Changes In Gene Levels Research Articles

Research in Speech Science and Voice Disorders: The Promise of Modern Genetic Approaches in Improving Clinical Diagnosis and Treatment

Much of the research in speech science and voice biology characterizes disorders through observations of functional behaviors, physiological measurements (e.g., videostroboscopy, subglottic pressure, noninvasive electroencephalography, acoustics, etc.), and outcome metrics. This body of research contributes to our understanding of disease presentation and informs clinical assessment and treatment paradigms. However, when existing treatments are not consistently effective in empirical testing, these techniques are limited in the information they can provide for revising clinical plans and improving patient outcomes. Investigation into gene mutations and protein and gene-level changes in speech science and voice disorders is starting to elucidate the pathophysiology underlying these conditions. In this article, we discuss the strengths and limitations of research relying on behavioral and functional assessment and treatment efficacy data in speech science and voice. We also provide a basic overview of modern genetic research approaches that may lend to greater mechanistic and etiological understanding of the disorders our patients face.

Effects of β-glucan Rich Barley Flour on Glucose and Lipid Metabolism in the Ileum, Liver, and Adipose Tissues of High-Fat Diet Induced-Obesity Model Male Mice Analyzed by DNA Microarray.

We evaluated whether intake of β-glucan-rich barley flour affects expression levels of genes related to glucose and lipid metabolism in the ileum, liver, and adipose tissues of mice fed a high-fat diet. C57BL/6J male mice were fed a high-fat diet supplemented with high β-glucan barley, for 92 days. We measured the expression levels of genes involved in glucose and lipid metabolism in the ileum, liver, and adipose tissues using DNA microarray and q-PCR. The concentration of short-chain fatty acids (SCFAs) in the cecum was analyzed by GC/MS. The metabolic syndrome indices were improved by barley flour intake. Microarray analysis showed that the expression of genes related to steroid synthesis was consistently decreased in the liver and adipose tissues. The expression of genes involved in glucose metabolism did not change in these organs. In liver, a negative correlation was showed between some SCFAs and the expression levels of mRNA related to lipid synthesis and degradation. Barley flour affects lipid metabolism at the gene expression levels in both liver and adipose tissues. We suggest that SCFAs are associated with changes in the expression levels of genes related to lipid metabolism in the liver and adipose tissues, which affect lipid accumulation.

Functional analysis of plasma membrane intrinsic protein ZmPIP1;1 involved in drought tolerance and photosynthesis in maize

<p indent=0mm>Plasma membrane intrinsic protein (PIP) is one of the main subfamily of aquaporin regulates diverse physiology functions during plant growth and development. In previous research, the expression of <italic>ZmPIP1</italic>;<italic>1</italic> was induced by osmosis or salt stress. However, the biological function of <italic>ZmPIP1</italic>;<italic>1</italic> was still unclear in maize. In this study, <italic>ZmPIP1</italic>;<italic>1</italic> overexpressed transgenic plants were obtained and exhibited less water loss rate and enhanced drought tolerance compared to wild type. Transcriptome sequencing indicated significant changes in the expression levels of genes involved in ABA biosynthesis and its signaling pathways. Photosynthetic activity, kernel width and kernel weight was increased in <italic>ZmPIP1</italic>;<italic>1</italic> overexpression maize, but not growth under normal condition compared with wild type. Moreover, interaction between ZmPIP1;1 and ZmPIP2;6 was observed by bimolecular fluorescence complementation (BiFC) experiment, resulting in re-localized on plasma membrane and chloroplast in maize mesophyll protoplast. Our study laid an important foundation for understanding the molecular mechanism of <italic>ZmPIP1</italic>;<italic>1</italic>, and provided a new method of molecular breeding for high photosynthetic efficiency.

Comparative expression profiling reveals the role of the hot pepper apoplast under drought conditions

Drought stress is the most important limiting factor of crop cultivation around the world and stress conditions will modulate the expression of many genes that play a significant role in the plant growth and development and to stress adaptation. The apoplast is a dynamic environment subject and considered as a ‘key information bridge’ between the environment and cells. In the present study we aimed to measure the changes in the expression levels of genes by RT-qPCR studies.Analysis shown the down-regulation of Peptidylprolyl isomerase and Pin II type protease inhibitor and there observed the huge increase in the expression of Pectinesterase and Alpha L fucosidase under treated conditions. These changes in the expression level of proteins under stress conditions implicate their possible role in stress tolerance and would prove to be useful for protein phenotyping.

The transcription factor WRKY22 is required during cryo-stress acclimation in Arabidopsis shoot tips.

Storage of meristematic tissue at ultra-low temperatures offers a mean to maintain valuable genetic resources from vegetatively reproduced plants. To reveal the biology underlying cryo-stress, shoot tips of the model plant Arabidopsis thaliana were subjected to a standard preservation procedure. A transcriptomic approach was taken to describe the subsequent cellular events which occurred. The cryoprotectant treatment induced the changes in the transcript levels of genes associated with RNA processing and primary metabolism. Explants of a mutant lacking a functional copy of the transcription factor WRKY22 were compromised for recovery. A number of putative downstream targets of WRKY22 were identified, some related to phytohormone-mediated defense, to the osmotic stress response, and to development. There were also alterations in the abundance of transcript produced by genes encoding photosynthesis-related proteins. The wrky22 mutant plants developed an open stomata phenotype in response to their exposure to the cryoprotectant solution. WRKY22 probably regulates a transcriptional network during cryo-stress, linking the explant’s defense and osmotic stress responses to changes in its primary metabolism. A model is proposed linking WRKY53 and WRKY70 downstream of the action of WRKY22.

Shikonin inhibits CEBPD downregulation in IL‑17‑treated HaCaT cells and in an imiquimod‑induced psoriasis model.

Psoriasis is a chronic inflammatory skin disease characterized by well-defined scaly papules and plaques. Interleukin (IL)-17 is involved in its pathogenesis and promotes the proliferation of epidermal keratinocytes through signal transducer and activator of transcription 3 (STAT3) activation. Shikonin, a natural naphthoquinone isolated from Lithospermum erythrorhizon, possesses anti-inflammatory and immunosuppressive properties and can suppress IL-17-induced vascular endothelial growth factor expression by inhibiting the JAK/STAT3 pathway. In the present study, MTS, iCELLigence and RT-qPCR were used to determine the optimal concentration and duration of IL-17 or shikonin acting on HaCaT cells. The changes in the expression levels of genes associated with the IL-6/STAT3 pathway in differentially treated cells were analyzed via RT2Profiler™ PCR Array. Small interfering RNA was used to silence the expression levels of the target gene CCAAT/enhancer-binding protein δ (CEBPD). Western blotting and immunohistochemistry were used to evaluate the effect of shikonin on imiquimod-induced psoriasis in mice and the expression levels of CEBPD. Shikonin reversed IL-17-mediated downregulation of the tumor suppressor CEBPD in HaCaT cells. Moreover, low levels of CEBPD in the imiquimod-induced mouse model of psoriasis were restored by shikonin treatment, which ameliorated excessive keratinocyte proliferation. Taken together, these findings suggest that CEBPD plays a key role in the pathogenesis of psoriasis and can be targeted by shikonin as a potential therapeutic strategy.

Gonadotropin-releasing hormone-independent effects of recombinant vertebrate ancient long opsin in the goldfish Carassius auratus reveal alternative reproduction pathways.

Vertebrate ancient long (VAL)-opsin is a green-sensitive photoreceptor that shows high sequence similarity to vertebrate ancient opsin, which is considered to play a role in sexual maturation via gonadotropin-releasing hormone (GnRH); however, the role of VAL-opsin in vertebrate sexual maturity remains unclear. Therefore, we investigated the possible role of VAL-opsin in reproduction in the goldfish Carassius auratus under a state of GnRH inhibition. Goldfish were injected with recombinant VAL-opsin protein (0.5μg/g body mass) and/or the GnRH antagonist cetrorelix (0.5μg/fish), and changes in the mRNA expression levels of genes associated with goldfish reproduction were measured by quantitative polymerase chain reaction, including those involved in the hypothalamus-pituitary-gonad (HPG) axis, VAL-opsin, GnRH, the gonadotropins (GTHs) luteinizing hormone and follicle-stimulating hormone, and estrogen receptor (ER). Moreover, the fish were irradiated with a green light-emitting diode (520nm) to observe the synergistic effect on the HPG axis with VAL-opsin. Green LED exposure significantly and slightly increased the VAL-opsin and GnRH levels, respectively; however, these effects were blocked in groups injected with cetrorelix at all time points. Cetrorelix significantly decreased the mRNA levels of GTHs and ER, whereas these hormones recovered by co-treatment with VAL-opsin. These results indicate that green LED is an effective light source to promote the expression of sex hormones in fish. Moreover, VAL-opsin not only affects activity of the HPG axis but also appears to act on the pituitary gland directly to stimulate a new sexual maturation pathway that promotes the secretion of GTHs independent of GnRH.

Abscisic Acid and Gibberellins Act Antagonistically to Mediate Epigallocatechin-3-Gallate-Retarded Seed Germination and Early Seedling Growth in Tomato

Germination is a crucial event in plant lifecycle mediated by a complex hormonal crosstalk. In this study, we revealed an antagonistic interaction between phytohormone abscisic acid (ABA) and gibberellins in epigallocatechin-3-gallate (EGCG)-retarded germination and early seedling growth in tomato. High concentrations of EGCG (0.5 mM and 1.0 mM) decelerated the seed germination and reduced the germination rate and biomass accumulation in seedlings. EGCG-induced inhibition in seedling growth was associated with oxidative stress and changes in antioxidant enzyme activity. Moreover, EGCG treatment increased the ABA content and decreased the GA3 content, leading to a significant reduction in the ratio of GA3/ABA in a dose-dependent manner. EGCG-induced changes in ABA and GA levels were attributed to the changes in expression levels of genes involved in their metabolism. Either exogenous GA application or endogenous ABA deficiency both alleviated EGCG-induced inhibition in early seedling growth. These results suggest that EGCG inhibits seed germination and early seedling growth by affecting the balance between ABA and GA in tomato. These findings are important to better understand the role of flavonoids in seed germination and their implications in controlling seed dormancy.

Oxytocin/Osteocalcin/IL-6 and NGF/BDNF mRNA Levels in Response to Cold Stress Challenge in Mice: Possible Oxytonic Brain-Bone-Muscle-Interaction.

Oxytocin (Oxt), osteocalcin (Ost), and NGF/BDNF have a role in bone homeostasis, reproduction, and cognition. Oxt/Ost is required for muscle repair. We investigated gene response of muscle and the inter-organ communication following cold stress (CS). The mRNA quantity of Ngf, Ost, Oxt, Bdnf, p75ntr, Ntrk1, Gprc6a, Oxtr, Ntrk2, UCP1, and Il-6 genes in bone, brain, soleus (SOL), and tibialis anterior (TA) muscles from adult mice following CS were investigated. The myosin heavy-chain Mhc2b, Mhc1, Mhc2x, and Mhc2a gene expression were investigated. Mice were maintained at T = 23°C or 4°C for 6 h and 5-days (5d). CS mice did not show signs of muscle degeneration. An upregulation of Ucp1 and Ngf genes by 2 and 1.5 folds, respectively, in TA after 6 h CS and Ntrk1 by 4 and 22 folds in SOL muscle after 6 h and 5d CS, respectively, was observed; while after 6 h CS p75Ntr was downregulated in either muscle. Bdnf was unaffected, while after 5d CS Ntrk2 was upregulated in TA. Ost was downregulated in SOL by 0.9-folds at 5d. Following 5d CS, Oxtr and Il-6 genes were upregulated, respectively, by 1 and 1.5 folds in SOL. A downregulation of Mhc2b, respectively, by 0.96 and 0.88-folds after 6 h and 5d CS in SOL and Mhc2a was also downregulated by 0.88-fold after 5d CS in TA. Mhc1 and Mhc2x were not affected. Changes in the expression levels of genes in TA and SOL muscles, bone, and brain following CS were regulated by IL6 and Oxt. CS potentiates the slow-twitch phenotype of SOL which is in line with the metabolic need of this muscle, and the potentiation of the slow-twitch phenotype in TA. Oxt and IL6 coordinate a phenotype-dependent tonic effect of slow-twitch muscle and Oxt regulates the inter-organ interaction between brain and SOL muscle. Muscle tropism is maintained by NGF signaling following CS.

Metabolic plasticity mediates differential responses to spring and autumn migrations: Evidence from gene expression patterns in migratory buntings.

What is the central question of this study? What are the molecular underpinnings of seasonal metabolic plasticity during spring and autumn migrations in songbirds? What is the main finding and its importance? We report differences in mRNA levels of genes involved in the regulation of glucose and fat metabolism between photoinduced non-migratory and migratory states and between the spring and autumn migratory states. Higher expression of genes associated with fat mobilization and energy generation in the spring than in the autumn migration suggests differential activation of the metabolic pathways or alteration in the efficiency of existing functional machinery during annual journeys between nearly fixed destinations. The molecular underpinnings of metabolic plasticity underlying differential responses to spring and autumn migrations are not well understood. We investigated this by examining the differences in mRNA levels of metabolic genes in the liver, muscle and adipose tissues of night-migratory red-headed buntings between photostimulated non-migratory and migratory states and between spring and autumn migratory states. Buntings accumulated more subcutaneous fat and hepatic lipid, had higher body mass, larger adipose cells and higher circulating triglyceride and free fatty acid levels and exhibited more intense Zugunruhe in the spring migratory state than in the autumn migratory state. More importantly, we found differences in the hepatic expression of pdc and pdk genes, indicating a differential acetyl-CoA requirement, and of the mdh and ogdh genes, suggesting differential oxidative phosphorylation between the non-migratory and migratory states and between the spring and autumn migratory states. Differences in fasn, bmal1 and glut1 mRNA levels were consistent with this and suggested seasonal differences in lipogenesis and/or glucose uptake. Likewise, differences in mRNA levels of genes coding for lipases (atgl and lpl) suggested that adipose triglycerides and free fatty acids serve largely as the metabolic substrate. Furthermore, changes in mRNA levels of genes coding for the fatty acid binding protein (fabp3) and fatty acid translocases (cd36) were consistent with differential fat fuel supply (via circulating free fatty acids) to aerobically exercising flight muscles between the spring and autumn migrations. These results show seasonal adaptation of genetic pathway(s) underlying seasonal metabolic plasticity that seems to mediate differential responses to spring and autumn migrations in latitudinal migratory songbirds.

Chlojaponilactone B Attenuates Lipopolysaccharide-Induced Inflammatory Responses by Suppressing TLR4-Mediated ROS Generation and NF-κB Signaling Pathway.

The lindenane-type sesquiterpenoid chlojaponilactone B (1), isolated from Chloranthus japonicus, has been reported to possess anti-inflammatory properties. The present study aimed to further explore the molecular mechanisms underlying the anti-inflammatory activity of 1. RNA-seq analyses revealed the significant changes in the expression levels of genes related to multiple inflammatory pathways upon treatment of lipopolysaccharide (LPS)-induced RAW 264.7 murine macrophages with 1. Real time PCR (RT-PCR) and Western blotting were used to confirm the modulations in the expression of essential molecules related to inflammatory responses. Compound 1 inhibited toll like receptor 4 (TLR4) and myeloid differentiation factor 88 (MyD88) activation upon LPS stimulation, influencing the expression of NF-κB and pro-inflammatory mediators. Molecular docking studies showed that 1 bound to TLR4 in a manner similar to that of TAK-242, a TLR4 inhibitor. Moreover, our results showed that 1 suppressed inflammatory responses by inhibiting TLR4 and subsequently decreasing reactive oxygen species (ROS) generation, downregulating the NF-κB, thus reducing the expression of the pro-inflammatory cytokines iNOS, NO, COX-2, IL-6 and TNF-α; these effects were similar to those of TAK-242. We proposed that 1 should be considered as a potential anti-inflammatory compound in future research.

Transcriptomic characterisation of the optimised rat model of Walker 256 breast cancer cell-induced bone pain.

In patients with breast cancer, metastases of cancer cells to the axial skeleton may cause excruciating pain, particularly in the advanced stages. The current drug treatments available to alleviate this debilitating pain condition often lack efficacy and/or produce undesirable side effects. Preclinical animal models of cancer-induced bone pain are key to studying the mechanisms that cause this pain and for the success of drug discovery programs. In a previous study conducted in our laboratory, we validated and characterised the rat model of Walker 256 cell-induced bone pain, which displayed several key resemblances to the human pain condition. However, gene level changes that occur in the pathophysiology of cancer-induced bone pain in this preclinical model are unknown. Hence, in this study, we performed the transcriptomic characterisation of the Walker 256 cell line cultured in vitro to predict the molecular genetic profile of this cell line. We also performed transcriptomic characterisation of the Walker 256 cell-induced bone pain model in rats using the lumbar spinal cord and lumbar dorsal root ganglia tissues. Here we show that the Walker 256 cell line resembles the basal-B molecular subtype of human breast cancer cell lines. We also identify several genes that may underpin the progression of pain hypersensitivities in this condition, however, this needs further confirmatory studies. These transcriptomic insights have the potential to direct future studies aimed at identifying various mechanisms underpinning pain hypersensitivities in this model that may also assist in discovery of novel pain therapeutics for breast cancer-induced bone pain.

An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of Bagging and Non-Bagging "Golden Delicious" Apple.

Apple skin russeting naturally occurs in many varieties, particularly in “Golden Delicious” and its pedigree, and is regarded as a non-invasive physiological disorder partly caused by excessive deposition of lignin. However, the understanding of its molecular mechanism is still limited. In this study, we used iTRAQ (isobaric tags for relative and absolute quantitation) and RNA-seq to detect the changes in the expression levels of genes and proteins in three developmental stages of russeting formation, in russeted (non-bagging) and non-russeted (bagging) skin of “Golden Delicious” apple. 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups were detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptomics and proteomics data revealed that four genes (MD03G1059200, MD08G1009200, MD17G1092400, and MD17G1225100) involved in lignin biosynthesis are significant changed during apple russeting formation. Additionally, 92 transcription factors, including 4 LIM transcription factors, may be involved in apple russeting formation. Among them, one LIM transcription factor (MD15G1068200) was capable of binding to the PAL-box like (CCACTTGAGTAC) element, which indicated it was potentially involved in lignin biosynthesis. This study will provide further views on the molecular mechanisms controlling apple russeting formation.

Schistosoma japonicum infection causes a reprogramming of glycolipid metabolism in the liver

BackgroundRecent investigations indicate that schistosome infection is closely associated with aberrant glycolipid metabolism. However, the actual glycolipid metabolism gene expression, as well as the possible pathways that regulate glycolipid metabolism in the schistosome-infected liver, has not been extensively explored.MethodsIn this study, we evaluated the dynamic expression of glycolipid metabolism-associated genes and proteins in the livers from mice infected with Schistosoma japonicum at the indicated time points using real-time PCR and immunofluorescence. Then, cultures of macrophages were treated with schistosome soluble egg antigen (SEA) to detect the expression levels of genes associated with glucose and lipid metabolism in order to identify macrophages metabolic characteristics in response to these antigens. Furthermore, SEA-stimulated macrophages were co-cultures with hepatocytes and detected the effects of macrophages on the gene expression of hepatocytes metabolism.ResultsThe expression of glycolysis-related genes (Ldha, Glut4, Pkm2, Glut1, Pfkfb3, Aldoc, HK2, Pfk) in the liver were upregulated but the gluconeogenesis gene (G6pc) was downregulated during S. japonicum infection. In addition, the mRNA levels of fatty acid (FA) oxidation-related genes (Ucp2, Atp5b, Pparg) in the liver were significantly upregulated; however, the FA synthesis genes (Fas, Acc, Scd1, Srebp1c) and lipid uptake gene (Cd36) were downregulated post-S. japonicum-infection. In consistence with these data, stimulation with SEA in vitro significantly enhanced the gene expression that involved in glycolysis and FA oxidation, but decreased genes related to gluconeogenesis, FA synthesis and lipid uptake in macrophages. The levels of phosphorylated AMPK, AKT and mTORC1 were increased in macrophages after SEA stimulation. Inhibition of phosphorylated AMPK, AKT and mTORC1 promoted SEA-treated macrophages to produce glucose. In addition, suppression of phosphorylated-AMPK, but not phosphorylated-AKT and phosphorylated-mTOR, induced the lipid accumulation in SEA-stimulated macrophages. Furthermore, SEA-treated macrophages significantly reduced the expression of Acc mRNA in hepatocytes in vitro.ConclusionsThese findings reveal S. japonicum infection induces dynamic changes in the expression levels of genes involved in catabolism (glucose uptake, glycolysis and fatty acid oxidation) and suppressing anabolism (glycogen synthesis) in the liver, which could occur via macrophages’ metabolic states, particularly those involved in the AMPK, AKT and mTORC1 pathways.

The Drosophila nuclear receptors EcR and ERR jointly regulate the expression of genes involved in carbohydrate metabolism

The rate of carbohydrate metabolism is tightly coordinated with developmental transitions in Drosophila, and fluctuates depending on the requirements of a particular developmental stage. These successive metabolic switches result from changes in the expression levels of genes encoding glycolytic, tricarboxylic acid cycle (TCA), and oxidative phosphorylation enzymes. In this report, we describe a repressive action of ecdysone signaling on the expression of glycolytic genes and enzymes of glycogen metabolism in Drosophila development. The basis of this effect is an interaction between the ecdysone receptor (EcR) and the estrogen-related receptor (ERR), a specific regulator of the Drosophila glycolysis. We found an overlapping DNA-binding pattern for the EcR and ERR in the Drosophila S2 cells. EcR was detected at a subset of the ERR target genes responsible for carbohydrate metabolism. The 20-hydroxyecdysone treatment of both the Drosophila larvae and the S2 cells decreased transcriptional levels of ERR targets. We propose a joint action mode for both the EcR and ERR, for at least a subset of the glycolytic genes. We find that both receptors bind to the same regulatory regions and may form or be part of a joint transcriptional regulatory complex in the Drosophila S2 cells.

The CD16A and CD16B mRNA level as potential immunological marker in colorectal cancer

The purpose of this study is to evaluate mRNA levels of genes encoding CD16A (FCGR3A) and CD16B (FCGR3B) in peripheral blood and tumors of colorectal cancer patients (CRC).Materials and methods. The study included 66 CRC patients from Nizhny Novgorod Regional Clinical Oncology Center and 111 people without cancer as a comparison group from Nizhny Novgorod Regional Blood Center named after N.Ya. Klimova. The mRNA relative levels in peripheral blood and tumor was detected by reverse transcription real-time polymerase chain reaction. The mRNA levels correlation and association with CRC clinical characteristics were assessed by statistic methods.Results. The study suggests that in the peripheral blood of CRC patients the levels of mRNA FCGR3A and FCGR3B were statistically significantly lower than in healthy individuals. The mRNA levels remained low at 7–10 days after surgery. The FCGR3A mRNA normalized level in the blood and tumors of CRC patients, as well as in the blood of healthy individuals, was several times higher than the FCGR3B mRNA level. At the II stage of tumor development in CRC patients, the FCGR3A and FCGR3B mRNA levels were statistically significantly decreased, but as the tumor progressed is normalized. Moderate degree of tumor differentiation was also characterized by a drop in mRNA levels of the tested genes. Reduced FCGR3A and FCGR3B mRNA levels in the blood of patients were observed in the absence of metastases. In tumor samples, FCGR3A mRNA was tested in 95.5% of cases, FCGR3B mRNA in 68.2% of cases. Progression of CRC was accompanied by an increase in FCGR3A mRNA level in tumors, the FCGR3B mRNA level did not change. Positive correlation of FCGR3A mRNA level with TNF and FOXP3 mRNA levels was found, which indicates the possible involvement of FCGR3A in the regulation of chronic inflammation in tumors of CRC patients.Conclusion. Changes in mRNA levels of genes encoding CD16A (FCGR3A) and CD16B (FCGR3A) molecules were detected in blood and tumor samples. The results indicate the potential for their use as monitoring immunological markers in CRC.

544 Alopecia areata lesions show significant changes in immune and keratin biomarkers that correlate with clinical improvement with oral Janus kinase inhibitors PF-06651600 (JAK3) and PF-06700841 (TYK2/JAK1)

Oral JAK3 (PF-06651600) and TYK2/JAK1 (PF-06700841) inhibitors were shown to be efficacious and well tolerated in patients with moderate to severe (≥50% scalp hair loss) alopecia areata (AA). A substudy of this Phase 2 trial (PF-06651600, n=18; PF-06700841, n=16; placebo, n=12) evaluated changes in lesional scalp biomarkers after 12 and 24 weeks of treatment using microarrays, qPCR, and immunohistochemistry. A total of 2264 genes were significantly up- or downregulated after 12 or 24 weeks of treatment across all patients and treatment groups (fold change >1.5; p<0.05). Significant gene-level changes from baseline in lesional transcriptomic profiles of 62% and 115% (12 weeks) and 162% and 104% (24 weeks) were obtained in the PF-06651600 and PF-06700841 groups, respectively, which differed significantly from those in the placebo group (week 12, 18%; week 24, 6%). With both treatments, patient-level T-cell activation, Th1, Th2, and IL12/23 pathways were significantly downregulated (p<0.05 at weeks 12 and/or 24) and hair keratins (KRT35, 40, 75, 83, 85, 86, KRTAP1) were significantly upregulated (p<0.05 at weeks 12 and/or 24). Most of these changes were significantly correlated (p<0.05) with clinical (Severity of Alopecia Tool score) improvements from baseline. No significant changes were seen with placebo. Greater improvements in clinical and transcriptomic parameters correlated with a shorter AA duration (<3.5 years). Overall, clinical improvements in patients with AA treated with PF-06651600 and PF-06700841 were associated with downregulation of Th1, Th2, and IL-12/23 immune responses and upregulation of hair keratins, with greater responses in patients with shorter disease duration.

Causal Disturbance Analysis: A Novel Graph Centrality Based Method for Pathway Enrichment Analysis.

Pathway enrichment analysis models (PEM) are the premier methods for interpreting gene expression profiles from high-throughput experiments. PEM often use a priori background knowledge to infer the underlying biological functions and mechanisms. A shortcoming of standard PEM is their disregarding of interactions for simplicity, which potentially results in partial and inaccurate inference. In this study, we introduce a graph-based PEM, namely Causal Disturbance Analysis (CADIA), that leverages gene interactions to quantify the topological importance of genes' expression profiles in pathways organizations. In particular, CADIA uses a novel graph centrality model, namely Source/Sink, to measure the topological importance. Source/Sink Centrality quantifies a gene's importance as a receiver and a sender of biological information, which allows for prioritizing the genes that are more likely to disturb a pathways functionality. CADIA infers an enrichment score for a pathway by deriving statistical evidence from Source/Sink centrality of the differentially expressed genes and combines it with classical over-representation analysis. Through real-world experimental and synthetic data evaluations, we show that CADIA can uniquely infer critical pathway enrichments that are not observable through other PEM. Our results indicate that CADIA is sensitive towards topologically central gene-level changes that and provides an informative framework for interpreting high-throughput data.

The Neuronal Overexpression of Gclc in Drosophila melanogaster Induces Life Extension With Longevity-Associated Transcriptomic Changes in the Thorax.

Some effects of aging in animals are tissue-specific. In D. melanogaster neuronal overexpression of Gclc increases lifespan and improves certain physiological parameters associated with health benefits such as locomotor activity, circadian rhythmicity, and stress resistance. Our previous transcriptomic analyses of Drosophila heads, primarily composed of neuronal tissue, revealed significant changes in expression levels of genes involved in aging-related signaling pathways (Jak-STAT, MAPK, FOXO, Notch, mTOR, TGF-beta), translation, protein processing in endoplasmic reticulum, proteasomal degradation, glycolysis, oxidative phosphorylation, apoptosis, regulation of circadian rhythms, differentiation of neurons, synaptic plasticity, and transmission. Considering that various tissues age differently and age-related gene expression changes are tissue-specific, we investigated the effects of neuronal Gclc overexpression on gene expression levels in the imago thorax, which is primarily composed of muscles. A total of 58 genes were found to be differentially expressed between thoraces of control and Gclc overexpressing flies. The Gclc level demonstrated associations with expression of genes involved in the circadian rhythmicity, the genes in categories related to the muscle system process and the downregulation of genes involved in proteolysis. Most of the functional categories altered by Gclc overexpression related to metabolism including Drug metabolism, Metabolism of xenobiotics by cytochrome P450, Glutathione metabolism, Starch and sucrose metabolism, Citrate cycle (TCA cycle), One carbon pool by folate. Thus, the transcriptomic changes caused by neuron-specific Gclc overexpression in the thorax were less pronounced than in the head and affected pathways also differed from previous results. Although these pathways don't belong to the canonical longevity pathways, we suggest that they could participate in the delay of aging of Gclc overexpressing flies.

RNA-seq analysis of the response of plant-pathogenic oomycete Phytophthora parasitica to the fungicide dimethomorph

Phytophthora parasitica is an important oomycete that causes disease in a variety of plants, dimethomorph fungicides being specific for oomycetes. The aim of this study was to use RNA-seq to rapidly discover the mechanism by which dimethomorph acts in the treatment of P. parasitica. We found that the expression of 832 genes changed significantly after the dimethomorph treatment, including 365 up-regulated genes and 467 down-regulated genes. According to the Gene Ontology (GO) enrichment analysis, pathway enrichment and verification test results, the following conclusions are obtained: (i) the treatment of P. parasitica with dimethomorph causes changes in the expression levels of genes associated with the cell wall and cell wall synthesis; (ii) dimethomorph treatment results in reduced permeability of the cell membrane and changes in the expression of certain transport-related proteins; (iii) dimethomorph treatment increased reactive oxygen species and reduced the expression of genes related to the control of oxidative stress.