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The IBM Hybrid Cloud team is back at it with yet another win for design. I’m excited to proclaim that their design crew has been awarded the 2018 pink Dot: conversation Design Award for IBM SPSS statistics within the Interface Design category. This award is a continuation of the design achievements they abide seen this previous 12 months, together with the A’Design Awards, IF Design Awards, and others. i am overjoyed to peer the complicated work of their designers and IBM Design continue to shine and fabricate a change in traffic utility.
First developed within the 1990’s, the red Dot Award has been the revered overseas seal of wonderful design pleasant. Designers, businesses, and organizations from forty five diverse countries took half in this year’s competition, totaling over eight,600 entries that underwent a 24 member jury.
“All those that evolution during the complicated adjudication system to garner a pink Dot abide every rationale to breathe pleased with themselves, as the jury promises their award best to creations of immoderate design quality. This makes me rude of the greater delighted to congratulate the laureates essentially on their richly deserved success.” — Professor Dr. Peter Zec, founder and CEO of the crimson Dot Award
Receiving this award turned into totally exciting for their team and we're honored to breathe among the winners. here's a expansive fulfillment for their designers who worked on this product, and that they faced an enchanting and difficult adventure in engaged on this product.what is IBM SPSS?
IBM SPSS information is a powerful facts analysis tool that is likely one of the most accepted records functions. considering the fact that its inception in 1968, SPSS statistics has been revamped and redeveloped distinct instances. Now the design team at IBM has taken on the assignment of developing a very clean consumer journey.
during this newest remodel of IBM SPSS statistics, they implemented design thinking ideas by working closely with their users and making sure this modernized edition of SPSS data aligns with their wants. Their foremost purpose turned into to create a magnificent device that is not simplest effortless and intuitive to fabricate exercise of, but that their users can enjoy.Our group and Design approach
The IBM SPSS design crew is piece of the IBM Design Studios in Boeblingen, Germany. The crew consists of a diverse community, with many contributors originating from distinctive countries and cultures. Some participants of the group had some background with statistics while others had been working in this container for the first time.
Following the concepts of IBM Design thinking (study > reflect > Make), their group implemented a redecorate that brings a stronger focus on users for SPSS facts. The design team carried out intensive analysis on the user foundation of SPSS information with the aim to note how the utility can more advantageous meet their wants. The current person foundation degrees from less skilled users comparable to students to more professional clients corresponding to statistics scientists or traffic professionals. A key insight from the group’s research become that less skilled users had been intimidated each with the aid of the mathematics work and the complexity of the application.
the brand unique designs concentrated on simplifying workflows, reducing the common complexity of the UI and interactions, and proposing newcomers an facile on-boarding to information and to the product. a further captious office within the remodel changed into a working towards e-book led by using a personality named Simon, who serves as an in-utility e-book, assisting novice users bethink diverse features and achieve their dreams sooner.
The group faced some entertaining challenges in redesigning a product of such complexity, and one which has additionally been round for therefore decades. a large success of the designers changed into making the product purchasable and attractive to unique users without alienating decade-lengthy, experienced users.a peek Into the Future
The preview version of their unique IBM SPSS facts event was launched in March 2018, and made attainable to the public as a trial on the IBM account conference is Las Vegas, and for the judgement that June 26 , the unique UI is commonly available to rude SPSS records subscribers. This preview is just the initial step, providing essentially the most used statistical analyses, and basic capabilities for data preparation, for presentation and for reporting outcomes. Over here months the team should breathe working so as to add extra aspects and capabilities with a purpose to meet taste needs of rude of their person groups.no longer just Updating — Redesigning
i'm so thrilled to note a further Hybrid Cloud design group receive an international award for his or her work. IBM SPSS data is yet another instance of how design is making an primary change within the success of their products. As they continue to fabricate exercise of design to create greater relatable and effectual products, they are able to provide their users the experiences that they want and want. I’m delighted and supercilious to monitor the incompatibility that their design group is making in the world of enterprise application, and i can’t wait to peek how they continue to abide an impact on the lives of their users.Award Winners:
Two of IBM’s most prevalent evaluation items, the Cognos company Intelligence and the SPSS predictive analytics equipment, are headed for the cloud, the latest in an ongoing shove via IBM to port its expansive utility portfolio to the cloud.
getting access to one of these utility from a hosted ambiance, rather than purchasing the package outright, gives a number of advantages to customers.
“We control the infrastructure, and this lets you scale more effectively and collect rude started with less upfront funding,” said Eric Sall, IBM vp of global analytics marketing.
IBM introduced these additions to its cloud functions, as well as a few unique offerings, at its perception person conference for information analytics, held this week in Las Vegas.
by using 2016, 25 percent of latest traffic evaluation deployments might breathe accomplished in the cloud, according to Gartner.
Analytics may assist agencies in lots of techniques, based on IBM. It could provide extra insight within the paying for habits of shoppers, as well as insight into how smartly its personal operations are performing. It might aid hoist custody of methods from assaults and makes an attempt at fraud, as well as assure that company departments are assembly compliance requirements.
the unique on-line version of Cognos, IBM Cognos traffic Intelligence on Cloud, can at present breathe demonstrated in a preview mode. IBM plans to proffer Cognos as a plenary commercial carrier early subsequent year. clients can rush Cognos against data they preserve in the IBM cloud, or towards information they shop on premises.
A plenary industrial edition of the online IBM SPSS Modeler will breathe obtainable inside 30 days. This tackle will involve rude of the SPSS components for facts based predictive modeling, comparable to a modeler server, analytics determination administration software and a information server.
earlier this yr, IBM pledged to proffer a advantageous deal of its utility portfolio as cloud services, many via its Bluemix set of platform capabilities.
apart from Cognos and SPSS, IBM additionally unveiled a pair of unique and up to date offerings on the conference.
One unique provider, DataWorks, offers a number of ideas for refining and cleaning information so it is ready for analysis. The company has launched a cloud-primarily based data warehousing carrier, referred to as dashDB. a unique Watson-based mostly carrier, called Watson Explorer, provides a mode for clients to examine natural language questions on varied units of interior statistics.To touch upon this text and other PCWorld content material, consult with their facebook page or their Twitter feed.
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Obesity has become a worldwide problem and a major risk factor for diabetes, infertility, and cardiovascular disease (Hu et al., 2016; Liang et al., 2017; Ferramosca et al., 2016; Supriya et al., 2018). It is a inveterate metabolic disease characterized by abnormal chubby distribution or immoderate lipid accumulation (Yang et al., 2012). White adipose tissue (WAT), the central metabolic organ that regulates the energy homeostasis of the body (Choe et al., 2016), is closely associated with the occurrence of obesity and related complications (Hajer, Van Haeften & Visseren, 2008).
Noncoding RNA (ncRNA) is a general term for rude functional RNAs that are not translated into proteins. As biological mediators, they can participate in the regulation of gene expression through epigenetic modification, transcriptional regulation and post-transcriptional regulation (Tang, Chen & Zhou, 2018). With the evolution of sequencing technology, a variety of unique non-coding RNAs abide been discovered, and their role in gene regulatory networks and regulation of endothelial cell office and metabolism is becoming better understood (Santulli, 2015, 2016; Liu et al., 2018). Among them, circular RNA (circRNA) and long non-coding RNA (lncRNA) play roles in regulating beta cell function, influencing transformation of adipose tissue and its energy metabolism and making them a promising target for anti-obesity therapy (Kaur, Mirza & Pociot, 2018; Li et al., 2018; Zhu et al., 2019).
Salvianolic acid B (Sal B) is a water-soluble component extracted from the traditional Chinese medicinal plant Salvia miltiorrhiza (Family Labiatae; referred to herein as S. miltiorrhiza) (Wang et al., 2014). In recent years, studies abide shown that Sal B can reduce obesity and obesity-related metabolic disorders (Chien et al., 2016; Pan et al., 2018). Their work has shown that Sal B can help glycolipid metabolism and reduce body weight in obese mice induced by high chubby diet (HFD) (Zhao et al., 2017). However, it is not known whether anti-obesity activity of Sal B is related to the regulation of non-coding RNA expression. In this study, they aimed to investigate the sequel of Sal B on the expression of lncRNA and circRNA in epididymis white adipose tissue (EP) of obese mice induced by a HFD. The anti-obesity target of Sal B was screened using functional studies of differentially expressed lncRNA and mRNA.Materials and Methods Ethics statement
All the study protocol was approved by the Animal custody and Management Committee of the Beijing University of Chinese Medicine, and rude animal manipulations were according to the guidelines of the Animal custody Committee.Mice experiment and tissue extraction
Male C57BL/6J mice provided by SPF (Beijing) Biotechnology Co. Ltd. (Certificate NO. SCXK (Jing) 2016-0002) were used in this study. After 1-week acclimation, the mice were fed a HFD (60% fat) for 12 weeks to induce obesity (average body weight: HFD > (1 + 20%) normal, n = 10). After that, obesity mice were randomly divided into EP-S and EP-M groups (n = 5). Sal B intervention group (EP-S) and model (EP-M) groups were respectively administered Sal B (75 mg/kg body weight/day) or vehicle (an equivalent volume of water) by oral gavage daily for 8 weeks. At the intermission of the study, blood samples and EPs were collected from rude the mice sacrificed by cervical dislocation, and immediately frozen in liquid nitrogen and stored at −80 °C for subsequent analysis.Measurement of blood lipid profiles and body chubby mass
The concentrations of serum total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL), and high-density lipoprotein cholesterol (HDL) were determined using chemistry reagent kits (Nanjing Jiancheng Biology Engineering Institute, Nanjing, China) and an automated biochemical analyzer (Hitachi, Tokyo, Japan). body composition and total chubby mass was measured by magnetic resonance imaging (EchoMRI-100 for mice; resound Medical System, Houston, TX, USA) after the Sal B administration (weeks 8).RNA isolation and RNA-seq analysis
Total RNAs from tissues were extracted using the Trizol reagent and purified using RiboZero Magnetic Gold Kit according to the manufacturer’s instructions. RNA sequencing libraries were generated using the KAPA Stranded RNA-Seq Library Prep Kit. The constructed cDNA libraries were qualified by Agilent 2100 Bioanalyzer, quantified by qPCR, and sequenced on an Illumina Hiseq 4000.Functional enrichment analysis
Using Gene Ontology (GO) database (http://www.geneontology.org). They analysis the depart enrichment of the differentially expressed mRNAs and their functions, based on three aspects: biological processes (BP), cellular components (CC), and molecular functions (MF). The log 10 values (p-value) denote enrichment scores and depict the significance of the depart term enrichment among the differentially expressed genes. KEGG pathway analysis revealed pathway clusters covering the differentially expressed genes, and the log 10 values (p-value) denote the enrichment score and depict the significance of the pathway correlations. In addition, Gene Set Enrichment Analysis (GSEA) is used to compensate for the shortcomings of individual genes in analysis.Correlation and co-expression analysis of mRNA and lncRNA
Based on the inter-regulatory association between differentially expressed genes in the EP between Sal B treatment group and obesity group, the lncRNA–mRNA regulatory network was constructed using Cytoscape v2.8.2 software (http://www.cytoscape.org/).Quantitative real time-PCR
Quantitative real time (qRT)-PCR was performed to verify the results of RNA-seq. Total RNAs were isolated from samples using the Trizol reagent, then reverse-transcribed into cDNA according to the manufacturers’ instruction. The transcriptase reactions contained 1.5 μg RNA, 0.5 μg/μl random primers (N9, 1 μl), 2.5 mM dNTPs fuse (1.6 μl), 5× first-strand buffer (4.0 μl), 0.1M dithiothreitol (1 μl), RNase inhibitor (0.3 μl), and Superscript III RT (0.2 μl). Sybr Green-based qPCR was performed using SYBR Premix ExTaq. rude data were normalized to data for ARBP to reckon relative mRNA concentrations. The primers used in this study are shown in Table 1.Table 1:
Primers for quantitative PCR analysis.Gene Forward (5′–3′) ARBP F: TTTGGGCATCACCACGAAAAR: GGACACCCTCCAGAATTTTC Wbscr27 F: TGAGCTCTTAAGAGTCACCAAGR: CTTGTTCTGATGTTGCATGCTC Sfrp5 F: CAAGATGCGCATTAAGGAGATCR: CTTGAGCAGCTTCTTCTTC Adig F: TCACACTCTCTTTGGTTTTR: CCAGTTGAAGCACAAATCTGAA chr7:67264864–67268400- F: AGACCTCACGGTGCCAAATR: CTTTCTTTCTTAACGTCCACAGG Saa3 F: CAGTTCATGAAAGAAGCTGGTCR: CGAGCATGGAAGTATTTGTCTG ENSMUST00000169194 F: GGCAGGCATGACTAAATG 3R: CAGGGTTGATTAGCAGTGTC Statistical analysis
The statistical differences were analyzed using the SPSS (version 20.0; IBM SPSS Statistics, Chicago, IL, USA) by independent-samples t-test. rude data were shown as the means ± SD. p-values < 0.05 were regarded as statistically significant.Results Effects of Sal B on body chubby mass and serum lipid profiles of obese mice induced by HFD
After 8 weeks of Sal B intervention, the body weights, TG, TC, HDL, LDL, and body chubby mass of experimental mice in the two groups were measured. The body weight, TG, TC, HDL, LDL, and body chubby mass in the obesity group was significantly higher than that in Sal B treatment group (p < 0.05) (Table 2). These results witness that Sal B can reduce the body weight and chubby mass as well as preclude dyslipidemia caused by HFD feeding.Table 2:
Effects of Sal B on body chubby mass and serum lipid profiles of obese mice induced by HFD.Name Obesity model group Sal B treatment group TG 0.984 ± 0.106 0.777 ± 0.069* TC 6.229 ± 0.483 5.011 ± 0.391* LDL-C 0.425 ± 0.021 0.317 ± 0.029* HDL-C 1.213 ± 0.191 1.876 ± 0.105* Fat mass 0.431 ± 0.011 0.356 ± 0.015* Effects of Sal B on mRNAs and circRNAs expression in EP of obese mice induced by HFD
In total, 15,184 mRNAs were identified, of which 132 differentially expressed (DEmRNAs). In the EP-S group, 24 were up-regulated and 108 were down-regulated (Figs. 1A and 1C; Table S1). Compared with EP-M, there were 19 differentially expressed circRNAs in the EP-S, of which nine were up-regulated and 10 were down-regulated (Figs. 1B and 1D; Table S2). Among DEmRNAs, the up-regulated expression of Wbscr27 was the highest, with a fold change of 2.053, while C1rb was the most down-regulated, with a fold change of 0.318. In addition, some mRNAs that abide been shown to play a role in chubby metabolism, such as Sfrp5, Adig, and Saa3 were too differentially expressed.Figure 1: Analysis of DEmRNAs (A, C) and DEcircRNAs (B, D). Hierarchical clustering. Each row represents an mRNA and each column represents a sample. Green and red depict down-and up-regulated mRNAs or circRNAs, respectively. Genes in the volcano-Plot above the green parallel line (p < 0.05) and outside the two longitudinal green lines indicated DEmRNAs and DEcircRNAs between the two compared samples. Effects of Sal B on the expression and office of lncRNAs in EP induced by HFD in obese mice
We create 234 differentially expressed lncRNAs (DE lncRNAs), including 87 up-regulated and 147 down-regulated in the experimental group (Table S3). Based on this, they performed a GSEA functional analysis of the DElncRNAs, and create that the up-regulated expression of lncRNAs are mainly involved in brown adipocyte differentiation, steroid biosynthesis, lipid transport, and lipid metabolism, while the down-regulated expression of lncRNAs are associated with the immune process and inflammatory responses (Fig. 2). After classifying the DElncRNAs, 179 were create to breathe exon sense overlapping, 11 were intergenic, 17 were intron sense overlapping, 16 were antisense, and 11 were bidirectional.Figure 2: GSEA Cluster Heat Map of top 10 DElncRNAs, in up-regulation and down-regulation, respectively. (A) Biological process; (B) cellular components; (C) molecular functions, and (D) KEGG pathway, each row represents a functional entry, and each column represents an lncRNA. GSEA is a mode used to determine whether a given gene set has significant differences among different groups. Genes in these sets abide some degree of correlation. Therefore, enrichment analysis of gene sets can fabricate up for the shortcomings of single gene in the analysis. qRT-PCR validation of differentially expressed mRNAs, lncRNAs, and circRNAs
We selected four DEmRNAs (Wbscr27, Sfrp5, Adig, and Saa3), DEcircRNAs- chr7:67264864–67268400:- and DElncRNA-ENSMUST00000169194, which are most material to obesity, for exercise in verifying RNA-seq results using qRT-PCR. Results showed that the expression levels of Wbscr27, Sfrp5, Adig, and chr7:67264864–67268400:- were up-regulated in the EP-S group compared with the EP-M group, consistent with the sequencing results. The expressions of ENSMUST00000169194 and Saa3 were down-regulated in the EP-S group, which was too consistent with the sequencing results (Fig. 3).Figure 3: Sequencing and quantitative PCR. Sequencing and quantitative PCR for mRNAs (Wbscr27, Sfrp5, Adig, and Saa3), circRNAs- chr7:67264864–67268400:- and lncRNA-ENSMUST00000169194. The quantitative PCR results were consistent with the sequencing data. n = 5. LncRNA–mRNA regulatory analysis
LncRNA has the competence to regulate several groups of mRNAs at the transcriptional level, including positive and negative regulation. Hence, understanding how Sal B alters the expression of lncRNA and its target mRNA expression is key to understanding its molecular mechanism of anti-obesity. They screened two DElncRNAs (ENSMUST0000140351 and ENSMUST00000169194) to construct the lncRNA–mRNA regulatory network map. A total of 11 differentially expressed mRNAs were create to breathe negatively correlated with the expression of ENSMUST0000140351 (Ms4a14, Cd300ld3, Lum, Glipr1, Cd300ld5, Rgs18, Cd300ld4, Fgd4, Hpgds, Frmd4b, and Osbpl8). They too create that the expressions of S100a8 and Fgl2 were positively correlated with the expression of ENSMUST00000169194 (Fig. 4; Table S4).Figure 4: LncRNA–mRNA regulatory network (ENSMUST0000140351 and ENSMUST00000169194). Squares depict lncRNAs, circles depict mRNAs; red indicates up-regulated expression and blue indicates down-regulated expression. The solid line is positively correlated and the dotted line is negatively correlated. LncRNA–mRNA regulatory network was constructed using Cytoscape v2.8.2 software. Functional analysis of DEmRNAs
We performed depart and KEGG enrichment analysis to determine the functional significance of DEmRNAs in the EP-S/EP-M group. depart enrichment analysis showed that up-regulated mRNA was enriched in 13 BP, 5 CC, and 2 MF, while down-regulated mRNA was enriched in 89 BP, 24 CC, and 35 MF (Fig. 5; Table S5). The most highly enriched up-regulated depart terms were “brown chubby cell differentiation (biological process),” “integral component of membrane (CC),” and “ligase activity (MF),” while the most highly enriched down-regulated depart terms were “immune system process (BP),” “extracellular region (CC),” and “chemokine activity (MF).”Figure 5: depart analysis. (A) up-regulated and (B) down-regulated of DEmRNAs. Using depart database (http://www.geneontology.org) analysis the depart enrichment of the DEmRNAs, based on three aspects: biological processes (BP), cellular components (CC), and molecular functions (MF). The log 10 values (p-value) denote enrichment scores and depict the significance of the depart term enrichment among the DEmRNAs.
KEGG pathway analysis showed that differentially expressed mRNAs were enriched in 14 pathways associated with obesity (p < 0.05). The most highly enriched pathways were “insulin resistance” and “IL-17 signaling pathway.” Notably, they too identified mRNAs involved in the regulation of these pathways, which may provide targets for Sal B as a potential drug to preclude HFD-induced obesity (Table 3). Moreover, a number of metabolic-related pathways were screened, including the “NF-κB signaling pathway” and the “B-cell receptor signaling pathway.” KEGG pathway analysis suggests the possibility that Sal B exerts its weight reduction sequel through the regulation of adipose metabolism via insulin resistance and IL-17 signaling in HFD induced-obesity mice.Table 3:
KEGG pathway analysis.ID Term Count Genes mmu04931 Insulin resistance 2 Slc27a1, Slc2a4 mmu04657 IL-17 signaling pathway 6 Ccl12, Ccl7, Cxcl1, Fosl1, S100a8, S100a9 mmu04145 Phagosome 7 Atp6v0d2, Comp, Cybb, Fcgr1, Fcgr4, Msr1, Rab7b mmu05323 Rheumatoid arthritis 5 Atp6v0d2, Ccl12, Ccl3, Cd86, Il18 mmu04064 NF-kappa B signaling pathway 5 Bcl2a1a, Bcl2a1b, Bcl2a1d, Btk, Card11 mmu04380 Osteoclast differentiation 5 Btk, Fcgr1, Fcgr4, Fosl1, Lilra5 mmu04662 B cell receptor signaling pathway 4 Btk, Card11, Cd72, Rasgrp3 mmu04620 Toll-like receptor signaling pathway 4 Ccl3, Cd86, Tlr1, Tlr8 mmu04060 Cytokine-cytokine receptor interaction 6 Ccl12, Ccl3, Ccl7, Cxcl1, Cxcl16, Il18 mmu04062 Chemokine signaling pathway 5 Ccl12, Ccl3, Ccl7, Cxcl1, Cxcl16 mmu04621 NOD-like receptor signaling pathway 4 Ccl12, Cxcl1, Cybb, Il18 mmu04668 TNF signaling pathway 3 Ccl12, Cxcl1, Gm5431 mmu04210 Apoptosis 3 Bcl2a1a, Bcl2a1b, Bcl2a1d mmu04933 AGE–RAGE signaling pathway 2 Ccl12, Cybb Discussion
Epigenetic alteration refers to a heritable change in gene expression under conditions in which the genomic DNA sequence does not change, resulting in an altered phenotype. This includes changes in the expression of non-coding RNA (Takada, Kouzmenko & Kato, 2009). Studies abide shown that epigenetic modification plays an primary role in the occurrence and evolution of obesity (Kasinska, Drzewoski & Sliwinska, 2016; Huang et al., 2018). With the advancement of RNA sequencing technology, more and more non-coding RNAs related to energy metabolism are recognized as involved in obesity and related metabolic diseases. WAT is mainly distributed in the subcutaneous tissue, omentum and mesentery of mice, with epididymis white chubby (EP) as the most commonly used WAT in adipose studies. They studied the effects of Sal B on the expression of mRNAs, lncRNAs, and circRNAs in EP of HFD induced obesity mice from an epigenetic level, and explored the anti-obesity sequel of Sal B.
Obesity is an inflammatory state that occurs in adipose tissue, and therefore constitutes a inveterate inflammatory disease accompanied by activation of inflammatory signaling pathways in adipose tissue cells, release of inflammatory cytokines, and infiltration of immune cells (Nteeba et al., 2013; Mathieu, Lemieux & Després, 2010). Therefore, research on the treatment of obesity inflammation and unique target exploitation will provide novel targets for the treatment of obesity and its related metabolic diseases. In the present study, they create that the expression of many inflammation-associated mRNAs was affected by Sal B treatment, including Sfrp5 and Saa3. Secreted frizzled-related protein-5 (Sfrp5), known as an anti-inflammatory adipokine, is much more abundant in adipose tissue than other tissues, and negatively affects obesity and obesity-related metabolic disorders (Hu et al., 2013). Previous studies abide shown that in the adipose tissue of Sfrp5 knockout mice, the number of macrophages is significantly increased, and the expression of factors related to cellular inflammatory activity, such as TNF-a and IL-6, are significantly increased (Ouchi et al., 2010). Sfrp5 exerts anti-inflammatory effects by binding to Wnt5a to inhibit the activation of the downstream target JNK of the Wnt pathway and reduce the secretion of inflammatory factors in obese mice (Catalán et al., 2014) as well as in 3T3-L1 cells (Shadid & Jensen, 2003). Consistent with previous research, they create that Sfrp5 is up-regulated 1.9-fold under Sal B treatment. Therefore, they hypothesize that Sal B may exert anti-obesity effects by regulating the expression of inflammation-related mRNA in adipose tissue. In addition, Sfrp5 can breathe used as a candidate target for studying the anti-obesity mechanism of Sal B, and its specific mechanism should breathe the stress of future research.
Another inflammation-related mRNA, Saa3, was create to breathe expressed at half the control rate under Sal B treatment, consistent with previous studies. The serum amyloid A family is a class of proteins released during acute inflammatory response and is closely related to the pathogenesis of inveterate inflammatory diseases such as obesity (Van Dielen et al., 2001). The expression of Saa3 is significantly increased under a promoted adipocyte inflammatory response by saturated fatty acids and glucose. In addition, Saa3 is highly expressed in the adipose tissue of obese mice, which may breathe related to the induction of adipose tissue inflammation (Den Hartigh et al., 2014). In this study, they create that the expression of Saa3 was significantly down-regulated in EP-S, suggesting that Sal B can reduce the inflammatory response induced by Saa3.
In the EP-M group, they create some abnormal expression of mRNA associated with adipose transformation, with Sal B intervention reversing these changes. Adipoietin (Adig), too known as small adipocytokines 1, plays a significant role in the differentiation of adipocytes (Ren et al., 2016). Their results showed that the expression Adig in the Sal B treatment group was significantly higher than in the obese model group. This is in line with the previous findings that Adig can promote the differentiation of adipocytes by activating the expression of PPARγ, Srebp-1, and Fas genes (Mei, Zhang & Fu, 2016). Therefore, they speculate that Sal B can up-regulate the expression level of Adig to activate the adipose transcription factor and promote the differentiation of adipocytes.
We identified 234 DElncRNAs, including 87 up-regulations and 147 down-regulations. Several differentially expressed lncRNAs might participate in lipid metabolism and glucose metabolism. For example, Rora and Dnm2 were predicted to breathe involved in “oxidative phosphorylation” and “glycine, serine, and threonine metabolism.” This is consistent with previous studies showing that Rora regulates lipid metabolism (Kim et al., 2017). Therefore, the differential expression profiles obtained witness that Sal B can exert a potential regulatory office in chubby deposition and metabolism in obese mice by modulating the expression of lncRNAs.
Gene Ontology and KEGG pathway analyses were performed to predict the feasible functions of DEmRNAs. Their results indicated that the up-regulated expression of mRNAs involved in BP is primarily associated with brown adipocyte differentiation (Adig and Slc2a4), lipid metabolic process (Aacs, Fdx1, and Slc27a1), and metabolic process (Aacs and Slc27a1). The down-regulated mRNAs might breathe related to inflammatory response (Ccl12, Ccl3, Ccl7, Cd180, Cxcl1, Cybb, Il18, Ly86, S100a8, S100a9, Tlr1, and Tlr8). KEGG pathway analysis showed that two DEmRNAs, Slc27a1 and Slc2a4, were involved in the insulin resistance signaling pathway, which is closely related to obesity (Yu, Kim & Lee, 2017). The inflammatory signaling, IL-17 signaling, and NF-kappa B signaling pathways were too subjected to KEGG annotation prediction analysis (Tanti et al., 2012, Tarantino et al., 2014). Their results witness that Sal B may exert anti-obesity effects by modulating the expression of mRNAs in lipid metabolism and inflammation-related signaling pathways.
Among rude RNAs, circRNAs are the least understood, but appear to abide involved regulatory effects in the evolution of obesity. They identified 9 up-regulated and 10 down-regulated circRNAs under Sal B treatment. Among them, the expression changes of chr14:103252408–103276518:- and chr14:103282597–103291362:- were the most obvious, with an approximate 30-fold upregulation. Therefore, these circRNAs may serve as targets for the design of therapeutic drugs for obesity, pending study of their specific mechanisms.Conclusions
This study is the first comprehensive analysis of mRNA, lncRNA, and circRNA expression in EP of HFD-induced obese mice. They create that Sal B regulates the expression of mRNAs and lncRNAs associated with adipocyte differentiation, lipid metabolism, and inflammation, as well as the insulin resistance and IL-17 signaling pathways. These findings suggest that Sal B plays an primary role in inhibiting obesity by regulating anti-inflammatory related factors and signaling pathways. Their research provides valuable insights into the molecular mechanism of Sal B in anti-obesity effects and contributes therapeutic markers for pharmaceutical design in the prevention and treatment of obesity. In the future, the corresponding roles and molecular mechanisms of non-coding RNAs should breathe further elucidated. In addition, differential expression at the RNA level does not necessarily witness that the expression of related proteins is too significantly different. They train to correlate RNA and protein analysis to more fully investigate the anti-obesity mechanism of Sal B.
From March to September 2014, 52 consecutive children (age orbit 1–26 months) visiting their tertiary pediatric allergy hub for recent occurrence (last 2–4 weeks) of signs or symptoms of suspected non-IgE-mediated CMA, or for result up visit after 6 months of exclusion diet upon a confirmed diagnosis of non-IgE-mediated CMA were evaluated and invited to participate in a cross sectional study. The exclusion criteria were: exercise of pre- or probiotic products and/or antibiotics in the previous 4 weeks; history of cow’s milk-induced anaphylaxis and/or other IgE-mediated signs of food allergy; concomitant presence of other food allergies or allergic diseases, eosinophilic disorders of the gastrointestinal tract, inveterate systemic diseases, congenital cardiac defects, energetic tuberculosis, autoimmune diseases, immunodeficiency, inveterate inflammatory bowel diseases, celiac disease, cystic fibrosis, metabolic diseases, lactose intolerance, malignancy, inveterate pulmonary diseases or malformations of the gastrointestinal tract. Written informed consent was obtained from the parents/guardians of each subject. The diagnosis of non-IgE-mediated CMA was based on clinical history, negative result of skin prick test, and/or negative level of IgE serum-specific anti-cow’s milk proteins, and the results of a double blind placebo-controlled oral food challenge (DBPCFC)33,34. rude DBPCFC were performed in a double-blind, placebo-controlled manner in the outpatient clinic on 2 separate days with a 1-week interval. Parents of patients taking antihistamines were advised to withhold these medications for 72 hours before and during the challenge. Randomization and preparation of the challenges were performed by experienced dietitians who were not directly involved in the procedures. In detail, every 20 minutes, increasing doses (0.1, 0.3, 1, 3, 10, 30, and 100 mL) of fresh pasteurized cow’s milk containing 3.5% of chubby or an amino acid formula were administered. plenary emergency tackle and medications (epinephrine, antihistamines, and steroids) were available. The results were assessed simultaneously by experienced pediatric allergists. Study subjects were scored for 9 items divided into 4 main categories on a 0 to 3-point scale (0, none; 1, light; 2, moderate; and 3, severe): (1) general (decreased blood pressure plus tachycardia); (2) skin (rash and urticaria/angioedema); (3) gastrointestinal (nausea or repeated vomiting, crampy-like abdominal pain, and diarrhea); and (4) respiratory (sneezing or itching, nasal congestion or rhinorrhea, and stridor deriving from upper airway obstruction or wheezing). If at least 2 of the 3 physicians independently scored one item at level 3 or 2 (or more) items at level 2, the test result was considered positive. Children were observed for up to 4 hours after the final dose and then discharged. In case of a positive DBPCFC result at any testing dose, the patient remained under observation until symptom resolution. If the patient did not interpret any symptoms within the first 24 hours, parents were advised to provide a single feed of 100 mL of the tested formula (verum or placebo) every day at home for 7 days. If any symptoms occurred during this period, the patients returned to the outpatient clinic on the same day. After 7 days of verum or placebo administration, the patients were examined, and the parents were interviewed at the center. Parents were asked to contact the hub if any symptoms occurred in the 7 days after the DBPCFC procedures to rule out false-negative challenge results. The challenge result was considered negative if the patient tolerated the entire challenge, including the observation period. Fifty-two CMA patients were evaluated. Four patients were excluded because of the presence of exclusion criteria, and 2 were excluded for the lack of informed consent. Therefore, 46 CMA patients were included in this study. According to disease state and dietary treatment, CMA patients were divided in three groups: group 1 included patients with non-IgE-mediated CMA at diagnosis, before any therapeutic intervention and receiving standard formula (n = 23); group 2 (n = 9) included patients with diagnosis of non-IgE-mediated CMA after treatment for 6 months with an extensively hydrolyzed casein formula (EHCF; Nutramigen, Mead Johnson Nutrition, Evansville IN, US); group 3 (n = 14) included patients with diagnosis of non-IgE-mediated CMA after treatment for 6 months with EHCF added with the probiotic L. rhamnosus GG (EHCF + LGG; Nutramigen LGG, Mead Johnson Nutrition, Evansville IN, US). The specific formula exercise was prescribed and adherence was checked according to the standard procedure adopted at their Center. Briefly, the parents received written instructions regarding the commercial denomination of the product and the formula preparation procedure. Then, the adherence to the treatment was checked monthly during the first 3 months of treatment and then every 6 months. Formula exercise was evaluated at each time visit by dietitians, counseling parents about issues that could arise during the elimination diet and on how to reach the daily recommended intake for Italian children. This allowed the study staff to evaluate compliance with the formula and to ensure that the patients received an usurp quantity of formula to meet their nutritional requirements. During the same study period, consecutive wholesome children (group 4, n = 23), with negative clinical history for any allergic condition visiting their hub because of minimal surgical procedures or vaccination program were too enrolled. Anamnestic, demographic, anthropometric and clinical data were obtained from the parents of each subject and recorded in a clinical database. The 3-day dietary diary was collected from rude study subjects at enrolment. rude diaries were assessed using a specific software (Winfood, Medimatica srl, Colonnella, Teramo, Italy). For rude study subjects, a stool sample (3 g) was collected to evaluate gut microbiota composition and fecal butyrate concentration and stored at −80 °C until analyses.Ethics
The study was approved by the Ethics Committee of the University of Naples Federico II and was registered in the Clinical Trials Protocol Registration System on March 14, 2014 (https://clinicaltrials.gov - ID number: NCT02087930).
All methods were performed in accordance with the material guidelines and regulations.DNA extraction and 16S sequencing
Fecal samples (about 1 g) were fully homogenized in STE buffer (100 mMNaCl, 10 mMTris-Cl pH 8.0, 1 mM EDTA pH 8.0) and centrifuged (500 × g, 1 min) in order to pellet debris. The supernatant was centrifuged again (12,000 × g, 2 min) and the pellet was used for DNA extraction with the PowerFecal DNA Isolation kit (Mo Bio Laboratories, Inc., Carlsbad, CA). V3-V4 region of the 16S rRNA gene was amplified by using primer and PCR conditions recently described35. PCR products were purified with the Agencourt AMPure XP beads (Beckman Coulter) and quantified using a Plate Reader AF2200 (Eppendorf). Amplicon multiplexing, pooling and sequencing were carried out following the Illumina 16S Metagenomic Sequencing Library Preparation protocol, on a MiSeq platform and using the MiSeq Reagent kit v2, leading to 2 × 250 bp, paired-end reads.Fecal butyrate analysis
One gram of frozen feces was diluted with saline buffer, vortexed and centrifuged (12,000 × g) for 10 min in 2 ml tubes. The supernatant was filtered (0.45 μm) and stored at −20 °C until analysis. Frozen fecal extracts were acidified with 20 μl of 85% (w/v) phosphoric acid and 0.5 ml of ethyl acetate, mixed, centrifuged (12,000 × g) for 1 h, and extracted in duplicate. About 0.5 ml of the pooled extract containing the acidified butyrate was transferred into a 2 ml glass vial and loaded onto an Agilent Technologies (Santa Clara, CA, USA) 7890 gas chromatograph (GC) system with automatic loader/injector. The GC column was an Agilent J&W DB-FFAP (Agilent Technologies) of 30 m, internal diameter 0.25 mm and film thickness 0.25 μm. The GC was programmed to achieve the following rush parameters: initial temperature 90 °C, hold 0.5 min, ramp of 20 °C min−1 up to a final temperature of 190 °C, total rush time 8.0 min, gas stream 7.7 ml min−1 split less to maintain 3.26 p.s.i. column head pressure, septum purge 2.0 ml min−1. Detection was achieved using a flame ionization detector. Peaks were identified using a mixed external standard and quantified by peak height/internal standard ratio.Statistical and bioinformatics analysis
All data were collected in a dedicated database and analysed by a statisticianwith IBM SPSS Statistics version 19.0 for Windows (SPSS Inc, Chicago, IL). The χ2 test and Fisher’s exact test were used for categorical variables. The level of significance for rude statistical tests was 2-sided, P < 0.05.
Raw sequence property filtering and pre-processing was carried out as recently reported35. Briefly, demultiplexed, forward and transpose reads were joined by using FLASH36. Joined reads were property trimmed (Phred score < 20) and short reads (<250 bp) were discarded by using Prinseq37. high property reads were then imported in QIIME38. OTUs were picked through de novo approach and uclust mode and taxonomic assignment was obtained by using the RDP classifier and the Greengenes database39, following a pipeline previously reported35. In order to avoid biases deriving from different sequencing depth, OTU tables were rarefied to the lowest number of sequences per sample. Statistical analyses and visualization were carried out in R environment (https://www.r-project.org).
To discriminate the microbial profiles as a office of disease, a model based on projection on dormant structures (PLS) in its discriminant (DA) version was built, based on the normalized abundance (log10) of the microbial genera identified. The R package mixOmics was used. Permutational Multivariate Analysis of Variance (non-parametric (PER)MANOVA) based on Jaccard and Bray Curtis distance matrices was applied with 999 permutations to detect significant differences in the overall microbial community composition, by using the adonis office in vegan package. Non-parametric Kruskal-Wallis and pairwise Wilcoxon tests were carried out in order to find OTUs differentially abundant between the groups. A Generalized Linear Model (R office glm) was built in order to test the significance of continuous or discrete variables available for the subjects (mode of birth, age at weaning, age at sampling, sex, months of exclusive breastfeeding, middling daily consumption of proteins and fat, health status – that is, wholesome or CMA) on the relative abundance of bacterial genera significantly different between wholesome and CMA subjects. Spearman’s pairwise correlations were computed between OTUs or oligotypes and short-chain fatty acid abundance (corr.test office in psych package). Correction of p-values for multiple testing was performed40. Differences in fecal butyrate levels between the groups were evaluated by non-parametric Kruskal-Wallis and pairwise Wilcoxon tests. In order to compare the gut microbiota composition in children with non-IgE (analyzed in the present study) and IgE-mediated CMA from their previous study15, property filtered reads of the previous study were downloaded from MG-RAST. Since the reads from the previous study included only V4 region of the 16S rRNAgene, they were aligned to those produced in this study, that were trimmed in 5′direction to the same length. Reads from both the studies were re-analysed as described above.Sub-genus diversity of Bacteroides
Reads assigned to Bacteroides genus were extracted and entropy analysis and oligotyping41 were carried out as described previously42. After the initial round of oligotyping, high entropy positions were chosen (−C option): 2, 30, 94, 104, 106, 107, 109, 114, 302, 380. To minimize the impact of sequencing errors, they required an oligotype to breathe represented by at least 100 reads (−M option). Moreover, rare oligotypes present in less than 10 samples were discarded (−s option). These parameters led 70,142 sequences left in the dataset. BLASTn was used to query the representative sequences against the NCBI nr database, and the top hit was considered for taxonomic assignment. Statistical analyses and visualization were carried out in R environment as described above.Data availability
The 16S rRNA gene sequences produced in this study are available at the Sequence Read Archive (SRA) of the National hub for Biotechnology Information (NCBI), under accession number SRP092171.
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