Gene Transcription In Response Research Articles

Structural insights into redox signal transduction mechanisms in the control of nitrogen fixation by the NifLA system

NifL is a conformationally dynamic flavoprotein responsible for regulating the activity of the σ54-dependent activator NifA to control the transcription of nitrogen fixation (nif) genes in response to intracellular oxygen, cellular energy, or nitrogen availability. The NifL-NifA two-component system is the master regulatory system for nitrogen fixation. NifL serves as a sensory protein, undergoing signal-dependent conformational changes that modulate its interaction with NifA, forming the NifL-NifA complex, which inhibits NifA activity in conditions unsuitable for nitrogen fixation. While NifL-NifA regulation is well understood, these conformationally flexible proteins have eluded previous attempts at structure determination. In work described here, we advance a structural model of the NifL dimer supported by a combination of scattering techniques and mass spectrometry (MS)-coupled structural analyses that report on the average structure in solution. Using a combination of small angle X-ray scattering-derived electron density maps and MS-coupled surface labeling, we investigate the conformational dynamics responsible for NifL oxygen and energy responses. Our results reveal conformational differences in the structure of NifL under reduced and oxidized conditions that provide the basis for a model for modulating NifLA complex formation in the regulation of nitrogen fixation in response to oxygen in the model diazotroph, Azotobacter vinelandii.

Recycling of bacterial RNA polymerase by the Swi2/Snf2 ATPase RapA

Free-living bacteria have regulatory systems that can quickly reprogram gene transcription in response to changes in the cellular environment. The RapA ATPase, a prokaryotic homolog of the eukaryotic Swi2/Snf2 chromatin remodeling complex, may facilitate such reprogramming, but the mechanisms by which it does so are unclear. We used multiwavelength single-molecule fluorescence microscopy in vitro to examine RapA function in the Escherichia coli transcription cycle. In our experiments, RapA at <5 nM concentration did not appear to alter transcription initiation, elongation, or intrinsic termination. Instead, we directly observed a single RapA molecule bind specifically to the kinetically stable post termination complex (PTC)-consisting of core RNA polymerase (RNAP)-bound sequence nonspecifically to double-stranded DNA-and efficiently remove RNAP from DNA within seconds in an ATP-hydrolysis-dependent reaction. Kinetic analysis elucidates the process through which RapA locates the PTC and the key mechanistic intermediates that bind and hydrolyze ATP. This study defines how RapA participates in the transcription cycle between termination and initiation and suggests that RapA helps set the balance between global RNAP recycling and local transcription reinitiation in proteobacterial genomes.

Ovarian Gene Transcriptional Responses To Antidepressant Drugs (Imipramine And Fluoxetine) In Female Wistar Rats

This study was designed to investigate ovarian gene transcriptional responses to selected antidepressant drugs (imipramine and fluoxetine) in female rats. Fifteen female rats (120 – 140 g) were used for this study. Imipramine (0.71 mg/kg) and fluoxetine (0.57 mg/kg) were given orally for 50 days. The method of RT-PCR was employed to investigate the expressions of FSH-R, p53 and Bcl-2 genes. Graphics were generated as mean +/- SEM using GraphPad Prism version 8.0. Results of the study revealed that the FSH-R, p53 and Bcl-2 expressions were significantly (p&lt;0.05) up-regulated in the imipramine-treated rats relative to their controls. Conclusively, it can be suggested that imipramine induced follicular growth and apoptosis in female Wistar rats.

A protonated cytidine stabilizes the ligand-binding pocket in the preQ1 riboswitch in thermophilic bacteria.

Riboswitches are bacterial mRNA structure elements regulating either transcription or translation of downstream genes in response to high-affinity binding of a low molecular weight ligand. Among this diverse group of RNA structures, the class-I preQ1sensing riboswitches (QSW) stand out since they are the smallest known natural riboswitches. QSW combine ligand sensing and functional control within a single structural domain that adopts a pseudoknot conformation encapsulating both the cognate ligand and the ribosome binding site. QSW also occur in thermophilic bacteria. In these cases, their tertiary structures have to be stable even at temperatures above 60 °C to be functional at the organism's optimal growth temperatures. Despite the available high-resolution structures of these riboswitches, it is not yet understood which tertiary interactions are primarily responsible for their exceptional temperature stability. Here, we show that an intricate three-dimensional network of non-canonical interactions involving various non-neighboring nucleobases is the origin of the riboswitch's thermostability. An essential part of this network is a so far undetected stably protonated cytidine. It is characterized by an exceptional high pKA value of >9.7 and could be unambiguously identified through the application of modern heteronuclear detected NMR experiments.

Transcriptional and Post-Translational Regulation of Plant bHLH Transcription Factors during the Response to Environmental Stresses.

Over the past decades, extensive research has been conducted to identify and characterize various plant transcription factors involved in abiotic stress responses. Therefore, numerous efforts have been made to improve plant stress tolerance by engineering these transcription factor genes. The plant basic Helix-Loop-Helix (bHLH) transcription factor family represents one of the most prominent gene families and contains a bHLH motif that is highly conserved in eukaryotic organisms. By binding to specific positions in promoters, they activate or repress the transcription of specific response genes and thus affect multiple variables in plant physiology such as the response to abiotic stresses, which include drought, climatic variations, mineral deficiencies, excessive salinity, and water stress. The regulation of bHLH transcription factors is crucial to better control their activity. On the one hand, they are regulated at the transcriptional level by other upstream components; on the other hand, they undergo various modifications such as ubiquitination, phosphorylation, and glycosylation at the post-translational level. Modified bHLH transcription factors can form a complex regulatory network to regulate the expression of stress response genes and thus determine the activation of physiological and metabolic reactions. This review article focuses on the structural characteristics, classification, function, and regulatory mechanism of bHLH transcription factor expression at the transcriptional and post-translational levels during their responses to various abiotic stress conditions.

JAK/STAT Signaling and Cervical Cancer: From the Cell Surface to the Nucleus.

The Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathway constitutes a rapid signaling module from the cell surface to the nucleus, and activates different cellular responses, such as proliferation, survival, migration, invasion, and inflammation. When the JAK/STAT pathway is altered, it contributes to cancer progression and metastasis. STAT proteins play a central role in developing cervical cancer, and inhibiting the JAK/STAT signaling may be necessary to induce tumor cell death. Several cancers show continuous activation of different STATs, including cervical cancer. The constitutive activation of STAT proteins is associated with a poor prognosis and overall survival. The human papillomavirus (HPV) oncoproteins E6 and E7 play an essential role in cervical cancer progression, and they activate the JAK/STAT pathway and other signals that induce proliferation, survival, and migration of cancer cells. Moreover, there is a crosstalk between the JAK/STAT signaling cascade with other signaling pathways, where a plethora of different proteins activate to induce gene transcription and cell responses that contribute to tumor growth. Therefore, inhibition of the JAK/STAT pathway shows promise as a new target in cancer treatment. In this review, we discuss the role of the JAK/STAT pathway components and the role of the HPV oncoproteins associated with cellular malignancy through the JAK/STAT proteins and other signaling pathways to induce tumor growth.

Beyond the reference: gene expression variation and transcriptional response to RNA interference in Caenorhabditis elegans.

Though natural systems harbor genetic and phenotypic variation, research in model organisms is often restricted to a reference strain. Focusing on a reference strain yields a great depth of knowledge but potentially at the cost of breadth of understanding. Furthermore, tools developed in the reference context may introduce bias when applied to other strains, posing challenges to defining the scope of variation within model systems. Here, we evaluate how genetic differences among 5 wild Caenorhabditis elegans strains affect gene expression and its quantification, in general and after induction of the RNA interference (RNAi) response. Across strains, 34% of genes were differentially expressed in the control condition, including 411 genes that were not expressed at all in at least 1 strain; 49 of these were unexpressed in reference strain N2. Reference genome mapping bias caused limited concern: despite hyperdiverse hotspots throughout the genome, 92% of variably expressed genes were robust to mapping issues. The transcriptional response to RNAi was highly strain- and target-gene-specific and did not correlate with RNAi efficiency, as the 2 RNAi-insensitive strains showed more differentially expressed genes following RNAi treatment than the RNAi-sensitive reference strain. We conclude that gene expression, generally and in response to RNAi, differs across C. elegans strains such that the choice of strain may meaningfully influence scientific inferences. Finally, we introduce a resource for querying gene expression variation in this dataset at https://wildworm.biosci.gatech.edu/rnai/.

104 Exposure to Environmental Pollutant GenX Chemical Modulates Innate and Adaptive Immunity Genes in Cow Neutrophils

Abstract GenX is an environmental contaminant with wide industrial use and found in drinking water. These chemicals have high bioaccumulation and cause adverse health effects in animals and humans. Previous study has shown that pre GenX perfluoroalkyl/polyfluoroalkyl substances (PFAS) and GenX affect immune cells but there is limited study on their impact on innate immune cells (neutrophils) in livestock, such as cows. This study evaluated the effect of GenX exposure on innate and adaptive immune response gene transcription in bovine neutrophils ex vivo. Whole blood was collected using Acid citrate dextrose as a coagulant from cows (n = 5). Neutrophils were isolated using differential centrifugation and hypotonic lysis of red cells. Isolated neutrophils were treated with GenX (100 ng), or untreated (control group) for hour at 37oC, 5%CO2 and 85% relative humidity. After treatment, total RNA was extracted using Trizol reagent, reverse transcribed to cDNA, and quantitative PCR was performed using the innate and adaptive immunity RT2 profiler array (Qiagen) with 84 genes. The qPCR data were analyzed using Livak’s method to calculate fold change (FC) in gene expression between GenX-treated and control neutrophils, and FC &amp;gt;2, (p &amp;lt; 0.05) was considered significant. Normalization of data was performed with GAPDH and Beta Actin as an internal control. Out of the 84 genes tested, 78 were expressed, 25 were upregulated and4 were downregulated, in response to GenX exposure. Exposure to GenX upregulated the expression of TLR8 (FC = 24.75), NOD2 (FC = 7.65), STAT1 (FC = 49.35), HLA-A (FC = 14.07), and NKB1A (FC = 16.52). Treatment with GenX decreased the expression TICAM1 (FC = -2.30), CD86 (FC = -2.27) and RAG1 (FC = -2.50). These results indicate that GenX exposure can activate and modulate the expression of innate and adaptive immune response genes in cow neutrophils. STAT1 is involved in transcriptional regulation and activation of TLR7/8 shifts neutrophil function from phagocytosis to NETosis. Thus, the mechanism of action of GenX on identified gene targets and their function and possible animal health consequences warrants further study.

Effects of ifosfamide and cisplatin exposure combined with a climate change scenario on the transcriptome responses of the mussel Mytilus galloprovincialis

Coastal ecosystems are currently exposed to pollutants and climate change. Namely, the increasing consumption of antineoplastic drugs and their potential release to aquatic ecosystems are raising concerns. Nevertheless, information regarding the toxicity of these drugs towards non-target species is scarce, especially considering climate change scenarios. Ifosfamide (IF) and cisplatin (CDDP) are among the antineoplastics already detected in aquatic compartments and due to their mode of action (MoA) can negatively affect aquatic organisms. This study evaluates the transcription of 17 selected target genes related to the MoA of IF and CDDP in Mytilus galloprovincialis gills exposed to environmentally relevant and toxicological meaningful concentrations (IF – 10, 100, 500 ng/L; CDDP – 10, 100, 1000 ng/L), under an actual (17 °C) and predicted warming scenario (21 °C). Results showed an upregulation of the cyp4y1 gene when exposed to the highest concentrations of IF, regardless of the temperature. Both drugs upregulated genes related to DNA damage and apoptosis (p53, caspase 8 and gadd45), especially under warmer conditions. Increased temperature also downregulated genes related to stress and immune responses (krs and mydd88). Therefore, the present results showed a gene transcriptional response of mussels to increasing concentrations of antineoplastics and that warmer temperatures modulated those effects.

Innate Immune Training Enhances the Reactivation of Latently Infected HIV-1 from Monocytic Cell lines

Abstract HIV virus can persist in a latent but activatable chronic state in resting CD4 +T-cells and macrophages that are more persistent, leading to the requirement of lifelong combination antiretroviral therapy (cART). The latency of HIV-1 in macrophage cells is associated with increased chromatin condensation induced by histone methylation at HIV-1 integration sites. Innate immune training of macrophages has been shown to relieve chromosome condensation through epigenetic rewiring. We hypothesized that training of macrophages could enhance the reactivation of HIV-1 by opening the chromatin to facilitate transcription in response to Latency Reversing Agents (LRAs). We used beta-glucan, Syk inhibitor and Rutaecarpine to train the THP89GFP cell line, which is an experimental model for latently infected HIV-1 monocytes. We found that these trained THP89GFP cells have higher transcription of HIV-1 specific genes in response to PMA stimulation. To check the epigenetic changes associated with training in the proviral HIV-1 DNA of THP89GFP, we performed a chromatin immunoprecipitation for the histone mark, H3K27Ac. Consistent with the higher induction of transcription of HIV-1 genes, we observed that multiple regions of the HIV-1 LTR had higher deposition of H3K27Ac in the trained macrophages. Our studies thus show that induction of trained innate immunity may be a viable approach to the reactivation of latently infected HIV-1. This finding supports the hypothesis that innate immune training stimuli could be developed as novel candidates for enhancing reactivation of latently infected HIV-1, which may facilitate elimination of macrophage reservoirs. This work was supported by the Intramural Research Program of NIAID, NIH This work was supported by the Intramural Research Program of NIAID, NIH and Office of AIDS research.

Addiction neuroscience goes nuclear: A role for the transcription factor RXRα

Building on work defining the cocaine-modulated transcriptional landscape in mice, Godino and colleagues focus in this issue of Neuron1 on the role of a specific nuclear receptor, RXRα. Results demonstrate that modifying accumbens RXRα expression profoundly alters gene transcription, neuronal activity, and cocaine-induced behavioral responses.

HIPK1 Inhibition Protects against Pathological Cardiac Hypertrophy by Inhibiting the CREB-C/EBPβ Axis.

Inhibition of pathological cardiac hypertrophy is recognized as an important therapeutic strategy for heart failure, although effective targets are still lacking in clinical practice. Homeodomain interacting protein kinase 1 (HIPK1) is a conserved serine/threonine kinase that can respond to different stress signals, however, whether and how HIPK1 regulates myocardial function is not reported. Here, it is observed that HIPK1 is increased during pathological cardiac hypertrophy. Both genetic ablation and gene therapy targeting HIPK1 are protective against pathological hypertrophy and heart failure in vivo. Hypertrophic stress-induced HIPK1 is present in the nucleus of cardiomyocytes, while HIPK1 inhibition prevents phenylephrine-induced cardiomyocyte hypertrophy through inhibiting cAMP-response element binding protein (CREB) phosphorylation at Ser271 and inactivating CCAAT/enhancer-binding protein β (C/EBPβ)-mediated transcription of pathological response genes. Inhibition of HIPK1 and CREB forms a synergistic pathway in preventing pathological cardiac hypertrophy. In conclusion, HIPK1 inhibition may serve as a promising novel therapeutic strategy to attenuate pathological cardiac hypertrophy and heart failure.

Imaging regional histone deacetylase expression in dementia with Lewy bodies with [11C]Martinostat (P13-6.008)

<h3>Objective:</h3> To image brain histone deacetylase (HDAC) expression using [¹¹C]Martinostat positron emission tomography (PET) in living participants with dementia with Lewy bodies (DLB). <h3>Background:</h3> Epigenetic modifications via HDACs and other mechanisms regulate transcription of specific genes in response to a cell’s environment or exposure, and epigenetic changes have been observed in postmortem brain tissue in Lewy body diseases. However, whether HDAC changes arise early in disease or only as a late phenomenon, and whether regional brain HDAC expression relates to the clinical or pathologic features of the disease remain uncertain. <h3>Design/Methods:</h3> Seven subjects with DLB and 17 age-matched healthy control (HC) subjects provided informed consent to participate. Participants underwent cognitive, motor, and neuropsychiatric evaluation followed by simultaneous MR and PET imaging with [¹¹C]Martinostat, a radioligand developed at the Massachusetts General Hospital (MGH) Martinos Center for Biomedical Imaging that binds class I HDACs with high affinity and selectivity. Data were reconstructed and standardized uptake value ratios computed using a global reference. A whole-brain voxelwise analysis was followed by region of interest-based analysis. <h3>Results:</h3> Compared to HC subjects, [¹¹C]Martinostat uptake in DLB was increased in regions enriched for Lewy body pathology, including the brainstem, medial temporal lobe, and anterior cingulate. Increased uptake was also observed in regions associated with motor function, including the striatum, motor cortex, and cerebellum. [¹¹C]Martinostat uptake was decreased in parietal cortex. <h3>Conclusions:</h3> These preliminary findings in living participants with DLB identify abnormal class I HDAC expression in regions associated with Lewy body pathology, motor circuitry, and cognition. They set the stage for planned comparisons with antemortem Parkinson’s disease (PD) and with postmortem regional HDAC expression in PD and DLB. <b>Disclosure:</b> The institution of Dr. Goodheart has received research support from American Academy of Neurology. Mr. Yoo has nothing to disclose. Ms. Striar has nothing to disclose. Ms. Quan has nothing to disclose. Prof. Wey has nothing to disclose. Dr. Wang has nothing to disclose. Dr. Gomperts has received personal compensation in the range of $0-$499 for serving as a Consultant for EIP. Dr. Gomperts has received personal compensation in the range of $0-$499 for serving on a Scientific Advisory or Data Safety Monitoring board for Jannsen. The institution of Dr. Gomperts has received research support from NIH. The institution of Dr. Gomperts has received research support from LBDA. The institution of Dr. Gomperts has received research support from DOD/CDMRP. The institution of Dr. Gomperts has received research support from FFFPRI. The institution of Dr. Gomperts has received research support from NIH. The institution of Dr. Gomperts has received research support from MJFF. The institution of Dr. Gomperts has received research support from NIH. The institution of Dr. Gomperts has received research support from NIH. The institution of Dr. Gomperts has received research support from MJFF. The institution of Dr. Gomperts has received research support from NIH. The institution of Dr. Gomperts has received research support from NIH.

DegS protease regulates the motility, chemotaxis, and colonization of Vibrio cholerae.

In bacteria, DegS protease functions as an activating factor of the σE envelope stress response system, which ultimately activates the transcription of stress response genes in the cytoplasm. On the basis of high-throughput RNA sequencing, we have previously found that degS knockout inhibits the expression of flagellum synthesis- and chemotaxis-related genes, thereby indicating that DegS may be involved in the regulation of V. cholerae motility. In this study, we examined the relationships between DegS and motility in V. cholerae. Swimming motility and chemotaxis assays revealed that degS or rpoE deletion promotes a substantial reduction in the motility and chemotaxis of V. cholerae, whereas these activities were restored in ΔdegS::degS and ΔdegSΔrseA strains, indicating that DegS is partially dependent on σE to positively regulate V. cholerae activity. Gene-act network analysis revealed that the cAMP-CRP-RpoS signaling pathway, which plays an important role in flagellar synthesis, is significantly inhibited in ΔdegS mutants, whereas in response to the overexpression of cyaA/crp and rpoS in the ΔdegS strain, the motility and chemotaxis of the ΔdegS + cyaA/crp and ΔdegS + rpoS strains were partially restored compared with the ΔdegS strain. We further demonstrated that transcription levels of the flagellar regulatory gene flhF are regulated by DegS via the cAMP-CRP-RpoS signaling pathway. Overexpression of the flhF gene in the ΔdegS strain partially restored motility and chemotaxis. In addition, suckling mouse intestinal colonization experiments indicated that the ΔdegS and ΔrpoE strains were characterized by the poor colonization of mouse intestines, whereas colonization efficacy was restored in the ΔdegSΔrseA, ΔdegS + cyaA/crp, ΔdegS + rpoS, and ΔdegS + flhF strains. Collectively, our findings indicate that DegS regulates the motility and chemotaxis of V. cholerae via the cAMP-CRP-RpoS-FlhF pathway, thereby influencing the colonization of suckling mouse intestines.

SlIAA23-SlARF6 module controls arbuscular mycorrhizal symbiosis by regulating strigolactone biosynthesis in tomato.

Auxins are a class of phytohormones with roles involved in the establishment and the maintenance of the arbuscular mycorrhizal symbiosis (AMS). AUXIN RESPONSE FACTORs (ARFs) and AUXIN/INDOLE-ACETIC ACIDs (AUX/IAAs), as two transcription factors of the auxin signaling pathway, co-regulate the transcription of auxin response genes. However, the inter-relation and regulatory mechanism of ARFs and AUX/IAAs in regulating AMS are still unclear. In this study, we found that the content of auxin in tomato roots increased sharply and revealed the importance of the auxin signaling pathway in the early stage of AMS. Notably, SlARF6 was found to play a negative role in AMF colonization. Silencing SlARF6 significantly increased the expression of AM-marker genes, as well as AMF-induced phosphorus uptake. SlIAA23 could interact with SlARF6 in vivo and in vitro, and promoted the AMS and phosphorus uptake. Interestingly, SlARF6 and SlIAA23 played a contrary role in strigolactone (SL) synthesis and accumulation in AMF-colonized roots of tomato plants. SlARF6 could directly bind to the AuxRE motif of the SlCCD8 promoter and inhibited its transcription, however, this effect was attenuated by SlIAA23 through interaction with SlARF6. Our results suggest that SlIAA23-SlARF6 co-regulated tomato-AMS via an SL-dependent pathway, thus affecting phosphorus uptake in tomato plants. This article is protected by copyright. All rights reserved.

A critical role for ecdysone response genes in regulating egg production in adult female Rhodnius prolixus.

Ecdysteroids control ovary growth and egg production through a complex gene hierarchy. In the female Rhodnius prolixus, a blood-gorging triatomine and the vector of Chagas disease, we have identified the ecdysone response genes in the ovary using transcriptomic data. We then quantified the expression of the ecdysone response gene transcripts (E75, E74, BR-C, HR3, HR4, and FTZ-F1) in several tissues, including the ovary, following a blood meal. These results confirm the presence of these transcripts in several tissues in R. prolixus and show that the ecdysone response genes in the ovary are mostly upregulated during the first three days post blood meal (PBM). Knockdown of E75, E74, or FTZ-F1 transcripts using RNA interference (RNAi) was used to understand the role of the ecdysone response genes in vitellogenesis and egg production. Knockdown significantly decreases the expression of the transcripts for the ecdysone receptor and Halloween genes in the fat body and the ovaries and reduces the titer of ecdysteroid in the hemolymph. Knockdown of each of these transcription factors typically alters the expression of the other transcription factors. Knockdown also significantly decreases the expression of vitellogenin transcripts, Vg1 and Vg2, in the fat body and ovaries and reduces the number of eggs produced and laid. Some of the laid eggs have an irregular shape and smaller volume, and their hatching rate is decreased. Knockdown also influences the expression of the chorion gene transcripts Rp30 and Rp45. The overall effect of knockdown is a decrease in number of eggs produced and a severe reduction in number of eggs laid and their hatching rate. Clearly, ecdysteroids and ecdysone response genes play a significant role in reproduction in R. prolixus.

Rock, scissors, paper: How RNA structure informs function.

RNA can fold back on itself to adopt a wide range of structures. These range from relatively simple hairpins to intricate 3D folds and can be accompanied by regulatory interactions with both metabolites and macromolecules. The last 50 yr have witnessed elucidation of an astonishing array of RNA structures including transfer RNAs, ribozymes, riboswitches, the ribosome, the spliceosome, and most recently entire RNA structuromes. These advances in RNA structural biology have deepened insight into fundamental biological processes including gene editing, transcription, translation, and structure-based detection and response to temperature and other environmental signals. These discoveries reveal that RNA can be relatively static, like a rock; that it can have catalytic functions of cutting bonds, like scissors; and that it can adopt myriad functional shapes, like paper. We relate these extraordinary discoveries in the biology of RNA structure to the plant way of life. We trace plant-specific discovery of ribozymes and riboswitches, alternative splicing, organellar ribosomes, thermometers, whole-transcriptome structuromes and pan-structuromes, and conclude that plants have a special set of RNA structures that confer unique types of gene regulation. We finish with a consideration of future directions for the RNA structure-function field.

Lactobacilli Probiotics Modulate Antibacterial Response Gene Transcription of Dendritic Cells Challenged with LPS.

Probiotics are beneficial bacteria that may modulate the immune response by altering the maturation and function of antigen-presenting cells, such as dendritic cells. This study aimed to evaluate the antibacterial gene expression of dendritic cells challenged with LPS and probiotics. Immature dendritic cells were obtained from human CD14+ monocytes and challenged with E. coli LPS and probiotics Lacticaseibacillus rhamnosus (LR-32) and Lactobacillus acidophilus (LA-5) at a ratio DC:bacteria of 1:10. The analysis of gene expression was performed by RT-qPCR using the Kit RT2 human antibacterial response. In the supernatant, the cytokines secretion was determined by ELISA. Tukey post-ANOVA with p at 5% was used for statistical analysis. LPS showed the higher upregulation of 29 genes compared with the groups where probiotics were added to LPS, including genes related to an inflammatory response like BIRC3, CASP1, CCL5, CXCL1, IL12B, IL18, MYD88, NLRP3, RIPK1, and TIRAP. Similarly, LPS increased the transcription of genes enrolled with apoptosis such as CARD6, CASP1, IRF5, MAP2K1, MAP2K4, MAPK1, MYD88, NLRP3, RIPK2, TNF, TNFRSF1A, and XIAP when compared to probiotics groups (p < 0.05). Although probiotics decrease several genes upregulated by LPS, the transcription of encoded cytokines IL12A, IL12B, IL1B, IL6, CXCL8, and TNF genes was maintained upregulated by probiotics, except for IL18, which was downregulated by LA-5. LA-5 led to a higher transcription of IL1B, IL6, and CXCL-8 which was followed by the secretion of these proteins by ELISA. The results suggest that probiotics attenuate the transcription of inflammatory and immune response genes caused by LPS.

Transcriptomic Profiling and Pathway Analysis of Mesenchymal Stem Cells Following Low Dose-Rate Radiation Exposure.

Low dose-rate radiation exposure can occur in medical imaging, as background from environmental or industrial radiation, and is a hazard of space travel. In contrast with high dose-rate radiation exposure that can induce acute life-threatening syndromes, chronic low-dose radiation is associated with Chronic Radiation Syndrome (CRS), which can alter environmental sensitivity. Secondary effects of chronic low dose-rate radiation exposure include circulatory, digestive, cardiovascular, and neurological diseases, as well as cancer. Here, we investigated 1-2 Gy, 0.66 cGy/h, 60Co radiation effects on primary human mesenchymal stem cells (hMSC). There was no significant induction of apoptosis or DNA damage, and cells continued to proliferate. Gene ontology (GO) analysis of transcriptome changes revealed alterations in pathways related to cellular metabolism (cholesterol, fatty acid, and glucose metabolism), extracellular matrix modification and cell adhesion/migration, and regulation of vasoconstriction and inflammation. Interestingly, there was increased hypoxia signaling and increased activation of pathways regulated by iron deficiency, but Nrf2 and related genes were reduced. The data were validated in hMSC and human lung microvascular endothelial cells using targeted qPCR and Western blotting. Notably absent in the GO analysis were alteration pathways for DNA damage response, cell cycle inhibition, senescence, and pro-inflammatory response that we previously observed for high dose-rate radiation exposure. Our findings suggest that cellular gene transcription response to low dose-rate ionizing radiation is fundamentally different compared to high-dose-rate exposure. We hypothesize that cellular response to hypoxia and iron deficiency are driving processes, upstream of the other pathway regulation.

Nature can still be the strongest help against aging and neurodegeneration: the sirtuins way.

Nature can still be the strongest help against aging and neurodegeneration: the sirtuins way.