Regulated Mechanism Research Articles

An Integrated Affinity Chromatography-Based Approach to Unravel the sRNA Interactome in Nitrogen-Fixing Rhizobia.

The activity mechanism and function of bacterial base-pairing small non-coding RNA regulators (sRNAs) are largely shaped by their main interacting cellular partners, i.e., proteins and mRNAs. We describe here an MS2 affinity chromatography-based procedure adapted to unravel the sRNA interactome in nitrogen-fixing legume endosymbiotic bacteria. The method consists of tagging of the bait sRNA at its 5'-end with the MS2 aptamer followed by pulse overexpression and immobilization of the chimeric transcript from cell lysates by an MS2-MBP fusion protein conjugated to an amylose resin. The sRNA-binding proteins and target mRNAs are further profiled by mass spectrometry and RNAseq, respectively.

Copper in Gynecological Diseases.

Copper (Cu) is an essential micronutrient for the correct development of eukaryotic organisms. This metal plays a key role in many cellular and physiological activities, including enzymatic activity, oxygen transport, and cell signaling. Although the redox activity of Cu is crucial for enzymatic reactions, this property also makes it potentially toxic when found at high levels. Due to this dual action of Cu, highly regulated mechanisms are necessary to prevent both the deficiency and the accumulation of this metal since its dyshomeostasis may favor the development of multiple diseases, such as Menkes' and Wilson's diseases, neurodegenerative diseases, diabetes mellitus, and cancer. As the relationship between Cu and cancer has been the most studied, we analyze how this metal can affect three fundamental processes for tumor progression: cell proliferation, angiogenesis, and metastasis. Gynecological diseases are characterized by high prevalence, morbidity, and mortality, depending on the case, and mainly include benign and malignant tumors. The cellular processes that promote their progression are affected by Cu, and the mechanisms that occur may be similar. We analyze the crosstalk between Cu deregulation and gynecological diseases, focusing on therapeutic strategies derived from this metal.

An Antidepressant Drug Increased TRAIL Receptor-2 Expression and Sensitized Lung Cancer Cells to TRAIL-induced Apoptosis.

TRAIL has emerged as a promising therapeutic target due to its ability to selectively induce apoptosis in cancer cells while sparing normal cells. Autophagy, a highly regulated cellular recycling mechanism, is known to play a cell survival role by providing a required environment for the cell. Recent studies suggest that autophagy plays a significant role in increasing TRAIL resistance in certain cancer cells. Thus, regulating autophagy in TRAIL-mediated cancer therapy is crucial for its role in cancer treatment. Our study explored whether the antidepressant drug desipramine could enhance the ability of TRAIL to kill cancer cells by inhibiting autophagy. The effect of desipramine on TRAIL sensitivity was examined in various lung cancer cell lines. Cell viability was measured by morphological analysis, trypan blue exclusion, and crystal violet staining. Flow cytometry analysis was carried out to measure apoptosis with annexin V-PI stained cells. Western blotting, rtPCR, and immunocytochemistry were carried out to measure autophagy and death receptor expression. TEM was carried out to detect autophagy inhibition. Desipramine treatment increased the TRAIL sensitivity in all lung cancer cell lines. Mechanistically, desipramine treatment induced death receptor expression to increase TRAIL sensitivity. This effect was confirmed when the genetic blockade of DR5 reduced the effect of desipramine in enhanced TRAIL-mediated cell death. Further investigation revealed that desipramine treatment increased the LC3 and p62 levels, indicating the inhibition of lysosomal degradation of autophagy. Notably, TRAIL, in combination with either desipramine or the autophagy inhibitor chloroquine, exhibited enhanced cytotoxicity compared to TRAIL treatment alone. Our findings revealed the potential of desipramine to induce TRAIL-mediated cell death by autophagy impairment. This discovery suggests its therapeutic potential for inducing TRAIL-mediated cell death by increasing the expression of death receptors, which is caused by impairing autophagy.

Quantitative Proteomics Analysis Reveals the Effect of a MarR Family Transcriptional Regulator AHA_2124 on Aeromonas hydrophila.

The transcriptional regulators of the MarR family play an important role in diverse bacterial physiologic functions, whereas their effect and intrinsic regulatory mechanism on the aquatic pathogenic bacterium Aeromonas hydrophila are, clearly, still unknown. In this study, we firstly constructed a deletion strain of AHA_2124 (ΔAHA_2124) of a MarR family transcriptional regulator in Aeromonas hydrophila ATCC 7966 (wild type), and found that the deletion of AHA_2124 caused significantly enhanced hemolytic activity, extracellular protease activity, and motility when compared with the wild type. The differentially abundant proteins (DAPs) were compared by using data-independent acquisition (DIA), based on a quantitative proteomics technology, between the ΔAHA_2124 strain and wild type, and there were 178 DAPs including 80 proteins up-regulated and 98 proteins down-regulated. The bioinformatics analysis showed that the deletion of gene AHA_2124 led to some changes in the abundance of proteins related to multiple biological processes, such as translation, peptide transport, and oxidation and reduction. These results provided a theoretical basis for better exploring the regulatory mechanism of the MarR family transcriptional regulators of Aeromonas hydrophila on bacterial physiological functions.

Investigation into actions of Xiebai and Zengye decoction on cough sensitivity, airway inflammation and gut microbiota in the rat model of post-infectious cough

This work was undertaken to observe therapeutic effect of Xiebai and Zengye (XBZY) decoction on post-infectious cough (PIC) in rats, as well as its effect on gut microbiota and the exploration of the intestinal microecological mechanisms of XBZY decoction in the treatment of PIC. Using a random number table, the rats that were successfully modelled were assigned to the PIC, XBZY group (14.8 g/kg/d), and montelukast sodium treatment (MAS) group (1 mg/kg/d). The cough sensitivity of rats and changes in fecal water content were assessed, and serum interleukin-8 (IL-8) and tumor necrosis factor-alpha (TNF-α) levels were determined by ELISA. The histopathological changes in the bronchus and colon tissues were observed under the microscope after hematoxylin-eosin staining. Short-chain fatty acids (SCFAs) in fecal samples were measured by gas chromatography, and changes in gut microbiota were observed using 16S rRNA sequencing. The PIC rats showed decreased fecal water content, increased cough sensitivity, elevated serum TNF-α and IL-8 levels, and higher bronchitis scores comparing to normal control group. The PIC rats showed reductions in SCFAs and significant changes in the structure of gut microbiota. XBZY decoction intervention led to increased fecal water content in rats, reduced cough sensitivity, decreased serum IL-8 and TNF-α levels, decreased bronchitis scores, and alleviated inflammatory cell infiltration was observed in the colonic mucosa. Additionally, elevated SCFAs levels were observed in the PIC rats. XBZY decoction intervention improved alpha-/beta-diversity, and corrected microbiota imbalance in PIC rats. SCFAs, TNF-α and IL-8, acetic acid was revealed to be positively associated with Allobaculum but inversely correlated with unclassified_f_Oscillospiraceae; propanoic acid was positively associated with Lactobacilli but negatively associated with Romboutsia; butanoic acid exhibited positive correlations with Akkermansia and Lactobacilli, but negative correlations with unclassified_f_Oscillospiraceae, Eubacterium_xylanophilum_group, and Lachnospiraceae_NK4A136_group; Additionally, TNF-α was inversely linked to Allobaculum, while IL-8 was positively related to Romboutsia and Turicibacter. In conclusion, XBZY decoction significantly reduced cough sensitivity and airway inflammation in PIC rats while ameliorating stool dryness and colonic inflammation. The protective effects of XBZY decoction could be linked to modulat gut microbiota in PIC rats, and regulat SCFAs contents in PIC rats, while the regulator mechanisms of XBZY decoction in gut microbiota still requires further in-depth investigation.

Autophagy: A Silent Protagonist in Kidney Transplantation.

Autophagy is a lysosome-dependent regulated mechanism that recycles unnecessary cytoplasmic components. It is now known that autophagy dysfunction may have a pathogenic role in several human diseases and conditions, including kidney transplantation. Both defective and excessive autophagy may induce or aggravate several complications of kidney transplantation, such as ischemia-reperfusion injury, alloimmune response, and immunosuppressive treatment and side effects. Although it is still complicated to measure autophagy levels in clinical practice, more attention should be paid to the factors that may influence autophagy. In kidney transplantation, the association of low doses of a mammalian target of rapamycin inhibitor with low doses of a calcineurin inhibitor may be of benefit for autophagy modulation. However, further studies are needed to explore the role of other autophagy regulators.

Dual‐mode event‐triggered predictive control for nonlinear systems with bounded disturbances

AbstractIn this article, we propose a dual‐mode event‐triggered predictive control method for nonlinear systems with bounded disturbances. The proposed method contains two triggering mechanisms, namely, the hybrid threshold‐based event‐triggered model predictive control (HETMPC) mechanism and the event‐triggered linear quadratic regulator mechanism. The former triggering mechanism is designed based on the error between the real state and the optimal state and also the disturbance information acted on the investigated system. Compared with the traditional fixed triggering threshold, the designed HETMPC has a fewer triggering numbers and reduces the computational burden of online real‐time optimization. This event‐triggered mechanism will be adopted before the states go into the terminal invariant set. The latter event‐triggered mechanism is designed based on the derivation of the system state and it will be adopted after the states enter the terminal invariant set. The feasibility and the input‐to‐state practical stability analysis of the designed strategy is presented. Some simulations, including the application to a mass‐spring‐damper system, are provided to show the correctness and feasibility of the designed algorithms.

Effect of cadmium on the regulatory mechanism of steroidogenic pathway of Leydig cells during spermatogenesis.

Cadmium is a male reproductive toxicant that interacts with a variety of pathogenetic mechanisms. However, the effect of cadmium on the regulatory mechanism of the steroidogenic pathway of Leydig cells during spermatogenesis is still ambiguous. Light microscopy, Western blot, immunohistochemistry, immunofluorescence, and quantitative polymerase chain reaction wereperformed to study the regulatory mechanism of the steroidogenic pathway of Leydig cells during spermatogenesis. The results indicated that in the control group, Leydig cells showed dynamic immunoreactivity and immunosignaling action with a strong positive significant secretion of 3β-hydroxysteroid hydrogenase (3β-HSD) in the interstitial compartment of the testis. Leydig cells showed a high active regulator mechanism of the steroidogenic pathway with increased the proteins and genes expression level of steroidogenic acute regulatory protein (STAR), cytochrome P450 cholesterol (CYP11A1), cytochrome P450 cholesterol (CYP17A1), 3β-hydroxysteroid hydrogenase (3β-HSD) 17β-hydroxysteroid hydrogenase (17β-HSD),and androgen receptor (AR) that maintained the healthy and vigorous progressive motile spermatozoa. However, on treatment with cadmium, Leydig cells were irregularly dispersed in the interstitial compartment of the testis. Leydig cells showed reduced immunoreactivity and immunosignaling of 3β-HSD protein. Meanwhile, cadmium impaired the regulatory mechanism of the steroidogenic process of the Leydig cells with reduced proteinand gene expression levels of STAR, CYP11A1, CYP17A1, 3β-HSD, 17β-HSD, and AR in the testis. Additionally, treatment with cadmium impaired the serum LH, FSH, and testosterone levels in blood as compared to control. This study explores the hazardous effect of cadmium on the regulatory mechanism of the steroidogenic pathway of Leydig cells during spermatogenesis.

YTHDF3as a prognostic predictive biomarker of thyroid cancer and its correlation with immune infiltration

PurposeThyroid cancer (TC) is one of the most common endocrine malignancies, and its morbidity continues to rise. N6-methyladenosine (m6A) RNA methylation, an epigenetic modification, is an important regulator of gene expression in TC. Therefore, it’s worth finding the characteristics and predictive value of the m6A RNA methylation regulators in thyroid cancer (TC).MethodRNA-seq data of TC was downloaded from the Cancer Genome Atlas (TCGA) database to screen out the differential expressed regulators. The absolute contraction selection operator (Lasso) Cox regression was used to construct the risk model of m6A methylation regulators. The predictive value of the risk scoring model was evaluated by Kaplan Meier (K-M) analysis and receiver operating characteristic (ROC) curves. The underlying mechanism of m6A methylation regulators in TC was predicted by gene set enrichment analysis (GSEA). Further validation was performed by using immunohistochemistry (IHC) and q-PCR. The correlation between risk-related gene and immune infiltration was evaluated by Tumour Immune Estimation Resource (TIMER).ResultsIGF2BP2, YTHDF1 and YTHDF3 were screened out as strong independent prognostic factors of TC. Then a risk score model was established to further screen the predictors. Finally, according to the results of overall survival (OS) and clinical characteristics of TC, YTHDF3 was screened out as a potential predictor. Meanwhile, IHC and qPCR confirmed that YTHDF3 was expressed differential in TC. The expression of YTHDF3 was positively associated with the infiltration level of CD4+ T cells and macrophages. It was strongly correlated with a variety of immune markers in TC.ConclusionWe confirmed that YTHDF3 can be used as a potential prognostic biomarker of TC. It not only plays a decisive role in the initiation and development of TC, but also provides a new perspective for understanding the modification of m6A RNA in TC.

Advances in the Study of the Transcriptional Regulation Mechanism of Plant miRNAs.

MicroRNAs (miRNA) are a class of endogenous, non-coding, small RNAs with about 22 nucleotides (nt), that are widespread in plants and are involved in various biological processes, such as development, flowering phase transition, hormone signal transduction, and stress response. The transcriptional regulation of miRNAs is an important process of miRNA gene regulation, and it is essential for miRNA biosynthesis and function. Like mRNAs, miRNAs are transcribed by RNA polymerase II, and these transcription processes are regulated by various transcription factors and other proteins. Consequently, the upstream genes regulating miRNA transcription, their specific expression, and the regulating mechanism were reviewed to provide more information for further research on the miRNA regulatory mechanism and help to further understand the regulatory networks of plant miRNAs.

Identify the potential driving mechanism of reconstructed bacterial community in reduce CO2 emissions and promote humus formation during cow manure composting

The mineralization of organic components releases CO2 during composting, which not only leads to the loss of organic carbon, but has a direct negative impact on the environment. Malonic acid as a competitive inhibitor of succinate dehydrogenase could affect the tricarboxylic acid (TCA) cycle and reduce CO2 emissions. However, the bacterial interaction and organic component transformation has less known how to malonic acid reduce CO2 and improve of humus synthesis in complex composting. The aim of this study was to investigated the malonic acid on organic carbon sequestration and transforming cow manure waste into products with high humus content. Humus content was elevated by 16.8% and cumulative CO2 emissions (30 d)d reduced by 13.6% after malonic acid addition compared to the CK. SparCC analysis of bacterial interaction presented that the network complexity and stability was more higher with malonic acid addition, while a greater concentration of keystones and their ecological metabolic functions was observed, suggesting they weaken the influence of TCA cycle inhibition by enhancing interactions. PICRUSt predictions indicate that malonic acid might enhance humus content by promoting the synthesis of polyphenols and polymerization with amino acids. This study investigated the potential mechanism of regulators to enhance quality and reduce emissions during humification process, providing a new strategy for the resource utilization of organic solid waste.

Molecular and biochemical biomarkers in the American oyster Crassostrea virginica exposed to herbicide Roundup® at high temperature.

Aquatic organisms are frequently exposed to various environmental stressors. Thus, the effects of high temperatures and herbicides on aquatic organisms are a major subject of interest. In this study, we studied the effects of short-term exposure (1week) to Roundup®, a glyphosate-based herbicide (concentrations: 0.5 and 5µg/L), on the morphology of gills, digestive glands, and connective tissues, and the expression of heat shock protein-70 (HSP70, a chaperone protein), cytochrome P450 (CYP450, a biomarker of environmental contaminants), dinitrophenyl protein (DNP, a biomarker of protein oxidation), nitrotyrosine protein (NTP, a biomarker of protein nitration), antioxidant enzymes such as superoxidase dismutase (SOD) and catalase (CAT) in tissues of American oyster, Crassostrea virginica (Gmelin, 1791) maintained at high temperature (30°C). Histological analyses showed an increase in mucous production in the gills and digestive glands, and in hemocyte aggregation in the connective tissues as well as a structural change of lumen in the digestive glands of oysters exposed to Roundup. Immunohistochemical and quantitative RT-PCR analyses showed significant (P < 0.05) increases in HSP70, CYP450, DNP, NTP, CAT, and SOD mRNA and protein expressions in the tissues of oysters exposed to Roundup. Taken together, these results suggest that exposure to Roundup at high temperature induces overproduction of reactive oxygen species/reactive nitrogen species which in turn leads to altered prooxidant-antioxidant activity in oyster tissues. Moreover, our results provide new information on protein oxidation/nitration and antioxidant-dependent mechanisms for HSP70 and CYP450 regulations in oysters exposed to Roundup at high temperature.

Exogenous glutathione can alleviate chromium toxicity in kenaf by activating antioxidant system and regulating DNA methylation

Glutathione (GSH) participates in plant response to heavy metals (HMs) stress, however, the epigenetic regulating mechanisms of GSH in HMs detoxification remains unclear. In this study, to reveal the potential epigenetic regulating mechanisms, kenaf seedlings were treated with/without GSH under chromium (Cr) stress. A comprehensive physiological, genome-wide DNA methylation and gene functional analysis were performed. Results showed that external GSH obviously recovered Cr-induced growth inhibition, significantly decreased H2O2, O2.- and MDA accumulation, increased the activities of antioxidant enzymes (SOD, CAT, GR and APX) in kenaf exposed to Cr. In addition, the expression level of the main DNA methyltransferase (MET1, CMT3 and DRM1) and demethylase (ROS1, DEM, DML2, DML3 and DDM1) genes were investigated by qRT-PCR. The result indicated that Cr stress decreased DNA methyltransferase genes expression while increased demethylase genes expression; however, apply exogenous GSH led to the recovery trend. These indicating exogenous GSH alleviation Cr stress on kenaf seedlings by increasing DNA methylation level. At the same time, the MethylRAD-seq genome-wide DNA methylation analysis showed the DNA methylation level was significantly increased after GSH treatment compared with Cr treatment alone. The differentially methylated genes (DMGs) were uniquely enriched in DNA repair, flavin adenine dinucleotide binding and oxidoreductase activity. Furthermore, a ROS homeostasis-associated DMG, HcTrx, was selected for further functional analysis. Results showed that the knock-down of HcTrx kenaf seedlings displayed yellow-green phenotype and impaired antioxidant enzyme activity; in contrast, the overexpression lines of HcTrx improved chlorophyll levels and enhanced Cr tolerance in Arabidopsis. Taken together, our results illustrate the novel role of GSH-mediated Cr detoxification in kenaf by modulating the DNA methylation, and thus further affect the activation of antioxidant defense systems. The present characterized Cr tolerant gene resource could be further used for kenaf Cr tolerant breeding via genetic improvement.

Type 2 Immunity Regulates Dermal White Adipose Tissue Function

Type 2 immune responses have been increasingly linked with tissue maintenance, regeneration, and metabolic homeostasis. The molecular basis of regulator and effector mechanisms of type 2 immunity in skin regeneration and homeostasis is still lacking. In this study, we analyzed the role of IL-4Rα signaling in the regeneration of diverse cellular compartments in the skin. Mutants with global IL-4Rα deficiency showed two major phenotypes: first, a pronounced atrophy of the interfollicular epidermis, and second, a significant increase in dermal white adipose tissue thickness in mice aged 3 weeks (postnatal day 21) compared with littermate controls. Notably, IL-4Rα deficiency decreased the activation of hormone-sensitive lipase, a rate-limiting step in lipolysis. Immunohistochemical and FACS analysis in IL-4/enhanced GFP reporter mice showed that IL-4 expression peaked on postnatal day 21 and that eosinophils are the predominant IL-4-expressing cells. Eosinophil-deficient mice recapitulated the lipolytic-defective dermal white adipose tissue phenotype of Il4ra-deficient mice, showing that eosinophils are necessary for dermal white adipose tissue lipolysis. Collectively, we provide mechanistic insights into the regulation of interfollicular epidermis and hormone-sensitive lipase-mediated lipolysis in dermal white adipose tissue in early life by IL-4Rα, and our findings show that eosinophils play a critical role in this process.

Numerical investigation on formation mechanism and flow law of droplet in T-junction by electric field

The mechanism of constant electric field regulation on droplet formation in a T-junction microchannel is investigated numerically, and the law of discrete phase fluid behavior in different viscosity systems is summarized. This research develops a two-phase-electrohydrodynamic solver in the OpenFOAM® framework. The solver uses a leaky medium model to simulate the microfluidic system and uses the volume of fluid method to trace the phase interface. It is found that the mechanism of droplet generation within the microfluidic system can be divided into squeeze and shear effect, where the shear mechanism will have transition to the squeeze mechanism under the influence of the electric field. Additionally, the effect of the electric field on the discrete phase fluid is significantly influenced by the viscosity of the continuous phase fluid. At low to medium viscosity, droplet length can be affected by wall shear resistance and undergo sudden changes at a certain electric field strength, but the mutation will decrease to disappear with the increase in the system viscosity. At high viscosity, droplets undergo significant agglomeration in the interaction of electric field force and viscous shear. Then, the regulating mechanism of constant electric field on a discrete phase fluid flow pattern in an ultra-high viscosity system is also studied. Finally, a map is proposed that adequately describes the variation of discrete phase fluid behavior with constant electric field strength with different continuous phase fluid viscosities.

Retinoic acid signaling pathway perturbation impacts mesodermal-tissue development in the zebrafish embryo: Biomarker candidate identification using transcriptomics.

The zebrafish embryo (ZE) model provides a developmental model well conserved throughout vertebrate embryogenesis, with relevance for early human embryo development. It was employed to search for gene expression biomarkers of compound-induced disruption of mesodermal development. We were particularly interested in the expression of genes related to the retinoic acid signaling pathway (RA-SP), as a major morphogenetic regulating mechanism. We exposed ZE to teratogenic concentrations of valproic acid (VPA) and all-trans retinoic acid (ATRA), using folic acid (FA) as a non-teratogenic control compound shortly after fertilization for 4 h, and performed gene expression analysis by RNA sequencing. We identified 248 genes specifically regulated by both teratogens but not by FA. Further analysis of this gene set revealed 54 GO-terms related to the development of mesodermal tissues, distributed along the paraxial, intermediate, and lateral plate sections of the mesoderm. Gene expression regulation was specific to tissues and was observed for somites, striated muscle, bone, kidney, circulatory system, and blood. Stitch analysis revealed 47 regulated genes related to the RA-SP, which were differentially expressed in the various mesodermal tissues. These genes provide potential molecular biomarkers of mesodermal tissue and organ (mal)formation in the early vertebrate embryo.

Are systemic risk measures effective? Evidence from macroeconomic downside risk prediction

ABSTRACT This paper studies the predictive power of a set of systemic risk measures for macroeconomic downside risks in China. The quantile single-index model (QSIM) is used to select and combine systemic risk measures to depict the lower tail of macroeconomy distribution. The out-of-sample results show that QSIM provides prominent and robust prediction, as it aggregates all relevant systemic risk measures information and captures parameter nonlinearity. Moreover, we uncover the risk drivers behind macroeconomic downturns using the variable selection technique. The results provide an early warning mechanism for regulators and a criterion for researchers to select systemic risk measures.

Mechanics of regulatable hydrogel adhesion with elastic heterogeneity

Hydrogel adhesion regulation remains a key challenge in applications of stretchable electronics, tissue engineering, and soft robotics. Whereas existing strategies are focused on enhancing adhesion, the underlying mechanics of on-demand mechanical regulation from adhesion promotion to adhesion reduction receives insufficient attention. We propose an effective method to manipulate the energy process zone near the crack front by invoking periodic elastic heterogeneity, whose adhesion toughness exhibits high dependence on the periodic structures and peeling direction. Without modifying surface chemistry, the adhesion of heterogeneous interfaces implemented by 3D printing can enhance peak force by 6-fold or weaken interfacial toughness to 1/30, as compared to the case of a homogeneous interface. Based on a variational principle, analytical formulations and finite element simulations are performed to quantify the heterogeneous behaviors. The analysis captures the instability phenomenon and predicts the maximum peel force. Combined experimental, theoretical, and finite element results demonstrate the effects of geometric parameters and peeling directions on the overall adhesion toughness. This data elucidates an energy storage mechanism, namely that the discrete elastic ligaments free of lateral constraints could enable the interface to accommodate large stretching and store intensified strain energy. The results also indicate the necessity and significance of peeling directions. The work provides a design guideline for on-demand enhancement and detachment in hydrogel interface applications.

Molecular dynamics simulation of the interaction of a raspberry polygalacturonase (RiPG) with a PG inhibiting protein (RiPGIP) isolated from ripening raspberry (Rubus idaeus cv. Heritage) fruit as a model to understand proteins interaction during fruit softening

Polygalacturonase (PG) is an important hydrolytic enzyme involved in pectin disassembly and the subsequent textural changes during fruit ripening. Although the interaction of fungal PGs with other proteins has been documented, the interaction of plant PGs with other plant proteins has not yet been studied. In this study, the molecular mechanisms involved in raspberry fruit ripening, particularly the polygalacturonase (RiPG) interaction with polygalacturonase inhibiting protein (RiPGIP) and substrate, were investigated with a structural approach. The 3D model of RiPG2 and RiPGIP3 was built using a comparative modeling strategy and validated using molecular dynamics (MD) simulations. The RiPG2 model structure comprises 11 complete coils of right-handed parallel β-helix architecture, with an average of 27 amino acid residues per turn. The structural model of the RiPGIP3 displays a typical structure of LRR protein, with the right-handed superhelical fold with an extended parallel β-sheet. The conformational interaction between the RiPG2 protein and RiPGIP3 showed that RiPGIP3 could bind to the enzyme and thereby leave the active site cleft accessible to the substrate. All this evidence indicates that RiPG2 enzyme could interact with RiPGIP3 protein. It can be a helpful model for evaluating protein-protein interaction as a potential regulator mechanism of hydrolase activity during pectin disassembly in fruit ripening.

Exploring proteasome inhibition using atomic weighted vector indices and machine learning approaches.

Ubiquitin-proteasome system (UPS) is a highly regulated mechanism of intracellular protein degradation and turnover. The UPS is involved in different biological activities, such as the regulation of gene transcription and cell cycle. Several researchers have applied cheminformatics and artificial intelligence methods to study the inhibition of proteasomes, including the prediction of UPP inhibitors. Following this idea, we applied a new tool for obtaining molecular descriptors (MDs) for modeling proteasome Inhibition in terms of EC50 (µmol/L), in which a set of new MDs called atomic weighted vectors (AWV) and several prediction algorithms were used in cheminformatics studies. In the manuscript, a set of descriptors based on AWV are presented as datasets for training different machine learning techniques, such as linear regression, multiple linear regression (MLR), random forest (RF), K-nearest neighbors (IBK), multi-layer perceptron, best-first search, and genetic algorithm. The results suggest that these atomic descriptors allow adequate modeling of proteasome inhibitors despite artificial intelligence techniques, as a variant to build efficient models for the prediction of inhibitory activity.