology(GO) analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway annotation in MATESCAPE. Cytoscape 3.8 was used to build the "component-target-pathway" network, on the basis of which the main active components, key targets, and pathways involved in the treatment of RA with SMP were predicted. Additionally, an HPLC-DAD method was established to simultaneously determine the content of berberine, atractylolide Ⅰ, atractylolide Ⅱ, ginsenoside Ro, and notoginsenoside R_1 in SMP. Furthermore, a rat model of collagen-induced arthritis(CIA) was established and the behavior test was carried out. Hematoxylin-eosin(HE) staining was conducted to reveal the pathological changes in the synovial tissue. Western blot was employed to determine the expression levels of proteins in the phosphatidylinositol 3-kinase(PI3K)/protein kinase B(AKT) pathway. A total of 126 chemical components were identified in SMP, and 332 targets were shared by SMP and RA. The PPI network predicted the key targets including AKT1 and TNF, which were mainly involved in 20 pathways including the PI3K/AKT pathway. Five components showed good linear relationships within the test concentration ranges, with RSD≤2%. The animal experiments revealed that SMP ameliorated synovial hyperplasia and down-regulated the expression levels of PI3K and p-AKT in CIA rats. The findings suggest that SMP may alleviate RA by modulating the PI3K/AKT pathway.

Effectiveness and Genetic Control of Trichoderma spp. as a Biological Control of Wheat Powdery Mildew Disease.

Wheat powdery mildew (WPM) is one of the most devasting diseases that affects wheat yield worldwide. Few efforts have been made to control such a serious disease. An effective way to control WPM is urgently needed. Biological control is an effective way to control plant diseases worldwide. In this study, the efficiency of three different Trichoderma spp. in controlling WPM at the seedling growth stage was tested using 35 highly diverse wheat genotypes. Highly significant differences were found in WPM resistance among the four treatments, confirming the efficiency of Trichoderma in controlling WPM. Of the three species, T. asperellum T34 (T34) was the most effective species in controlling WPM, as it reduced the symptoms by 50.56%. A set of 196 wheat genotypes was used to identify the genetic control of the WPM resistance induced by T34. A total of 39, 27, and 18 gene models were identified to contain the significant markers under Pm, T34, and the improvement in powdery mildew resistance due to T34 (T34_improvement) conditions. Furthermore, no gene model was common between T34 and Pm, suggesting the presence of completely different genetic systems controlling the resistance under T34 and Pm. The functional annotation and biological process pathways of the detected gene models confirm their association with the normal and induced resistance. This study, for the first time, confirms the efficiency of T34 in controlling WPM and provides a deep understanding of the genetic control of induced and normal resistance to WPM.

Transcriptomic profiling under poly (L-lactide) polymer degradation of the thermophilic filamentous bacterium Laceyella sacchari LP175 and its potential for polymer film hydrolysis

Polylactide or polylactic acid (PLA) is a hydrolysable polymer used in many applications including medical devices, agricultural films, and packaging materials. Biological methods that completely decompose biodegradable polymers are environmentally beneficial. Laceyella sacchari LP175, a thermophilic filamentous bacterium, had a high potential producing poly (L-lactide) (PLLA)-degrading enzyme which is characterized as a serine protease. This study demonstrated that this strain is an effective degrader of PLLA at a high temperature of 50 °C, which resulted in an increase in enzyme activity within the initial 24 h of incubation. The alterations in the physical and structural characteristics of the PLLA polymer film were verified to occur when incubated with a culture supernatant of this strain. Transcriptomic profiling revealed the differentially expressed genes of Laceyella sacchari LP175 under PLLA degradation, showing 289 and 296 up-regulated and down-regulated genes, respectively. Findings indicated that serine protease and transport-related genes played a key role in the biodegradation of PLLA in Laceyella sacchari LP175. The functions and metabolic pathway annotation of the enriched expression genes showed that propanoate metabolism, protein secretion, and membrane transportation were the main pathways induced when cells were grown in the presence of PLLA powder. Therefore, transcriptome data will be helpful in the development and manipulation of microbial systems to improve the degradation of biodegradable polymers.

To Explore the Mechanism of Maiwei Dihuang Decoction in the Treatment of Non-small Cell Lung Cancer based on Network Pharmacology Combined with LC-MS.

To explore the mechanism of Maiwei Dihuang decoction in the treatment of non-small cell lung cancer (NSCLC) by using network pharmacology and LC-MS technology. The effective components in Maiwei Dihuang decoction were detected by liquid chromatography- mass spectrometry (LC-MS). Use the SuperPred database to collect the relevant targets of the active ingredients of Mai Wei Di Tang, and then collect the relevant targets of nonsmall cell lung cancer from GeneCards, DisgenNET and OMIM databases. On this basis, PPI network construction, GO enrichment analysis and KEGG pathway annotation analysis were carried out for target sites. Finally, AutoDock Vina is used for molecular docking. We further screened 16 effective Chinese herbal compounds through LC-MS combined with ADME level. On this basis, we obtained 77 core targets through protein interaction network analysis. Through GO, KEGG analysis and molecular docking results, we finally screened out the potential targets of Maiwei Dihuang Decoction for NSCLC: TP53, STAT3, MAPK3. Maiwei Dihuang decoction may play a role in the treatment of NSCLC by coregulating TP53/STAT3/MAPK3 signal pathway.

Exogenous strigolactones alleviate low-temperature stress in peppers seedlings by reducing the degree of photoinhibition.

The growth and yield of pepper, a typical temperature-loving vegetable, are limited by low-temperature environments. Using low-temperature sensitive 'Hangjiao No. 4' (Capsicum annuum L.) as experimental material, this study analyzed the changes in plant growth and photosynthesis under different treatments: normal control (NT), low-temperature stress alone (LT), low-temperature stress in strigolactone pretreated plants (SL_LT), and low-temperature stress in strigolactone biosynthesis inhibitor pretreated plants (Tis_LT). SL pretreatment increased the net photosynthetic rate (Pn) and PSII actual photochemical efficiency (φPSII), reducing the inhibition of LT on the growth of pepper by 17.44% (dry weight of shoot). Due to promoting the accumulation of carotenoids, such as lutein, and the de-epoxidation of the xanthophyll cycle [(Z + A)/(Z + A + V)] by strigolactone after long-term low-temperature stress (120h), non-photochemical quenching (NPQ) of pepper was increased to reduce the excess excitation energy [(1-qP)/NPQ] and the photoinhibition degree (Fv/Fm) of pepper seedlings under long-term low-temperature stress was alleviated. Twelve cDNA libraries were constructed from pepper leaves by transcriptome sequencing. There were 8776 differentially expressed genes (DEGs), including 4473 (51.0%) upregulated and 4303 (49.0%) downregulated genes. Gene ontology pathway annotation showed that based on LT, the DEGs of SL_LT and Tis_LT were significantly enriched in the cellular component, which is mainly related to the photosystem and thylakoids. Further analysis of the porphyrin and chlorophyll biosynthesis, carotenoid biosynthesis, photosynthesis-antenna protein, and photosynthetic metabolic pathways and the Calvin cycle under low-temperature stress highlighted 18, 15, 21, 29, and 31 DEGs for further study, which were almost all highly expressed under SL_LT treatment and moderately expressed under LT treatment, whereas Tis_LT showed low expression. The positive regulatory effect of SLs on the low-temperature tolerance of pepper seedlings was confirmed. This study provided new insights for the development of temperature-tolerant pepper lines through breeding programs.

Potential functions and mechanisms of lysine crotonylation modification (Kcr) in tumorigenesis and lymphatic metastasis of papillary thyroid cancer (PTC).

To examine the putative functions and mechanisms of lysine crotonylation (Kcr) during the development and progression of papillary thyroid cancer (PTC). Samples of thyroid cancer tissues were collected and subjected to liquid chromatography-tandem mass spectrometry. Crotonylated differentially expressed proteins (DEPs) and differentially expressed Kcr sites (DEKSs) were analyzed by Motif, dynamic expression model analysis (Mfuzz), subcellular localization, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation, Go Ontology (GO) annotation, and protein-protein interaction analysis (PPI). Validation was performed by immunohistochemistry (IHC). A total of 262 crotonylated DEPs and 702 DEKSs were quantitated. First, for the tumor/normal comparison, a dynamic expression model analysis (Mfuzz) of the DEKSs revealed that clusters 1, 3, and 4 increased with the progression of thyroid cancer; however, cluster 6 showed a dramatic increase during the transition from N0-tumor to N1-tumor. Furthermore, based on GO annotation, KEGG, and PPI, the crotonylated DEPs were primarily enriched in the PI3K-Akt signaling pathway, Cell cycle, and Hippo signaling pathway. Of note, crosstalk between the proteome and Kcr proteome suggested a differential changing trend, which was enriched in Thyroid hormone synthesis, Pyruvate metabolism, TCA cycle, Cell cycle, and Apoptosis pathways. Similarly, for the LNM comparison group, the DEKSs and related DEPs were primarily enriched in Hydrogen peroxide catabolic process and Tight junction pathway. Finally, according to The Cancer Genome Atlas Program (TCGA) database, the differential expression of Kcr DEPs were associated with the prognosis of thyroid cancer, indicating the prognostic significance of these proteins. Moreover, based on the clinical validation of 47 additional samples, Kcr was highly expressed in thyroid tumor tissues compared with normal tissue (t = 9.792, P < 0.001). In addition, a positive correlation was observed between Kcr and N-cadherin (r = 0.5710, P = 0.0015). Moreover, N-cadherin expression was higher in the relatively high Kcr expression group (χ2 = 18.966, P < 0.001). Higher Kcr expression was correlated with thyroid tumorigenesis and lymphatic metastasis, which may regulate thyroid cancer progression by Pyruvate metabolism, TCA cycle, Cell cycle, and other pathways.