Search results for: STAT pathway

Authors: Bikram K. Das, Kalyan K. Chattopadhyay

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The advent of 2-D materials in the last decade has induced a fresh spur of growth in fuel cell technology as these materials have some highly promising traits that can be exploited to felicitate Oxygen Reduction Reaction (ORR) in an efficient way. Among the various 2-D carbon materials, graphyne (Gy) and graphdiyne (Gdy)1 with their intrinsic non-uniform charge distribution holds promises in this purpose and it is expected2 that substitutional Nitrogen (N) doping could further enhance their efficiency. In this regard, dispersive force corrected density functional theory is used to map the oxygen reduction reaction (ORR) kinetics of five different kinds of N doped graphyne and graphdiyne systems (namely αGy, βGy, γGy, RGy and 6,6,12Gy and Gdy) in alkaline medium. The best doping site for each of the Gy/ Gdy system is determined comparing the formation energies of the possible doping configurations. Similarly, the best di-oxygen (O₂) adsorption sites for the doped systems are identified by comparing the adsorption energies. O₂ adsorption on all N doped Gy/ Gdy systems is found to be energetically favorable. ORR on a catalyst surface may occur either via the Eley-Rideal (ER) or the Langmuir–Hinschelwood (LH) pathway. Systematic studies performed on the considered systems reveal that all of them favor the ER pathway. Further, depending on the nature of di-oxygen adsorption ORR can follow either associative or dissociative mechanism; the possibility of occurrence of both the mechanisms is tested thoroughly for each N doped Gy/ Gdy. For the ORR process, all the Gy/Gdy systems are observed to prefer the efficient four-electron pathway but the expected monotonically exothermic reaction pathway is found only for N doped 6,6,12Gy and RGy following the associative pathway and for N doped βGy, γGy and Gdy following the dissociative pathway. Further computation performed for these systems reveals that for N doped 6,6,12Gy, RGy, βGy, γGy and Gdy the overpotentials are 1.08 V, 0.94 V, 1.17 V, 1.21 V and 1.04 V respectively depicting N doped RGy is the most promising material, to carry out ORR in alkaline medium, among the considered ones. The stability of the ORR intermediate states with the variation of pH and electrode potentials is further explored with Pourbiax diagrams and the activities of these systems in the alkaline medium are compared with the prior reported B/N doped identical systems for ORR in an acidic medium in terms of a common descriptor.

Keywords: graphdiyne, graphyne, nitrogen-doped, ORR

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Authors: Amel M. A. Osman, Roy Mahony, Lisa Dann, McKenna S.

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Background: Computed Tomography (CT) is a significant source of radiation in the pediatric population. A new head injury (HI) pathway was introduced in 2021, which altered the previous process of HI being jointly admitted with general pediatrics and surgery to admit these patients under the Emergency Medicine Team. Admitted patients included those with positive CT findings not requiring immediate neurosurgical intervention and those who did not meet current criteria for urgent CT brain as per NICE guidelines but were still symptomatic for prolonged observations. This approach aims to decrease the number of CT scans performed. The main aim is to assess the variation in CT scanning rates since the change in the admitting process. A retrospective review of patients presenting to CHI PECU with HI over 6-month period (01/01/19-31/05/19) compared to a 6-month period post introduction of the new pathway (01/06/2022-31/12/2022). Data was collected from the electronic record databases, symphony, and PACS. Results: In 2019, there were 869 presentations of HI, among which 32 (3.68%) had CT scans performed. 2 (6.25%) of those scanned had positive findings. In 2022, there were 1122 HI presentations, with 47 (4.19%) CT scans performed and positive findings in 5 (10.6%) cases. 57 patients were admitted under the new pathway for observation, with 1 having a CT scan following admission. Conclusion: Quantitative lifetime radiation risks for children are not negligible. While there was no statistically significant reduction in CTs performed amongst HIs presenting to our department, a significant group met the criteria for admission under the PECU consultant for prolonged monitoring. There was also a greater proportion of abnormalities on CT scans performed in 2022, demonstrating improved patient selection for imaging. Further data analysis is ongoing to determine if those who were admitted would have previously been scanned under the old pathway.

Keywords: head injury, CT, admission, guidline

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Authors: Razieh Zareia, Hassan ZMB, Darush Moslemic, Amrollah Mostafa-Zaded

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Introduction: Shark is a murine organism and its cartilage has antitumor peptides to prevent angiogenesis, at least, in vitro. The purpose of our research was to evaluate the immune-effectiveness on imbalance between IL-23/IL-17 axis, as an inflammatory pathway and TGF/Foxp3 T regulatory as a inhibitory pathway of commercial shark cartilage that is available as a non-common dietary supplement in IRAN. Materials and Methods: First investigated an imbalanced supernatant of cytokines exist in patients with gastric cancer by ELISA. Associated with cytokines measuring such as IL-23, IL-17, TGF-β, IL-4, and γ-IFN, then flow cytometry was employed to determine whether the peripheral blood mononuclear cells such as CD4+CD25+Foxp3highT regulatory cells in patients with gastric cancer were changed correspondingly. Results: The simultaneously presented up-regulation IL-17A indicated, at least cytokine level without changing in TGF-β amount or CD4+CD25+Foxp3 T regulatory cells, that there are not a direct correlation between IL-23/IL-17 axis and Treg/TGF-β pathway in patients with gastric cancer treated by shark cartilage, but IL-23 was not expressed differentially in this group. So, accompany these changes, an imbalance between Th1 immunity (γ-IFN production) and TH2 immunity (IL-4 secretion) evaluated in patients with gastric cancer treated by shark cartilage. Conclusion: On the basis of results, we propose that shark cartilage, by reducing IL-4, decreasing IL-17 a central cytokine in angiogenesis and increasing γ-IFN amplify anti-tumor immune responses in patients with gastric cancer.

Keywords: IL-23/IL17 axis, TGF-β/CD4+CD25+Foxp3high T regulatory pathway, γ-IFN, IL-4, shark cartilage, gastric cancer

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Authors: Aida Kalantari, Boyang Ji, Tao Chen, Ivan Mijakovic

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3-hydroxypropanoic acid (3-HP) is one of the most important biomass-derivable platform chemicals that can be converted into a number of industrially important compounds. There have been several attempts at production of 3-HP from renewable sources in cell factories, focusing mainly on Escherichia coli, Klebsiella pneumoniae, and Saccharomyces cerevisiae. Despite the significant progress made in this field, commercially exploitable large-scale production of 3-HP in microbial strains has still not been achieved. In this study, we investigated the potential of Bacillus subtilis to be used as a microbial platform for bioconversion of glycerol into 3-HP. Our recombinant B. subtilis strains overexpress the two-step heterologous pathway containing glycerol dehydratase and aldehyde dehydrogenase from various backgrounds. The recombinant strains harboring the codon-optimized synthetic pathway from K. pneumoniae produced low levels of 3-HP. Since the enzymes in the heterologous pathway are sensitive to oxygen, we had to perform our experiments in micro-aerobic conditions. Under these conditions, the cell produces lactate in order to regenerate NAD+, and we found the lactate production to be in competition with the production of 3-HP. Therefore, based on the in silico predictions, we knocked out the glycerol kinase (glpk), which in combination with growth on glucose, resulted in improving the 3-HP titer to 1 g/L and the removal of lactate. Cultivation of the same strain in an enriched medium improved the 3-HP titer up to 7.6 g/L. Our findings provide the first report of successful introduction of the biosynthetic pathway for conversion of glycerol into 3-HP in B. subtilis.

Keywords: bacillus subtilis, glycerol, 3-hydroxypropanoic acid, metabolic engineering

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Authors: Kwangman Park, Jinhee Kang, Suhee Kim, Dohyeon Yu, Kyoungseong Choi, Jinho Park

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Statement of the Problem: Diarrhea is a major cause of death in young calves. This causes great economic damage to the livestock industry. These diarrhea cause dehydration, decrease blood flow, lower the pH and degrade enzyme function. In the past, serum screening was not possible in the field. However, now with the spread of portable serum testing devices, it is now possible to conduct tests directly on field. Thus, accurate serological changes can be identified and used in the field of large animals. Methodology and Theoretical Orientation: The test groups were calves from 1 to 44 days old. The status of the feces was divided into four grade to determine the severity of diarrhea (grade 0,1,2,3). Grade 0, 1 is considered to have no diarrhea. Grade 2, 3 is considered to diarrhea positive group. One or more viruses were detected in this group. Diarrhea negasitive group consisted of 57 calves (Asan=30, Samrye=27). Diarrhea positive group consisted of 34 calves (Kimje=27, Geochang=7). The feces of all calves were analyzed by PCR Test. Blood sample was measured using an automatic blood analyzer(i-STAT, Abbott inc. Illinois, US). Calves were divided into 3 groups according to age. Group 1 is 1 to 14 days old. Group 2 is 15 to 28 days old. Group 3 is more than 28 days old. Findings: Diarrhea caused an increase in HCT due to dehydration. The difference from normal was highest in 15 to 28 days old (p < 0.01). At all ages, bicarbonate decreased compared to normal, and therefore pH decreased. Similar to HCT, the largest difference was observed between 15 and 28 days (p < 0.01). The pCO₂ decreases to compensate for the decrease in pH. Conclusion and Significance: At all ages, HCT increases, and bicarbonate, pH, and pCO₂ decrease in diarrhea calves. The calf from 15 days to 28 days shows the most difference from normal. Over 28 days of age, weight gain and homeostasis ability increase, diarrhea is seen in the stool, there are fewer hematologic changes than groups below 28 days of age.

Keywords: calves, diarrhea, hematological changes, i-STAT

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Authors: Chengcao Sun, Shujun Li, Dejia Li

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Sulforaphane (SFN) possesses powerful chemo-preventive effects and plays a crucial role on oxidative stress and inflammatory. In our recent study, SFN treatment could relieve muscular dystrophy in mdx mice by activating Nrf2 (NF-E2 related factor 2). Moreover, our findings indicated that SFN-activated Nrf2 alleviated muscle inflammation in dystrophin-deficient mdx mice through suppressing NF-κB signaling pathway. Collectively, SFN-induced Nrf2 molecular pathway might be a promising approach for treatment of the patients with Duchenne muscular dystrophy.

Keywords: sulforaphane, Duchenne muscular dystrophy, Nrf2, inflammation, fibrosis, oxidative stress

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Authors: Hyun Lim, Dong Sook Min, Han Eul Yun, Kil Tae Kim, Ya Nan Sun, Young Ho Kim, Hyun Pyo Kim

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Matrix metalloproteinase (MMP)-13 has an important role for degrading cartilage materials under inflammatory conditions such as arthritis. Since the 70% ethanol extract of Acanthopanax koreanum inhibited MMP-13 expression in IL-1β-treated human chondrocyte cell line, SW1353, two major constituents including acanthoic acid and impressic acid were initially isolated from the same plant materials and their MMP-13 down-regulating capacity was examined. In IL-1β-treated SW1353 cells, acanthoic acid and impressic acid significantly and concentration-dependently inhibited MMP-13 expression at 10 – 100 μM and 0.5 – 10 μM, respectively. The potent one, impressic acid, was found to inhibit MMP-13 expression by blocking the phosphorylation of signal transducer and activator of transcription-1/-2 (STAT-1/-2) and activation of c-Jun and c-Fos among cellular signaling pathway involved, but did not affect the activation of mitogen-activated protein kinases (MAPKs) and nuclear transcription factor-κB (NF-κB). Further, impressic acid was also found to inhibit the expression of MMP-13 mRNA (47.7% inhibition at 10 μM), the glycosaminoglycan release (42.2% reduction at 10 μM) and proteoglycan loss in IL-1-treated rabbit cartilage explants culture. For a further study, 21 impressic acid derivatives were isolated from the same plant materials and their suppressive activities against MMP-13 expression were examined. Among the derivatives, 3α-hydroxy-lup-20(29)-en-23-oxo,28-oic acid, (20R)-3α-hydroxy-29-dimethoxylupan-23,28-dioic acid, acankoreoside F and acantrifoside A clearly down-regulated MMP-13 expression, but impressic acid being most potent. All these results suggest that impressic acid, 3α-hydroxy-lup-20(29)-en-23-oxo,28-oic acid, (20R)-3α-hydroxy-29-dimethoxylupan-23,28-dioic acid, acankoreoside F, acantrifoside A and A. koreanum may have a potential for therapeutic agents to prevent cartilage degradation possibly by inhibiting matrix protein degradation.

Keywords: acanthoic acid, Acanthopanax koreanum, cartilage, impressic acid, matrix metalloproteinase

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Authors: Han-Qin Zheng, Yi-Fan Chiang-Hsieh, Chia-Hung Chien, Wen-Chi Chang

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As the most important non-vascular plants, algae have many research applications, including high species diversity, biofuel sources, adsorption of heavy metals and, following processing, health supplements. With the increasing availability of next-generation sequencing (NGS) data for algae genomes and transcriptomes, an integrated resource for retrieving gene expression data and metabolic pathway is essential for functional analysis and systems biology in algae. However, gene expression profiles and biological pathways are displayed separately in current resources, and making it impossible to search current databases directly to identify the cellular response mechanisms. Therefore, this work develops a novel AlgaePath database to retrieve gene expression profiles efficiently under various conditions in numerous metabolic pathways. AlgaePath, a web-based database, integrates gene information, biological pathways, and next-generation sequencing (NGS) datasets in Chlamydomonasreinhardtii and Neodesmus sp. UTEX 2219-4. Users can identify gene expression profiles and pathway information by using five query pages (i.e. Gene Search, Pathway Search, Differentially Expressed Genes (DEGs) Search, Gene Group Analysis, and Co-Expression Analysis). The gene expression data of 45 and 4 samples can be obtained directly on pathway maps in C. reinhardtii and Neodesmus sp. UTEX 2219-4, respectively. Genes that are differentially expressed between two conditions can be identified in Folds Search. Furthermore, the Gene Group Analysis of AlgaePath includes pathway enrichment analysis, and can easily compare the gene expression profiles of functionally related genes in a map. Finally, Co-Expression Analysis provides co-expressed transcripts of a target gene. The analysis results provide a valuable reference for designing further experiments and elucidating critical mechanisms from high-throughput data. More than an effective interface to clarify the transcript response mechanisms in different metabolic pathways under various conditions, AlgaePath is also a data mining system to identify critical mechanisms based on high-throughput sequencing.

Keywords: next-generation sequencing (NGS), algae, transcriptome, metabolic pathway, co-expression

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Authors: Irma Gabriela Lopez-Moreno, Elva Perez-Luque, Herlinda Aguilar-Zavala

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Introduction: Type 2 Diabetes Mellitus (T2DM) is characterized by combination of insulin resistance and deterioration of insulin secretion. Sfrp5 is a protein that antagonizes Wnt5a proteins by preventing it from reaching its receptor and activating the Wnt/β-catenin signaling pathway, this pathway is one of the most important regulators of adipogenesis. Although metformin decreases glucose levels its mechanisms of action are not fully known but it has been implicated in the inhibition of the Wnt/β-catenin signaling pathway. Objective: The objective was evaluating the effects of metformin on serum levels of Sfrp5 in patients with T2DM treated and not treated with metformin. Methods: Two groups of patients were selected: one group of T2DM patients treated with metformin (n = 35) and another group of subjects with recent diagnosis of T2DM untreated (n = 35) with a mean age of 48 ± 9 years. In these subjects anthropometric measures were taken as weight, height, waist and hip circumference, were calculated the percentage of body fat, visceral fat and muscle mass. In addition, were measured glucose levels, lipid profile, adiponectin and Sfrp5. Results: Sfrp5 were higher in metformin-treated patients compared to the untreated group (19.9 vs 13.6 ng/mL p < 0.001), a negative correlation was found between Sfrp5 levels and total cholesterol levels (r= -0.25, p = 0.03) and percentage of visceral fat (r = -0.26, p = 0.03) and a positive correlation with HDL cholesterol levels (r = 0.31, p = 0.01) and adiponectin (r=0.65, p = < 0.001). Conclusions: The findings show that metformin consumption increased levels of Sfrp5, which may lead to a decrease in the activation of the WNT/β-catenin pathway impacting on adipogenesis.

Keywords: adiponectin, diabetes, metformin, Sfrp5

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Authors: Jiahui Song, Ravindra Joshi

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High-intensity, nanosecond, pulsed electric fields have been shown to be useful non-thermal tools capable of producing a variety of specific cellular responses. While reversible and temporary changes are often desired based on electromanipulation, irreversible effects can also be important objectives. These include elimination of tumor cells and bacterial decontamination. A simple model-based rate-equation treatment of the various cellular biochemical processes was used to qualitatively predict the pulse number-dependent caspase activation and cell survival trends. The model incorporated the caspase-8 associated extrinsic pathway, the delay inherent in its activation, cytochrome c release, and the internal feedback mechanism between caspase-3 and Bid. Results were roughly in keeping with the experimental cell-survival data. A pulse-number threshold was predicted followed by a near-exponential fall-off. The intrinsic pathway was shown to be much weaker as compared to the extrinsic mechanism for electric pulse induced cell apoptosis. Also, delays of about an hour are predicted for detectable molecular concentration increases following electrical pulsing.

Keywords: apoptosis, cell survival, model, pathway

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Authors: Wenxing Chen, Guangying Chen, Yin Lu, Shile Huang

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Cryptotanshinone (CPT), a fat-soluble tanshinone from Salvia miltiorrhiza Bunge, has been demonstrated to inhibit mTOR pathway, resulting in inhibition of cancer cell proliferation. However, the molecular mechanism how CPT acts on mTOR is unknown. Here, cancer cells expressing rapamycin-resistant mutant mTOR are also sensitive to CPT, while phosphorylation of AMPK and TSC2 was activated, suggesting that CPT inhibition of mTOR maybe due to activating upstream of mTOR, AMPK, but not directly binding to and inhibiting mTOR. Further results indicated that Compound C, inhibitor of AMPK, could partially reversed CPT inhibition effect on cancer cells, and dominant-negative AMPK in cancer cells conferred resistance to CPT inhibition of 4EBP1 and phosphorylation of S6K1, as well as sh-AMPK. Furthermore, compared with MEF cells with AMPK positive, MEF cells with AMPK knock out are less sensitive to CPT by the findings that 4E-BP1 and phosphorylation of S6K1 express comparatively much. Furthermore, downexpression of TSC2 slightly recovered expression of 4EBP1 and phosphorylation of S6K1, while co-immunoprecipitation of TSC2 did not affect expression of TSC1 by CPT. Collectively, the above-mentioned results suggest that CPT inhibited mTOR pathway mostly was due to activation of AMPK-TSC2 pathway rather than specific inhibition of mTOR and then induction of subsequent lethal cellular effect.

Keywords: cryptotanshinone, AMPK, TSC2, mTOR, cancer cells

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Authors: Seham Alsaif, Susan Wray

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Obesity is a worldwide disorder influencing women’s health and childbearing. There is a close relation between obesity and pregnancy related complications. Dyslipidemia and adipokine dysregulation are core environmental changes that may mechanistically link these complications with obesity in pregnant women. We have previously found that visfatin has a relaxant effect on mouse, rat and human myometrial contractility. We hypothesised that visfatin inhibits mouse myometrial contractility through the NAD+ pathway. This study was designed to examine the mechanism of action of visfatin on myometrial contractility. To examine the NAD+ pathway, FK866 which is a potent inhibitor of NAD+ biosynthesis was used. Methods: Myometrial strips from term pregnant mice were dissected, superfused with physiological saline and the effects of visfatin (10nM) on oxytocin-induced contractions (0.5nM) alone and after the infusion of FK866 (10uM) were studied. After regular contractions were established, contractility was examined for control (100%) and test response at 37 °C for 10 min each. Results: FK866 was found to inhibit the effect of visfatin on myometrial contractility (the AUC increased from 89±2% of control, P=0.0009 for visfatin alone to 97±4% of control, P>0.05 for visfatin combined with FK866, n=8). In conclusion, NAD+ pathway appears to be involved in the mechanism of action of visfatin on mouse myometrium. This could have a role in making new targets to prevent obesity-related complications.

Keywords: myometrium, obesity, oxytocin, pregnancy, visfatin

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Authors: Maryam Saeidi, Ehsan Motamedian, Seyed Abbas Shojaosadati

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Zymomonas mobilis is known as an example of the uncoupled growth phenomenon. This microorganism also has a unique metabolism that degrades glucose by the Entner–Doudoroff (ED) pathway. In this paper, a genome-scale metabolic model including 434 genes, 757 reactions and 691 metabolites was reconstructed to simulate uncoupled growth and study its effect on flux distribution in the central metabolism. The model properly predicted that ATPase was activated in experimental growth yields of Z. mobilis. Flux distribution obtained from model indicates that the major carbon flux passed through ED pathway that resulted in the production of ethanol. Small amounts of carbon source were entered into pentose phosphate pathway and TCA cycle to produce biomass precursors. Predicted flux distribution was in good agreement with experimental data. The model results also indicated that Z. mobilis metabolism is able to produce biomass with maximum growth yield of 123.7 g (mol glucose)-1 if ATP synthase is coupled with growth and produces 82 mmol ATP gDCW-1h-1. Coupling the growth and energy reduced ethanol secretion and changed the flux distribution to produce biomass precursors.

Keywords: genome-scale metabolic model, Zymomonas mobilis, uncoupled growth, flux distribution, ATP dissipation

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Authors: Joshua W. Edefo, Shafiul Azam, Murray D. Smith.

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Introduction: In April 2022, the Welsh Government introduced the six goals for urgent and emergency care programs. One of these goals was to provide access to clinically safe alternatives, leading to the establishment of the Same Day Emergency Care (SDEC) program. The SDEC initiative aims to offer viable options that maintain patient safety while avoiding unnecessary hospital stays. The aim of the study is to determine the duration of patient stay in SDEC and compare it with that of Emergency department (ED) stay to ascertain if one of the objectives of SDEC is achieved. Methods: Patient stays and attendance datasets were constructed from Withybush SDEC and ED patient records. These records were provided by Hywel Dda University Health Board Informatics. Some hypothetical pathways were identified, notably SDEC visits involving a single attendance and ED visits then immediately transferred to SDEC. Descriptive statistics were used to summarise the data, and hypothesis tests for mean differences used the student t-test. Propensity scoring was employed to match a set of ED patient stays to SDEC patient stays which were then used to determine the average treatment effect (ATE) to compare durations of stay in SDEC with ED. Regression methods were used to model the natural logarithm of the duration of SDEC attendance, and the level of statistical significance was set to 0.05. Results: SDEC visits involving a single attendance (170 of 384; 44.3%) is the most frequently observed pathway with patient length of stay at 256 minutes (95%CI 237.4 - 275.1). The next most frequently observed pathway of patient stay was SDEC attendance after presenting to ED (80 of 384; 20.8%) and gave the length of stay of 440 minutes (95%CI 351.6 - 529.2). Time spent in this pathway significantly increased by 184 minutes (95%CI 118.0 - 250.2, support for no difference p<0.001) compared to the most seen pathway. When SDEC data were compared with ED, the estimate for the ATE from SDEC single attendance was -272 minutes (95%CI -334.1 - -210.5; p<0.001), while that of ED then SDEC pathway was -50.6 min (95%CI -182.7-81.5; p=0.453). Conclusion: When patients are admitted to SDEC and successfully discharged, their stays are significantly shorter, approximately 4.5 hours, compared to patients who spend their entire stay in the Emergency Department. That difference vanishes when the patient stay includes a period spent previously in ED before transfer to SDEC.

Keywords: attendance, emergency-department, patient-stay, same-day-emergency-care

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Authors: Kamran Jawed, Anu Jose Mattam, Zia Fatma, Saima Wajid, Malik Z. Abdin, Syed Shams Yazdani

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Worldwide demand of natural and sustainable fuels and chemicals have encouraged researchers to develop microbial platform for synthesis of short chain fatty acids as they are useful precursors to replace petroleum-based fuels and chemicals. In this study, we evaluated the role of fatty acid synthesis and β-oxidation cycle of Escherichia coli to produce butyric acid, a 4-carbon short chain fatty acid, with the help of three thioesterases, i.e., TesAT from Anaerococcus tetradius, TesBF from Bryantella formatexigens and TesBT from Bacteroides thetaiotaomicron. We found that E. coli strain transformed with gene for TesBT and grown in presence of 8 g/L glucose produced maximum butyric acid titer at 1.46 g/L, followed by that of TesBF at 0.85 g/L and TesAT at 0.12 g/L, indicating that these thioesterases were efficiently converting short chain fatty acyl-ACP intermediate of fatty acid synthesis pathway into the corresponding acid. The titer of butyric acid varied significantly depending upon the plasmid copy number and strain genotype. Deletion of genes for fatty acyl-CoA synthetase and acyl-CoA dehydrogenase, which are involved in initiating the fatty acid degradation cycle, and overexpression of FadR, which is a dual transcriptional regulator and exerts negative control over fatty acid degradation pathway, reduced up to 30% of butyric acid titer. This observation suggested that β-oxidation pathway is working synergistically with fatty acid synthesis pathway in production of butyric acid. Moreover, accelerating the fatty acid elongation cycle by overexpressing acetyl-CoA carboxyltransferase (Acc) and 3-hydroxy-acyl-ACP dehydratase (FabZ) or by deleting FabR, the transcription suppressor of elongation, did not improve the butyric acid titer, rather favored the long chain fatty acid production. Finally, a balance between cell growth and butyric acid production was achieved with the use of phosphorous limited growth medium and 14.3 g/L butyric acid, and 17.5 g/L total free fatty acids (FFAs) titer was achieved during fed-batch cultivation. We have engineered an E. coli strain which utilizes the intermediate of both fatty acid synthesis and degradation pathway, i.e. butyryl-ACP and -CoA, to produce butyric acid from glucose. The strategy used in this study resulted in highest reported titers of butyric acid and FFAs in engineered E. coli.

Keywords: butenoic acid, butyric acid, Escherichia coli, fed-batch fermentation, short chain fatty acids, thioesterase

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Authors: Naif Al-Jomah, Falah H Al-Mohanna, Abdelilah Aboussekhra

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Active breast cancer-associated fibroblasts (CAFs), the most influential cells in breast tumor microenvironment, express/secrete high levels of the proinvasive/metastatic interleukin-6 (IL-6). Therefore, we have tested here the effect of the IL-6 receptor (IL-6R) inhibitor tocilizumab (TCZ; Actemra) on different active breast CAFs. We have shown that TCZ potently and persistently suppresses the expression of various CAF biomarkers, namely α-SMA, SDF-1 as well as the STAT3 pathway and its downstream target AUF1. TCZ also inhibited the proliferation, migration and invasion abilities of active breast CAF cells. Additionally, TCZ repressed the ability of CAF cells in promoting epithelial-to-mesenchymal transition, and enhancing the migratory/invasive and proliferative capacities of breast cancer cells in vitro. Importantly, these findings were confirmed in orthotopic humanized breast tumors in mice. Furthermore, TCZ suppressed the expression of the pro-angiogenic factor VEGF-A and its transactivator HIF-1α in CAF cells, and consequently inhibited the angiogenic-promoting effect of active CAFs both in vitro and in orthotopic tumor xenografts. These results indicate that inhibition of the IL-6/STAT3/AUF1 pathway by TCZ can normalize active breast CAFs and suppress their paracrine pro-carcinogenic effects, which paves the way toward development of specific CAF-targeting therapy, badly needed for more efficient breast cancer treatments.

Keywords: angiogenesis, interleukin-6, paracrine, cancer-associated fibroblasts

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Authors: Samantha Jeffries, Chontit Chuenurah

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Thailand incarcerates the largest number of women and has the highest female incarceration rate in South East Asia. Since the 1990s, there has been a substantial increase in the number, rate and proportion of women imprisoned. Thailand places a high priority on the gender specific contexts out of which offending arises and the different needs of women in the criminal justice system. This is manifested in work undertaken to guide the development of the United Nations Rules for the Treatment of Women Prisoners and Non-Custodial Measures for Women Offenders (the Bangkok Rules); adopted by the United Nations General Assembly in 2010. The Bangkok Rules make a strong statement about Thailand’s recognition of and commitment to the fair and equitable treatment of women throughout their contact with the criminal justice system including at sentencing and in prison. This makes the comparatively high use of imprisonment for women in Thailand particularly concerning and raises questions about the relationship between gender, crime and criminal justice. While there is an extensive body of research in Western jurisdictions exploring women’s pathways to prison, there is a relative dearth of methodologically robust research examining the possible gendered circumstances leading to imprisonment in Thailand. In this presentation, we will report preliminary findings from a qualitative study of women’s pathways to prison in Thailand. Our research aims were to ascertain: 1) the type, frequency, and context of criminal behavior that led to women’s incarceration, 2) women’s experiences of the criminal justice system, 3) the broader life experiences and circumstances that led women to prison in Thailand. In-depth life history interviews (n=77) were utilized to gain a comprehensive understanding of women’s journeys into prison. The interview schedule was open-ended consisting of prisoner responses to broad discussion topics. This approach provided women with the opportunity to describe significant experiences in their lives, to bring together distinct chronologies of events, and to analyze links between their varied life experiences, offending, and incarceration. Analyses showed that women’s journey’s to prison take one of eight pathways which tentatively labelled as follows, the: 1) harmed and harming pathway, 2) domestic/family violence victimization pathway, 3) drug connected pathway, 4) street woman pathway, 5) economically motivated pathway, 6) jealousy anger and/or revenge pathway, 7) naivety pathway, 8) unjust and/or corrupted criminal justice pathway. Each will be fully discussed during the presentation. This research is significant because it is the first in-depth methodologically robust exploration of women’s journeys to prison in Thailand and one of a few studies to explore gendered pathways outside of western contexts. Understanding women’s pathways into Thailand’s prisons is crucial to the development of effective planning, policy and program responses not only while women are in prison but also post-release. To best meet women’s needs in prison and effectively support their reintegration, we must have a comprehensive understanding of who these women are, what offenses they commit, the reasons that trigger their confrontations with the criminal justice system and the impact of the criminal justice system on them.

Keywords: pathways, prison, women, Thailand

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Authors: M. Marjaneh, M. Y. Narazah, H. Shahrul

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Array-based gene expression analysis is a powerful tool to profile expression of genes and to generate information on therapeutic effects of new anti-cancer compounds. Anti-apoptotic effect of thymoquinone was studied in MCF7 breast cancer cell line using gene expression profiling with cDNA micro array. The purity and yield of RNA samples were determined using RNeasyPlus Mini kit. The Agilent RNA 6000 Nano LabChip kit evaluated the quantity of the RNA samples. AffinityScript RT oligo-dT promoter primer was used to generate cDNA strands. T7 RNA polymerase was used to convert cDNA to cRNA. The cRNA samples and human universal reference RNA were labelled with Cy-3-CTP and Cy-5-CTP, respectively. Feature Extraction and GeneSpring software analysed the data. The single experiment analysis revealed involvement of 64 pathways with up-regulated genes and 78 pathways with down-regulated genes. The MAPK and p38-MAPK pathways were inhibited due to the up-regulation of PTPRR gene. The inhibition of p38-MAPK suggested up-regulation of TGF-ß pathway. Inhibition of p38 - MAPK caused up-regulation of TP53 and down-regulation of Bcl2 genes indicating involvement of intrinsic apoptotic pathway. Down-regulation of CARD16 gene as an adaptor molecule regulated CASP1 and suggested necrosis-like programmed cell death and involvement of caspase in apoptosis. Furthermore, down-regulation of GPCR, EGF-EGFR signalling pathways suggested reduction of ER. Involvement of AhR pathway which control cytochrome P450 and glucuronidation pathways showed metabolism of Thymoquinone. The findings showed differential expression of several genes in apoptosis pathways with thymoquinone treatment in estrogen receptor-positive breast cancer cells.

Keywords: cDNA microarray, thymoquinone, CARD16, PTPRR, CASP10

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Authors: Kai-Yao Huang, Tzong-Yi Lee, Pin-Hao Ho, Tzu-Hao Chang, Cheng-Wei Chang

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Background: Human cytomegalovirus (HCMV) infects much people around the world, and there were many researches mention that many diseases were caused by HCMV. To understand the mechanism of HCMV lead to diseases during infection. We observe a microRNA (miRNA) – miRNA interaction between HCMV and host during infection. We found HCMV miRNA sequence component complementary with host miRNA precursors, and we also found that the host miRNA abundances were decrease in HCMV infection. Hence, we focus on the host miRNA which may target by the other HCMV miRNA to find theirs target mRNAs expression and analysis these mRNAs affect what kind of signaling pathway. Interestingly, we found the affected mRNA play an important role in some diseases related pathways, and these diseases had been annotated by HCMV infection. Results: From our analysis procedure, we found 464 human miRNAs might be targeted by 26 HCMV miRNAs and there were 291 human miRNAs shows the concordant decrease trend during HCMV infection. For case study, we found hcmv-miR-US22-5p may regulate hsa-mir-877 and we analysis the KEGG pathway which built by hsa-mir-877 validate target mRNA. Additionally, through survey KEGG Disease database found that these mRNA co-regulate some disease related pathway for instance cancer, nerve disease. However, there were studies annotated that HCMV infection casuse cancer and Alzheimer. Conclusions: This work supply a different scenario of miRNA target interactions(MTIs). In previous study assume miRNA only target to other mRNA. Here we wonder there is possibility that miRNAs might regulate non-mRNA targets, like other miRNAs. In this study, we not only consider the sequence similarity with HCMV miRNAs and human miRNA precursors but also the expression trend of these miRNAs. Then we analysis the human miRNAs validate target mRNAs and its associated KEGG pathway. Finally, we survey related works to validate our investigation.

Keywords: human cytomegalovirus, HCMV, microRNA, miRNA

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Authors: Jae-Hyung Jin, Kyung-Tae Lee, Yee-Seul So, Eunji Jeong, Yeonseon Lee, Dongpil Lee, Dong-Gi Lee, Yong-Sun Bahn

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Cryptococcus neoformans causes cryptococcal meningoencephalitis mainly in immunocompromised patients as well as immunocompetent people. But therapeutic options are limited to treat cryptococcosis. Some signaling pathways including cyclic AMP pathway, MAPK pathway, and calcineurin pathway play a central role in the regulation of the growth, differentiation, and virulence of C. neoformans. To understand signaling networks regulating the virulence of C. neoformans, we selected the 114 putative phosphatase genes, one of the major components of signaling networks, in the genome of C. neoformans. We identified putative phosphatases based on annotation in C. neoformans var. grubii genome database provided by the Broad Institute and National Center for Biotechnology Information (NCBI) and performed a BLAST search of phosphatases of Saccharomyces cerevisiae, Aspergillus nidulans, Candida albicans and Fusarium graminearum to Cryptococcus neoformans. We classified putative phosphatases into 14 groups based on InterPro phosphatase domain annotation. Here, we constructed 170 signature-tagged gene-deletion strains through homologous recombination methods for 91 putative phosphatases. We examined their phenotypic traits under 30 different in vitro conditions, including growth, differentiation, stress response, antifungal resistance and virulence-factor production.

Keywords: human fungal pathogen, phosphatase, deletion library, functional genomics

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Authors: Jianming Cai

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Exposure to ionizing radiation causes severe damage to human body and an safe and effective radioprotector is urgently required for alleviating radiation damage. In 2008, flagellin, an agonist of TLR5, was found to exert radioprotective effects on radiation injury through activating NF-kB signaling pathway. From then, the radioprotective effects of TLR ligands has shed new lights on radiation protection. CpG-ODN is an unmethylated oligonucleotide which activates TLR9 signaling pathway. In this study, we demonstrated that CpG-ODN has therapeutic effects on radiation injuries induced by γ ray and 12C6+ heavy ion particles. Our data showed that CpG-ODN increased the survival rate of mice after whole body irradiation and increased the number of leukocytes as well as the bone marrow cells. CpG-ODN also alleviated radiation damage on intestinal crypt through regulating apoptosis signaling pathway including bcl2, bax, and caspase 3 etc. By using a radiation-induced pulmonary fibrosis model, we found that CpG-ODN could alleviate structural damage, within 20 week after whole–thorax 15Gy irradiation. In this model, Th1/Th2 imbalance induced by irradiation was also reversed by CpG-ODN. We also found that TGFβ-Smad signaling pathway was regulated by CpG-ODN, which accounts for the therapeutic effects of CpG-ODN in radiation-induced pulmonary injury. On another hand, for high LET radiation protection, we investigated protective effects of CpG-ODN against 12C6+ heavy ion irradiation and found that after CpG-ODN treatment, the apoptosis and cell cycle arrest induced by 12C6+ irradiation was reduced. CpG-ODN also reduced the expression of Bax and caspase 3, while increased the level of bcl2. Then we detected the effect of CpG-ODN on heavy ion induced immune dysfunction. Our data showed that CpG-ODN increased the survival rate of mice and also the leukocytes after 12C6+ irradiation. Besides, the structural damage of immune organ such as thymus and spleen was also alleviated by CpG-ODN treatment. In conclusion, we found that TLR9 ligand, CpG-ODN reduced radiation injuries in response to γ ray and 12C6+ heavy ion irradiation. On one hand, CpG-ODN inhibited the activation of apoptosis induced by radiation through regulating bcl2, bax and caspase 3. On another hand, through activating TLR9, CpG-ODN recruit MyD88-IRAK-TRAF6 complex, activating TAK1, IRF5 and NF-kB pathway, and thus alleviates radiation damage. This study provides novel insights into protection and therapy of radiation damages.

Keywords: TLR9, CpG-ODN, radiation injury, high LET radiation

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Authors: Ming Ma, Rui Li

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In the highly urbanized district, green open space is playing an important role in human’s health and wellbeing as a physical, aesthetic and natural environment resources. The aim of this paper is to close this gap through providing a comprehensive, qualitative meta-analysis of existing studies related to this issue. A systematic scoping of current quantitative research is conducted which mostly focused on cross-sectional survey and experimental studies. Health benefits from contact with green open space could be categorized into physical health, psychological health and social wellbeing. Mechanism for the health related to green open space could be clearly identified with the regard to natural restoration, physical activities and social capital. These results indicate a multiple pathways framework between the health benefits and mechanism. In order to support design and planning, the most evident relationship was picked up that people could psychologically benefit from green open space through outdoors physical activities. Additionally, three design and planning strategies are put forward. Various and multi-level contacts with green open space would be considered as an explanation of the pathway results and tie to bridge the health to design and planning. There is a need to carry out long-term research emphasizing on causal relationship between health and green open space through excluding cofounding factors such as self-selection.

Keywords: urban green open space, planning and design, health benefit, mechanism, pathway framework

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Authors: Cuili Yang, Chengcao Sun, Ruilin Xue, Yongyong Xi, Liang Wang, Dejia Li

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Backgrounds: Previous studies showed that Sirt1 plays an important role in C2C12 myoblast cell proliferation, but the mechanism(s) involved in this process remains unclear. This work was undertaken to determine if Myostatin participates in the regulation of C2C12 proliferation by Sirt1. Methods: We administrated the Sirt1 activator resveratrol, inhibitor Nicotinamide (NAM) and Myostatin inhibitor SB431542 on C2C12 myoblast cells. Cell viability was evaluated by CCK8 assay. The expression of Sirt1 and MyoD were detected by qRT-PCR. Utilizing western blot to determinate the expression of myostatin, P107 and p-P107. Results: Our results showed that resveratrol promoted the proliferation of C2C12 myoblast cells, while NAM suppressed the proliferation of C2C12 myoblast cells; SB431542 promoted the proliferation of C2C12 myoblast cells and attenuated the inhibition effect of NAM on C2C12 myoblast cells proliferation; Resveratrol can significantly increase the expression of Sirt1 and MyoD, decrease the expression of Myostatin, while NAM can significantly down-regulate the expression of Sirt1, MyoD and the phosphorylation of P107(p-P107), but up-regulate the expression of Myostatin and the protein P107; SB431542 can significantly mitigate the effect of NAM on the expression of MyoD, P107, and p-P107. Conclusions: Taken together, these results indicate that Sirt1 promotes the proliferation of C2C12 myoblast cells via Myostatin signaling pathway.

Keywords: Sirt1, C2C12 cells, proliferation, myostatin signaling pathway

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Authors: Laura Ulitzky, Dougbeh-Chris Nyan, Manuel M. Lafer, Erica Silberstein, Nicoleta Cehan, Deborah R. Taylor

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Hepatitis C virus (HCV)-associated hepatocellular carcinoma, fibrosis and cirrhosis are more frequent in men and postmenopausal women than in premenopausal women and women receiving hormone replacement therapy, suggesting that β-estradiol (estrogen) plays an innate role in preventing viral infection and liver disease. Estrogen classically acts through nuclear estrogen receptors or, alternatively, through the membrane-bound G-protein-coupled estrogen receptor (GPR30 or GPER). We observed a marked decrease in detectable virus when HCV-infected human hepatoma cells were treated with estrogen. The effect was mimicked by both Tamoxifen (Tam) and G1, a GPR30-specific agonist, and was reversed by the GPR30-specific antagonist, G15. Through GPR30, estrogen-mediated the down-regulation of occludin; a tight junction protein and HCV receptor, by promoting activation of matrix metalloproteinases (MMPs). Activated MMP-9 was secreted in response to estrogen, cleaving occludin in the extracellular Domain D, the motif required for HCV entry and spread. This pathway gives new insight into a novel innate immune pathway and the disparate host-virus responses to HCV demonstrated by the two sexes. Moreover, these data suggest that hormone replacement therapy may have beneficial antiviral properties for HCV-infected postmenopausal women and show promise for new antiviral treatments for both men and women.

Keywords: HCV, estrogen, occludin, MMPs

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Authors: Claudia Schier, Arvid Biallas, Bernd Friedrich

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The demand for Li-ion-batteries owing to their benefits, such as; fast charging time, high energy density, low weight, large temperature range, and a long service life performance is increasing compared to other battery systems. These characteristics are substantial not only for battery-operated portable devices but also in the growing field of electromobility where high-performance energy storage systems in the form of batteries are highly requested. Due to the sharp rising production, there is a tremendous interest to recycle spent Li-Ion batteries in a closed-loop manner owed to the high content of valuable metals such as cobalt, manganese, and lithium as well as regarding the increasing demand for those scarce applied metals. Currently, there are just a few industrial processes using hydrometallurgical methods to recover valuable metals from Li-ion-battery waste. In this study, the extraction of valuable metals from spent Li-ion-batteries is investigated by pretreated and subsequently leached battery wastes using different precipitation methods in a comparative manner. For the extraction of lithium, cobalt, and other valuable metals, pelletized battery wastes with an initial Li content of 2.24 wt. % and cobalt of 22 wt. % is used. Hydrochloric acid with 4 mol/L is applied with 1:50 solid to liquid (s/l) ratio to generate pregnant leach solution for subsequent precipitation steps. In order to obtain pure precipitates, two different pathways (pathway 1 and pathway 2) are investigated, which differ from each other with regard to the precipitation steps carried out. While lithium carbonate recovery is the final process step in pathway 1, pathway 2 requires a preliminary removal of lithium from the process. The aim is to evaluate both processes in terms of purity and yield of the products obtained. ICP-OES is used to determine the chemical content of leach liquor as well as of the solid residue.

Keywords: hydrochloric acid, hydrometallurgy, Li-ion-batteries, metal recovery

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Authors: Michael Huber, Maximilian J. Poller, Jens Tochtermann, Wolfgang Korth, Andreas Jess, Jakob Albert

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Aside from the desulfurisation, the denitrogenation of fuels is of great importance to minimize the environmental impact of transport emissions. The oxidative reaction pathway of organic nitrogen in the catalytic oxidative denitrogenation could be successfully elucidated. This is the first time such a pathway could be traced in detail in non-microbial systems. It was found that the organic nitrogen is first oxidized to nitrate, which is subsequently reduced to molecular nitrogen via nitrous oxide. Hereby, the organic substrate serves as a reducing agent. The discovery of this pathway is an important milestone for the further development of fuel denitrogenation technologies. The United Nations aims to counteract global warming with Net Zero Emissions (NZE) commitments; however, it is not yet foreseeable when crude oil-based fuels will become obsolete. In 2021, more than 50 million barrels per day (mb/d) were consumed for the transport sector alone. Above all, heteroatoms such as sulfur or nitrogen produce SO₂ and NOx during combustion in the engines, which is not only harmful to the climate but also to health. Therefore, in refineries, these heteroatoms are removed by hy-drotreating to produce clean fuels. However, this catalytic reaction is inhibited by the basic, nitrogenous reactants (e.g., quinoline) as well as by NH3. The ion pair of the nitrogen atom forms strong pi-bonds to the active sites of the hydrotreating catalyst, which dimin-ishes its activity. To maximize the desulfurization and denitrogenation effectiveness in comparison to just extraction and adsorption, selective oxidation is typically combined with either extraction or selective adsorption. The selective oxidation produces more polar compounds that can be removed from the non-polar oil in a separate step. The extraction step can also be carried out in parallel to the oxidation reaction, as a result of in situ separation of the oxidation products (ECODS; extractive catalytic oxidative desulfurization). In this process, H8PV5Mo7O40 (HPA-5) is employed as a homogeneous polyoxometalate (POM) catalyst in an aqueous phase, whereas the sulfur containing fuel components are oxidized after diffusion from the organic fuel phase into the aqueous catalyst phase, to form highly polar products such as H₂SO₄ and carboxylic acids, which are thereby extracted from the organic fuel phase and accumulate in the aqueous phase. In contrast to the inhibiting properties of the basic nitrogen compounds in hydrotreating, the oxidative desulfurization improves with simultaneous denitrification in this system (ECODN; extractive catalytic oxidative denitrogenation). The reaction pathway of ECODS has already been well studied. In contrast, the oxidation of nitrogen compounds in ECODN is not yet well understood and requires more detailed investigations.

Keywords: oxidative reaction pathway, denitrogenation of fuels, molecular catalysis, polyoxometalate

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Authors: Ren-Jye Lin, Li-Hsiung Lin, Bing-Cheng Liu, Ching-Len Liao

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The human zinc finger protein 36-like protein family, containing zinc finger protein 36-like 1 (ZFP36L1) and zinc finger protein 36-like 2 (ZFP36L2), belongs to CCCH-type zinc-finger protein identified as an RNA-binding protein that participates in controlling posttranscriptional regulation via RNA decay pathways. Recently, we demonstrated that human ZFP36L1 showed potent antiviral activity against flavivirus Infection by both 5´-3´ XRN1 and 3´-5´RNA-exosome RNA decay pathways (Journal of Virology 2022 Jan 12;96(1): e0166521). However, another zinc finger protein 36-like protein member, ZFP36L2, in the host defense response against flaviviruses has yet to be addressed. Here, we also demonstrate that ZFP36L2 functions as a host innate defender against flaviviruses, including Japanese encephalitis virus (JEV) and dengue virus (DENV). Overexpression of ZFP36L2 reduced JEV and DENV infection, and ZFP36L2 knockdown significantly promoted viral replication. Distinct from the antiviral mechanism of ZFP36L1, ZFP36L2 inhibits flavivirus infection by only a 5´-3´ XRN1-mediated RNA decay pathway but not the 3´-5´RNA-exosome RNA decay pathway. Human ZFP36L1 and ZFP36L2 can restrict flavivirus replication by directly binding and destabilizing viral RNA. Thus, for the first time, human zinc finger protein 36-like family members, ZFP36L1 and ZFP36L2, are identified as host antiviral factors that can bind and degrade flavivirus viral RNA by diverse antiviral mechanisms.

Keywords: ZFP36L1, ZFP36L2, 5'-3' exonuclease XRN1, antiviral mechansim

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Authors: Ozlem Oral, Seval Kilic, Ozlem Yedier, Serap Dokmeci, Devrim Gozuacik

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Autophagy is a degradation pathway, activating under stress conditions. It digests macromolecules, such as abnormal proteins and long-lived organelles by engulfing them and by subsequent delivery of the cargo to lysosomes. The members of the phospholipid-dependent serine/threonine kinases, involved in many signaling pathways, which are necessary for the regulation of cellular metabolic activation. Previous studies implicate that, serine/threonine kinases have crucial roles in the mechanism of many diseases depend on the activated and/or inactivated signaling pathway. Data indicates, the signaling pathways activated by serine/threonine kinases are also involved in activation of autophagy mechanism. However, the information about the effect of serine/threonine kinases on autophagy mechanism and the roles of these effects in disease formation is limited. In this study, we investigated the effect of activated serine/threonine kinases on autophagic pathway. We performed a commonly used autophagy technique, GFP-LC3 dot formation and by using microscopy analyses, we evaluated promotion and/or inhibition of autophagy in serine/threonine kinase-overexpressed fibroblasts as well as cancer cells. In addition, we carried out confocal microscopy analyses and examined autophagic flux by utilizing the differential pH sensitivities of RFP and GFP in mRFP-GFP-LC3 probe. Based on the shRNA-library based screening, we identified autophagy-related proteins affected by serine/threonine kinases. We further studied the involvement of serine/threonine kinases on the molecular mechanism of newly identified autophagy proteins and found that, autophagic pathway is indirectly controlled by serine/threonine kinases via specific autophagic proteins. Our data indicate the molecular connection between two critical cellular mechanisms, which have important roles in the formation of many disease pathologies, particularly cancer. This project is supported by TUBITAK-1001-Scientific and Technological Research Projects Funding Program, Project No: 114Z836.

Keywords: autophagy, GFP-LC3 dot formation assay, serine/threonine kinases, shRNA-library screening

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Authors: Naseer Iqbal, Mukesh Kumar, Pradeep Sharma, Satya Prakash Yadav, Punit Kaur, Sujata Sharma, T. P. Singh

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Dehydroquinase (3-dehydroquinate dehydratase, DHQD, EC 4.2.1.10) is involved in shikimate pathway and catalyzes the conversion of dehydroquinate to dehydroshikimate. Shikimate pathway is important drug target as this pathway is absent in mammals. DHQD from Acinetobacter baumannii (AbDHQD) was cloned, expressed and purified to homogeneity. The binding studies showed that compounds quinic acid and citrazinic acid bound to AbDHQD at micromolar concentrations. AbDHQD was crystallized using 30% PEG-3350, 50mM tris-HCl, and 1.0M MgSO4 at PH 8.0. Crystals of AbDHQD were stabilized by transferring them into reservoir solution to which 25% glycerol was added for data collection at 100K. The X-ray intensity data were collected to 2.0Å resolution. The crystals belong to monoclinic space group P21 with cell dimensions, a = 82.3, b = 95.3, c = 132.3Å and β = 95.7°. The structure was solved with molecular replacement method and refined to Rcryst/Rfree factors of 0.200/0.232. The structures of 12 crystallographically independent molecules in the asymmetry unit were identical with r.m.s shifts for the C atoms ranging from 0.3 Å to 0.8 Å. They formed a dodecamer with four trimers arranged in a tetrahedral manner. The classical lid adopted an open conformation although a sulfate ion was observed in the substrate binding site. As a result of which, the compounds quinic acid and citrazinic acid did not bind to AbDHQD.

Keywords: acinetobacter Bauman Nii, dehydroquinate dehydratase, dodecamer, open conformation

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Authors: Angela U. Makolo, Temitayo A. Olagunju

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The knowledge of signaling pathways is central to understanding the biological mechanisms of organisms since it has been identified that in eukaryotic organisms, the number of signaling pathways determines the number of ways the organism will react to external stimuli. Signaling pathways are studied using protein interaction networks constructed from protein-protein interaction data obtained using high throughput experimental procedures. However, these high throughput methods are known to produce very high rates of false positive and negative interactions. In order to construct a useful protein interaction network from this noisy data, computational methods are applied to validate the protein-protein interactions. In this study, a computational technique to identify signaling pathways from a protein interaction network constructed using validated protein-protein interaction data was designed. A weighted interaction graph of the Saccharomyces cerevisiae (Baker’s Yeast) organism using the proteins as the nodes and interactions between them as edges was constructed. The weights were obtained using Bayesian probabilistic network to estimate the posterior probability of interaction between two proteins given the gene expression measurement as biological evidence. Only interactions above a threshold were accepted for the network model. A pathway was formalized as a simple path in the interaction network from a starting protein and an ending protein of interest. We were able to identify some pathway segments, one of which is a segment of the pathway that signals the start of the process of meiosis in S. cerevisiae.

Keywords: Bayesian networks, protein interaction networks, Saccharomyces cerevisiae, signalling pathways

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