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Stress is a primary risk factor for psychiatric disorders such as Major Depressive Disorder (MDD) and Post Traumatic Stress Disorder (PTSD). The response to stress involves the regulation of transcriptional programs, which is supposed to play a role in coping with stress. To evaluate transcriptional processes implemented after exposure to unavoidable traumatic stress, we applied microarray expression analysis to the PFC of rats exposed to acute footshock (FS) stress that were sacrificed immediately after the 40 min session or 2 h or 24 h after. While no substantial changes were observed at the single gene level immediately after the stress session, gene set enrichment analysis showed alterations in neuronal pathways associated with glia development, glia–neuron networking, and synaptic function. Furthermore, we found alterations in the expression of gene sets regulated by specific transcription factors that could represent master regulators of the acute stress response. Of note, these pathways and transcriptional programs are activated during the early stress response (immediately after FS) and are already turned off after 2 h—while at 24 h, the transcriptional profile is largely unaffected. Overall, our analysis provided a transcriptional landscape of the early changes triggered by acute unavoidable FS stress in the PFC of rats, suggesting that the transcriptional wave is fast and mild, but probably enough to activate a cellular response to acute stress.

Bovine mastitis is a complex infectious disease that develops in the mammary gland, predominantly by a bacterial infection of mammary tissue. Mastitis is economically important in the context of a long-lasting decrease in milk yield (in the range of 5-25%), cost of treatment, and effect on cow’s health. Genetic variability of mastitis is well established and depends upon different quantitative trait loci (QTL) related to mastitis resistance or susceptibility. The susceptibility is often attributed to single nucleotide polymorphisms (SNPs) in the variable cow breed genomes. Several global investigative attempts have resulted in studies mapping mastitis to the variations in the relevant genes. Reports have been attributed to dramatic genetic expression changes in Toll Like Receptor 4 (TLR4) genes in mastitis-positive cows. However, the mechanism behind this variable genetic expression of TLR4 genes has been studied poorly. This study aims to investigate possible mechanisms behind this variable expression of TLR4 by comparative SNP evaluation and transcriptional factor profile mining. So that the important genetic mutations and effects thereof can be exploited in selecting specific breeds with higher mastitis resistance and milk yields, this paper identifies several mutations of prominence and almost sixteen SNPs falling in TLR4 promoter and 5` untranslated region (5`UTR) sequences in mastitis-positive genotypes compared to reference genomes. The study also investigates the potential transcriptional factor program deployed in response to variable mastitis development resistance. This paper combines the classic parameters of mastitis like somatic cell count (SCC), milk electric conductivity (EC), milk pH, California mastitis test (CMT) and attempts to attribute a genetic cause in relation to variable TLR4 promoter and 5`UTR sequence SNPs. The results of this paper have wide applicability for researchers developing mastitis-resistant breeding programs and the data generated may aid in the selection of better genetic breeds. The transcription factor binding profiles given in the paper will serve as concrete leads about the studies on bovine mastitis at the molecular level and may also aid global research groups working on transcription factor (TF) -based molecular pathology of mastitis.

Streptococcus gordonii and Streptococcus mutans are oral bacteria that grow as a plaque biofilm on the tooth surface. The metabolic production of hydrogen peroxide produced by S. gordonii can inhibit the growth of S. mutans, the primary causative agent of human dental caries. [1] Manganese ions (Mn2+) are an essential nutrient for pathogenic bacteria and has been linked to virulence in many species. [2] The expression of Mn2+-selective ABC transporters in streptococci is under the regulatory control of a group of homologous metalloregulatory proteins, including ScaR from S. gordonii, and SloR from S. mutans. [3] To investigate the influence of Mn2+ ion binding on structural and dynamical properties of SloR and ScaR, we conducted molecular dynamic simulations of both proteins. The computational results were validated by experimental methods: circular dichrosim (CD) and differential scanning calorimetry (DSC)

One of the major mysteries in science is how it is possible to pack the cellular chromatin with a total length of over 1 m, into a small sphere with a diameter of 5 mm “the nucleus”, and even more difficult to envisage how to make it functional. Although we know that compaction is achieved through the histones, however, the DNA needs to be accessible to the transcription machinery and this is allowed thanks to a variety of very complex epigenetic mechanisms. Either DNA (methylation) or post-translational modifications of histone proteins (acetylation, methylation, ubiquitination and sumoylation) play a crucial role in chromatin remodelling and consequently on gene expression. Recently the serotonylation and dopaminylation of the histone 3, catalyzed by the Transglutaminase type 2 (TG2), has been reported. These novel post-translational modifications catalyzed by a predominantly cytoplasmic enzyme opens a new avenue for future investigations on the enzyme function itself and for the possibility that other biological amines, substrate of TG2, can influence the genome regulation under peculiar cellular conditions. In this review we analyzed the nuclear TG2’s biology by discussing both its post-translational modification of various transcription factors and the implications of its epigenetic new face. Finally, we will focus on the potential impact of these events in human diseases.

Objective The current research was aimed to identify candidate genes associated with development and progression of epithelial ovarian carcinoma using bioinformatics analysis. Materials and methods We screened and validated candidate genes associated with carcinogenesis and development of epithelial ovarian carcinoma via bioinformatic analysis in three microarray datasets (GSE14407, GSE29450, and GSE54388) downloaded from the Gene Expression Omnibus (GEO) database. Results Our bioinformatic analysis identified 514 differentially expressed genes (DEGs) and nine candidate hub genes (CCNB1, CDK1, BUB1, CDC20, CCNA2, BUB1B, AURKA, RRM2, and TTK). Survival analysis using the Kaplan-Meier plotter showed that high expression levels of seven candidate genes (CCNB1, RRM2, BUB1, CCNA2, AURKA, CDK1, and BUB1B) were associated with poor overall survival (OS). Gene Expression Profiling Interactive Analysis (GEPIA) revealed a higher expression level of these seven candidate genes in ovarian carcinoma samples than in normal ovarian samples. Immunostaining results from the Human Protein Atlas (HPA) database suggested that the protein expression levels of CCNB1, CCNA2, AURKA, and CDK1 were increased in ovarian cancer tissues. No difference was observed in RRM2 protein expression level between normal ovarian and ovarian cancer samples. Oncomine analysis revealed an association between the expression patterns of BUB1B, CCNA2, AURKA, CCNB1, CDK1, and BUB1 and patient clinicopathological information. Finally, six genes, namely CCNB1, CCNA2, AURKA, BUB1, BUB1B, and CDK1, were identified as hub genes and a transcription factor (TF)-gene regulatory network was constructed to identify TFs, including POLR2A, ZBTB11, KLF9, and ELF1, that were implicated in regulating these hub genes. Conclusion Six significant hub DEGs associated with a poor prognosis in epithelial ovarian cancer were identified. These could be potential biomarkers for ovarian cancer patients.

Salt stress-induced limitation in crop growth and produce is a critical problem worldwide. The prerequisite to developing salt-tolerant plants of commercial importance is understanding the plant responses to salinity exposure at physiological, biochemical, and molecular levels, integrating various approaches to understanding underlying salt tolerance mechanisms, and utilizing naturally occurring genetic resources available for salt tolerance. In this review, plant responses and associated salt tolerance, at physiological and biochemical levels through ion homeostasis, osmolyte accumulation, hormonal regulation, antioxidant responses, and mitogen-activated protein kinase cascade signaling and molecular responses through transcription factors, different gene expressions, non-coding RNA production, and epigenetic modifications are presented.

Flower color is one of the most important qualitative characteristics of ornamental horticultural plants, which mainly depends on anthocyanins and carotenoids. Modification of flower color in ornamental plants involves many aspects, including complicated structural gens, transcription factors and metabolic pathways. Anthocyanins are important secondary metabolites in the flavonoid biosynthesis pathway, which mainly derive from six anthocyanidins. Anthocyanin has antioxidant activity, protects plants and performs some other functions. Studying the genes and regulatory factors in the biosynthesis pathway will contribute to cultivating novel flower color plants and to improving plants’ resistance. To date, a series of structural and regulatory genes that are involved in anthocyanin synthesis and color formation have been reported, whose functions have also been revealed. Some color-related transgenic flowers have been successfully obtained. Carotenoids are the source of the yellow pigments in the petals of many flowers. The carotenoid biosynthesis pathway as well as its major enzymes and genes are conducive to regulate its biosynthesis via genetic engineering methods and thereby changing the color of flowers. In this paper, we review the plant flower color in terms of mechanisms of plant pigment formation, classification of flower color, biosynthesis pathway, and genes related to anthocyanin formation. Subsequently, we analyze the regulating mechanism of the expression of these genes, including transcription regulation and post-transcription regulation. The methods and achievements in flower color improvement in recent years are summarized. Finally, analyzing the molecular regulatory network in flower color formation provides a theoretical basis for the improvement and modification of flower color.

Background Polyploidy is widespread in angiosperms and has a significant impact on plant evolution, diversity, and breeding program. However, the changes in the flower development regulatory mechanism in autotetraploid plants remains relatively limited. In this study, RNA-seq analysis was used to investigate changes in signaling pathways at flowering in autotetraploid Brassica rapa. Results The study findings showed that the key genes such as CO, CRY2, and FT which promotes floral formation were down-regulated, whereas floral transition genes FPF1 and FD were up-regulated in autotetraploid B. rapa. The data also demonstrated that the positive regulators GA1 and ELA1 in the gibberellin’s biosynthesis pathway were negatively regulated by polyploidy in B. rapa. Furthermore, transcriptional factors (TFs) associated with flower development were significantly differentially expressed including the up-regulated CIB1 and AGL18, and the down-regulated AGL15 genes, and by working together such genes affected the expression of the down-stream flowering regulator FLOWERING LOCUS T in polyploid B. rapa. Compared with that in diploids autotetrapoid plants consist of differential expression within the signaling transduction pathway, with 13 TIFY gens up-regulated and 17 genes related to auxin pathway down-regulated. Conclusion Therefore, polyploidy is more likely to integrate multiple signaling pathways to influence flowering in B. rapa after polyploidization. In general, the present results shed new light on our global understanding of flowering regulation in polyploid plants during breeding program.

Circulating free-cell miRNAs are increasingly important as potential non-invasive biomarkers due to the easy accessibility of clinical materials. Moreover, their epigenetic role may provide insight into the mechanisms of pathogenesis. Nevertheless, these aspects are mostly studied in the area of oncological diseases. Therefore, this research aimed to find the potential association of selected miRNAs in serum with the expression of Th17/Treg transcription factors and clinical features in RA patients. Accordingly, experiments was conducted on rheumatoid arthritis (RA), osteoarthritis (OA) and healthy subjects (HC). Analysis of miRNAs level in serum was performed using LNA miRNA PCR assays. mir-10 was detected only in RA patients. Furthermore, its expression was correlated with IL-35 serum concentration and the mRNA level of STAT5a in whole blood in RA. Additionally, a tendency of the raised level of miR-10 was noted in RA patients with high activity disease. miR-326 was significantly upregulated in RA patients with rheumatoid factor presence. In HC the correlation between miR-26 and IL-21 serum levels and expression of SMAD3 have been found. In OA patients, correlations between miR-126 and HIF1 expression and between miR-146 and RORc have been noted. The differential association of transcription factor expression with serum miRNA levels may be important in the diagnosis and progression of RA and OA.

Destruction and death of neurons can lead to neurodegenerative diseases. One possible way to treat neurodegenerative diseases and damage of the nervous system is replacing damaged and dead neurons by cell transplantation. If new neurons can replace the lost neurons, patients may be able to regain the lost functions of memory, motor, and so on. Therefore, acquiring neurons conveniently and efficiently is vital to treat neurological diseases. In recent years, studies on reprogramming human fibroblasts into neurons have emerged one after another, and this paper summarizes all these studies. Scientists find small molecules and transcription factors playing a crucial role in reprogramming and inducing neuron production. At the same time, both the physiological microenvironment in vivo and the physical and chemical factors in vitro play an essential role in the induction of neurons. Therefore, this paper summarized and analyzed these relevant factors. In addition, due to the unique advantages of physical factors in the process of reprogramming human fibroblasts into neurons, such as safe and minimally invasive, it has a more promising application prospect. Therefore, this paper also summarizes some successful physical mechanisms of utilizing fibroblasts to acquire neurons, which will provide new ideas for somatic cell reprogramming.

Transcription factors represent the crucial role of controlling gene transcription in cancer development and progression. However, their functions in gastric cancer have not been thoroughly characterized. For this study, we comprehensively evaluated the correlation between infiltration patterns of tumor microenvironment (TME) cells and TFs expression in the cohort of stomach adenocarcinoma (STAD) from TCGA database. We integrally explored differential expression panel and prognostic value of candidate TFs in TCGA‐STAD cohort. Notably, we found a key transcription factor named HEYL, which its expression level was correlated with stromal component transformation of TME. HEYL was regularly high expressed in gastric cancer and correlated with patients’ poor prognosis. Knockdown of HEYL prominently abrogated the tendency of cell proliferation, migration, and progression in gastric cancer. Consistently, overexpression of HEYL strikingly accelerated the gastric carcinoma development through activating oncogenic signaling pathways and transcriptional activation of cadherin 11 (CDH11). Our findings not only identified the close relationship between TFs and TME phenotype, but also emphasized the crucial importance of TFs, especially HEYL, which could be identified as a candidate biomarker to evaluate prognostic risk and therapeutic effect in gastric cancer., Our data highlighted that TME‐related TFs, especially HEYL, may represent a potentially promising target of diagnosis and clinical interventions for gastric cancer patients.

Caspase-1 is an evolutionarily conserved inflammatory mediated enzyme that cleaves and activates inflammatory cytokines. It can be activated through the assembly of inflammasome and its major effect is to activate the pro-inflammatory cytokines; interleukin 1β (IL-1β) and interluekine-18 (IL-18). In addition to IL-1β and IL-8, several lines of evidence showed that caspase-1 targets the substrates that are involved in different metabolic pathways, including lipid metabolism. Caspase-1 regulates lipid metabolism through cytokine dependent or cytokine independent regulation of genes that involved in lipid metabolism and its regulation. To date, there are several reports on the role of caspase-1 in lipid metabolism. Therefore, this review is aimed to summarize the role of caspase-1 in lipid metabolism and its regulation.

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers with a poor response to current treatment regimens. The multifunctional DNA repair-redox signaling protein Ref-1 has a redox signaling function that activates several transcriptional factors (TFs) including NF-κB (RelA), STAT3, AP-1. These have been implicated in signaling in PDAC and associated with cancer progression and therapy resistance. Numerous studies have shown a role for RelA in PDAC inflammatory responses and therapy resistance, little is known as to how these inflammatory responses are modulated through Ref-1 redox signaling pathways during pancreatic pathogenesis. RelA and STAT3 are two major targets of Ref-1 and are important in PDAC pathogenesis. To decipher the mechanistic role of RelA in response to Ref-1 inhibition, we used PDAC cells (KC3590) from a genetically engineered KrasG12D-driven mouse model that also is functionally deficient for RelA (Parent/Vector) or KC3590 cells with fully functional RelA added back (clone 13; C13). We demonstrated that RelA deficient cells are more resistant to Ref-1 redox inhibitors APX3330, APX2009, and APX2014, and their sensitivity is restored in the RelA proficient cells. Knockdown of STAT3 did not change cellular sensitivity to Ref-1 redox inhibitors in either cell type. Gene expression analysis demonstrated that Ref-1 inhibitors significantly decreased IL-8, FOSB, and c-Jun when functional RelA is present. We also demonstrated that PRDX1, a known Ref-1 redox modulator, contributes to Ref-1 inhibitor cellular response. Knockdown of PRDX1 when functional RelA is present resulted in dramatically increased PDAC killing in response to Ref-1 inhibitors. The enhanced cell killing was not due to increased intracellular ROS production. Although Ref-1 inhibition decreased the NADP/NADPH ratio in the cells, the addition of PRDX1 knockdown did not further this redox imbalance. This data suggests that the mechanism of cell killing following Ref-1 inhibition is at least partially mediated through RelA and not STAT3. Further imbalancing of the redox signaling through disruption of the PRDX1-Ref-1 interaction may have therapeutic implications. Our data further support a pivotal role of RelA in mediating Ref-1 redox signaling in PDAC cells with the KrasG12D genotype and provide novel therapeutic strategies to combat PDAC drug resistance.

Autism spectrum disorder (ASD) is a collection of neurological disabilities marked by difficulties with behavior, speech, language, and interaction. It is a complicated and behaviorally defined static disorder of the developing brain. Recently it has become a serious concern across the world. The goal of this project was to use bioinformatics tools and network biology to uncover the molecular signatures and pathways of ASD. We investigated brain transcriptomics gene expression datasets and determined 47 dysregulated differentially expressed common genes. Several kinds of crucial neurodegeneration-related molecular mechanisms in the signaling structures were determined as a result of these investigations. We implemented gene set enrichment analysis (GSEA) using bimolecular pathways and gene ontology (GO) terms to determine the role of these differentially expressed genes (DEGs), as well as protein-protein interactions (PPI), transcriptional factor interactions, and post-transcriptional factor interactions. PPI network collected the top ten hub genes including KIT, PIN1, GATA1, GRIN2A, PBX2, BLK, ATP6V1B1, TCF7L1, TRAF1, and HSPG2. The PPI network also revealed the existence of two sub-networks. Moreover, several transcription factors (NFIC, USF2, TFAP2A, RELA, FOXL1, GATA2, YY1, FOXC1, NFKB1, and E2F1) and post-transcription factors (mir-335-5p, mir-26b-5p, mir-124-3p, mir-192-5p, mir-1-3p, mir-215-5p, mir-6825-5p, mir-146a-5p, mir-8485, and mir-93-5p) were found throughout this study. Some drug-like molecules were also predicted that might have a beneficial effect against ASD. We detected potentially novel links between pathogenic conditions in ASD patient's brain tissues. This work offers molecular biomarkers at the gene expression level and protein bases that could aid in a better understanding of molecular pathways, as well as potential pharmacological approaches and therapies for developing effective ASD treatments.

Transposable elements (TEs) and transcription factors (TFs) are involved in the precise regulation of gene expression during the preimplantation stage. Activation of TEs is a key event for mammalian embryonic genome activation and preimplantation early embryonic development. TFs are involved in the regulation of drastic changes in gene expression patterns, but an inventory of the interplay between TEs and TFs during normal/abnormal human embryonic development is still lacking. Here we used single-cell RNA sequencing data generated from biparental and uniparental embryos to perform an integrative analysis of TE and TF expression. Our results showed that endogenous retroviruses (ERVs) are mainly expressed during the minor embryonic genome activation (EGA) process of early embryos, while Alu is gradually expressed in the middle and later stages. Some important ERVs (e.g., LTR5_Hs, MLT2A1) and Alu TEs are expressed at significantly lower levels in androgenic embryos. Integrative analysis revealed that the expression of the transcription factors CTCF and POU5F1 is correlated with the differential expression of ERV TEs. Comparative coexpression network analysis further showed distinct expression levels of important TFs (e.g., LEUTX and ZSCAN5A) in dizygotic embryos vs. parthenogenetic and androgenic embryos. This systematic investigation of TE and TF expression in human early embryonic development by single-cell RNA sequencing provides valuable insights into mammalian embryonic development.

Chronic venous disease (CVD) is an often underestimated inflammatory pathological condition that can have a serious impact on quality of life. Many therapies have been proposed to deal with CVD, but unfortunately the symptoms recur with increasing frequency and intensity as soon as treatments are stopped. Previous studies have shown that the common inflammatory transcription factor AP-1 (activator protein-1) and nuclear factor kappa-activated B-cell light chain enhancer (NF-kB) play key roles in the initiation and progression of this vascular dysfunction. The aim of this research was to develop a herbal product that acts simultaneously on different aspects of CVD-related inflammation. Based on the evidence that several natural components of plant origin are used to treat venous insufficiency and that magnolol has been suggested as a putative modulator of AP-1, two herbal preparations based on Ruscus aculeatus root extracts, and Vitis vinifera seed extracts, as well as diosmetin and magnolol, were established. A preliminary MTT-based evaluation of the possible cytotoxic effects of these preparations led to the selection of one of them, named DMRV-2, for further investigation. First, the anti-inflammatory efficacy of DMRV-2 was demonstrated by monitoring its ability to reduce cytokine secretion from endothelial cells subjected to LPS-induced inflammation. Furthermore, using a real-time PCR-based protocol, the effect of DMRV-2 on AP-1 expression and activity was also evaluated; the results obtained demonstrated that the incubation of the endothelial cells with this preparation almost completely nullified the effects exerted by the treatment with LPS on AP-1. Similar results were also obtained for NF-kB, whose activation was evaluated by monitoring its distribution between the cytosol and the nucleus of endothelial cells after the different treatments.

Simple Summary One of the most important health problems in the paediatric population, due to its prevalence worldwide, is the occurrence of congenital heart defects. The integration of multidisciplinary approaches to clinical diagnosis will allow us to detect this type of problem in patients in a timely way. The TBX5 gene has an important participation in cardiogenesis. Therefore, we performed a case-control study, that involved the DNA methylation assessment of the TBX5 gene promoter region in patients that were non-syndromic with congenital septal defects, to identify an epigenetic marker. Moreover, we evaluated the exposure to environmental factors during pregnancy in mothers of these patients. Additionally, we used bioinformatic tools to identify transcription factors binding to the TBX5 gene region of interest and to learn their possible functional effect. These results could help to clarify the mechanisms that regulate these pathologies and establish risk markers, which can be used in future in clinical practice. Abstract The TBX5 gene regulates morphological changes during heart development, and it has been associated with epigenetic abnormalities observed in congenital heart defects (CHD). The aim of this research was to evaluate the association between DNA methylation levels of the TBX5 gene promoter and congenital septal defects. DNA methylation levels of six CpG sites in the TBX5 gene promoter were evaluated using pyrosequencing analysis in 35 patients with congenital septal defects and 48 controls. Average methylation levels were higher in individuals with congenital septal defects than in the controls (p < 0.004). In five CpG sites, we also found higher methylation levels in patients than in the controls (p < 0.05). High methylation levels were associated with congenital septal defects (OR = 3.91; 95% CI = 1.02–14.8; p = 0.045). The analysis of Receiver Operating Characteristic (ROC) showed that the methylation levels of the TBX5 gene could be used as a risk marker for congenital septal defects (AUC = 0.68, 95% CI = 0.56–0.80; p = 0.004). Finally, an analysis of environmental factors indicated that maternal infections increased the risk (OR = 2.90; 95% CI = 1.01–8.33; p = 0.048) of congenital septal defects. Our data suggest that a high DNA methylation of the TBX5 gene could be associated with congenital septal defects.

Droughts represent one of the main challenges that climate change imposes on crop production. As a globally cultivated staple crop, wheat (Triticum aestivum L.) is prone to drought environments. Therefore, improvement in drought tolerance represents a growing concern to ensure food security, especially for wheat. In this perspective, the application of Phyto-phillic exogenous materials such as glycine-betaine (GB) has been attracting attention, particularly in stress-related studies. Since roots procure the water and nutrients for plants, any improvements in their response and capacity against drought stress could induce stress tolerance in plants. However, the knowledge about the changes in root architecture, defense mechanism, hormonal metabolism, and downstream signaling, in response to GB-mediated root priming, is still limited. Therefore, we designed the present study to investigate the role of GB-mediated root priming in improving the water stress tolerance in wheat (cv. Jimai-22) under in-vitro conditions. The roots of twelve days old wheat seedlings were treated with Hoagland’s solution (GB-0), 50 mM GB (GB-1), and 100 mM GB (GB-2) for 48 h and subjected to well-watered (WW) and water-stress (WS) conditions. The osmotic stress substantially impaired shoot/root growth, dry matter accumulation, and increased malondialdehyde (MDA) and hydrogen-peroxide (H2O2) production in the roots of wheat seedlings. However, GB-mediated root priming improved the redox homeostasis of wheat roots by boosting the activities of SOD and POD and triggering the significantly higher accumulation of abscisic acid (ABA) and salicylic acid (SA) in the roots of GB-primed plants. Consequently, it modified the root architecture system and improved plant growth, dry matter accumulation, and water-stress tolerance of wheat seedlings. Moreover, GB-mediated root priming increased root sensitivity to water stress and induced overexpression of stress-responsive genes involved in ABA metabolism (TaNECD1, TaABA’OH2), their downstream signal transduction (TaPP2C, TaSNRK2.8), and activation of different transcriptional factors (TabZIP60, TaAREB3, TaWRKY2, TaERF3, and TaMYB3) that are associated with plant metabolite accumulation and detoxification of ROS under water stress conditions. Overall, our results demonstrated that GB-priming improved the physiological and biochemical attributes of wheat plants under WS conditions by improving the drought perception capacity of wheat roots, ultimately enhancing the water stress tolerance. Thus, the GB-priming of roots could help to enhance the water-stress tolerance of economically important crops (i.e., wheat).

ilustraciones, tablas, gráficas De acuerdo con el centro de control de enfermedades de los Estados Unidos (CDC’s) en su reporte de resistencia a antibióticos, las infecciones causadas por P. aeruginosa multi-fármaco resistente comprometieron alrededor de 32,600 pacientes y generaron 2,700 muertes durante el 2017. En Colombia el Sistema Nacional de Vigilancia de Resistencia Antimicrobiana (IAAS) en su informe del 2018 mostró que la P. aeruginosa es el patógeno con mayor recurrencia de la métalo β-lactamasa VIM en el territorio colombiano, alcanzando 840 casos contabilizados y dificultando el tratamiento de las infecciones de este patógeno. Como parte de la búsqueda de nuevas soluciones contra este patógeno, el mecanismo de comunicación intercelular denominado quorum sensing y los factores de transcripción que intervienen en él resultan ser blancos promisorios como adyuvantes en el tratamiento de infecciones por este patógeno. Por esta razón, en la presente investigación se seleccionaron los factores de transcripción LasR, PqsR y RhlR como blancos de estudio en el control de esta vía de comunicación. A través de la construcción de bases de datos con moléculas a las que se les ha demostrado su actividad biológica y su análisis mediante diversas herramientas del diseño de fármacos basado en el ligando, se encontraron múltiples características estructurales involucradas con la actividad contra estos factores de transcripción. Para LasR, anillos de 5 y 6 miembros (lactónicos y fenílicos), cadenas carbonadas de 10 o más carbonos, dos aceptores y un donador de puente de hidrogeno y el tamaño molecular superior a los 15 átomos fueron las características estructurales mínimas asociadas a moléculas con actividad sobre este factor. Adicionalmente se identificaron las interacciones con los residuos Tyr 47, ala 105, Thr 80, Leu 36, Ile 36, Ile 52 y Tyr 56 como posibles responsables de la actividad antagonista utilizando herramientas como fingerprints de interacción proteína-ligando y simulación de dinámicas molecular; siendo estos asociados al diseño de fármacos basado en la estructura. Los compuestos con actividad sobre PqsR exhibieron las siguientes características estructurales: biciclos nitrogenados de 6 miembros (quinoleína y quinazolina), cadenas alifáticas de un tamaño mínimo de 10 carbonos, mínimo un aceptor y donador de puente de hidrogeno y se debe igualar o superar a los 15 átomos; las interacciones con los aminoácidos que podrían estar involucrados en la actividad antagonista sobre este factor son: Tyr 258, Phe 221, Ala 102, Leu 207, Ile 149, siendo estas caracterizadas con los instrumentos del diseño e fármacos basado en la estructura. A partir de la base de datos construida para RhlR y los análisis quimioinformáticos se detectó que las moléculas con un anillo de 5 o 6 miembros (lactonas y fenilos), cadenas carbonadas de 3 a 6 carbonos; al menos 2 aceptores de puente de hidrogeno, 1 donador de puente de hidrogeno y que el conteo de átomos oscile entre 8 y 12. Como en las bases de datos públicas al momento no se encuentra elucidada la estructura terciaria de este factor de transcripción, en este trabajo se planteó y validó un modelo de estructura: con la anterior se procedió a hacer los análisis de fingerprints interacción proteína-ligando y la simulación de dinámica molecular para encontrar los residuos involucrados con la actividad antagonista, encontrado a las interacciones con la Val 60, Leu 69, Tyr 64, Tyr 72 y Ala 83 como las posibles responsables. Con el fin de complementar las características estructurales encontradas anteriormente, se crearon los farmacóforos a través del alineamiento estructural de las conformaciones obtenidas con los acoplamientos de las 10 moléculas con mejor actividad antagonista sobre cada uno de los factores de transcripción. Adicionalmente, se construyeron modelos de aprendizaje de maquina supervisados, donde los compuestos de la base de datos fueron clasificados como activos e inactivos y con el molecular fingerprint ECFP4 se caracterizó cada una de las moléculas para el entrenamiento posterior de 14 modelos; los cuales fueron clasificados según 6 métricas diferentes. De lo anterior se encontró que los mejores clasificadores fueron extreme gradient boosting y k-nearest neighbors classifier para todos los factores de transcripción y se propone el uso conjunto para la clasificación de los compuestos con posible actividad. Para integrar la información anterior, se realizó un cribado virtual sobre una base de datos molecular de productos naturales; encontrando a los compuestos: litseanolido C2, 1-hidroxi-3-metoxi-N-metil acridona y hematomato de metilo como los mejores clasificados para ser antagonistas contra LasR, PqsR y RhlR; además se identificó a las familias Rutaceae, Lauraceae y Piperaceae como una fuente potencial de compuestos con actividad contra estos factores de transcripción. (Texto tomado de la fuente). According to the United States Center for Disease Control (CDC's) in its report of antibiotic resistance, infections caused by multi-drug resistant P. aeruginosa affected around 32,600 patients and generated 2,700 deaths during 2017. In Colombia the National Antimicrobial Resistance Surveillance System (IAAS) in its 2018 report showed that P. aeruginosa is the pathogen with the highest recurrence of Metallo β-lactamase VIM in the Colombian territory, reaching 840 counted cases and making it difficult to treat the infections of this pathogen. As part of the search for new solutions against this pathogen, the intercellular communication mechanism called quorum sensing and the transcription factors involved in it turn out to be promising targets as adjuvants in the treatment of infections caused by this pathogen. For this reason, in this research, the transcription factors LasR, PqsR, and RhlR were selected as study targets in the control of this communication pathway. Through the construction of databases with active molecules. In this thesis using various tools of drug design based on the ligand, multiple structural characteristics involved with the activity against these transcription factors were found. For LasR, 5 and 6-membered rings (lactonic and phenyl), carbon chains of 10 or more carbons, two acceptors and a hydrogen bridge donor, and molecular size greater than 15 atoms were the minimum structural characteristics associated with molecules with activity on this factor. Additionally, interactions with residues Tyr 47, ala 105, Thr 80, Leu 36, Ile 36, Ile 52, and Tyr 56 were identified as possibly responsible for the antagonist activity using tools such as protein-ligand interaction fingerprints and molecular dynamics simulation; these being associated with structure-based drug design. Compounds with activity on PqsR exhibited the following structural characteristics: 6-membered nitrogenous bicycles (quinoline and quinazoline), aliphatic chains of a minimum size of 10 carbons, at least one hydrogen bridge acceptor and donor, and should equal or exceed those 15 atoms; the interactions with the amino acids that could be involved in the antagonist activity on this factor are: Tyr 258, Phe 221, Ala 102, Leu 207, Ile 149, being these characterized with the instruments of design and drugs based on the structure. From the database built for RhlR and the chemoinformatics analyzes, it was detected that molecules with a 5 or 6-membered ring (lactones and phenyl), carbon chains of 3 to 6 carbons; at least 2 hydrogen bridge acceptors, 1 hydrogen bridge donor, and that the atom count ranges between 8 and 12. As in the public databases at the moment the tertiary structure of this transcription factor is not elucidated. This work proposed and validated a structure model: with the previous one, we proceeded to do the analysis of protein-ligand interaction fingerprints and the simulation of molecular dynamics to find the residues involved with the antagonist activity, found in the interactions with Val 60, Leu 69, Tyr 64, Tyr 72 and Ala 83 as the possible culprits. In order to complement the structural characteristics, found previously, the pharmacophores were created through the structural alignment of the conformations obtained with the couplings of the 10 molecules with the best antagonist activity on each of the transcription factors. Additionally, supervised machine learning models were built, where the compounds in the database were classified as active and inactive, and with the molecular fingerprint ECFP4, each of the molecules was characterized for the subsequent training of 14 models; which were classified according to 6 different metrics. From the above, it was found that the best classifiers were extreme gradient boosting and k-nearest neighbor’s classifier for all transcription factors, and joint use is proposed for the classification of compounds with possible activity. To integrate the above information, virtual screening was performed on a molecular database of natural products; finding the compounds: C2 litseanolide, 1-hydroxy-3-methoxy-N-methyl acridone, and methyl hematomate as the best classified to be antagonists against LasR, PqsR, and RhlR; Furthermore, the Rutaceae, Lauraceae, and Piperaceae families were identified as a potential source of compounds with activity against these transcription factors. MinCiencias FPIT - Fundación para la promoción de la investigación y la tecnología Maestría Magíster en Ciencias Farmacéuticas Química medicinal y modelamiento molecular

Background Isatidis Radix, the root of Isatis indigotica Fort. (Chinese woad) can produce a variety of efficacious compound with medicinal properties. The tetraploid I. indigotica plants exhibit superior phenotypic traits, such as greater yield, higher bioactive compounds accumulation and enhanced stress tolerance. In this study, a comparative transcriptomic and metabolomic study on Isatidis Radix autotetraploid and its progenitor was performed. Results Through the targeted metabolic profiling, 283 metabolites were identified in Isatidis Radix, and 70 polyploidization-altered metabolites were obtained. Moreover, the production of lignans was significantly increased post polyploidization, which implied that polyploidization-modulated changes in lignan biosynthesis. Regarding the transcriptomic shift, 2065 differentially expressed genes (DEGs) were identified as being polyploidy-responsive genes, and the polyploidization-altered DEGs were enriched in phenylpropanoid biosynthesis and plant hormone signal transduction. The further integrative analysis of polyploidy-responsive metabolome and transcriptome showed that 1584 DEGs were highly correlated with the 70 polyploidization-altered metabolites, and the transcriptional factors TFs-lignans network highlighted 10 polyploidy-altered TFs and 17 fluctuated phenylpropanoid pathway compounds. Conclusions These results collectively indicated that polyploidization contributed to the high content of active compounds in autotetraploid roots, and the gene–lignan pathway network analysis highlighted polyploidy–responsive key functional genes and regulators.

Background Recent evidences indicated that shear stress is critical in orchestrating gene expression in cardiovascular disease. It is necessary to identify the mechanism of shear stress influencing gene expression in physiology and pathophysiology conditions. This paper aimed to identify candidate hub genes and its transcription factors with bioinformatics. Methods We analyzed microarray expression profile of GSE16706 to identify differentially expressed genes (DEGs) in low shear stress (1 dyne/cm2) treated human umbilical vein endothelial cells (HUVECs) compared with static condition for 24 h. Results 652 DEGs, including 333 up-regulated and 319 down-regulated DEGs, were screen out. Functional enrichment analysis indicated enrichment items mainly included cytokine-cytokine receptor interaction and cell cycle. Five hub genes (CDC20, CCNA2, KIF11, KIF2C and PLK1) and one significant module (score = 17.39) were identified through protein–protein interaction (PPI) analysis. Key transcriptional factor FOXC1 displayed close interaction with all the hub genes via gene-transcriptional factor network. Single-gene GSEA analysis indicated that CDC20 was linked to the G2M_CHECKPOINT pathway and cell cycle pathway. Conclusions By using integrated bioinformatic analysis, a new transcriptional factor and hub-genes network related to HUVECs treated with low shear stress were identified. The new regulation mechanism we discovered may be a promising potential therapeutic target for cardiovascular disease.

Simple Summary In aquatic biological models, the communication between cells from the immune system remains poorly characterized. In this work, to determine the gene expression of master transcriptional factors that coordinate the polarization of T cells, co-cultures of rainbow trout splenocytes are analyzed after stimulation with Interferon-gamma and/or Piscirickettsia salmonis. The results showed an upregulation of foxp3 compared to the other transcriptional factors, suggesting a potential communication between cells in the spleen, which may induce a Treg phenotype. Abstract In fish, the spleen is one of the major immune organs in the animal, and the splenocytes could play a key role in the activation and modulation of the immune response, both innate and adaptive. However, the crosstalk between different types of immune cells in the spleen has been poorly understood. In this work, an in vitro strategy is carried out to obtain and characterize mononuclear splenocytes from rainbow trout, using biomarkers associated with lymphocytes (CD4 and IgM) and antigen-presenting cells (CD83 and MHC II). Using these splenocytes, co-cultures of 24 and 48 h are used to determine the gene expression of master transcriptional factors that coordinate the polarization of T cells (t-bet, gata3, and foxp3). The results show a proportional upregulation of foxp3 (compared to t-bet and gata3) in co-cultures (at 24 h) of IFNγ-induced splenocytes with and without stimulation of Piscirickettsia salmonis proteins. In addition, foxp3 upregulation was established in co-cultures with IFNγ-induced cells and in cells only stimulated previously with P. salmonis proteins at 48 h of co-culture. These results show a potential communication between antigen-presenting-like cells and lymphocyte in the spleen, which could be induced towards a Treg phenotype.

Different types of post-translational modifications are present in bacteria that play essential roles in bacterial metabolism modulation. Nevertheless, limited information is available on these types of modifications in actinobacteria, particularly on their effects on secondary metabolite biosynthesis. Recently, phosphorylation, acetylation, or phosphopantetheneylation of transcriptional factors and key enzymes involved in secondary metabolite biosynthesis have been reported. There are two types of phosphorylations involved in the control of transcriptional factors: (1) phosphorylation of sensor kinases and transfer of the phosphate group to the receiver domain of response regulators, which alters the expression of regulator target genes. (2) Phosphorylation systems involving promiscuous serine/threonine/tyrosine kinases that modify proteins at several amino acid residues, e.g., the phosphorylation of the global nitrogen regulator GlnR. Another post-translational modification is the acetylation at the epsilon amino group of lysine residues. The protein acetylation/deacetylation controls the activity of many short and long-chain acyl-CoA synthetases, transcriptional factors, key proteins of bacterial metabolism, and enzymes for the biosynthesis of non-ribosomal peptides, desferrioxamine, streptomycin, or phosphinic acid-derived antibiotics. Acetyltransferases catalyze acetylation reactions showing different specificity for the acyl-CoA donor. Although it functions as acetyltransferase, there are examples of malonylation, crotonylation, succinylation, or in a few cases acylation activities using bulky acyl-CoA derivatives. Substrates activation by nucleoside triphosphates is one of the central reactions inhibited by lysine acetyltransferases. Phosphorylation/dephosphorylation or acylation/deacylation reactions on global regulators like PhoP, GlnR, AfsR, and the carbon catabolite regulator glucokinase strongly affects the expression of genes controlled by these regulators. Finally, a different type of post-translational protein modification is the phosphopantetheinylation, catalized by phosphopantetheinyl transferases (PPTases). This reaction is essential to modify those enzymes requiring phosphopantetheine groups like non-ribosomal peptide synthetases, polyketide synthases, and fatty acid synthases. Up to five PPTases are present in S. tsukubaensis and S. avermitilis. Different PPTases modify substrate proteins in the PCP or ACP domains of tacrolimus biosynthetic enzymes. Directed mutations of genes encoding enzymes involved in the post-translational modification is a promising tool to enhance the production of bioactive metabolites.

Made available in DSpace on 2022-05-01T10:18:54Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-11-01 Bundesministerium für Bildung und Forschung American Historical Association Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Deutsche Forschungsgemeinschaft National Institutes of Health Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Adipose tissue has been classified based on its morphology and function as white, brown, or beige/brite. It plays an essential role as a regulator of systemic metabolism through paracrine and endocrine signals. Recently, multiple adipocyte subtypes have been revealed using RNA sequencing technology, going beyond simply defined morphology but also by their cellular origin, adaptation to metabolic stress, and plasticity. Here, we performed an in-depth analysis of publicly available single-nuclei RNAseq from adipose tissue and utilized a workflow template to characterize adipocyte plasticity, heterogeneity, and secretome profiles. The reanalyzed dataset led to the identification of different subtypes of adipocytes including three subpopulations of thermogenic adipocytes, and provided a characterization of distinct transcriptional profiles along the adipocyte trajectory under thermogenic challenges. This study provides a useful resource for further investigations regarding mechanisms related to adipocyte plasticity and trans-differentiation. Department of Genetics Ribeirão Preto Medical School University of São Paulo Center for Cell-Based Therapy (CEPID/FAPESP) National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq) Regional Blood Center of Ribeirão Preto Institute for Cancer Research IPEC Department of Structural and Functional Biology Institute of Biosciences São Paulo State University (UNESP) Department of Translational Genomics Medical Faculty University of Cologne Department of Biochemistry School of Medicine Boston University Department of Integrated Biotechnology University of Mogi das Cruzes Department of Structural and Functional Biology Institute of Biosciences São Paulo State University (UNESP) Bundesministerium für Bildung und Forschung: 01ZX1901A American Historical Association: 17POST33660875 CNPq: 311319/2018-1 CNPq: 311530/2019-2 Deutsche Forschungsgemeinschaft: 413326622 CNPq: 870415/1997-2 National Institutes of Health: DK117161 National Institutes of Health: DK117163 National Institutes of Health: P30-DK-046200 Deutsche Forschungsgemeinschaft: SFB1399

Background Normal-weight polycystic ovary syndrome (PCOS) women exhibit adipose resistance in vivo accompanied by enhanced subcutaneous (SC) abdominal adipose stem cell (ASC) development to adipocytes with accelerated lipid accumulation per cell in vitro. The present study examines chromatin accessibility, RNA expression and fatty acid (FA) synthesis during SC abdominal ASC differentiation into adipocytes in vitro of normal-weight PCOS versus age- and body mass index-matched normoandrogenic ovulatory (control) women to study epigenetic/genetic characteristics as well as functional alterations of PCOS and control ASCs during adipogenesis. Results SC abdominal ASCs from PCOS women versus controls exhibited dynamic chromatin accessibility during adipogenesis, from significantly less chromatin accessibility at day 0 to greater chromatin accessibility by day 12, with enrichment of binding motifs for transcription factors (TFs) of the AP-1 subfamily at days 0, 3, and 12. In PCOS versus control cells, expression of genes governing adipocyte differentiation (PPARγ, CEBPα, AGPAT2) and function (ADIPOQ, FABP4, LPL, PLIN1, SLC2A4) was increased two–sixfold at days 3, 7, and 12, while that involving Wnt signaling (FZD1, SFRP1, and WNT10B) was decreased. Differential gene expression in PCOS cells at these time points involved triacylglycerol synthesis, lipid oxidation, free fatty acid beta-oxidation, and oxidative phosphorylation of the TCA cycle, with TGFB1 as a significant upstream regulator. There was a broad correspondence between increased chromatin accessibility and increased RNA expression of those 12 genes involved in adipocyte differentiation and function, Wnt signaling, as well as genes involved in the triacylglycerol synthesis functional group at day 12 of adipogenesis. Total content and de novo synthesis of myristic (C14:0), palmitic (C16:0), palmitoleic (C16:1), and oleic (C18:1) acid increased from day 7 to day 12 in all cells, with total content and de novo synthesis of FAs significantly greater in PCOS than controls cells at day 12. Conclusions In normal-weight PCOS women, dynamic chromatin remodeling of SC abdominal ASCs during adipogenesis may enhance adipogenic gene expression as a programmed mechanism to promote greater fat storage.

One common and reversible type of post-translational modification (PTM) is the addition of O-linked β-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation), and its dynamic balance is controlled by O-GlcNAc transferase (OGT) and glycoside hydrolase O-GlcNAcase (OGA) through the addition or removal of O-GlcNAc groups. A large amount of research data confirms that proteins regulated by O-GlcNAcylation play a pivotal role in cells. In particularly, imbalanced levels of OGT and O-GlcNAcylation have been found in various types of cancers. Recently, increasing evidence shows that imbalanced O-GlcNAcylation directly or indirectly impacts the process of cancer metastasis. This review summarizes the current understanding of the influence of O-GlcNAc-proteins on the regulation of cancer metastasis. It will provide a theoretical basis to further elucidate of the molecular mechanisms underlying cancer emergence and progression.

Steroid microbial degradation plays a significant ecological role for biomass decomposition and removal/detoxification of steroid pollutants. In this study, the initial steps of cholesterol degradation and lithocholate bioconversion by a strain with enhanced 3-ketosteroid dehydrogenase (3-KSD) activity, Nocardioides simplex VKM Ac-2033D, were studied. Biochemical, transcriptomic, and bioinformatic approaches were used. Among the intermediates of sterol sidechain oxidation cholest-5-en-26-oic acid and 3-oxo-cholesta-1,4-dien-26-oic acid were identified as those that have not been earlier reported for N. simplex and related species. The transcriptomic approach revealed candidate genes of cholesterol and lithocholic acid (LCA) catabolism by the strain. A separate set of genes combined in cluster and additional 3-ketosteroid Δ1-dehydrogenase and 3-ketosteroid 9α-hydroxylases that might be involved in LCA catabolism were predicted. Bioinformatic calculations based on transcriptomic data showed the existence of a previously unknown transcription factor, which regulates cholate catabolism gene orthologs. The results contribute to the knowledge on diversity of steroid catabolism regulation in actinobacteria and might be used at the engineering of microbial catalysts for ecological and industrial biotechnology.

One common and reversible type of post-translational modification (PTM) is the addition of O-linked β-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation), and its dynamic balance is controlled by O-GlcNAc transferase (OGT) and glycoside hydrolase O-GlcNAcase (OGA) through the addition or removal of O-GlcNAc groups. A large amount of research data confirms that proteins regulated by O-GlcNAcylation play a pivotal role in cells. In particularly, imbalanced levels of OGT and O-GlcNAcylation have been found in various types of cancers. Recently, increasing evidence shows that imbalanced O-GlcNAcylation directly or indirectly impacts the process of cancer metastasis. This review summarizes the current understanding of the influence of O-GlcNAc-proteins on the regulation of cancer metastasis. It will provide a theoretical basis to further elucidate of the molecular mechanisms underlying cancer emergence and progression.

In most plants, major unsaturated fatty acids (UFAs) are three C18 species, namely, oleic (18:1), linoleic (18:2), and α-linolenic (18:3) acids. These simple compounds play multiple crucial roles in planta and are also important economic traits of oil crops. The enzymatic steps of C18 UFA biosynthesis have been well established. However, the associated FA/lipid trafficking between the plastid and the endoplasmic reticulum remains largely unclear, as does the regulation of the expression and activities of the involved enzymes. In this review, we will revisit the biosynthesis of C18 UFAs with an emphasis on the trafficking, and present an overview of the key enzymes and their regulation. Of particular interest is the emerging regulatory network composed of transcriptional factors and upstream signaling pathways. The review thereby provides the promise of using physical, biochemical and/or genetic means to manipulate FA composition and increase oil yield in crop improvement.

Soil dwelling Streptomyces species are faced with large variations in carbon or nitrogen sources, phosphate, oxygen, iron, sulfur, and other nutrients. These drastic changes in key nutrients result in an unbalanced metabolism that have undesirable consequences for growth, cell differentiation, reproduction, and secondary metabolites biosynthesis. In the last decades evidence has accumulated indicating that mechanisms to correct metabolic unbalances in Streptomyces species take place at the transcriptional level, mediated by different transcriptional factors. For example, the master regulator PhoP and the large SARP-type regulator AfsR bind to overlapping sequences in the afsS promoter and, therefore, compete in the integration of signals of phosphate starvation and S-adenosylmethionine (SAM) concentrations. The cross-talk between phosphate control of metabolism, mediated by the PhoR–PhoP system, and the pleiotropic orphan nitrogen regulator GlnR, is very interesting; PhoP represses GlnR and other nitrogen metabolism genes. The mechanisms of control by GlnR of several promoters of ATP binding cassettes (ABC) sugar transporters and carbon metabolism are highly elaborated. Another important cross-talk that governs nitrogen metabolism involves the competition between GlnR and the transcriptional factor MtrA. GlnR and MtrA exert opposite effects on expression of nitrogen metabolism genes. MtrA, under nitrogen rich conditions, represses expression of nitrogen assimilation and regulatory genes, including GlnR, and competes with GlnR for the GlnR binding sites. Strikingly, these sites also bind to PhoP. Novel examples of interacting transcriptional factors, discovered recently, are discussed to provide a broad view of this interactions. Altogether, these findings indicate that cross-talks between the major transcriptional factors protect the cell metabolic balance. A detailed analysis of the transcriptional factors binding sequences suggests that the transcriptional factors interact with specific regions, either by overlapping the recognition sequence of other factors or by binding to adjacent sites in those regions. Additional interactions on the regulatory backbone are provided by sigma factors, highly phosphorylated nucleotides, cyclic dinucleotides, and small ligands that interact with cognate receptor proteins and with TetR-type transcriptional regulators. We propose to define the signal integration DNA regions (so called integrator sites) that assemble responses to different stress, nutritional or environmental signals. These integrator sites constitute nodes recognized by two, three, or more transcriptional factors to compensate the unbalances produced by metabolic stresses. This interplay mechanism acts as a safety net to prevent major damage to the metabolism under extreme nutritional and environmental conditions.

The ability of microorganisms to colonise and display an intracellular lifestyle within a host body increases their fitness to survive and avoid extinction. This host−pathogen association drives microbial evolution, as such organisms are under selective pressure and can become more pathogenic. Some of these microorganisms can quickly spread through the environment via transmission. The non-transmittable fungal pathogens, such as Cryptococcus, probably return into the environment upon decomposition of the infected host. This review analyses whether re-entry of the pathogen into the environment causes restoration of its non-pathogenic state or whether environmental factors and parameters assist them in maintaining pathogenesis. Cryptococcus (C.) neoformans is therefore used as a model organism to evaluate the impact of environmental stress factors that aid the survival and pathogenesis of C. neoformans intracellularly and extracellularly.

As a central player of the hypothalamic-pituitary-adrenal (HPA) axis, the corticotropin -releasing hormone (CRH) neurons in the hypothalamic paraventricular nucleus (PVN) determine the state of HPA axis and play a key role in stress response. Evidence supports that during stress response the transcription and expression of CRH was finely tuned, which involved cis-element-transcriptional factor (TF) interactions and epigenetic mechanisms. Here we reviewed recent progress in CRH transcription regulation from DNA methylation to classic TFs regulation, in which a number of paired receptors were involved. The imbalance of multiple paired receptors in regulating the activity of CRH neurons indicates a possible molecular network mechanisms underlying depression etiology and directs novel therapeutic strategies of depression in the future. Keywords: Stress, Corticotropin-releasing hormone, Transcriptional factors, Paraventricular nucleus

Transcription factors (TFs) play a central role in the gene regulation associated with a plant's development and its response to the environmental factors. The work of TFs is well regulated at each stage of their activities. TFs usually consist of three protein domains required for DNA binding, dimerization, and transcriptional regulation. Alternative splicing (AS) produces multiple proteins with varying composition of domains. Recent studies have shown that AS of some TF genes form small proteins (small interfering peptide/small interfering protein, siPEP/siPRoT), which lack one or more domains and negatively regulate target TFs by the mechanism of protein interference (peptide interference/protein interference, PEPi/PROTi). The presence of an alternative form for the transcription factor CCA1 of Arabidopsis thaliana, has been shown to be involved in the regulation of the response to cold stress. For the PtFLC protein, one of the isoforms was found, which is formed as a result of alternative splicing and acts as a negative repressor, binding to the full-length TF PtFLC and therefore regulating the development of the Poncirus trifoliata. For A. thaliana, a FLM gene was found forming the FLM-б isoform, which acts as a dominant negative regulator and stimulates the development of the flower formation process due to the formation of a heterodimer with SVP TF. Small interfering peptides and proteins can actively participate in the regulation of gene expression, for example, in situations of stress or at different stages of plant development. Moreover, small interfering peptides and proteins can be used as a tool for fundamental research on the function of genes as well as for applied research for permanent or temporary knockout of genes. In this review, we have demonstrated recent studies related to siPEP/siPROT and their involvement in the response to various stresses, as well as possible ways to obtain small proteins.

Introduction: The programmed death receptor ligand 1 (PD-L1) immunohistochemistry (IHC) assay is a widely used selection method for pembrolizumab treatment in gastric cancer (GC) patients. PD-L1 is the main regulator of immunity in oncogenesis. Material and methods: The study included 38 patients with GC. The combined treatment consisted of neoadjuvant FOLFOX6, or FLOT, chemotherapy and surgery. PD-L1 + tumor status was recorded in 12 patients (CPS &gt, 5), with a negative status recorded in 26 patients. RT-PCR determined the expression of molecular markers. The level of LC3B protein was detected by Western Blotting analysis. Results: An overexpression of PD-1, PD-L2 in the tumor is associated with AKT/mTOR mRNA profile change and autophagy initiation in IHC PD-L1 positive GCs. NACT influences these biological features, modifying the expression of AKT/mTOR components and autophagic flux. In PD-L1 positive cancers, the effect of NACT and molecular markers rearrangements are essential compared to the PD-L1 negative cancers. Conclusion: The IHC PD-L1 status in gastric cancers is the significant marker of cancer progression, recovering the multiple inner mechanisms of cancer spreading and leading to ineffective therapy. Autophagy induction and angiogenesis are found in PD-L1 positive gastric cancers.

The present study aimed to identify the involvement of critical genes in systemic vasculitis, to gain an improved understanding of the molecular circuity and to investigate novel potential gene targets for systemic vasculitis treatment. The dual-color cDNA microarray data of GSE16945, consisting of peripheral mononuclear blood cell specimens from 13 patients with systemic vasculitis and 16 healthy controls, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened in systemic vasculitis compared with controls using BRB ArrayTools, followed by the construction of a protein-protein interaction (PPI) network using the clusterProfiler package, and significant functional interaction (FI) module selection. Furthermore, transcriptional factors (TFs) among the identified DEGs were predicted and a transcriptional regulation network was constructed. A total of 173 up- and 93 downregulated genes were identified, which were mainly associated with immune response pathways. FBJ murine osteosarcoma viral oncogene homolog (FOS), ubiquitin B (UBB), signal transducer and activator of transcription 1 (STAT1) and MX dynamin-like GTPase 1 (MX1) were identified as hub proteins in the PPI network. Furthermore, UBB, FOS, and STAT1 were hub proteins in the three identified FI modules, respectively. In total, nine TFs were predicted among the DEGs. Of the DEGs that were predicted to be TFs, STAT1, v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog B (MAFB) and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein Z (YWHAZ), which interacted with each other, were identified to regulate further DEGs as target genes. Various genes, including FOS, UBB, MX1, STAT1, MAFB, and YWHAZ may be potential targets useful for the treatment of systemic vasculitis.

// Li Min 1, 2, 3, * , Cheng Zhang 1, * , Like Qu 1 , Jialiang Huang 2, 3 , Lan Jiang 2, 3 , Jiafei Liu 1 , Luca Pinello 2, 3 , Guo-Cheng Yuan 2, 3 , Chengchao Shou 1 1 Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Departments of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing 100036, P. R. China 2 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA 3 Harvard T. H. Chan School of Public Heath, Boston, MA 02115, USA * These authors have contributed equally to this work Correspondence to: Chengchao Shou, email: scc@bjcancer.org Guo-Cheng Yuan, email: gcyuan@jimmy.harvard.edu Keywords: gene regulatory pattern, network analysis, transcriptional factors, TNBC Received: October 27, 2016 Accepted: January 10, 2017 Published: February 27, 2017 ABSTRACT Background: Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype. Genome-scale molecular characteristics and regulatory mechanisms that distinguish TNBC from other subtypes remain incompletely characterized. Results: By combining gene expression analysis and PANDA network, we defined three different TF regulatory patterns. A core TNBC-Specific TF Activation Driven Pattern (TNBCac) was specifically identified in TNBC by computational analysis. The essentialness of core TFs (ZEB1, MZF1, SOX10) in TNBC was highlighted and validated by cell proliferation analysis. Furthermore, 13 out of 35 co-targeted genes were also validated to be targeted by ZEB1, MZF1 and SOX10 in TNBC cell lines by real-time quantitative PCR. In three breast cancer cohorts, non-TNBC patients could be stratified into two subgroups by the 35 co-targeted genes along with 5 TFs, and the subgroup that more resembled TNBC had a worse prognosis. Methods: We constructed gene regulatory networks in breast cancer by Passing Attributes between Networks for Data Assimilation (PANDA). Co-regulatory modules were specifically identified in TNBC by computational analysis, while the essentialness of core translational factors (TF) in TNBC was highlighted and validated by in vitro experiments. Prognostic effects of different factors were measured by Log-rank test and displayed by Kaplan-Meier plots. Conclusions: We identified a core co-regulatory module specifically existing in TNBC, which enabled subtype re-classification and provided a biologically feasible view of breast cancer.

Complications due to malaria are caused mostly by host immunological responses. Plasmodium falciparum subverts host immunity by various strategies, including modulation in the host immune responses by regulating cytokines. The transcriptional alterations of major cytokines and immunoregulators were analyzed in this study through gene expression profiling in clinically defined subgroups of P. falciparum patients. Malaria patients were included from Dhalai district hospital of Tripura with uncomplicated malaria (UC) and severe malaria (SM) and healthy controls from endemic and non-endemic areas of India. qPCR gene expression analysis was performed for all factors and they were grouped into three clusters based on their altered expressions. The first cluster was downregulated with an increased parasitic burden which included T-BET, GATA3, EOMES, TGF-&beta, STAT4, STAT6 and cytokines IFN-&gamma, IL-12, IL-4, IL-5, and IL-13. RANTES, IL-8, CCR8, and CXCR3 were decreased in the SM group. The second cluster was upregulated with severity and included TNF-&alpha, IL-10, IL-1&beta, and IL-7. PD-1 and BCL6 were increased in the SM group. The third cluster comprised of NF-&kappa, B and was not altered. The level of perforin was suppressed while GrB expression was elevated in SM. P. falciparum malaria burden is characterized by the modulation of host immunity via compromization of T cell-mediated responses and suppression of innate immune-regulators.

Background RNA-binding proteins (RBPs) play important roles in cellular homeostasis by regulating the expression of thousands of transcripts, which have been reported to be involved in human tumorigenesis. Despite previous reports of the dysregulation of RBPs in cancers, the degree of dysregulation of RBPs in cancers and the intrinsic relevance between dysregulated RBPs and clinical TNM information remains unknown. Furthermore, the co-expressed networks of dysregulated RBPs with transcriptional factors and lncRNAs also require further investigation. Results Here, we firstly analyzed the deviations of expression levels of 1,542 RBPs from 20 cancer types and found that (1) RBPs are dysregulated in almost all 20 cancer types, especially in BLCA, COAD, READ, STAD, LUAD, LUSC and GBM with proportion of deviation larger than 300% compared with non-RBPs in normal tissues. (2) Up- and down-regulated RBPs also show opposed patterns of differential expression in cancers and normal tissues. In addition, down-regulated RBPs show a greater degree of dysregulated expression than up-regulated RBPs do. Secondly, we analyzed the intrinsic relevance between dysregulated RBPs and clinical TNM information and found that (3) Clinical TNM information for two cancer types—CHOL and KICH—is shown to be closely related to patterns of differentially expressed RBPs (DE RBPs) by co-expression cluster analysis. Thirdly, we identified ten key RBPs (seven down-regulated and three up-regulated) in CHOL and seven key RBPs (five down-regulated and two up-regulated) in KICH by analyzing co-expression correlation networks. Fourthly, we constructed the co-expression networks of key RBPs between 1,570 TFs and 4,147 lncRNAs for CHOL and KICH, respectively. Conclusions These results may provide an insight into the understanding of the functions of RBPs in human carcinogenesis. Furthermore, key RBPs and the co-expressed networks offer useful information for potential prognostic biomarkers and therapeutic targets for patients with cancers at the N and M stages in two cancer types CHOL and KICH.

Complications due to malaria are caused mostly by host immunological responses. Plasmodium falciparum subverts host immunity by various strategies, including modulation in the host immune responses by regulating cytokines. The transcriptional alterations of major cytokines and immunoregulators were analyzed in this study through gene expression profiling in clinically defined subgroups of P. falciparum patients. Malaria patients were included from Dhalai district hospital of Tripura with uncomplicated malaria (UC) and severe malaria (SM) and healthy controls from endemic and non-endemic areas of India. qPCR gene expression analysis was performed for all factors and they were grouped into three clusters based on their altered expressions. The first cluster was downregulated with an increased parasitic burden which included T-BET, GATA3, EOMES, TGF-β, STAT4, STAT6 and cytokines IFN-γ, IL-12, IL-4, IL-5, and IL-13. RANTES, IL-8, CCR8, and CXCR3 were decreased in the SM group. The second cluster was upregulated with severity and included TNF-α, IL-10, IL-1β and IL-7. PD-1 and BCL6 were increased in the SM group. The third cluster comprised of NF-κB and was not altered. The level of perforin was suppressed while GrB expression was elevated in SM. P. falciparum malaria burden is characterized by the modulation of host immunity via compromization of T cell-mediated responses and suppression of innate immune-regulators.

Background The incidence of nasopharyngeal carcinoma (NPC) is rare, but a certain amount of mortality remains in NPC patients. Our study aimed to identify candidate genes as biomarkers for NPC screening, diagnosis, and therapy. Methods We investigated two microarray profile datasets GSE64634 and GSE12452 to screen the potential differentially expressed genes (DEGs) in NPC. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the DEGs were also performed. A protein-protein interaction (PPI) network of DEGs was constructed by STRING and visualized by Cytoscape software. The associated transcriptional factor regulatory network of the DEGs was also constructed. Results A total of 152 DEGs were identified from the GSE64634 and GSE12452 datasets, including 10 upregulated and 142 downregulated genes. Gene functional enrichment analysis indicated that these DEGs were enriched in the cilium movement, antimicrobial humoral response, O-glycan processing, mucosal immune response, carbohydrate transmembrane transporter activity, hormone biosynthetic process, neurotransmitter biosynthetic process, and drug metabolism-cytochrome P450 pathway. Five hub genes (DNALI1, RSPH4A, RSPH9, DNAI2, and ALDH3A1) and one significant module (score = 5.6) were obtained from the PPI network. Key transcriptional factors, such as SPI1, SIN3B, and GATA2, were identified with close interactions with these five hub DEGs from the gene-transcriptional factor network. Conclusions With the integrated bioinformatic analysis, numerous DEGs related to NPC were screened, and the hub DEGs we identified may be potential biomarkers for NPC.

Nature has evolved exquisite sensing mechanisms to detect cellular and environmental signals surrounding living organisms. These biosensors have been widely used to sense small molecules, detect environmental cues and diagnose disease markers. Metabolic engineers and synthetic biologists have been able to exploit metabolites-responsive transcriptional factors (MRTFs) as basic tools to rewire cell metabolism, reprogram cellular activity as well as boost cell’s productivity. This is commonly achieved by integrating sensor-actuator systems with biocatalytic functions and dynamically allocating cellular resources to drive carbon flux toward the target pathway. Up to date, most of identified MRTFs are derived from bacteria. As an endeavor to advance intelligent biomanufacturing in yeast cell factory, we will summarize the opportunities and challenges to transfer the bacteria-derived MRTFs to expand the small-molecule sensing capability in eukaryotic cells. We will discuss the design principles underlying MRTF-based biosensors in eukaryotic cells, including the choice of reliable reporters and the characterization tools to minimize background noise, strategies to tune the sensor dynamic range, sensitivity and specificity, as well as the criteria to engineer activator and repressor-based biosensors. Due to the physical separation of transcription and protein expression in eukaryotes, we argue that nuclear import/export mechanism of MRTFs across the nuclear membrane plays a critical role in regulating the MRTF sensor dynamics. Precisely-controlled MRTF response will allow us to repurpose the vast majority of transcriptional factors as molecular switches to achieve temporal or spatial gene expression in eukaryotes. Uncovering this knowledge will inform us fundamental design principles to deliver robust cell factories and enable the design of reprogrammable and predictable biological systems for intelligent biomanufacturing, smart therapeutics or precision medicine in the foreseeable future.

Streptococcus pyogenes (group A streptococci; GAS) is an exclusively human pathogen. It causes a variety of suppurative and non-suppurative diseases in people of all ages worldwide. Not all can be successfully treated with antibiotics. A licensed vaccine, in spite of its global importance, is not yet available. GAS express an arsenal of virulence factors responsible for pathological immune reactions. The transcription of all these virulence factors is under the control of three types of virulence-related regulators: (i) two-component systems (TCS), (ii) stand-alone regulators, and (iii) non-coding RNAs. This review summarizes major TCS and stand-alone transcriptional regulatory systems, which are directly associated with virulence control. It is suggested that this treasure of knowledge on the genetics of virulence regulation should be better harnessed for new therapies and prevention methods for GAS infections, thereby changing its global epidemiology for the better.

Background Dextrorotatory borneol (D-borneol), a cyclic monoterpene, is widely used in traditional Chinese medicine as an efficient topical analgesic drug. Fresh leaves of Cinnamomum trees, e.g., C. burmannii and C. camphor, are the main sources from which D-borneol is extracted by steam distillation, yet with low yields. Insufficient supply of D-borneol has hampered its clinical use and production of patent remedies for a long time. Biological synthesis of D-borneol offers an additional approach; however, mechanisms of D-borneol biosynthesis remain mostly unresolved. Hence, it is important and necessary to elucidate the biosynthetic pathway of D-borneol. Results Comparative analysis on the gene expression patterns of different D-borneol production C. burmannii samples facilitates elucidation on the underlying biosynthetic pathway of D-borneol. Herein, we collected three different chemotypes of C. burmannii, which harbor different contents of D-borneol.A total of 100,218 unigenes with an N50 of 1,128 bp were assembled de novo using Trinity from a total of 21.21 Gb clean bases. We used BLASTx analysis against several public databases to annotate 45,485 unigenes (45.38%) to at least one database, among which 82 unigenes were assigned to terpenoid biosynthesis pathways by KEGG annotation. In addition, we defined 8,860 unigenes as differentially expressed genes (DEGs), among which 13 DEGs were associated with terpenoid biosynthesis pathways. One 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and two monoterpene synthase, designated as CbDXS9, CbTPS2 and CbTPS3, were up-regulated in the high-borneol group compared to the low-borneol and borneol-free groups, and might be vital to biosynthesis of D-borneol in C. burmannii. In addition, we identified one WRKY, two BHLH, one AP2/ERF and three MYB candidate genes, which exhibited the same expression patterns as CbTPS2 and CbTPS3, suggesting that these transcription factors might potentially regulate D-borneol biosynthesis. Finally, quantitative real-time PCR was conducted to detect the actual expression level of those candidate genes related to the D-borneol biosynthesis pathway, and the result showed that the expression patterns of the candidate genes related to D-borneol biosynthesis were basically consistent with those revealed by transcriptome analysis. Conclusions We used transcriptome sequencing to analyze three different chemotypes of C. burmannii, identifying three candidate structural genes (one DXS, two monoterpene synthases) and seven potential transcription factor candidates (one WRKY, two BHLH, one AP2/ERF and three MYB) involved in D-borneol biosynthesis. These results provide new insight into our understanding of the production and accumulation of D-borneol in C. burmannii.

Submitted by Loreana Sanches Silveira (loreana.silveira@unesp.br) on 2019-01-18T17:07:49Z No. of bitstreams: 1 Tese Loreana S Silveira.pdf: 27685757 bytes, checksum: b7f466a0a49a2de5a3d97e63da20dcd1 (MD5) Rejected by ALESSANDRA KUBA OSHIRO ASSUNÇÃO (alessandra@fct.unesp.br), reason: Solicitamos que realize correções na submissão seguindo as orientações abaixo: - Realizar as modificações nos agradecimentos dependendo da situação: 1- Caso o auxílio financeiro tenha sido recebido através do Convênio Fapesp/Capes, verificar no termo de outorga como fazer o agradecimento ou 2- Caso tenha recebido auxílio de cada agência separadamente, a Capes, através da portaria nº 206, de 04/09/2018, exige que nos agradecimentos seja colocada a frase abaixo, exatamente como está: O presente trabalho foi realizado com apoio da Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Código de Financiamento 001 - No repositório, no campo 'Agência de Fomento', selecionar também a Capes - Qualquer dúvida entrar em contato através do e-mail bibaqu.fct@unesp.br Agradecemos a compreensão. on 2019-01-21T10:54:57Z (GMT) Submitted by Loreana Sanches Silveira (loreana.silveira@unesp.br) on 2019-01-21T16:00:24Z No. of bitstreams: 1 Loreana Silveira TESE de Doutorado vs FINAL.pdf: 15598811 bytes, checksum: 2611e4a4c1b9483ddba98487e00395e5 (MD5) Approved for entry into archive by ALESSANDRA KUBA OSHIRO ASSUNÇÃO (alessandra@fct.unesp.br) on 2019-01-21T18:07:24Z (GMT) No. of bitstreams: 1 silveira_ls_dr_prud_par.pdf: 702225 bytes, checksum: de43cd8ff1b38924f24cda2f2687c935 (MD5) Made available in DSpace on 2019-01-21T18:07:24Z (GMT). No. of bitstreams: 1 silveira_ls_dr_prud_par.pdf: 702225 bytes, checksum: de43cd8ff1b38924f24cda2f2687c935 (MD5) Previous issue date: 2018-12-11 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) O treinamento físico aeróbio é considerado uma terapia para doenças inflamatórias crônicas de baixo grau devido sua resposta anti-inflamatória mediada por células do sistema imunológico. O receptor ativado por proliferador de peroxissomo gama (PPAR-γ) é capaz de regular a polarização M1 (caráter pró-inflamatório) e M2 (caráter anti-inflamatório), assim como a resposta imunometabólica dos macrófagos. Desta maneira, propusermos na presente tese verificar se a deleção condicional do PPAR-γ em macrófagos teria algum efeito sobre o papel anti-inflamatório do exercício aeróbio moderado. Para testar nossa hipótese, foram utilizadas duas linhagens de animais: PPAR-γ LyzCre+/+ (KO) e animais controle da mesma ninhada (WT). Cada genótipo foi dividido em 1) dieta controle sedentário; 2) dieta controle e treinamento moderado; 3) dieta hiperlipídica sedentário (HF) e 4) dieta hiperlipídica e treinamento moderado (HFT). O protocolo experimental teve duração de doze semanas, sendo quatro semanas apenas de dieta e oito semanas de dieta e exercício. Foram avaliados o perfil metabólico dos animais e o perfil inflamatório de macrófagos peritoneais e do tecido adiposo subcutâneo (TAS). A deleção do PPAR-y não afetou a composição corporal ou o desempenho no teste físico em animais alimentados com dieta controle, no entanto o treinamento não apenas proporcionou melhoras metabólicas mas também na resposta imune de animais nocaute. A indução da obesidade promoveu hipertrofia no TAS de animais KO, no entanto o perfil inflamatório não foi exacerbado. Macrófagos peritoneais de animais KO exibiram acentuado ambiente inflamatório após estimulo com LPS. A adoção do programa de treinamento físico aeróbio moderado protegeu ambos os genótipos do ganho de peso, reduziu a ingestão calórica e a hipertrofia do TAS de animais KO. O treinamento físico modulou a produção de citocinas em macrófagos peritoneais, embora a polarização M2 tenha exibido atenuação na ausência de PPAR-γ. Tomados em conjunto, nossos achados demonstram importante papel modulador do fator de transcrição PPAR-γ em marcadores M2 de macrófagos, porém sua deleção não impediu os efeitos anti-inflamatórios mediados pelo exercício físico. Aerobic physical training is considered a therapy for chronic low-grade inflammatory diseases due to its anti-inflammatory response mediated by immune cells. The peroxisome proliferator-activated receptor gamma (PPAR-γ) is able to regulate the M1 (pro-inflammatory) and M2 (anti-inflammatory) polarization, as well as the immunometabolic response of macrophages. Thus, we propose in the present thesis to verify whether the conditional deletion of PPAR-γ in macrophages would have any effect on the anti-inflammatory role of moderate aerobic exercise. To test our hypothesis, two animal strains were used: PPAR-γ LyzCre+/+ (KO) and littermates control animals (WT). Each genotype was divided into 1) sedentary control diet; 2) control diet and moderate training (T); 3) sedentary high fat diet (HF) and 4) high fat diet and moderate training (HFT). The experimental protocol lasted for 12 weeks, four weeks of diet only and eight weeks of diet and exercise. The metabolic profile of the animals and the inflammatory profile of peritoneal macrophages and subcutaneous adipose tissue (SAT) were evaluated. The PPAR-γ deletion did not affect body composition or physical test performance in control diet fed animals, however the training not only provided metabolic but also the immune response enhancements on knockout animals. The induction of obesity promoted hypertrophy in the SAT, though the inflammatory profile was not exacerbated in KO animals. Peritoneal macrophages of KO animals exhibited a marked inflammatory environment after LPS stimulation. The moderate aerobic training program protected both genotypes from weight gain, reduced caloric intake and hypertrophy of SAT from KO animals. Training modulated cytokine production in peritoneal macrophages, although M2 polarization exhibited attenuation in the absence of PPAR-γ. In summary, our findings demonstrate an important modulatory role of the transcription factor PPAR-γ in macrophages M2 markers, but its deletion did not prevent the exercise-mediated anti-inflammatory effect. FAPESP 2014/01246-6 FAPESP 2017/08530-0 CAPES - Código de Financiamento 001

Trigonella foenum-graecum L. (fenugreek) is a valuable resource of producing diosgenin which serves as a substrate for synthesizing more than two hundred kinds of steroidal drugs. Phytochemical analysis indicated that methyl jasmonate (MeJA) efficiently induced diosgenin biosynthesis in fenugreek seedlings. Though early steps up to cholesterol have recently been elucidated in plants, cytochrome P450 (CYP)- and glycosyltransferase (GT)-encoding genes involved in the late steps from cholesterol to diosgenin remain unknown. This study established comparative fenugreek transcriptome datasets from the MeJA-treated seedlings and the corresponding control lines. Differential gene expression analysis identified a number of MeJA-induced CYP and GT candidate genes. Further gene expression pattern analysis across a different MeJA-treating time points, together with a phylogenetic analysis, suggested specific family members of CYPs and GTs that may participate in the late steps during diosgenin biosynthesis. MeJA-induced transcription factors (TFs) that may play regulatory roles in diosgenin biosynthesis were also discussed. This study provided a valuable genetic resource to functionally characterize the genes involved in diosgenin biosynthesis, which will push forward the production of diosgenin in microbial organisms using a promising synthetic biology strategy.

The NAC (NAM, ATAF, and CUC) genes encode transcription factors involved with the control of plant morph-physiology and stress responses. The release of the last soybean (Glycine max) genome assembly (Wm82.a2.v1) raised the possibility that new NAC genes would be present in the soybean genome. Here, we interrogated the last version of the soybean genome against a conserved NAC domain structure. Our analysis identified 32 putative novel NAC genes, updating the superfamily to 180 gene members. We also organized the genes in fifteen phylogenetic subfamilies, which showed a perfect correlation among sequence conservation, expression profile, and function of orthologous Arabidopsis thaliana genes and NAC soybean genes. To validate our in silico analyses, we monitored the stress-mediated gene expression profiles of eight new NAC-genes by qRT-PCR and monitored the GmNAC senescence-associated genes by RNA-seq. Among ER stress, osmotic stress and salicylic acid treatment, all the novel tested GmNAC genes responded to at least one type of stress, displaying a complex expression profile under different kinetics and extension of the response. Furthermore, we showed that 40% of the GmNACs were differentially regulated by natural leaf senescence, including eight (8) newly identified GmNACs. The developmental and stress-responsive expression profiles of the novel NAC genes fitted perfectly with their phylogenetic subfamily. Finally, we examined two uncharacterized senescence-associated proteins, GmNAC065 and GmNAC085, and a novel, previously unidentified, NAC protein, GmNAC177, and showed that they are nuclear localized, and except for GmNAC065, they display transactivation activity in yeast. Consistent with a role in leaf senescence, transient expression of GmNAC065 and GmNAC085 induces the appearance of hallmarks of leaf senescence, including chlorophyll loss, leaf yellowing, lipid peroxidation and accumulation of H2O2. GmNAC177 was clustered to an uncharacterized subfamily but in close proximity to the TIP subfamily. Accordingly, it was rapidly induced by ER stress and by salicylic acid under late kinetic response and promoted cell death in planta. Collectively, our data further substantiated the notion that the GmNAC genes display functional and expression profiles consistent with their phylogenetic relatedness and established a complete framework of the soybean NAC superfamily as a foundation for future analyses.

Submitted by José Gerosa Neto (netoef@yahoo.com.br) on 2019-01-23T22:43:37Z No. of bitstreams: 1 TESE Doutorado - Jose Gerosa-Neto.pdf: 4166451 bytes, checksum: 9467b29300e3017cb7ce1f3f148f9cb4 (MD5) Rejected by Claudia Adriana Spindola null (claudia@fct.unesp.br), reason: Solicitamos que realize correções na submissão seguindo as orientações abaixo: - Acrescentar a seguinte expressão do financiador nos agradecimentos das páginas iniciais : O presente trabalho foi realizado com apoio da Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Código de Financiamento 001 on 2019-01-24T10:17:09Z (GMT) Submitted by José Gerosa Neto (netoef@yahoo.com.br) on 2019-01-24T16:24:57Z No. of bitstreams: 1 TESE DOUTORADO Jose Gerosa Neto.pdf: 4179804 bytes, checksum: f64d466e42591976b7af1d28623b30f8 (MD5) Approved for entry into archive by ALESSANDRA KUBA OSHIRO ASSUNÇÃO (alessandra@fct.unesp.br) on 2019-01-24T16:55:06Z (GMT) No. of bitstreams: 1 gerosaneto_j_dr_prud.pdf: 4179804 bytes, checksum: f64d466e42591976b7af1d28623b30f8 (MD5) Made available in DSpace on 2019-01-24T16:55:06Z (GMT). No. of bitstreams: 1 gerosaneto_j_dr_prud.pdf: 4179804 bytes, checksum: f64d466e42591976b7af1d28623b30f8 (MD5) Previous issue date: 2018-10-03 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Estudos anteriores evidenciaram associações da obesidade e o desenvolvimento de dislipidemia e inflamação crônica de baixo grau. Dessa forma, é possível que alterações imunometabólicas, sistêmicas e teciduais, coordenadas por fatores de transcrição gênica, favoreçam a instalação e progressão de diversas doenças e que o nível de condicionamento físico esteja diretamente envolvido nessas alterações. Diante desses fatos, o objetivo do presente projeto foi examinar a resposta imunometabólica de indivíduos obesos frente a dois programas de exercícios físicos em esteira rolante e a possível participação do fator de transcrição gênica PPAR-γ em monócitos. Homens obesos e inativos (IMC≥ 30 kg/m2, entre 18 e 35 anos) foram recrutados e randomizados em dois grupos: Treinamento intermitente de alta intensidade (HIIT) (10 x 1:1' a 100% - VO2max) ou Treinamento contínuo moderado (MICT) (65% - VO2max). O treinamento foi realizado três vezes por semana, durante seis semanas e o gasto energético das sessões foi equalizado. Os valores de VO2max e velocidade máxima foram obtidos em teste incremental máximo em esteira rolante. Os parâmetros de composição corporal foram avaliados por bioimpedância e ultrassonografia, as concentrações sanguíneas de IL-6, IL-10, TNF-ɑ, insulina, cortisol, leptina e PAI-1 por ELISA, e perfil lipídico e glicose por ensaio enzimático colorimétrico. As coletas de sangue foram realizadas Pré e Pós seis semanas de treinamento em cinco situações: 1) Jejum e 2) Pré-Sessão; 3) Pós-Sessão; 4) 30min e 5) 60min após uma sessão de treinamento. Para cultura de células, amostras foram coletadas nos momentos Pré e Pós e a expressão dos genes IKK, TLR-4, PPAR-γ, PGC-1α e CD36 realizada por RT-PCR. Após seis semanas de treinamento, aumentos significativos ocorreram no VO2max, Velocidade Máxima e Massa Livre de Gordura (%). A Gordura Subcutânea, Pressão Arterial Sistólica e Diastólica foram reduzidas. No Jejum não houve alterações nas concentrações sanguíneas das citocinas. Nas situações de exercício a IL-6 permaneceu elevada até 60 min após a sessão e a IL-10 apresentou menores concentrações em relação a sessão Pré treinamento. Apesar dos resultados positivos encontrados, uma intervenção com maior duração parece mais indicada para adaptações significativas na composição corporal e nos parâmetros sanguíneos avaliados. Os resultados indicaram que a via do fator de transcrição PPAR-y, em monócitos, não gerou alterações significativas nos mecanismos estudados. Dessa forma, para melhor entender as implicações dos dois modelos de treinamento propostos, novos estudos devem respeitar a equiparação do gasto energético das sessões e ampliar o período de intervenção e avaliar a via do PPAR-y em outras células do sistema imunológico. Previous studies have demonstrated associations of obesity and the development of dyslipidemia and low-grade inflammation. Thus, it is possible that immunometabolic, systemic and tissue changes, coordinated by gene transcription factors, favor the establishment and progression of several diseases and that the level of physical activity is directly involved in these alterations. Thus, the aim of this project was to evaluate the immunometabolic response of obese individuals front of two programs of exercise on a treadmill and the possible participation of the gene transcription factor PPAR-γ in monocytes. Obese and inactive men (BMI ≥ 30 kg/m2, 18-35 years old) were recruited and randomized into two groups: High-intensity Intermittent Training (HIIT) (10 x 1:1´ to 100% - VO2max) or Moderate Continuous Training (MICT) (65% - VO2max). The training was performed three times a week for six weeks and the energy expenditure of the sessions was equalized. The values of VO2max and maximum velocity were obtained in maximum incremental test in treadmill. The body composition parameters were evaluated by bioimpedance and ultrasonography, blood concentrations of IL-6, IL-10, TNF-ɑ, insulin, cortisol, leptin and PAI-1 by ELISA, and lipid profile and glucose by enzymatic colorimetric assay. The blood collections were performed Pre and Post six weeks of training in five moments: 1) Fasting and 2) Pre-Session; 3) Post-Session; 4) 30min and 5) 60min after a training session. For cell culture, samples were collected at Pre and Post and expression of genes IKK, TLR-4, PPAR-γ, PGC-1α and CD36 performed by RT-PCR. After six weeks of training, significant increases occurred in VO2max, Maximum Velocity and Fat Free Mass (%). Subcutaneous fat, Systolic and Diastolic Blood Pressure were reduced. In fasting there were no changes in blood concentrations of cytokines. In exercise sessions IL-6 remained elevated up to 60min after the session and IL-10 presented lower concentrations in relation to the Pre-training session. Despite the positive results found, an intervention with longer duration seems more appropriate for significant adaptations in body composition and blood parameters evaluated. The results indicated that the PPAR-γ transcription factor pathway, in monocytes, did not generate significant changes in the mechanisms studied. Thus, in order to better understand the implications of the two training models proposed, new studies should respect the equalization of the energy expenditure of the sessions and extend the intervention period and evaluate the PPAR-y pathway in other cells of the immune system. CAPES - Código de Financiamento 001

Made available in DSpace on 2018-12-11T17:20:29Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-09-01 The epithelial-mesenchymal transition (EMT) is a dynamic process linked to metastasis in many tumor types, including mammary tumors. In this study, we evaluated E-cadherin and vimentin immunolocalization in primary canine mammary carcinomas (20 cases) and their respective metastases, as well as their relationship with the core regulators SNAIL/SLUG. To assess the number of cells undergoing the process of EMT, we quantitated double-positive (E-cadherin+/vimentin+) cells using immunofluorescence, via cell counting and image analysis. In addition, SNAIL/SLUG expression was evaluated by established immunohistochemical methods. Primary tumors had significantly more E-cadherin+/vimentin+ co-expression than their paired respective lymph node or distant metastasis, respectively. Furthermore, the percentage of E-cadherin+/vimentin+ cells in grade II and III carcinomas was significantly higher than in grade I tumors. Primary tumors had significantly higher SNAIL/SLUG expression when analyzed based on the percentage of positive cells compared with their respective distant metastases in pairwise comparisons. An inverse correlation was noted between SNAIL/SLUG immunoreactivity and percentage of E-cadherin+/vimentin+ immunopositive cells in primary tumor samples when SNAIL/SLUG immunoreactivity was grouped into 2 categories (high versus low) based on percentage-positive staining. These results show a positive correlation between E-cadherin+/vimentin+ cells and higher tumor grade, establish differences between primary tumor and their respective metastases, and provide further support that EMT plays a critical role in the metastasis of canine mammary carcinoma. Furthermore, these data suggest that modulation of this process could provide greater therapeutic control and provide support for further research to determine if E-cadherin+/vimentin+ co-immunoreactivity imparts predictive value in the clinical outcome of patients with canine mammary carcinomas. Department of Veterinary Clinic and Surgery School of Agricultural and Veterinarian Sciences São Paulo State University (UNESP) Department of Clinical Sciences and Advanced Medicine School of Veterinary Medicine University of Pennsylvania Department of Pathobiology School of Veterinary Medicine University of Pennsylvania Penn Vet Cancer Center University of Pennsylvania Department of Veterinary Clinic School of Veterinary Medicine and Animal Science São Paulo State University (UNESP) Department of Companion Animal Clinical Sciences Faculty of Veterinary Medicine and Biosciences Norwegian University of Life Sciences Department of Biomedical Sciences School of Veterinary Medicine University of Pennsylvania Department of Veterinary Clinic and Surgery School of Agricultural and Veterinarian Sciences São Paulo State University (UNESP) Department of Veterinary Clinic School of Veterinary Medicine and Animal Science São Paulo State University (UNESP)

The ability of Mycobacterium tuberculosis (M. tb) to survive and persist in the host for decades in an asymptomatic state is an important aspect of tuberculosis pathogenesis. Although adaptation to hypoxia is thought to play a prominent role underlying M. tb persistence, how the bacteria achieve this goal is largely unknown. Rv0081, a member of the DosR regulon, is induced at the early stage of hypoxia while Rv3334 is one of the enduring hypoxic response genes. In this study, we uncovered genetic interactions between these two transcription factors. RNA-seq analysis of ΔRv0081 and ΔRv3334 revealed that the gene expression profiles of these two mutants were highly similar. We also found that under hypoxia, Rv0081 positively regulated the expression of Rv3334 while Rv3334 repressed transcription of Rv0081. In addition, we demonstrated that Rv0081 formed dimer and bound to the promoter region of Rv3334. Taken together, these data suggest that Rv0081 and Rv3334 work in the same regulatory pathway and that Rv3334 functions immediately downstream of Rv0081. We also found that Rv3334 is a bona fide regulator of the enduring hypoxic response genes. Our study has uncovered a regulatory pathway that connects the early and the enduring hypoxic response, revealing a transcriptional cascade that coordinates the temporal response of M. tb to hypoxia.

Z izrazom pluripotentne matične celice označujemo nediferencirane celice, ki se lahko razvijejo v vse tri tipe zarodnih tkiv (endoderm, ektoderm in mezoderm), ne pa tudi v ekstra embrionalna tkiva. To pomeni sposobnost razvoja v več kot 200 različnih tipov celic. Njihova glavna značilnost je zmožnost neskončnega samoobnavljanja in vitro in plastičnost, saj preko celičnih delitev ne izgubijo potenciala za diferenciacijo v različne tipe tkiv. In vivo je pluripotentno stanje embrionalnih celic in je le kratko prehodno stanje v razvoju zarodka, ki nato vodi v nadaljno diferenciacijo celic in embrionalnih tkiv. Regulacija pluripotentnosti poteka na nivoju epigenetskih modifikacij, inhibicije z miRNA, različnih transkripcijskih faktorjev in majhnih molekul. Pluripotent stem cells are undifferentiated cells, which can then evolve into all three germ layers (endoderm, ectoderm and mesoderm) but not to extraembryonic tissue. This means that they can differentiate into more than 200 types of cells. Their main characteristics is the ability to self-renew in vitro and their plasticity, as they do not lose the ability to differentiate even after multiple cell divisions. In vivo, pluripotency is a short transitional phase of the embryo, that then leads to further differentiation of cells and tissues. The cells regulate their pluripotency trough epigenetic modifications, miRNA interference, various transcriptional factors and small molecules.