Search results for: Sonic hedgehog signaling

Authors: Vineet Gairola

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In many cultures, ethnographers have tried to set up a tight link between music and possession. However, they rarely informed us about the psychology of interactions between music and the possessed. Ancient myths and the archetypal find expression through the rituals practiced in Uttarakhand. In Uttarakhand (a part of the Central Himalayan region), an intriguing archetypal healing mechanism takes place. Some people get 'possessed' by a deity and shower blessings onto people gathered for a puja in a temple, where invocation of deity takes place through two archetypal drumming instruments played together named dhol-damaun. There is devi-doli (palanquin of the goddess) worship, which is carried on the shoulders of two people and is said to be tilting and shaking on its own. Archetypal in the modern mind survives effortlessly. The 'oceanic' of religious feelings are explored through an oral text of Dholsagar. The method of ethnography along with case-studies has been used. A substantial part of fieldwork was carried out in Rudraprayag, Uttarakhand. The research suggests that the collective unconscious is also sonic in nature, which is characterized by sounds and rhythms—not only symbols and images, as Dr. Jung suggested.

Keywords: archetypal, music, myth, mysticism, possession, sonic collective unconscious

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Authors: Usha Kiran, M. Z. Abdin

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Osmotin is an abundant cationic multifunctional protein discovered in cells of tobacco (Nicotiana tabacum L. var Wisconsin 38) adapted to an environment of low osmotic potential. It provides plants protection from pathogens, hence placed in the PRP family of proteins. The osmotin induced proline accumulation has been reported in plants including transgenic tomato and strawberry conferring tolerance against both biotic and abiotic stresses. The exact mechanism of induction of proline by osmotin is however, not known till date. These observations have led us to hypothesize that osmotin induced proline accumulation could be due to its involvement as transcription factor and/or cell signal pathway modulator in proline biosynthesis. The present investigation was therefore, undertaken to analyze the osmotin protein as transcription factor /cell signalling modulator using bioinformatics tools. The results of available online DNA binding motif search programs revealed that osmotin does not contain DNA-binding motifs. The alignment results of osmotin protein with the protein sequence from DATF showed the homology in the range of 0-20%, suggesting that it might not contain a DNA binding motif. Further to find unique DNA-binding domain, the superimposition of osmotin 3D structure on modeled Arabidopsis transcription factors using Chimera also suggested absence of the same. We, however, found evidence implicating osmotin in cell signaling. With these results, we concluded that osmotin is not a transcription factor but regulating proline biosynthesis and accumulation through cell signaling during abiotic stresses.

Keywords: osmotin, cell signaling modulator, bioinformatic tools, protein

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Authors: Mohammad I. Hossain, Omar F. Hamim

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This paper presents a case study on a pile integrity test for assessing the integrity of piles as well as a physical dimension (e.g., cross-sectional area, length), continuity, and consistency of the pile materials. The recent boom in the socio-economic condition of Bangladesh has given rise to the building of high-rise commercial and residential infrastructures. The advantage of the pile integrity test lies in the fact that it is possible to get an approximate indication regarding the quality of the sub-structure before commencing the construction of the super-structure. This paper aims at providing a classification of cast-in-situ piles based on characteristic reflectograms obtained using the Sonic Integrity Testing program for the sub-soil condition of Narayanganj, Bangladesh. The piles have been classified as 'Pile Type-1', 'Pile Type-2', 'Pile Type-3', 'Pile type-4', 'Pile Type-5' or 'Pile Type-6' from the visual observations of reflections from the generated stress waves by striking the pile head with a handheld hammer. With respect to construction quality and integrity, piles have been further classified into three distinct categories, i.e., satisfactory, may be satisfactory, and unsatisfactory.

Keywords: cast-in-situ piles, characteristic reflectograms, pile integrity test, sonic integrity testing program

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Authors: Shih-Hao Chen, Chi-Wai Chow

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Visible light communication combined with spread spectrum modulation is demonstrated in this study. Differential signaling method also ensures the proposed system that can support high immunity to ambient light interference. Experiment result shows the proposed system has 6 dB gain comparing with the original On-Off Keying modulation scheme.

Keywords: Visible Light Communication (VLC), Spread Spectrum Modulation (SSM), On-Off Keying, visible light communication

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Authors: Jayahar Sivasubramanian

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Understanding laminar-turbulent transition process in hyper-sonic boundary layers is crucial for designing viable high speed flight vehicles. The study of transition becomes particularly important in the high speed regime due to the effect of transition on aerodynamic performance and heat transfer. However, even after many years of research, the transition process in hyper-sonic boundary layers is still not understood. This lack of understanding of the physics of the transition process is a major impediment to the development of reliable transition prediction methods. Towards this end, spatial Direct Numerical Simulations are conducted to investigate the instability waves generated by a localized disturbance in a hyper-sonic flat plate boundary layer. In order to model a natural transition scenario, the boundary layer was forced by a short duration (localized) pulse through a hole on the surface of the flat plate. The pulse disturbance developed into a three-dimensional instability wave packet which consisted of a wide range of disturbance frequencies and wave numbers. First, the linear development of the wave packet was studied by forcing the flow with low amplitude (0.001% of the free-stream velocity). The dominant waves within the resulting wave packet were identified as two-dimensional second mode disturbance waves. Hence the wall-pressure disturbance spectrum exhibited a maximum at the span wise mode number k = 0. The spectrum broadened in downstream direction and the lower frequency first mode oblique waves were also identified in the spectrum. However, the peak amplitude remained at k = 0 which shifted to lower frequencies in the downstream direction. In order to investigate the nonlinear transition regime, the flow was forced with a higher amplitude disturbance (5% of the free-stream velocity). The developing wave packet grows linearly at first before reaching the nonlinear regime. The wall pressure disturbance spectrum confirmed that the wave packet developed linearly at first. The response of the flow to the high amplitude pulse disturbance indicated the presence of a fundamental resonance mechanism. Lower amplitude secondary peaks were also identified in the disturbance wave spectrum at approximately half the frequency of the high amplitude frequency band, which would be an indication of a sub-harmonic resonance mechanism. The disturbance spectrum indicates, however, that fundamental resonance is much stronger than sub-harmonic resonance.

Keywords: boundary layer, DNS, hyper sonic flow, instability waves, wave packet

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Authors: Anita Jäger, Andrew Salazar, Jörg von Hagen, Harald Kolmar

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In the treatment of individuals with sensitive and psoriatic skin, several inflammation and itch-related molecular and cellular targets have been identified, but many of these have yet to be characterized. In this study, we present two potential targets in the skin that can be linked to the inflammation and itch cycle. 11ßHSD1 is the enzyme responsible for converting inactive cortisone to active cortisol used to transmit signals downstream. The activation of the receptor NK1R correlates with promoting inflammation and the perception of itch and pain in the skin. In this study, both targets have been investigated based on their involvement in inflammation. The role of both identified targets was characterized based on the secretion of inflammation cytokine- IL6, IL-8, and CCL2, as well as phosphorylation and signaling pathways. It was found that treating skin cells with molecules able to inhibit inflammatory pathways results in the reduction of inflammatory signaling molecules secreted by skin cells and increases their proliferative capacity. Therefore, these molecular targets and their associated pathways show therapeutic potential and can be mitigated via small molecules. This research can be used for further studies in inflammation and itch pathways and can help to treat pathological symptoms.

Keywords: inflammation, itch, signaling pathway, skin

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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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Authors: Faustina Masocha, Vusani Moyo

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For decades, dividend announcements have been presumed to contain important signals about the future prospects of companies. Similarly, the same has been presumed about management earnings announcements. Despite both dividend and earnings announcements being considered informative, a number of researchers questioned their credibility and found both to contain short-term signals. Pertaining to dividend announcements, some authors argued that although they might contain important information that can result in changes in share prices, which consequently results in the accumulation of abnormal returns, their degree of informativeness is less compared to other signaling tools such as earnings announcements. Yet, this claim in favor has been refuted by other researchers who found the effect of earnings to be transitory and of little value to shareholders as indicated by the little abnormal returns earned during the period surrounding earnings announcements. Considering the above, it is apparent that both dividends and earnings have been hypothesized to have a signaling impact. This prompts one to question which between these two signaling tools is more informative. To answer this question, two follow-up questions were asked. The first question sought to determine the event which results in the most effect on share prices, while the second question focused on the event that influenced trading volume the most. To answer the first question and evaluate the effect that each of these events had on share prices, an event study methodology was employed on a sample made up of the top 10 JSE-listed companies for data collected from 2012 to 2019 to determine if shareholders gained abnormal returns (ARs) during announcement dates. The event that resulted in the most persistent and highest amount of ARs was considered to be more informative. Looking at the second follow-up question, an investigation was conducted to determine if either dividends or earnings announcements influenced trading patterns, resulting in abnormal trading volumes (ATV) around announcement time. The event that resulted in the most ATV was considered more informative. Using an estimation period of 20 days and an event window of 21 days, and hypothesis testing, it was found that announcements pertaining to the increase of earnings resulted in the most ARs, Cumulative Abnormal Returns (CARs) and had a lasting effect in comparison to dividend announcements whose effect lasted until day +3. This solidifies some empirical arguments that the signaling effect of dividends has become diminishing. It was also found that when reported earnings declined in comparison to the previous period, there was an increase in trading volume, resulting in ATV. Although dividend announcements did result in abnormal returns, they were lesser than those acquired during earnings announcements which refutes a number of theoretical and empirical arguments that found dividends to be more informative than earnings announcements.

Keywords: dividend signaling, event study methodology, information content of earnings, signaling theory

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Authors: Xingxin Wu, Fenli Shao, Tao Tan, Yang Tan, Yang Sun, Qiang Xu

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Psoriasis is a chronic inflammatory skin disease that affects about 2% of the world's population. IL-23 signaling plays a key role in the pathogenesis of psoriasis. Control of IL-23 release by small molecule compounds during developing psoriasis has not been well established. Here, we show that compound 1, a small molecule nature product, protected mice from imiquimod-induced psoriasis with improved skin lesions, reduced skin thickness, and reduced IL-23 mRNA expression in the skin tissue. FACS results showed compound 1 reduced the number of dendritic cells in the skin. Interestingly, compound 1 was not able to ameliorate IL-23-induced psoriasis-like skin inflammation in mice. Further, compound 1 inhibited MyD88-dependent IL-23 mRNA expression induced by LPS, CpG and imiquimod in BMDC cells, but not MyD88-independent CD80 and CD86 expression induced by LPS. The methods included real-time PCR, western blot, H & E staining, FACS and ELISA et al. In conclusion, compound 1 regulates MyD88-dependent signaling to control IL-23 release in dendritic cells, which improves imiquimod-induced psoriasis.

Keywords: dendritic cells, IL-23, toll-like receptor signaling, psoriasis

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Authors: Nihal Atif Salim

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To improve the quality of life in cities, a variety of interventions are used. Noise is a substantial and important sort of pollution that has a negative impact on the urban environment and human health. According to the complaint survey, it ranks second among environmental contamination complaints (conducted by EEAA in 2019). The most significant source of noise in the city is traffic noise. In order to improve the sound urban environment, many physical techniques are applied. In the local area, noise barriers are considered as one of the most appropriate physical techniques along existing traffic routes. Alexandria is Egypt's second-largest city after Cairo. It is located along the Mediterranean Sea, and El- Gish Road is one of the city's main arteries. It impacts the waterfront promenade that extends along with the city by a high level of traffic noise. The purpose of this paper is to clarify the design considerations for the most appropriate noise barrier type along with the promenade, with the goal of improving the Quality of Life (QOL) and the sonic urban environment specifically. The proposed methodology focuses on how noise affects human perception and the environment. Then it delves into the various physical noise control approaches. After that, the paper discusses sustainable design decisions making. Finally, look into the importance of incorporating sustainability into design decisions making. Three stages will be followed in the case study. The first stage involves doing a site inspection and using specific sound measurement equipment (a noise level meter) to measure the noise level along the promenade at many sites, and the findings will be shown on a noise map. The second step is to inquire about the site's user experience. The third step is to investigate the various types of noise barriers and their effects on QOL along existing routes in order to select the most appropriate type. The goal of this research is to evaluate the suitable design of noise barriers that fulfill environmental and social perceptions while maintaining a balanced approach to the noise issue in order to improve QOL along existing roadways in the local area.

Keywords: noise pollution, sonic urban environment, traffic noise, noise barrier, acoustic sustainability, noise reduction techniques

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Authors: Monika Rawat, Rahul Kumar

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Input output Buffer Information Specification (IBIS) models are used for describing the analog behavior of the Input Output (I/O) buffers of a digital device. They are widely used to perform signal integrity analysis. Advantages of using IBIS models include simple structure, IP protection and fast simulation time with reasonable accuracy. As design complexity of driver and receiver increases, capturing exact behavior from transistor level model into IBIS model becomes an essential task to achieve better accuracy. In this paper, an improvement in existing methodology of generating IBIS model for complex I/O interfaces such as Inter-Integrated Circuit (I2C) and Low Voltage Differential Signaling (LVDS) is proposed. Furthermore, the accuracy and computational performance of standard method and proposed approach with respect to SPICE are presented. The investigations will be useful to further improve the accuracy of IBIS models and to enhance their wider acceptance.

Keywords: IBIS, signal integrity, open-drain buffer, low voltage differential signaling, behavior modelling, transient simulation

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Authors: Mohammad Hossein Habibi, Atena Sadat Hosseini

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Colorectal cancer is the third leading cause of cancer-related death in the world. Colorectal cancer screening, early detection, and treatment programs could benefit from the most up-to-date information on the disease's burden, given the present worldwide trend of increasing colorectal cancer incidence. Tumor recurrence and resistance are exacerbated by the presence of chemotherapy-resistant cancer stem cells that can generate rapidly proliferating tumor cells. In addition, tumor cells can evolve chemoresistance through adaptation mechanisms. In this work, we used in silico analysis to select suitable GEO datasets. In this study, we compared slow-growing cancer stem cells with high-growth colorectal cancer-derived cancer stem cells. We then evaluated the signal pathways, transcription factors, and kinases associated with these two types of cancer stem cells. A total of 980 upregulated genes and 870 downregulated genes were clustered. MAPK signaling pathway, AGE-RAGE signaling pathway in diabetic complications, Fc gamma R-mediated phagocytosis, and Steroid biosynthesis signaling pathways were observed in upregulated genes. Also, caffeine metabolism, amino sugar and nucleotide sugar metabolism, TNF signaling pathway, and cytosolic DNA-sensing pathway were involved in downregulated genes. In the next step, we evaluated the best transcription factors and kinases in two types of cancer stem cells. In this regard, NR2F2, ZEB2, HEY1, and HDGF as transcription factors and PRDM5, SMAD, CBP, and KDM2B as critical kinases in upregulated genes. On the other hand, IRF1, SPDEF, NCOA1, and STAT1 transcription factors and CTNNB1 and CDH7 kinases were regulated low expression genes. Using bioinformatics analysis in the present study, we conducted an in-depth study of colorectal cancer stem cells at low and high growth rates so that we could take further steps to detect and even target these cells. Naturally, more additional tests are needed in this direction.

Keywords: colorectal cancer, bioinformatics analysis, transcription factor, kinases, cancer stem cells

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Authors: Su Bin Wang, Jin Hee Ahn, Tong-Shin Chang

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The peroxisome proliferator-activated receptors (PPARs) are member of nuclear receptor superfamily that act as a ligand-activated transcription factors. Although platelets lack a nucleus, previous studies have shown that PPARγ agonists, rosiglitazone, inhibited platelet activation induced by collagen. In this study, we investigated the inhibitory effects of KR-62980, a newly synthesized PPARγ agonist, on collagen receptor-stimulated platelet activation. The specific tyrosine phosphorylations of key components (Syk, Vav1, Btk and PLCγ2) for collagen receptor signaling pathways were suppressed by KR-62980. KR-62980 also attenuated downstream responses including cytosolic calcium elevation, P-selectin surface exposure, and integrin αIIbβ3 activation. PPARγ was found to associate with multiple proteins within the LAT signaling complex in collagen-stimulated platelets. This association was prevented by KR-62980, indicating a potential mechanism for PPARγ function in collagen-stimulated platelet activation. Furthermore, KR-62980 inhibited platelet aggregation and adhesion in response to collagen in vitro and prolonged in vivo thrombotic response in carotid arteries of mice. Collectively, these data suggest that KR-62980 inhibits collagen-stimulated platelet activation and thrombus formation through modulating the collagen receptor signaling pathways.

Keywords: KR-62980, PPARγ, antiplatelet, thrombosis

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Authors: Sudeshna Mukherjee, Leena Fageria, R. Venkataramana Dilip, Rajdeep Chowdhury, Jitendra Panwar

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Metal nanoparticles in recent years have gained importance in cancer therapy due to their enhanced permeability retention effect. Among various nanomaterials, silver nanoparticles (AgNPs) have received considerable attention due to their unique properties like conductivity, chemical stability, relative lower toxicity and outstanding therapeutic potential, such as anti-inflammatory, antimicrobial and anti-cancerous activities. In this study, we took a greener approach to synthesize silver nanoparticle from fungus and analyze its effects on both epithelial and mesenchymal derived cancer cells. Much research has been done on nanoparticle-induced apoptosis, but little is known about its role in autophagy. In our study, the silver nanoparticles were seen to induce autophagy which was analyzed by studying the expression of several autophagy markers like, LC3B-II and ATG genes. Monodansylcadaverine (MDC) assay also revealed the induction of autophagy upon treatment with AgNPs. Inhibition of autophagy by chloroquine resulted in increased cell death suggesting autophagy as a survival strategy adopted by the cells. In parallel to autophagy induction, silver nanoparticles induced ROS accumulation. Interestingly, autophagy inhibition by chloroquine increased ROS level, resulting in enhanced cell death. We further analyzed MAPK signaling upon AgNP treatment. It was observed that along with autophagy, activation of JNK signaling served as pro-survival while ERK signaling served as a pro-death signal. Our results provide valuable insights into the role of autophagy upon AgNP exposure and provide cues to probabilistic strategies to effectively sensitize cancer cells.

Keywords: autophagy, JNK signalling, reactive oxygen species, silver nanoparticles

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Authors: Michael P. Mannino, Gerald W. Hart

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The majority of glucose metabolism proceeds through glycolytic pathways such as glycolysis or pentose phosphate pathway, however, about 5% is shunted through the hexosamine biosynthetic pathway, producing uridine diphosphate N-acetyl glucosamine (UDP-GlcNAc). This precursor can then be incorporated into complex oligosaccharides decorating the cell surface or remain as an intracellular post-translational-modification (PTM) of serine/threonine residues (O-GlcNAcylation, OGN), which has been identified on over 4,000 cytosolic or nuclear proteins. Intracellular OGN has major implications on cellularprocesses, typically by modulating protein localization, protein-protein interactions, protein degradation, and gene expression. Additionally, OGN is known to have an extensive cross-talk with phosphorylation, be in a competitive or cooperative manner. Unlike other PTMs there are only two cycling enzymes that are capable of adding or removing the GlcNAc moiety, O-linked N-aceytl glucosamine Transferase (OGT) and O-linked N-acetyl glucoamidase (OGA), respectively. The activity of OGT has been shown to be sensitive to cellular UDP-GlcNAc levels, even changing substrate affinity. Owing to this and that the concentration of UDP-GlcNAc is related to the metabolisms of glucose, amino acid, fatty acid, and nucleotides, O-GlcNAc is often referred to as a nutrient sensing rheostat. Indeed OGN is known to regulate several signaling pathways as a result of nutrient levels, such as insulin signaling. Dysregulation of OGN is associated with several disease states such as cancer, diabetes, and neurodegeneration. Improvements in glycomics over the past 10-15 years has significantly increased the OGT substrate pool, suggesting O-GlcNAc’s involvement in a wide variety of signaling pathways. However, O-GlcNAc’s role at the receptor level has only been identified in a case-by-case basis of known pathways. Examining the OGN of the plasma membrane (PM) may better focus our understanding of O-GlcNAc-effected signaling pathways. In this current study, PM fractions were isolated from several cell types via ultracentrifugation, followed by purification and MS/MS analysis in several cell lines. This process was repeated with or without OGT/OGA inhibitors or with increased/decreased glucose levels in media to ascertain the importance of OGN. Various pathways are followed up on in more detailed studies employing methods to localize OGN at the PM specifically.

Keywords: GlcNAc, nutrient sensitive, post-translational-modification, receptor

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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: Saud Al Taj

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Employer branding is considered as a useful tool for addressing the global-local problem facing complex organisations that have operations scattered across the globe and face challenges of dealing with the local environment alongside. Despite being an established field of study within the Western developed world, there is little empirical evidence concerning the relevance of employer branding to global companies that operate in the under-developed economies. This paper fills this gap by gaining rich insight into the implementation of employer branding programs in a foreign multinational operating in Pakistan dealing with the global-local problem. The study is qualitative in nature and employs semi-structured and focus group interviews with senior/middle managers and local frontline employees to deeply examine the phenomenon in case organisation. Findings suggest that authenticity is required in employer brands to enable them to respond to the local needs thereby leading to the resolution of the global-local problem. However, the role of signaling theory is key to the development of authentic employer brands as it stresses on the need to establish an efficient and effective signaling environment wherein signals travel in both directions (from signal designers to receivers and backwards) and facilitate firms with the global-local problem. The paper also identifies future avenues of research for the employer branding field.

Keywords: authenticity, counter-signals, employer branding, global-local problem, signaling theory

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Authors: Gholamreza Hashemitabr, Reza Valadan, Alireza Rafiei, Mohammad Reza Bassami

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Breast cancer is the most common malignancy among women worldwide. Cancer cells use a complex multilayer network of epidermal growth factor receptors (EGFRs) signaling pathways to support their survival and growth. The overlapping networks of EGFRs signaling pathways account for the failure of most ErbB-targeted therapies. The aim of this study was to enrich a pool of recombinant antibody fragments against common epitopes of ErbB1 and ErbB2 in order to simultaneous blockade of ErbBs signaling pathways. ErbB1 and ErbB2 were expressed stably in VERO cells. Selection of recombinant antibodies was performed on live cells expressing either of ErbB1 and ErbB2 receptors using subtractive phage display approach. The results of PCR and DNA fingerprinting in the last round of panning showed that most clones contained insert (80% and 85% for ErbB1 and ErbB2 respectively) with an identical restriction pattern. The selected clones showed positive reaction to both ErbB1 and ErbB2 receptors in phage-ELISA test. Furthermore, the resulting soluble antibody fragments recognized common epitopes of both immunoprecipitated ErbB1 and ErbB2 in western blot. Additionally, the antibodies directed against the dimerization domain of ErbB1 demonstrated a significant absorbance in EGF-stimulated VERO/ErbB1 cells than non-stimulated cells (1.91 and 1.09 respectively). Moreover, the results of dimerization inhibition test showed that these antibodies blocked ErbB1 and ErbB2 dimerization on the surface of ErbB1 and ErbB2 expressing VERO cells. Regarding the importance of pan-ErbB approach to cancer therapy, the antibodies developed here might provide novel therapeutics for simultaneous blockade of ErbBs signaling pathways.

Keywords: breast cancer, single-chain antibody, ErbB1, ErbB2, epitope

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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: Bing Yan

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Nanomaterials are widely used in various industrial sectors, biomedicine, and more than 1300 consumer products. Although there is still no standard safety regulation, their potential toxicity is a major concern worldwide. We discovered that nanoparticles target and enter human cells1, perturb cellular signaling pathways2, affect various cell functions3, and cause malfunctions in animals4,5. Because the majority of atoms in nanoparticles are on the surface, chemistry modification on their surface may change their biological properties significantly. We modified nanoparticle surface using nano-combinatorial chemistry library approach6. Novel nanoparticles were discovered to exhibit significantly reduced toxicity6,7, enhance cancer targeting ability8, or re-program cellular signaling machineries7. Using computational chemistry, quantitative nanostructure-activity relationship (QNAR) is established and predictive models have been built to predict biocompatible nanoparticles.

Keywords: nanoparticle, nanotoxicity, nano-bio, nano-combinatorial chemistry, nanoparticle library

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Authors: Blanche Aguida, Marootpong Pooam, Nathalie Jourdan, Margaret Ahmad

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COVID-19-related morbidity is associated with exaggerated inflammation and cytokine production in the lungs, leading to acute respiratory failure. The cellular mechanisms underlying these so-called ‘cytokine storms’ are regulated through the Toll-like receptor 4 (TLR4) signaling pathway and by reactive oxygen species (ROS). Both light (photobiomodulation) and magnetic fields (e.g., pulsed electromagnetic field) stimulation are non-invasive therapies known to confer anti-inflammatory effects and regulate ROS signaling pathways. Here we show that daily exposure to two 10-minute intervals of moderate-intensity infra-red light significantly lowered the inflammatory response induced via the TLR4 receptor signaling pathway in human cell cultures. Anti-inflammatory effects were likewise achieved by electromagnetic field exposure of cells to daily 10-minute intervals of either pulsed electromagnetic fields (PEMF) or to low-level static magnetic fields. Because current illumination and electromagnetic field therapies have no known side effects and are already approved for some medical uses, we have here developed protocols for verification in clinical trials of COVID 19 infection. These treatments are affordable, simple to implement, and may help to resolve the acute respiratory distress of COVID 19 patients both in the home and in the hospital.

Keywords: COVID 19, electromagnetic fields therapy, inflammation, photobiomodulation therapy

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Authors: M. Cardenas-Garcia, P. P. Gonzalez-Perez

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Intercellular communication is a necessary condition for cellular functions and it allows a group of cells to survive as a population. Throughout this interaction, the cells work in a coordinated and collaborative way which facilitates their survival. In the case of cancerous cells, these take advantage of intercellular communication to preserve their malignancy, since through these physical unions they can send signs of malignancy. The Wnt/β-catenin signaling pathway plays an important role in the formation of intercellular communications, being also involved in a large number of cellular processes such as proliferation, differentiation, adhesion, cell survival, and cell death. The modeling and simulation of cellular signaling systems have found valuable support in a wide range of modeling approaches, which cover a wide spectrum ranging from mathematical models; e.g., ordinary differential equations, statistical methods, and numerical methods– to computational models; e.g., process algebra for modeling behavior and variation in molecular systems. Based on these models, different simulation tools have been developed from mathematical ones to computational ones. Regarding cellular and molecular processes in cancer, its study has also found a valuable support in different simulation tools that, covering a spectrum as mentioned above, have allowed the in silico experimentation of this phenomenon at the cellular and molecular level. In this work, we simulate and explore the complex interaction patterns of intercellular communication in cancer cells using the Cellulat bioinformatics tool, a computational simulation tool developed by us and motivated by two key elements: 1) a biochemically inspired model of self-organizing coordination in tuple spaces, and 2) the Gillespie’s algorithm, a stochastic simulation algorithm typically used to mimic systems of chemical/biochemical reactions in an efficient and accurate way. The main idea behind the Cellulat simulation tool is to provide an in silico experimentation environment that complements and guides in vitro experimentation in intra and intercellular signaling networks. Unlike most of the cell signaling simulation tools, such as E-Cell, BetaWB and Cell Illustrator which provides abstractions to model only intracellular behavior, Cellulat is appropriate for modeling both intracellular signaling and intercellular communication, providing the abstractions required to model –and as a result, simulate– the interaction mechanisms that involve two or more cells, that is essential in the scenario discussed in this work. During the development of this work we made evident the application of our computational simulation tool (Cellulat) for the modeling and simulation of intercellular communication between normal and cancerous cells, and in this way, propose key molecules that may prevent the arrival of malignant signals to the cells that surround the tumor cells. In this manner, we could identify the significant role that has the Wnt/β-catenin signaling pathway in cellular communication, and therefore, in the dissemination of cancer cells. We verified, using in silico experiments, how the inhibition of this signaling pathway prevents that the cells that surround a cancerous cell are transformed.

Keywords: cancer cells, in silico approach, intercellular communication, key molecules, modeling and simulation

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Authors: Qiaoyue Kuang, Yang Li, Mizuki Endo, Takeaki Ozawa

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G protein-coupled receptors (GPCR) are the largest family of receptor proteins that detect molecules outside the cell and activate cellular responses. Of the GPCRs, dopamine receptors, which recognize extracellular dopamine, are essential to mammals due to their roles in numerous physiological events, including autonomic movement, hormonal regulation, emotions, and the reward system in the brain. To precisely understand the physiological roles of dopamine receptors, it is important to spatiotemporally control the signaling mediated by dopamine receptors, which is strongly dependent on their surface expression. Conventionally, chemical-induced interactions were applied to trigger the endocytosis of cell surface receptors. However, these methods were subjected to diffusion and therefore lacked temporal and special precision. To further understand the receptor-mediated signaling and to control the plasma membrane expression of receptors, an optogenetic tool called E-fragment was developed. The C-terminus of a light-sensitive photosensory protein cyptochrome2 (CRY2) was attached to β-Arrestin, and the E-fragment was generated by fusing the C-terminal peptide of vasopressin receptor (V2R) to CRY2’s binding partner protein CIB. The CRY2-CIB heterodimerization triggered by blue light stimulation brings β-Arrestin to the vicinity of membrane receptors and results in receptor endocytosis. In this study, the E-fragment system was applied to dopamine receptors 1 and 2 (DRD1 and DRD2) to control dopamine signaling. First, confocal fluorescence microscope observation qualitatively confirmed the light-induced endocytosis of E-fragment fused receptors. Second, NanoBiT bioluminescence assay verified quantitatively that the surface amount of E-fragment labeled receptors decreased after light treatment. Finally, GloSensor bioluminescence assay results suggested that the E-fragment-dependent receptor light-induced endocytosis decreased cAMP production in DRD1 signaling and attenuated the inhibition effect of DRD2 on cAMP production. The developed optogenetic tool was able to induce receptor endocytosis by external light, providing opportunities to further understand numerous physiological activities by controlling receptor-mediated signaling spatiotemporally.

Keywords: dopamine receptors, endocytosis, G protein-coupled receptors, optogenetics

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Authors: Michal Kielbik, Izabela Szulc-Kielbik, Anna Brzostek, Jaroslaw Dziadek, Magdalena Klink

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The goal of many research groups in the world is to find new components that are important for survival of mycobacteria in the host cells. Mycobacterium tuberculosis (Mtb) possesses a number of enzymes degrading cholesterol that are considered to be an important factor for its survival and persistence in host macrophages. One of them - cholesterol oxidase (ChoD), although not being essential for cholesterol degradation, is discussed as a virulence compound, however its involvement in macrophages’ response to Mtb is still not sufficiently determined. The recognition of tubercle bacilli antigens by pathogen recognition receptors is crucial for the initiation of the host innate immune response. An important receptor that has been implicated in the recognition and/or uptake of Mtb is Toll-like receptor type 2 (TLR2). Engagement of TLR2 results in the activation and phosphorylation of intracellular signaling proteins including IRAK-1 and -4, TRAF-6, which in turn leads to the activation of target kinases and transcription factors responsible for bactericidal and pro-inflammatory response of macrophages. The aim of these studies was a detailed clarification of the role of Mtb cholesterol oxidase as a virulence factor affecting the TLR2 signaling pathway in human macrophages. As human macrophages the THP-1 differentiated cells were applied. The virulent wild-type Mtb strain (H37Rv), its mutant lacking a functional copy of gene encoding cholesterol oxidase (∆choD), as well as complimented strain (∆choD–choD) were used. We tested the impact of Mtb strains on the expression of TLR2-depended signaling proteins (mRNA level, cytosolic level and phosphorylation status). The cytokine and bactericidal response of THP-1 derived macrophages infected with Mtb strains in relation to TLR2 signaling pathway dependence was also determined. We found that during the 24-hours of infection process the wild-type and complemented Mtb significantly reduced the cytosolic level and phosphorylation status of IRAK-4 and TRAF-6 proteins in macrophages, that was not observed in the case of ΔchoD mutant. Decreasement of TLR2-dependent signaling proteins, induced by wild-type Mtb, was not dependent on the activity of proteasome. Blocking of TLR2 expression, before infection, effectively prevented the induced by wild-type strain reduction of cytosolic level and phosphorylation of IRAK-4. None of the strains affected the surface expression of TLR2. The mRNA level of IRAK-4 and TRAF-6 genes were significantly increased in macrophages 24 hours post-infection with either of tested strains. However, the impact of wild-type Mtb strain on both examined genes was significantly stronger than its ΔchoD mutant. We also found that wild-type strain stimulated macrophages to release high amount of immunosuppressive IL-10, accompanied by low amount of pro-inflammatory IL-8 and bactericidal nitric oxide in comparison to mutant lacking cholesterol oxidase. The influence of wild-type Mtb on this type of macrophages' response strongly dependent on fully active IRAK-1 and IRAK-4 signaling proteins. In conclusion, Mtb using cholesterol oxidase causes the over-activation of TLR2 signaling proteins leading to the reduction of their cytosolic level and activity resulting in the modulation of macrophages response to allow its intracellular survival. Supported by grant: 2014/15/B/NZ6/01565, National Science Center, Poland

Keywords: Mycobacterium tuberculosis, cholesterol oxidase, macrophages, TLR2-dependent signaling pathway

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Authors: Chang-Bin Ha, Young-Min Ko, Seongjoo Lee, Hyoung-Kyu Song

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In this paper, the signaling scheme using phase shifting is proposed for the improved performance of the Wi-Fi backscatter system. Because the communication in the Wi-Fi backscatter system is based on on-off modulation and impedance modulation by unit of packet, the data rate is very low compared to the conventional wireless systems. Also, because the Wi-Fi backscatter system is based on the RF-powered device, the achievement of high reliability is difficult. In order to increase the low data rate, the proposed scheme transmits information of multiple bits during one packet period. Also, in order to increase the reliability, the proposed scheme shifts the phase of signal in according to the transmitting information. The simulation result shows that the proposed scheme has the improved throughput performance.

Keywords: phase shifting, RF-powered device, Wi-Fi backscatter system, IoT

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Authors: W. Hamaidia, T. Zebbiche

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This paper presents the design of axisymmetric supersonic nozzles, in order to accelerate a supersonic flow to the desired Mach number and that having a small weight, in the same time gives a high thrust. The concerned nozzle gives a parallel and uniform flow at the exit section. The nozzle is divided into subsonic and supersonic regions. The supersonic portion is independent to the upstream conditions of the sonic line. The subsonic portion is used to give a sonic flow at the throat. In this case, nozzle gives a uniform and parallel flow at the exit section. It’s named by minimum length Nozzle. The study is done at high temperature, lower than the dissociation threshold of the molecules, in order to improve the aerodynamic performances. Our aim consists of improving the performances both by the increase of exit Mach number and the thrust coefficient and by reduction of the nozzle's mass. The variation of the specific heats with the temperature is considered. The design is made by the Method of Characteristics. The finite differences method with predictor-corrector algorithm is used to make the numerical resolution of the obtained nonlinear algebraic equations. The application is for air. All the obtained results depend on three parameters which are exit Mach number, the stagnation temperature, the chosen mesh in characteristics. A numerical simulation of nozzle through Computational Fluid Dynamics-FASTRAN was done to determine and to confirm the necessary design parameters.

Keywords: flux supersonic flow, axisymmetric minimum length nozzle, high temperature, method of characteristics, calorically imperfect gas, finite difference method, trust coefficient, mass of the nozzle, specific heat at constant pressure, air, error

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Authors: Jiangang Shen

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Olfactory dysfunction is a common symptom companied by anxiety- and depressive-like behaviors in depressive patients. Chronic stress triggers hormone responses and inhibits the proliferation and differentiation of neural stem cells (NSCs) in the hippocampus and subventricular zone (SVZ)-olfactory bulb (OB), contributing to depressive behaviors and olfactory dysfunction. However, the cellular signaling molecules to regulate chronic stress mediated olfactory dysfunction are largely unclear. Adaptor proteins containing the pleckstrin homology domain, phosphotyrosine binding domain, and leucine zipper motif (APPLs) are multifunctional adaptor proteins. Herein, we tested the hypothesis that APPL2 could inhibit hippocampal neurogenesis by affecting glucocorticoid receptor (GR) signaling, subsequently contributing to depressive and anxiety behaviors as well as olfactory dysfunctions. The major discoveries are included: (1) APPL2 Tg mice had enhanced GR phosphorylation under basic conditions but had no different plasma corticosterone (CORT) level and GR phosphorylation under stress stimulation. (2) APPL2 Tg mice had impaired hippocampal neurogenesis and revealed depressive and anxiety behaviors. (3) GR antagonist RU486 reversed the impaired hippocampal neurogenesis in the APPL2 Tg mice. (4) APPL2 Tg mice displayed higher GR activity and less capacity for neurogenesis at the olfactory system with lesser olfactory sensitivity than WT mice. (5) APPL2 negatively regulates olfactory functions by switching fate commitments of NSCs in adult olfactory bulbs via interaction with Notch1 signaling. Furthermore, baicalin, a natural medicinal compound, was found to be a promising agent targeting APPL2/GR signaling and promoting adult neurogenesis in APPL2 Tg mice and chronic corticosterone-induced depression mouse models. Behavioral tests revealed that baicalin had antidepressant and olfactory-improving effects. Taken together, APPL2 is a critical therapeutic target for antidepressant treatment.

Keywords: APPL2, hippocampal neurogenesis, depressive behaviors and olfactory dysfunction, stress

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Authors: Shrikant Ghadage

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Study of shock waves generated in the Scramjet engine is typically restricted to pressure, temperature, density, entropy and Mach number variation across the shock wave. The present work discusses the impact of inlet shock wave angles on the specific impulse of the Scramjet engine. A mathematical analysis has done for the isentropic hypersonic flow of air flowing through a Scramjet with hydrogen fuel at an altitude of 30 km. Analysis has been done in order to get optimum shock wave angle to achieve maximum impulse. Since external drag has excluded from the analysis, the losses due to friction are not considered for the present analysis. When Mach number of the airflow at the entry of the nozzle reaches unity, then that flow is choked. This condition puts limitations on increasing the inlet shock wave angle. As inlet shock wave angle increases, speed of the flow entering into the nozzle decreases, which results in an increase in the specific impulse of the engine. When the speed of the flow at the entry of the nozzle reduces below sonic speed, then there is no further increase in the specific impulse of the engine. Here the Conclusion is the thrust and specific impulse of a scramjet engine, which increases gradually with an increase in inlet shock wave angle up to the condition when airflow speed reaches sonic velocity at the exit of the combustor. In addition to that, variation in drag force at the inlet of the scramjet and variation in hypersonic flow conditions at every stage of the scramjet also studied in order to understand variation on flow characteristics with respect to flow deflection angle. Essentially, it helps in designing inlet profile for the Scramjet engine to achieve optimum specific impulse.

Keywords: hypersonic flow, scramjet, shock waves, specific impulse, mathematical analysis

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Authors: Ireneusz Majsterek, Dariusz Pytel, J. Alan Diehl

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PKR-like ER kinase (PERK) is serine/threonie endoplasmic reticulum (ER) transmembrane kinase activated during ER-stress. PERK can activate signaling pathways known as unfolded protein response (UPR). Attenuation of translation is mediated by PERK via phosphorylation of eukaryotic initiation factor 2α (eIF2α), which is necessary for translation initiation. PERK activation also directly contributes to activation of Nrf2 which regulates expression of anti-oxidant enzymes. An increased phosphorylation of eIF2α has been reported in Alzheimer disease (AD) patient hippocampus, indicating that PERK is activated in this disease. Recent data have revealed activation of PERK signaling in non-Hodgkins lymphomas. Results also revealed that loss of PERK limits mammary tumor cell growth in vitro and in vivo. Consistent with these observations, activation of UPR in vitro increases levels of the amyloid precursor protein (APP), the peptide from which beta-amyloid plaques (AB) fragments are derived. Finally, proteolytic processing of APP, including the cleavages that produce AB, largely occurs in the ER, and localization coincident with PERK activity. Thus, we expect that PERK-dependent signaling is critical for progression of many types of diseases (human cancer, neurodegenerative disease and other). Therefore, modulation of PERK activity may be a useful therapeutic target in the treatment of different diseases that fail to respond to traditional chemotherapeutic strategies, including Alzheimer’s disease. Our goal will be to developed therapeutic modalities targeting PERK activity.

Keywords: PERK kinase, small molecule inhibitor, neurodegenerative disease, Alzheimer’s disease

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Authors: Sylvia Huang

Abstract:

Contemporary Buddhist music has been emerged at the new forms of large-scale public Buddhist ritual ceremonies that may involve up to 10,000 participants at a time. Since 2007, the Buddha’s Birthday ceremony (Sanskrit, Vesak) by the Buddhist Tzu Chi Foundation has being held at major cities in Taiwan and many affiliated Tzu Chi offices around the world. Analysis of this modern and technologically-dependent ceremony sheds new light on the significance of music in contemporary Buddhist ritual, and also on recently enhanced and increasingly intimate connections between music and Buddhism. Through extensive ethnographic research of ten years (2007-2017), the research explores how the form of contemporary Buddhist music relates to the role of music in participants’ experience of the ritual and the way in which they construct meaning. The theoretical approach draws on both ethnomusicology and Buddhist teachings, Dharma. As soundscape is defined as the entire sonic energy produced by a landscape, the concept of soundscape is utilised to examine the contemporary ritual music in the Tzu Chi Vesak ceremony. The analysis opens new territory in exploring how analysis of Buddhist music can benefit from incorporating Buddhist philosophy within the methodological approach. Main findings are: 1) music becomes a method for Buddhist understanding through a focus in particular on how the ceremonial program is followed by music, and 2) participants engage with each other and entrain with music in the Vesak ceremony. As Buddhist sounding, such as scripture reading, liturgical chanting, and ceremonial music singing, is a sonic epistemological knowing of the conditions in which Buddhism is practiced, experienced, and transmigrated, the research concludes by showing that studies of Buddhist music have the potential to reveal distinctively Buddhist concepts, meaning, and values. Certain principles of Buddhist philosophy are adopted within ethnomusicological analysis to further enhance understandings of the crucial function of music within such a ritual context. Finally, the contemporary Buddhist music performance in the ceremony is possessed as a means of direct access to the spiritual experience in Buddhism.

Keywords: buddhist music, Taiwan, soundscape, Vesak ceremony

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