ARTICLE | doi:10.20944/preprints202009.0459.v1
Online: 19 September 2020 (11:34:12 CEST)
The COVID-19 global pandemic has created dire consequences with an alarming rate of morbidity and mortality. There are not yet vaccine or efficacious treatment options to combat the causative SARS-CoV-2 infection. This paper describes the identification of potentially repurposable drugs for COVID-19 treatment by conducting pathway enrichment analysis on publicly available Gene Expression Omnibus datasets. We first determined SARS-CoV-2 infection-induced alterations of host gene expressions and pathways. We then identified drugs or compounds that target and counter virus-triggered cellular perturbations, suggesting their potential repurposing for COVID-19 treatment. The key findings are that SARS-CoV-2 infection in host cells induces mitochondrial dysfunction, inhibits oxidative phosphorylation, and activates several immune response and pro-inflammatory pathways. Triptolide, the major bioactive component of a traditional Chinese medicine herb, may rescue mitochondrial dysfunction by activating oxidative phosphorylation. Further in vitro and in vivo studies are necessary to verify these results prior to clinical application.
ARTICLE | doi:10.20944/preprints201810.0268.v1
Subject: Life Sciences, Genetics Keywords: Turner’s syndrome; chromosomal aneuploidy; amniotic fluid; cell-free RNA; ingenuity pathway analysis
Online: 12 October 2018 (12:07:26 CEST)
Genetic disorders are quite a major topic of discussion and debate in the recent world of biological sciences. Turner’s syndrome is one such disorder caused by a chromosome aneuploidy and it has characteristic symptoms in the patient or the affected individual. The amniotic fluid is a complex biological material found in the amniotic sac of pregnant women and they can provide valuable knowledge and understanding of the pathogenesis of this particular chromosomal abnormality. In this study, global gene expression analysis of cell-free RNA in amniotic fluid supernatant was used to detect genes/organ systems which may be significant in the pathophysiology of Turner’s syndrome. The cell-free RNA from the amniotic fluid of five mid-trimester Turner’s syndrome fetuses and five euploid female fetuses matched for age of gestation were extracted, amplified and hybridized onto Affymetrix U33 Plus 2.0. array. The paired t-test was used to identify the significantly differentially regulated genes. Biological interpretation was conducted using ingenuity pathway analysis and BioGPS gene expression atlas. Of the genes, XIST was especially downregulated and SHOX was not expressed differentially. One of the most highly represented organ systems was the hematologic/immune system, differentiating the transcriptome of Turner’s syndrome from other chromosomal aneuploidies that are discussed in this area of science. The differences in the transcriptome of the Turner’s syndrome are due to genome-wide dysregulation. The hematologic/immune system differences are significant in early-onset autoimmune dysfunction. There are other genes which have been identified that are associated with the cardiovascular and the skeletal system, as these are often seen to be affected in the female patients with turner’s syndrome. Hopefully, such knowledge gained from this study will help us to understand the deeper mechanisms of this disorder and the possible treatments of this disease.
ARTICLE | doi:10.20944/preprints202006.0261.v1
Subject: Life Sciences, Molecular Biology Keywords: adverse outcome pathway; toxicity pathway; computational toxicology
Online: 21 June 2020 (11:10:34 CEST)
Background: Targeted methods that dominated toxicological research until recently did not allow for screening of all molecular changes involved in toxic response. Therefore, it is difficult to infer if all major mechanisms of toxicity have already been discovered, or if some of them are still overlooked. Objectives: To identify molecular mechanisms sensitive to chemical exposures in an unbiased manner. Methods: We used data on 641,516 unique chemical-gene interactions from the Comparative Toxicogenomic Database. Only data from high-throughput gene expression experiments with human, rat or mouse cells/tissues were extracted. The total number of chemical-gene interactions was calculated for every gene, and used as a measure of gene sensitivity to chemical exposures. These values were further used in enrichment analyses to identify molecular mechanisms sensitive to chemical exposures. Results: Remarkably, use of different input subsets with non-overlapping lists of chemical compounds identified largely the same genes and molecular pathways as most sensitive to chemical exposures, indicative of an unbiased nature of our analysis. One of the most important findings of this study is that almost every known molecular mechanism may be affected by chemical exposures. Predictably, xenobiotic metabolism pathways and mechanisms of cellular response to stress and damage were among the most sensitive. Additionally, our analysis identified a range of highly sensitive molecular pathways, which are not widely recognized by modern toxicology as major targets of toxicants, including lipid metabolism pathways, longevity regulation cascade and cytokine mediated signaling. Discussion: Molecular mechanisms identified as the most sensitive to chemical exposures are relevant for significant public health problems, such as aging, cancer, metabolic and autoimmune disease. Thus, public health system will likely benefit from future research focus on these sensitive molecular mechanisms. Additionally, approach used in this study may guide identification of priority adverse outcome pathways (AOP) for in-vitro and in-silico toxicity testing methods.
REVIEW | doi:10.20944/preprints202009.0276.v1
Subject: Biology, Plant Sciences Keywords: Citral; essential oil; integrated pest management; insect-repellent; lemongrass; MEP pathway; mevalonate pathway
Online: 13 September 2020 (11:30:41 CEST)
Lemongrass (Cymbopogon flexuosus) is an aromatic perennial grass grown extensively for its essential oil. Lemongrass oil is chiefly a mixture of various cyclic and acyclic bioactive monoterpenes. We reviewed lemongrass oil and its biosynthesis in the present chapter along with its biochemical composition. Furthermore, we attempted to explore both the possible routes for essential oil biosynthesis in lemongrass, i.e. mevalonate and non-mevalonate pathways and how these pathways interwind with each other. Lemongrass oil has high commercial potential in medicinal, cosmetic, food and energy industries. Regarding the pharmacological properties, a wide array of biological activities has been observed in lemongrass oil such as antimicrobial, insecticidal, analgesic and anti-cancer properties as well as its efficacy as insect-repellent. The later sections were dedicated for the analysis of insecticidal property of the lemongrass oil and the mechanism working behind this phenomenon where it was observed that in addition to synergistic effects, various components of lemongrass oil can also induce specific neurotoxic and cytotoxic responses in the insects.
REVIEW | doi:10.20944/preprints201908.0229.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: paracellular permeability; tight junction; Pore Pathway; Leak Pathway; occludin; ZO-1; ZO-2; claudin
Online: 22 August 2019 (03:58:59 CEST)
The epithelial cell tight junction structure is the site of the transepithelial movement of solutes and water between epithelial cells (paracellular permeability). Paracellular permeability can be divided into two distinct pathways, the Pore Pathway mediating the movement of small ions and solutes and the Leak Pathway mediating the movement of large solutes. Claudin proteins form the basic paracellular permeability barrier and mediate the movement of small ions and solutes via the Pore Pathway. The Leak Pathway remains less understood. Several proteins have been implicated in mediating the Leak Pathway, including occludin, ZO proteins, tricellulin, and actin filaments, but the proteins comprising the Leak Pathway remain unresolved. The properties of the Leak Pathway, such as its molecular mechanism, its regulation, and whether or not it has a size limit, remain controversial. This review will trace the evolution of the Leak Pathway concept from its origins, will discuss the current information about the properties of the Leak Pathway, and will discuss recent research suggesting a possible molecular basis for the Leak Pathway. Based on these findings, we propose a model for the molecular mechanism underlying the Leak Pathway and its regulation.
ARTICLE | doi:10.20944/preprints202204.0082.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Caco2/HT-29 cells; lipopolysaccharide(LPS); mucins; focal adhesion pathway; ECM receptor in-teraction pathway
Online: 8 April 2022 (14:04:17 CEST)
Endotoxins are toxic substances that widely exist in the environment and can enter the intestine with food and other substances. Intestinal epithelial cells are protected by a mucus layer that contains MUC2 as its main structural component. However, a detailed understanding of the mechanisms involved in the function of the mucus barrier in endotoxin penetration is lacking. Here, we established the most suitable proportion of Caco-2/HT-29 co-culture cells as a powerful tool to evaluate the intestinal mucus layer. Our findings significantly advance current knowledge as focal adhesion and ECM-receptor interaction were identified as the two most significantly implicated pathways in MUC2 small interfering RNA (siRNA)-transfected Caco-2/HT-29 co-culture cells after 24 h of LPS stimulation. When the mucus layer was not intact, LPS was found to damage the tight junctions of Caco-2/HT29 co-cultured cells. Furthermore, LPS was demonstrated to inhibit the integrin-mediated focal adhesion structure and damage the matrix network structure of the extracellular and actin microfilament skeletons. Ultimately, LPS inhibited the interactive communication between the extracellular matrix and the cytoskeleton for 24 h in the siMUC2 group compared with the LPS(+) and LPS(-) groups. Overall, we recognized the potential of MUC2 as a tool for barrier function in several intestinal bacterial diseases.
ARTICLE | doi:10.20944/preprints202010.0373.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Fungi; ergosterol pathway; dermatophytes; chelerythrine; sanguinarine
Online: 19 October 2020 (11:10:30 CEST)
The ergosterol pathway is a prime antifungal target. The minimum inhibitory concentration (MIC) assay is a simple research tool that determines the lowest concentration at which a novel antimicrobial with limited scope to determine the mechanism of action for a drug. In this study, we show that by adding hydrogen peroxide, an oxidative stressor, or glutathione (GSH), an antioxidant, to modify a commonly performed MIC assay allowed us to screen selectively for new antifungal drugs that target ergosterol biosynthesis in fungi. A human pathogen, Microsporum gypseum, was used as a test organism. When exposed to ergosterol targeting drugs, the hydrogen peroxide treatment significantly decreased fungal survival by reducing ergosterol in the cell wall, whereas GSH increased survival of M. gypseum. Further, by performing a series of experiments with M. gypseum, it was determined that the oxidative stress from hydrogen peroxide causes cell death at different developmental stages. These findings allow us to describe a simple, high-throughput method for simultaneously screening new antifungal drugs for activity and effects on the ergosterol pathway. By using this tool, two isoquinoline alkaloids were discovered to be potent inhibitors of ergosterol biosynthesis by reducing the amount of ergosterol without affecting the expression of 1,3-β-glucan.
ARTICLE | doi:10.20944/preprints201906.0130.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: breast cancer; Wnt pathway; TCF1; NHERF1
Online: 14 June 2019 (05:00:53 CEST)
Wnt pathway is involved in breast cancer (BC) progression. Our aim was to evaluate the expression of some components of the Wnt pathway (β-catenin, FZD4, LRP5, LRP6 and TCF1) in order to detect potential associations with NHERF1 protein. In addition, we assessed their impact on patients’clinical outcome. We evaluated 220 primary BC samples by immunohistochemistry (IHC) and protein localization by immunofluorescence. We found a significant correlation between NHERF1 and FZD4, LRP5, LRP6 and TCF1. Univariate analysis showed that β-catenin (p<0.0001), FZD4 (p=0.0001), LRP5, LRP6 and TCF1 over-expression (p<0.0001 respectively) was related to poor disease free survival (DFS). A Kaplan-Meier analysis confirmed univariate data and showed a poor DFS for cNHERF1+/FZD4+ (p=0.0007), cNHERF1+/LRP5+ (p=0.0002), cNHERF1+/LRP6+ (p<0.0001) and cNHERF1+/TCF1+ phenotypes (p=0.0034). In multivariate analysis, TCF1 and β-catenin expression were independent prognostic variable of worse DFS (p=0.009 and p=0.027, respectively). In conclusion, we found that β-catenin, FZD4, LRP5, LRP6 and TCF1 overexpression was associated to poor prognosis. Furthermore, we first identified TCF1 as independent prognostic factor of poor outcome, indicating it as a new potential biomarker for BC patients management. In addition, Wnt pathway proteins expression, both alone and in association with NHERF1, suggests original associations of biological significance for new studies.
ARTICLE | doi:10.20944/preprints201905.0020.v1
Online: 5 May 2019 (12:41:30 CEST)
Euglenids are a group of algae of great interest for biotechnology, with a large and complex metabolic capability. To study the metabolic network, it is necessary to know the subcellular locations of the component enzymes, but despite a long history of research into Euglena, the subcellular locations of many major pathways are only poorly defined. Euglena is phylogenetically distant from other commonly studied algae, they have secondary plastids bounded by three membranes, and they can survive after destruction of their plastids. These unusual features make it difficult to assume that the subcellular organization of the metabolic network will be equivalent to that of other photosynthetic organisms. Moreover, we show here that the presence of the secondary chloroplast means that it is not possible to make reliable predictions of the subcellular locations of enzymes in Euglena using existing informatics tools. In order to generate a model of the central metabolic pathway operating in Euglena we analysed biochemical and proteomic information from a variety of sources to assess the subcellular location of relevant enzymes. We use these assignments to propose the compartmentation of the core metabolic pathways in Euglena, a prerequisite for the further study of the metabolic network of Euglena. This model of the metabolic network shows that, other than photosynthesis, all major pathways present in the chloroplast are duplicated elsewhere in the cell, and that several biosynthetic pathways confined to plastids in higher plants are localized elsewhere in Euglena. Our model demonstrates how this organism can synthesise all the metabolites required for growth from simple carbon inputs, and can survive in the absence of chloroplasts.
REVIEW | doi:10.20944/preprints202011.0563.v2
Subject: Medicine & Pharmacology, Allergology Keywords: Chromosomal instability; FA pathway; Radial figures; TGF pathway; MYC; p53; Bone marrow failure; cancer; physical abnormalities; infertility.
Online: 22 December 2020 (10:58:20 CET)
Abstract: Fanconi anemia (FA), a chromosomal instability syndrome, is caused by inherited pathogenic variants in any of 22 FANC genes, that cooperate in the FA/BRCA pathway. This pathway regulates the repair of DNA interstrand crosslinks (ICLs) through homologous recombination. In FA proper repair of ICLs is impaired, and accumulation of toxic DNA double strand breaks occurs. In order to repair this type of DNA damage, FA cells activate alternative error-prone DNA repair pathways, that may lead to the formation of gross structural chromosome aberrations of which radial figures are the hallmark of FA and their segregation during cell division are the origin of subsequent aberrations like translocations, dicentrics and acentric fragments. The deficiency in DNA repair has pleiotropic consequences in the phenotype of patients with FA, including developmental alterations, bone marrow failure and an extreme risk to develop cancer. The mechanisms leading to the physical abnormalities during embryonic development have not been clearly elucidated, however FA has features of premature aging with chronic inflammation mediated by pro-inflammatory cytokines, that results in tissue attrition, selection of malignant clones and cancer onset. Moreover, the effect of the FA/BRCA pathway in germinal cells, evidenced by infertility in patients with FA attests of chromosomal instability and cell death also occurring in the germinal compartment.
ARTICLE | doi:10.20944/preprints202011.0709.v1
Subject: Life Sciences, Biochemistry Keywords: Sphingosine-1-phosphate receptor analogue; fingolimod phosphate; neuroprotection; mitochondrial damage; glycolytic pathway; pentose phosphate pathway; REDOX homeostasis.
Online: 30 November 2020 (08:31:50 CET)
Imbalance in the oxidative status in neurons, along with mitochondrial damage, are common characteristics in some neurodegenerative diseases. The maintenance in energy production is crucial to face and recover from the oxidative damage and the coexistence of different sources of energy production, such as mitochondrial and glycolytic ATP, allows faster adaptative mechanisms to situations of high energy demand and may help in the maintenance of neuronal function in stress situations. Fingolimod phosphate is a drug with neuroprotective and antioxidant actions, used in the treatment of Multiple Sclerosis. This work has been performed in a model of oxidative damage on neuronal cell cultures exposed to menadione, in presence or absence of fingolimod phosphate. We have studied the mitochondrial function and several pathways related with glucose metabolism, including oxidative, glycolytic and pentose phosphate in neuronal cells cultures. Our results showed a beneficial effect on neuronal survival probably based in the recovery of all, oxidative balance, glycolysis and pentose phosphate, promoted by fingolimod phosphate. These effects are mediated, at least in part by the interaction with its specific receptor. These actions would make this drug a potential tool to the treatment of neurodegenerative processes, either to slow progression or alleviate symptoms.
REVIEW | doi:10.20944/preprints202201.0186.v2
Subject: Behavioral Sciences, Behavioral Neuroscience Keywords: Habituation; Genelist; Molecular pathway; Cognition; Neurodevelopmental disorders
Online: 6 May 2022 (08:58:50 CEST)
Habituation is the most ancient and fundamental form of learning. As a firewall that protects our brain from sensory overload, it is indispensable for higher cognitive processes. Studies in humans and animal models provide a growing body of evidence that habituation is affected in autism and related monogenic neurodevelopmental disorders (NDDs). An integrated application of habituation assessment in NDDs and their animal models has currently unexploited potential for fundamental neuroscience and medical care.With the aim to gain mechanistic insights, we systematically retrieved genes that have been demonstrated in the literature to underlie habituation. We identified 258 evolutionarily conserved genes across species, describe the biological processes they converge on, and highlight regulatory pathways and drugs that may alleviate the habituation deficits associated with their dysregulation. We also summarize current habituation paradigms and extract the most decisive arguments from the literature that support the crucial role of habituation for cognition in health and disease. We conclude that habituation is a conserved, quantitative, cognition- and disease-relevant process that can connect preclinical and clinical work, and hence is a powerful tool to advance research, diagnostics,’’ and treatment of NDDs.
REVIEW | doi:10.20944/preprints202201.0134.v1
Subject: Medicine & Pharmacology, Psychiatry & Mental Health Studies Keywords: TRYCATs; MDD; MDE; Suicidal behavior; Kynurenine pathway
Online: 11 January 2022 (10:39:25 CET)
Kynurenine or tryptophan catabolite (TRYCAT) pathway contributes to the pathophysiology of major depression disorder (MDD) and major depressive episodes (MDE) in bipolar disorder and suicidal behaviors. The consequences of the overactivation of this pathway large reduced tryptophan (TRP) levels in peripheral blood and the CNS and increased levels of neurotoxic TRYCATs including kynurenine (KYN), 3-hydroxy kynurenine (3HK), quinolinic acid (QA), xanthurenic acid (XA), and picolinic acid (PA). However, other TRYCATs are protective, such as kynurenic acid (KA) and anthranilic acid (AA). Inflammation and cell-mediated immune activation along with oxidative and nitrosative stress (O&NS) may stimulate the first and rate-limiting enzyme of this pathway, namely indoleamine-2,3-dioxygenase (IDO). Therefore, during depression, balancing neuroprotective versus neurotoxic TRYCATs and balancing activation of the immune response system (IRS) versus the compensatory immune response system is crucial for achieving better treatment outcomes. Furthermore, targeting the causes of TRYCAT pathway activation (immune activation and O&NS) is probably the most effective strategy to treat depression. In the present review, we aim to provide a comprehensive explanation of the impact of TRYCATs in terms of pathophysiology and treatment of MDD and MDE.
ARTICLE | doi:10.20944/preprints202103.0742.v1
Subject: Life Sciences, Biochemistry Keywords: Salinity; wheat; organellar antioxidant; SOS pathway; RBOH
Online: 30 March 2021 (13:49:12 CEST)
The response of salt tolerant wheat genotype (Kharchia 65), and sensitive cultivars (HD2687, HD2009, WL711) to vegetative stage salinity stress (for 4 weeks) were studied at 1.1 (control), 9.1 (S1) and 14.2 (S2) dSm-1 salinity levels. Based on relative change in Membrane stability, PSII efficiency, retention of chlorophyll and carotenoid contents, Kharchia 65 showed better tolerance to salinity than other genotypes considered. To understand the role of different component mechanisms, expression of genes involved in ion exclusion, antioxidant defence and compatible osmolyte synthesis were analysed. Expression of SOS1 (plasma membrane Na+/H+ antiporter), NHX (vacuolar Na+/H+ antiporter), Ionic (sodium exclusion) and tissue tolerance (Sodium compartmentation, compatible solute accumulation and antioxidant defence) mechanisms were analysed in leaves of the genotypes after 4 weeks of salinity stress. Expression assay and the content of respective constituents indicated that apart from the well-known ion exclusion ability, Kharchia 65 also showed high level of tissue tolerance resulting in high early vigour and maintenance of growth rate afterwards. In Kharchia 65, sensing of salinity stress at plasma membrane activates NADPH Oxidase (RBOH) genes and generate ROS at apoplast. Apoplastic ROS triggers calcium influx and activates calcium signaling genes of SOS pathway (SOS1 and NHX). ROS generated from organelles chloroplast, peroxisome and mitochondria triggers cellular oxidative burst. ROS and calcium activates MAPK genes and downstream transcription factors, NAC and bZIP. MAPK signaling induces cellular antioxidant and compatible osmolyte biosynthesis and imparts tissue tolerance to salinity.
ARTICLE | doi:10.20944/preprints202005.0495.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Hedgehog pathway; Smoothened; Promoter; Methylation; Transcription factors
Online: 31 May 2020 (19:14:59 CEST)
Background: The hedgehog (HH) signaling pathway is a key regulator of embryonic patterning, tissue regeneration, stem cell renewal, and cancer growth. The smoothened (SMO) protein regulates the HH signaling pathway and has demonstrated oncogenic activity. Methods: To clarify the role of the HH signaling pathway in tumorigenesis, the expression profile of key HH signaling molecules, including SMO, PTCH1, GLI1, GLI2, and GLI3, were determined in thirty-three cancer cell lines. We performed a computational analysis of the upstream region of the SMO gene to identify the regulatory elements. Results: Three potential CpG islands and several putative SMO promoter elements were identified. Luciferase reporter assays mapped key SMO promoter elements, and functional binding sites for SP1, AP1, CREB, and AP-2a transcription factors in the core SMO promoter region were confirmed. A hypermethylated SMO promoter was identified in several cancer cell lines suggesting an important role for epigenetic silencing of SMO expression in certain cancer cells. Discussion: These results have important implications for our understanding of regulatory mechanisms controlling HH pathway activity and the molecular basis of SMO gene function. Moreover, this study may prove valuable for future research aimed at producing therapeutic downregulation of SMO expression in cancer cells.
ARTICLE | doi:10.20944/preprints202002.0423.v1
Subject: Life Sciences, Molecular Biology Keywords: ITF2_TCF4; chemotheraoy resistance; NSCLC; HOXD9; Wnt pathway
Online: 28 February 2020 (11:58:28 CET)
Despite often leading to platinum resistance, platinum-based chemotherapy continues to be the standard treatment for many epithelial tumors. In this study we analyze and validated the cytogenetic alterations that arise after treatment in four lung and ovarian paired cisplatin-sensitive/resistant cell lines by 1-million array-CGH and qRT-PCR methodologies. RNA-sequencing, functional transfection assays and gene-pathway activity analysis were used to identify genes with a potential role in the development of this malignancy. Results were further explored in 55 lung and ovarian primary tumors and control samples and in two extensive in silico databases. Long-term cell exposure to platinum induces the frequent deletion of ITF2 gene. Its expression re-sensitizes tumor cells to platinum and recovers the levels of Wnt/β-catenin transcriptional activity. ITF2 expression was also frequently downregulated in epithelial tumors, predicting a worse overall survival. We also identified an inverse correlation between ITF2 and HOXD9 expression, revealing that NSCLC patients with lower expression of HOXD9 have a better overall survival rate. We define the implication of ITF2 as a molecular mechanism behind the development of cisplatin resistance probably through the activation of the Wnt-signaling pathway. This data highlights the possible role of ITF2 and HOXD9 as novel therapeutic targets for platinum resistant tumors.
REVIEW | doi:10.20944/preprints201805.0404.v2
Subject: Life Sciences, Other Keywords: microbiota; kynurenine pathway; serotonin; inflammation; gut motility
Online: 22 June 2018 (06:29:42 CEST)
The human gastrointestinal tract is inhabited by trillions of commensal bacteria collectively known as the gut microbiota. Our recognition of the significance of the complex interaction between the microbiota, and its host has grown dramatically over the past years. A balanced microbial community is a key regulator of the immune response, and metabolism of dietary components, which in turn, modulates several brain processes impacting mood and behavior. Consequently, it is likely that disruptions within the composition of the microbiota would remotely affect the mental state of the host. Here, we discuss how intestinal bacteria and their metabolites can orchestrate gut-associated neuroimmune mechanisms that influence mood and behavior leading to depression. In particular, we focus on microbiota-triggered gut inflammation and its implications in shifting the tryptophan metabolism towards kynurenine biosynthesis while disrupting the serotonergic signaling. We further investigate the gaps to be bridged in this exciting field of research in order to clarify our understanding of the multifaceted crosstalk in the microbiota-gut-brain interphase, bringing about a novel microbiota-targeted therapeutics for mental illnesses.
ARTICLE | doi:10.20944/preprints201804.0344.v1
Subject: Chemistry, General & Theoretical Chemistry Keywords: Chevron-Phillips; chromium; trimerization; polymerization; reaction pathway
Online: 26 April 2018 (16:55:12 CEST)
In the present work, effect of basic components on the energy pathway of ethylene oligomerization by landmark Chevron-Phillips catalyst has been explored in detail using density functional theory (DFT). Studied factors were chosen considering the main components of Chevron-Phillips catalyst, i.e. ligand, cocatalyst and halocarbon compounds, comprising i) the type of alkyl substituents in pyrrole ligand as methyl, iso-propyl, tert-butyl, and phenyl, as well as the simple hydrogen, and the electronwithdrawing fluoro and trifluoromethyl; ii) the number of Cl atoms in Al-compound (as AlMe2Cl, AlMeCl2 and AlCl3) which indicates halocarbon amount and iii) cocatalyst type as alkylboron, alkylaluminium, or alkylgallium. Besides main ingredients, solvent effect, from toluene or methylcyclohexane, on oligomerization pathway was explored as well. In this regard, the full catalytic cycles for the main product (1-hexene) formation as well as side reactions, i.e. 1-butene release and chromacyclononane formation, were calculated on the basis of the metallacycle based mechanism. Based on results, a modification on the Chevron-Phillips catalyst system, to reach higher 1-hexene selectivity and activity, is suggested.
REVIEW | doi:10.20944/preprints202209.0458.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: kynurenine pathway; inflammatory biomarkers; inflammation; ADHD; neurobiology; kynurenine
Online: 29 September 2022 (08:11:33 CEST)
Attention deficit hyperactivity disorder (ADHD) is a prevalent neurodevelopmental disorder that can diminish the quality of life of both children and adults in academic, occupational, and social contexts. The kynurenine pathway (KP) contains a set of enzymatic reactions involved in tryptophan (TRP) degradation. It is known to be associated with the risk of developing ADHD. This review will address the KP and underlying mechanism of inflammation in ADHD. Potential inflammatory biomarkers reported in the most recent studies are summarized. Although a strong neuroimmunological basis has been established due to advances of recent neurobiological research, the pathophysiology of ADHD remains unclear.
ARTICLE | doi:10.20944/preprints202207.0067.v1
Subject: Medicine & Pharmacology, Cardiology Keywords: restenosis; foam cells; NLRP3 inflammasome; MAPK signaling pathway
Online: 5 July 2022 (08:15:38 CEST)
The accumulation of foam cells in arterial intima and the accompanied chronic inflammation are considered major causes of neoatherosclerosis and restenosis. However, both the underlying mechanism and effective treatment for the disease are yet to be uncovered. In this study, we combined transcriptome profiling of restenosis artery tissue and bioinformatic analysis to reveal that NLRP3 inflammasome is markedly upregulated in restenosis and that several restenosis re-lated DEGs are also targets of mulberry extract, a natural dietary supplement used in traditional Chinese medicine to improve liver vitality. Further pathway enrichment analysis identified MAPK signaling pathway to be involved in the inflammatory response of foam cells. Consistently, immunofluorescence microscopy shows co-localization of NLRP3 with CD68+ macrophages. We then evaluated the efficacy of mulberry extract in inhibiting both the formation of foam cells and their inflammatory response. We demonstrated that mulberry extract suppresses the formation of ox-LDL induced foam cells, possibly by upregulating the cholesterol efflux genes ABCA1 and ABCG1 to inhibit intracellular lipid accumulation. In addition, mulberry extract dampens NLRP3 inflammasome activation by stressing the MAPK signaling pathway. Collectively, our mecha-nistic and functional studies unveil the therapeutic value of mulberry extract in neoatherosclerosis and restenosis treatment by regulating lipid metabolism and inflammatory response of foam cells.
REVIEW | doi:10.20944/preprints202111.0127.v1
Subject: Biology, Animal Sciences & Zoology Keywords: Apoptosis; preclinical research; diabetes type 2; HIPPO pathway
Online: 8 November 2021 (11:45:49 CET)
Diabetes mellitus is a heterogeneous disease of complex etiology and pathogenesis. Hyperglycemia leads to many serious complications, but also directly initiates the process of β cell apoptosis. A potential strategy for the preservation of pancreatic β cells in diabetes may be to inhibit the implementation of pro-apoptotic pathways or to enhance the action of pancreatic protective factors. The HIPPO signaling pathway is proposed and selected as a target to manipulate the activity of its core proteins in therapy - basic research. MST1 and LATS2 as major upstream signaling kinases of the Hippo pathway are considered as target candidates for pharmacologically induced tissue regeneration and inhibition of apoptosis. Manipulating the activity of components of the HiPPO pathway offers a wide range of possibilities, and thus is a potential tool in the treatment of diabetes and the regeneration of β cells. Therefore, it is important to fully understand the processes involved in apoptosis in diabetic states and to fully characterize the role of this pathway in diabetes. Therapy consisting in slowing down or stopping the mechanisms of apoptosis may be an important direction of diabetes treatment shortly.
ARTICLE | doi:10.20944/preprints202011.0311.v1
Subject: Medicine & Pharmacology, Allergology Keywords: autism genetics; family microarrays; pathway enrichment; network biology
Online: 10 November 2020 (12:33:35 CET)
The genetic heterogeneity of autism has stymied the search for causes and cures. Whole-genomic studies on large numbers of families have helped identify combinations of inherited and de novo signal. In the present work, we re-analyze DNA microarrays using a novel strategy that takes prior knowledge of genetic relationships into account and that was designed to boost signal important to our understanding of the molecular basis of autism. Our strategy was designed to identify significant genomic variation within a priori defined biological concepts and improves signal detection while lessening the severity of multiple test correction seen in standard analysis of genome-wide association data. Upon application of our approach using 3,244 biological concepts, we detected genomic variation in 68 biological concepts with significant association to autism in comparison to family-based controls. These concepts clustered naturally into a total of 19 classes, principally including cell adhesion, cancer, and immune response. The top-ranking concepts contained high percentages of genes already suspected to play roles in autism or in a related neurological disorder. In addition, many of the sets associated with autism at the DNA level also proved to be predictive of changes in gene expression within a separate population of autistic cases, suggesting that the signature of genomic variation may also be detectable in blood-based transcriptional profiles. This cross-validation with gene expression data from individuals with autism coupled with the enrichment within autism-related neurological disorders supported the possibility that the mutations play important roles in the onset of autism and should be given priority for further study. Our work provides new leads into the genetic underpinnings of autism and highlights the importance of reanalysis of genomic studies of complex disease using prior knowledge of genetic organization.
ARTICLE | doi:10.20944/preprints201805.0076.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Oral cancer; mTOR pathway; secreted glycoprotein; drug resistance
Online: 3 May 2018 (12:47:14 CEST)
Oral cancer is a major public health burden worldwide. The lack of biomarkers for early diagnosis has increased the difficulty in managing this disease. Recent studies have reported that neutrophil gelatinase-associated lipocalin (NGAL), a secreted glycoprotein, is upregulated in various tumors. In our study we found that NGAL was significantly downregulated in primary malignant and metastatic tissues of oral cancer compared to normal tissues. The downregulation of NGAL was strongly correlated with the degree of differentiation and stage (I-IV), and can serve as a prognostic biomarker for oral cancer. Tobacco carcinogens were also found to be involved in the downregulation of NGAL. Mechanistic studies revealed that knockdown of NGAL increased oral cancer cell proliferation, survival, and migration, and also induced resistance against cisplatin. Silencing of NGAL activated mTOR signaling and reduced autophagy by the LKB1-AMPK-p53-Redd1 signaling axis. Moreover, cyclin-D1, Bcl-2, and MMP-9 were upregulated, and caspase-9 was downregulated, suggesting that silencing of NGAL increases oral cancer cell proliferation, survival, and migration. Thus, from our study it is evident that downregulation of NGAL activates the mTOR pathway and helps in the progression of oral cancer.
ARTICLE | doi:10.20944/preprints201608.0011.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: curcumin; furazolidone; oxidative stress; DNA damage; mitochondrial pathway
Online: 2 August 2016 (05:59:38 CEST)
Furazolidone (FZD) is a synthetic nitrofuran with the antiprotozoal and antibacterial activity. The proper mechanism of FZD induced toxicity is still unclear. This study aimed to investigate the protective effect of curcumin on FZD induced oxidative stress, DNA injury and apoptosis in human hepatocyte L02 cells. The results showed that curcumin treatment significantly ameliorated FZD induced cytotoxicity, characterized by decreasing the production of reactive oxygen species (ROS) and malondialdehyde, as well as increasing superoxide dismutase, catalase activities and glutathione contents. Moreover, curcumin pretreatment significantly inhibited FZD induced the loss of mitochondrial membrane potential, the activation caspase-9 and -3 and apoptosis. Comet assay showed that curcumin attenuated FZD induced DNA injury in a dose-dependent manner. Correspondingly, curcumin markedly reversed the up-regulation of p53, Bax, caspase-9 and -3 mRNA expressions and the down-regulation of Bcl-2 mRNA (all p<0.05 or 0.01). These results reveal that curcumin protects against FZD induced oxidative stress, DNA injury and cell apoptosis via inhibiting oxidative stress and mitochondrial pathway, which may be attributed to ROS scavenging and anti-oxidative ability of curcumin. Importantly, our study highlights that curcumin may be a potential way to prevent FZD-mediated oxidative DNA injury and apoptosis in human or animals.
ARTICLE | doi:10.20944/preprints202004.0053.v1
Subject: Life Sciences, Genetics Keywords: calcium signaling; chemokine signaling; gap junction; NOD-like receptor signaling; oli-neu cells; pannexin1; PI3K-Akt pathway; thyroid hormone pathway
Online: 6 April 2020 (12:36:20 CEST)
We profiled the transcriptomes of primary mouse cortical astrocytes cultured alone or co-cultured with immortalized precursor oligodendrocytes. The experimental set-up (insert systems) prevented formation of gap junction channels but allowed free exchange of the two culture media. The study complements our previously published reports that the genomic fabrics of major functional pathways in oligodendrocytes are substantially remodeled by the proximity of non-touching astrocytes. Here, we present new analysis indicating that the transcriptomic landscape of astrocytes likewise changes significantly in the proximity of non-touching oligodendrocytes. The research was stimulated by the reported transcriptomic similarity between the brains of Cx43KO and Cx32KO mice, both substantially different from that of the Cx36KO mice. Since the three connexins are expressed in different cell types (Cx43 in astrocytes, Cx32 in oligodendrocytes and Cx36 in neurons), altogether these findings support the idea of a “panglial transcriptomic syncytium” in the mouse brain. Going further, our results suggest that integration in a heterocellular tissue modulates not only the expression profile but also the expression control and networking of the genes in each cell phenotype.
ARTICLE | doi:10.20944/preprints202102.0602.v1
Online: 26 February 2021 (09:38:28 CET)
Knee Osteoarthritis (KOA) is a chronic disease characterized by progressive disability and joint pain. Meniscus chondrocytes apoptosis is the main cause of reduced chondrocyte number and self-repair function. The purpose of this study was to investigate the role of miR-27b-3p in KOA.In this study, we found that the expression of miR-27b-3p was downregulated in cultured IL-1β treated chondrocyte and cartilage tissues in KOA. KOA overexpression evidently reduced IL-1β induced chondrocyte apoptosis and caspase-3 and caspase-9 expression.The upregulated iNOS and COX-2 mRNA and proteins expression was also inhibited by miR-27b-3p mimics. The expression of nitric oxide, PGE2, TNF-α and IL-6 was also inhibited by miR-27b-3p mimics. The target gene of miR-27b-3p was confirmed to be BDNF. TrkB/CREB pathway was proved to be the downstream pathway of miR-27b-3p/BDNF axis.The apoptotic cell percentage and nitric oxide, PGE2, TNF-α and IL-6 expression was induced by BDNF+IL-1β. This induction was inhibited by miR-27b-3p mimics. The cartilage tissues stained with safranin O results showed miR-27b-3p greatly decreased KOA induced cartilage degradation. The expression of BDNF、TrkB and p-CREB was inhibited by len-miR-27b-3p. MiR-27b-3p also reduced the expression of TNF-α、IL-6 and Bax, and increased Bcl-2 expression. These results indicated miR-27b-3p could applied to inhibit the development of KOA and miR-27b-3p/BDNF/TrkB/CREB pathway could serve as novel treatment target to handle KOA.
ARTICLE | doi:10.20944/preprints202101.0130.v1
Subject: Life Sciences, Biochemistry Keywords: Geniposide; NF-ĸB; IEC-6; Signaling pathway; Cell migration
Online: 8 January 2021 (08:35:25 CET)
The nuclear factor-ĸB (NF-ĸB) transcriptional system is a major effector pathway involved in inflammatory responses. Previous studies found that a Gardenia decoction (GD) inhibited the expression of NF-κB in a lipopolysaccharide (LPS)-stimulated mouse intestinal injury model. Herein, we hypothesized that geniposide (GE), a component of Gardenia jasminoides Ellis, also exerts anti-inflammatory effects and inhibits NF-ĸB activity in LPS-induced intestinal epithelial cells (IEC-6). IEC-6 cells were stimulated with LPS, following which the effects of GE on NF-ĸB signaling in the IEC-6 cells were examined by western blotting to detect IĸB phosphorylation/degradation. The expression of NF-κB was determined by immunofluorescence assay (IFA). Enzyme-linked immunosorbent assay (ELISA) was used to detect the inhibitory effect of GE on the release of tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and interleukin-1β (IL-1β) activated by LPS in IEC-6 cells. In addition, the migration ability of IEC-6 cells was observed by the scratch method. These results showed that GE dose-dependently downregulated levels of the proinflammatory cytokines TNF-α, IL-6 and IL-1β that had been upregulated by LPS and suppressed the phosphorylation of IĸB and NF-ĸB induced by LPS. Our findings indicated that GE could reduce LPS-induced NF-ĸB signaling and proinﬂammatory expression in IEC-6 cells and significantly enhance the migration of IEC-6 cells. Moreover, GE inhibited the expression of NF-κB, nuclear transfer, and transcriptional activity in IEC-6 cells. GE could block the synthesis of inflammatory factors of IEC-6 cells by inhibiting activation of the IĸB/NF-κB signaling pathway induced by LPS.
ARTICLE | doi:10.20944/preprints202011.0497.v1
Subject: Medicine & Pharmacology, Allergology Keywords: ONC201; colorectal cancer cells; DDIT3; CHOP; BAK/BAX pathway
Online: 19 November 2020 (08:42:43 CET)
The imipramine ONC201 exerts a novel anti-proliferative activity over a wide spectrum of cancer cell types. ONC201 activates integrated stress response pathway that is associated with induction of Damage Inducible Transcript 3 (DDIT3, also known as C/EBP homologous protein or CHOP). We questioned whether the ONC201/CHOP crosstalk is regulated by diverse signaling pathways in non-metastatic versus metastatic cancer cell lines. Therefore, the Dukes' type B colorectal adenocarcinoma non-metastatic (SW480) and metastatic (LS-174T) cell lines were treated with ONC201. Cell proliferation and apoptosis were evaluated by MTT assay, flow cytometry analysis, gene expression was assessed by Affymetrix microarray, and key regulatory proteins were validated by Western blot assays. Unlike LS-174T cells, SW480 cells were resistant to ONC201 treatment. Gene ontology pathway enrichment analysis of differentially expressed genes revealed substantial differences between LS-174T and SW480 responsiveness to ONC201 treatment. In both cell lines, CHOP expression was upregulated in response to ONC201 treatment, however, its upstream regulatory mechanisms were not identical. Although, PERK, ATF6 and IRE1 ER-stress pathways were found to upregulated CHOP in both cell types, the BAK/BAX pathway was a notable regulator of CHOP in the metastatic LS-174T cells alone. In addition, CHOP RNA splicing profiles were varied between the two cell lines, which was further modified in response to ONC201 treatments. In conclusion, we delineated the signaling mechanisms regulating the expression of CHOP in non-metastatic versus metastatic colorectal cells in response to ONC201 treatment. The observed differences were related to cellular plasticity and metabolic reprogramming.
REVIEW | doi:10.20944/preprints202004.0294.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: signaling pathway; microRNA; long-noncoding RNA; chemoresistence; cervical cancer
Online: 17 April 2020 (08:12:52 CEST)
Cervical cancer is known as one of the most important cancers in women worldwide. Chemotherapy is a standard treatment for advanced/recurrent cervical cancer in which the prognosis of the disease is really poor and the 1-year survival chance in these patients is maximally 20%. However, resistance to anticancer drugs is a major problem in treating cancer. Cervical cancer stem cells are considered as a fundamental cause of chemo and radio-resistance and also relapse after primary successful treatment. Signaling pathways include a wide range of molecular mechanisms contribute to drug resistance. Recently, microRNAs (miRNAs) are announced as a group of molecular biomarkers involving in response to chemotherapy in cancer patients. As the miRNAs, there are some long non-coding RNAs (LncRNAs) which their aberrant expression is considered as a biomarker for monitoring chemoresistance. In this review, we summarized current reports about the involvement of signaling pathways during chemoresistance in cervical cancer. Then, genes that have been demonstrated their involvement during drug resistance in cervical cancer were tabulated. Further, miRNAs that have been reported as biomarkers during treatment are listed. By bioinformatic analysis, we predictedmiR-335-5p and miR-16-5p as the most potential biomarkers for monitoring resistance to chemotherapy. Finally, long non-coding RNAs that have been introduced in recent studies as novel biomarkers during the response to chemotherapy were mentioned.
ARTICLE | doi:10.20944/preprints201809.0274.v1
Subject: Chemistry, Food Chemistry Keywords: rice bran; rice genes; rice cultivars; metabolic pathway; metabolomics
Online: 15 September 2018 (19:34:43 CEST)
Rice (Oryza sativa L.) processing yields ~60 million metric tons of bran annually. Rice genes producing bran metabolites of nutritional and human health importance were assessed across 17 diverse cultivars from seven countries using non-targeted metabolomics and resulted in 378-430 metabolites. Gambiaka cultivar had the highest number and Njavara had the lowest number of metabolites. The 71 rice bran compounds of significant variation by cultivar included 21 amino acids, seven carbohydrates, two metabolites from cofactors and vitamins, 33 lipids, six nucleotides, and two secondary metabolites. Tryptophan, -ketoglutarate, γ-tocopherol/β-tocopherol and γ-tocotrienol are example bran metabolites with extensive cultivar variation and genetic information. 34 rice bran components that varied between cultivars linked to 535 putative biosynthetic genes using to the OryzaCyc 4.0, Plant Metabolic Network database. Rice genes responsible for bran composition with animal and human health importance is available for rice breeding programs to utilize in crop improvement.
ARTICLE | doi:10.20944/preprints201804.0158.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: Cholera toxin; exosomes; endocytic pathway; Caveolin-1; GM1 ganglioside
Online: 12 April 2018 (05:58:31 CEST)
Here we first report, how cholera toxin (CT) A subunit (CTA), the bacterial enzyme moiety responsible of cell signaling alteration, can take over the exosomal pathway, spread extracellularly and be transmitted in a cell population. A first evidence for long-term transmission of CT toxic effect via extracellular vesicles was obtained in CHO cells. To follow CT intracellular route towards exosome secretion we adopted a strategy apt to convert multivesicular body (MVB) derived exosomes in traceable fluorescent vectors. CT treated Me665 cells, a human melanoma cell line highly expressing caveolin-1 (Cav-1) and GM1, were used to purify and characterize fluorescent exosomes. Our results clearly show association of CT with exosomes together with typical exosomal markers and the HSP90 and PDI molecules, the required membrane translocation elements of CTA to the cytoplasm. Confocal microscopy proved direct CT containing fluorescent exo transfer into CHO cells coupled with the morphological cell change characteristic of CT action. Moreover, direct assessment of cAMP levels in Me665 cells treated with CT containing exo showed an efficient induction of cAMP increase comparable with CT alone. From our results, we can infer that CT can exploit exosome-mediated cell communication to target and extend its pathophysiological action throughout cell tissues.
ARTICLE | doi:10.20944/preprints202206.0385.v1
Subject: Life Sciences, Molecular Biology Keywords: UxuR; ExuR; Ashwell pathway; uxuAB; fliC; proteome; motility; biofilm formation
Online: 28 June 2022 (10:42:44 CEST)
ExuR and UxuR are paralogous proteins belonging to the GntR family of transcriptional regulators. Both are known to control hexuronic acid metabolism in a variety of Gammaproteobacteria but the relative impact of each of them is still unclear. Here, we apply 2D difference electrophoresis followed by mass-spectrometry to characterise the changes in the Escherichia coli proteome in response to the uxuR or exuR deletion. Our data clearly show that the effects are different: deletion of uxuR resulted in significantly enhanced expression of D-mannonate dehydratase UxuA and flagellar protein FliC, and inhibition of outer membrane porin OmpF, while the absence of ExuR did not significantly alter the spectrum of detected proteins.This suggests that the roles of proteins predicted as homologs are far from identical. Effects of uxuR deletion were largely dependent on the cultivation conditions: during growth with glucose, UxuA and FliC were dramatically altered, while during growth with glucuronate activation of both was not so prominent. During growth on glucose, the maximal activation was detected for FliC. This was further confirmed by expression analysis and physiological tests thus suggesting involvement of UxuR in the regulation of bacterial motility and biofilm formation.
ARTICLE | doi:10.20944/preprints202201.0359.v1
Subject: Chemistry, Medicinal Chemistry Keywords: JAK/STAT3 signaling pathway; Meridianin derivatives; Isothiouronium; Anti-tumor activity
Online: 24 January 2022 (14:06:38 CET)
Hyperactivation of Janus kinase (JAK)/signal transducer and activator of transcription 3 (STAT3) signaling is an attractive therapeutic target for tumor therapy. Herein, forty-eight novel meridianin derivatives were designed and synthesized, and their anti-tumor activity were evaluated in vitro both for activity optimization and structure-activity relationship (SAR) study. The results indicated that most derivatives exhibited significantly improved anti-tumor activity, especially for compound 6e. The compound 6e contains an isothiouronium linked by an alkyl chain consisting of 6 carbon atoms with IC50 ranging from 1.11 to 2.80 μM on various cancer cell lines. Consistently, 6e dose dependently induced the apoptosis of A549 and DU145 cells, in which STAT3 are constitutively active. Western blotting assays indicated that the phosphorylation levels of JAK1, JAK2 and STAT3 were inhibited by 6e at 5 μM without significant change in total STAT3 level. Moreover, 6e also suppressed the expressions of STAT3 downstream genes, including c-Myc, Cyclin D1 and Bcl-XL at 10 μM. An additional in vivo study revealed that 6e at the dose of 10 mg/kg could potently inhibit the DU145 xenograft tumor without obvious body-weight loss. These results clearly indicate that 6e could be a potential anti-tumor agent by targeting JAK/STAT3 signaling pathway.
ARTICLE | doi:10.20944/preprints202109.0105.v1
Subject: Medicine & Pharmacology, Obstetrics & Gynaecology Keywords: endometrial cancer; tumor microenvironment; Wnt/β-catenin pathway; SATB1; SATB2
Online: 6 September 2021 (14:29:35 CEST)
Wnt/β-catenin signaling pathway plays an established role in various diseases and is considered a hallmark of endometrial cancer (EC). Special AT-rich sequence-binding protein 1 and 2 (SATB1 and SATB2) are nuclear matrix-associated proteins involved in chromatin remodeling and regulation of gene expression. SATB1 promotes the progression of numerous types of cancers, whereas SATB2 acts as a tumor suppressor. Despite a recent progress in our knowledge about EC, the exact mechanisms that control their proliferation and metastatic potential still remain unknown. The aim of our study was to investigate the association between Wnt3A, β-catenin, SATB1 and SATB2 protein level and the clinicopathological features of EC patients. 92 EC patients, aged 37-84, were enrolled to our study. The immunoexpression of WNT3A was found in specimens from all EC patients, β-catenin was expressed in 97% of the cases, SATB1 in 87%. The significant association between Wnt3a expression and tumor grade was found; moreover mean IRS for Wnt3a turned out to be significantly lower in high-grade tumors than in low-grade malignancies (p=0.038). In turn, immunoexpression of β-catenin varied significantly across FIGO stages and was associated with the presence of lymph node metastases. Mean IRS for β-catenin in patients with lymph node metastases was significantly lower than in those without (p = 0.028). The Kaplan-Meier analyses demonstrated a stepwise impairment of cancer overall survival with increasing SATB1 expression. In conclusion, both Wnt/β-catenin signaling pathway and SATB1 contribute to progression of EC. Downregulation of β-catenin may predispose to lymphatic spread of EC. In turn, downregulation of Wnt3a seems to be characteristic for high-grade tumors, but probably does not play a role in formation of lymph node metastases. The important role of SATB1 as a predictor of poor survival and could be helpful in establishing a more accurate prognosis in endometrial cancer patients.
Subject: Social Sciences, Accounting Keywords: course pathway modeling; student-centered classroom; course evaluation; course design
Online: 10 February 2021 (09:01:23 CET)
Student-centered teaching practices such as active learning continue to gain momentum in college science education. Many instructors committed to these innovative practices transform their classroom beyond the standard lecture. Nevertheless, widespread implementation of these practices is limited because the learning benefits for students are often attained through increased instructional complexity to which many instructors cannot commit. When co-instructors are teaching the course, the level of commitment to building a student-centered classroom may be even more profound. For these reasons, new tools are needed to help instructors and co-instructors plan, organize, evaluate, and communicate their classroom innovations. Pathway modeling is a tool with potential to fill this gap. Unlike curriculum mapping -- which identifies academic content gaps, redundancies, and misalignments by examining a series of courses within a plan of study – course pathway modeling creates a visual map of a single course and reveals how teaching practices influence short-, mid-, and long-term student learning outcomes. This essay demonstrates how course pathway modeling can help co-instructors better represent the complexity of student-centered teaching practices. We include guides for creating course pathway models and discuss how this approach offers the potential to improve curricular design, course evaluation, student assessment, and communication between co-instructors.
REVIEW | doi:10.20944/preprints202010.0338.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Urothelial carcinoma; immune checkpoint inhibitors; immunotherapy; tumor microenvironment; metabolic pathway
Online: 16 October 2020 (08:00:41 CEST)
Cisplatin-based chemotherapy has long been viewed as the first-line chemotherapy for advanced and metastatic urothelial carcinoma (UC). However, many patients with UC have been classified as “cisplatin-ineligible patient”, which requires alternative chemotherapy due to their poor responses. In fact, vast majority of those who initially responded to cisplatin-based chemotherapy eventually progressed. Understanding of UC tumor immunology provided an immunopathogenic bases for immune checkpoint inhibitors, targeting PD-1 and CTLA-4, to treat cisplatin ineligible metastatic UC and patients with platinum-refractory metastatic UC. In 2020, data from the trail further showed that PD-L1 inhibitors benefit prolonged survival and progression-free survival as maintenance therapy. Besides immune-targeting therapies, manipulation of tumor microenvironment via metabolic pathways alternation, such as inhibiting tumor glycolysis, lactate accumulation and exogenous glutamine uptake, has been investigated in the past few years. In this comprehensive review, we started by introducing traditional chemotherapy of UC, and summarized current evidences supporting the use of immune checkpoint inhibitors and highlighted ongoing clinical trials. Lastly, we reviewed the tumor metabolic characteristic and the anti-tumor treatments targeting metabolic pathways.
Subject: Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; coronavirus; signaling pathway; molecular alteration
Online: 21 September 2020 (04:17:24 CEST)
Emerging viruses description have grown at an unprecedented rate since the beginning of the 21st century. The emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and its related illness, Coronavirus Disease 2019 (COVID-19) has been reported as the third highly pathogenic coronavirus introducing itself into human population in the current era after the SARS-CoV and Middle East Respiratory Syndrome (MERS-CoV). Molecular and cellular studies considering the pathogenesis of this novel coronavirus are still in the early stages of research, however, regarding the similarity of SARS-CoV-2 and other coronaviruses, it could be hypothesized that the NF-κB, Cytokine regulation, ERK, and TNF-α signaling pathways are the more likely causes of inflammation upon onset of COVID-19. There are several drugs prescribed and used to alleviate the activity of these inflammatory cellular signaling pathways which might be beneficial for developing novel therapeutic modalities against COVID-19. In this review, we briefly summarized the alteration of cellular signaling pathways affected by coronavirus infection, particularly SARS-CoV and MERS-CoV and tabulated the current therapeutic agents approved for previous human diseases.
REVIEW | doi:10.20944/preprints202008.0699.v1
Subject: Life Sciences, Biochemistry Keywords: heterologous production; shikimic acid pathway; phenolic acids; flavonoids; anthocyanins; stilbenes
Online: 31 August 2020 (05:02:19 CEST)
Secondary phenolic metabolites are defined as valuable natural products synthesized by different organisms that are not essential for growth and development. These compounds play an essential role in plant defense mechanisms, and an important role in the pharmaceutical, cosmetics, food, and agricultural industries. Despite the vast chemical diversity of natural compounds, their content in plants is very low, in consequence, it eliminates the possibility of the production of these interesting secondary metabolites from plants. Therefore, microorganisms are widely used as cell factories by industrial biotechnology to the production of different non-native compounds. Among microorganisms commonly used in biotechnological applications, yeasts are prominent host for the diverse secondary metabolite biosynthetic pathways. Saccharomyces cerevisiae is often regarded as the better host organism for the heterologous production of phenolics compounds, especially if the expression of different plant genes is necessary.
REVIEW | doi:10.20944/preprints202007.0123.v1
Subject: Life Sciences, Other Keywords: causal interactions; databases; interoperability; biological pathway; logical modeling; computational biology
Online: 7 July 2020 (09:50:40 CEST)
Causal molecular interactions represent key building blocks used in computational modeling, where they facilitate the assembly of regulatory networks. These regulatory networks can then be used to predict biological and cellular behavior by system perturbations and in silico simulations. Today, broad sets of these interactions are being made available in a variety of biological knowledge resources. Moreover, different visions, based on distinct biological interests, have led to the development of multiple ways to describe and annotate causal molecular interactions. Therefore, data users can find it challenging to efficiently explore resources of causal interaction and to be aware of recorded contextual information that ensures valid use of the data. This manuscript presents a review of public resources collecting causal interactions and the different views they convey, together with a thorough description of the export formats established to store and retrieve these interactions. Our goal is to raise awareness amongst the targeted audience, i.e., logical modelers, but also any scientist interested in molecular causal interactions, about existing data resources and how to get familiar with them.
Subject: Life Sciences, Other Keywords: neural differentiation; regulatory motif; feedback regulation; signaling pathway; mathematical models
Online: 24 December 2019 (11:20:25 CET)
Computational simulation using mathematical models is a useful method for understanding the complex behavior of a living system. The majority of studies using mathematical models to reveal biological mechanisms uses one of the two main approaches: the bottom-up or the top-down approach. When we aim to analyze a large-scale network, such as a comprehensive knowledge-integrated model of a target phenomenon, for example a whole-cell model, the variation of analyses is limited to particular kind of analysis because of the size and complexity of the model. To analyze a large-scale regulatory network of neural differentiation, we developed a hybrid method that combines both approaches. To construct a mathematical model, we extracted network motifs, subgraph structures that recur more often in a metabolic network or gene regulatory network than in a random network, from a large-scale regulatory network, detected regulatory motifs among them, and combined these motifs. We confirmed that the model reproduced the known dynamics of HES1 and ASCL1 before and after differentiation, including oscillation and equilibrium of their concentrations. The model also reproduced the effects of overexpression and knockdown of the Id2 gene. Our model suggests that the characteristic change in HES1 and ASCL1 expression in the large-scale regulatory network is controlled by a combination of four feedback loops, including a large loop which has not been focused on. The model extracted by our hybrid method has the potential to reveal the critical mechanisms of neural differentiation. The hybrid method is applicable to other biological events.
ARTICLE | doi:10.20944/preprints201910.0063.v1
Subject: Biology, Plant Sciences Keywords: lilium sp.; in vitro protocol; conventional pathway; bulb production; timeline
Online: 7 October 2019 (11:16:43 CEST)
Lily–belong to the genus Lilium is one of the top cut flowers worldwide. Production and propagation of bulblets in vitro is an important approach for high-volume production, but not proved satisfactory. Hence, the aim of this study was to describe and compare the performances of morphological characteristics of the lily bulb in vivo produced by in vitro and conventional culture method and compare the production timelines in vitro vs conventional culture method. In results, it seems clear that in vitro re-culture of lily bulblet was able to be sustained and maintained its growth and so, ontogenic development after their performance in soil. Our results demonstrate that in the conventional pathway, the course of bulblet growth to bulb and ontogenic development took 3–4 growing seasons to reach the adult flowering phase. On the other hand, along with the re-culture in vitro, the course of bulb growth and ontogenic development took 1–2 growing seasons to reach the adult flowering phase because of the increasing initial bulb size and advancement of ontogenic development. Other than bulblet production through bulb scale explant, this study represents the first report on the method of in vitro bulb production of lily through re-culture by in vitro pathway with a comparison of the timelines and ontogenic development obtained from in vitro versus conventional pathway.
REVIEW | doi:10.20944/preprints202207.0436.v1
Subject: Biology, Physiology Keywords: SUMO; MSC; osteoblast; chondrocyte; osteoclast; signaling pathway; arthritis; osteosarcoma; developmental disorders
Online: 28 July 2022 (09:04:33 CEST)
The modification of proteins by small ubiquitin-related modifier (SUMO) molecules, SUMOylation, is a key post-translational modification involved in a variety of biological processes such as chromosomes organization, DNA replication and repair, transcription, nuclear transport, and cell signaling transduction. In recent years, emerging evidence has shown that SUMOylation regulates the development and homeostasis of the skeletal system, with its dysregulation causing skeletal diseases, suggesting that SUMOylation pathways may serve as a promising therapeutic target. In this review, we summarize the current understanding of the molecular mechanisms by which SUMOylation pathways regulate skeletal cells in the physiological and disease contexts.
REVIEW | doi:10.20944/preprints202110.0026.v1
Subject: Biology, Other Keywords: Halotolerant/halophilic fungi; Hortaea werneckii; Wallemia ichthyophaga; HOG signal transduction Pathway
Online: 1 October 2021 (14:52:54 CEST)
Sensing and responding to changes in NaCl concentration in hypersaline environments is vital for cell survival. We have identified and characterized key components of the high-osmolarity glycerol (HOG) signal transduction pathway, which is crucial in sensing hypersaline conditions in the extremely halotolerant black yeast Hortaea werneckii and in the obligate halophilic fungus Wallemia ichthyophaga. Both organisms were isolated from solar salterns, their predominating ecological niche. The identified components included homologous proteins of both branches involved in sensing high osmolarity (SHO1 and SLN1) and the homologues of mitogen-activated protein kinase module (MAPKKK Ste11, MAPKK Pbs2, and MAPK Hog1). Functional complementation of the identified gene products in S. cerevisiae mutant strains revealed some of their functions. Structural protein analysis demonstrated important structural differences in the HOG pathway components between halotolerant/halophilic fungi isolated from solar salterns, salt-sensitive S. cerevisiae, the extremely salt-tolerant H. werneckii, and halophilic W. ichthyophaga. Known and novel gene targets of MAP kinase Hog1 were uncovered particularly in halotolerant H. werneckii. Molecular studies of many salt-responsive proteins confirm unique and novel mechanisms of adaptation to changes in salt concentration.
Subject: Materials Science, Biomaterials Keywords: bismuth selenide nanoparticles; photothermal killing; apoptosis; autophagy; stress-related signaling pathway
Online: 10 May 2021 (10:52:30 CEST)
With a highly efficient optical absorption capability, bismuth selenide (Bi2Se3) nanomaterial can be used as an outstanding photothermal agent for anti-tumor treatment and shows promise in the field of nanotechnology-based biomedicine. However, little research has been done on the relevant mechanism underlying the photothermal killing effect of Bi2Se3 nanomaterial. Herein, the photothermal effects of Bi2Se3 nanoparticles on A549 cells were explored with emphasis put on autophagy. Firstly, we characterized the structure and physicochemical property of the synthesized Bi2Se3 and confirmed their excellent photothermal conversion efficiency (35.72%), photostability, biocompatibility and ability of photothermal killing on A549 cells. Enhanced autophagy was detected in Bi2Se3-exposed cells under an 808 nm laser. Consistently, an elevated expression ratio of LC3-II to LC3-I, a marker of autophagy occurrence, was induced in Bi2Se3-exposed cells upon NIR irradiation. Meanwhile, the expression of cleaved-PARP was increased in the irradiated cells dependently on the exposure concentrations of Bi2Se3 nanoparticles. Pharmacological inhibition of autophagy by 3-methyladenine (3-MA) further strengthened the photothermal killing effect of Bi2Se3. Meanwhile, stress-related signaling pathways including p38 and SAPK/JNK were activated coupled with the attenuated PI3K/Akt signaling. Our study figures out that autophagy and the activation of stress-related signaling pathways were involved in the photothermal killing of cancerous cells by Bi2Se3, which provides a more understanding of photothermal nanomaterials.
REVIEW | doi:10.20944/preprints202008.0455.v1
Subject: Life Sciences, Molecular Biology Keywords: Hedgehog signaling pathway; GLI family; protein arginine methyl transferase; signal transduction
Online: 20 August 2020 (09:58:05 CEST)
The glioma-associated oncogene (GLI) family consists of GLI1, GLI2, and GLI3 in mammals, and is the effector in the Hedgehog signaling pathway. This family has important roles in the development and homeostasis of various tissues. To achieve these roles, the GLI family has widespread outputs. GLI activity is therefore strictly regulated at multiple levels, including via post-translational modifications for context-dependent GLI target gene expression. Conversely, dysregulated GLI activation has strong links with a variety of cancers. The protein arginine methyl transferase (PRMT) family is also associated with embryogenesis, homeostasis, and cancer via epigenetic modifications and signal transduction. In the PRMT family, PRMT1, PRMT5, and PRMT7 reportedly regulate GLI1 and GLI2 activity. PRMT1 methylates GLI1 to upregulate its activity and target gene expression. Cytoplasmic PRMT5 methylates GLI1 and is involved in GLI1 protein stabilization. In contrast, nucleic PRMT5 interacts with MENIN to suppress growth arrest-specific protein 1 expression, which assists Hedgehog ligand binding to Patched, indirectly resulting in downregulated GLI1 activity. PRMT7-mediated GLI2 methylation upregulates its activity through the dissociation of GLI2 and Suppressor of Fused. Therefore, PRMT1, PRMT5, and PRMT7 regulate GLI activity at multiple levels, and PRMT-mediated GLI dysregulation may be involved in cancer formation.
ARTICLE | doi:10.20944/preprints201909.0045.v1
Subject: Biology, Animal Sciences & Zoology Keywords: Prostate cancer, post-GWAS, functional variants, pathway analysis, upstream analysis, Oncomine
Online: 4 September 2019 (14:13:15 CEST)
Understanding the role of risk regions identified by genome-wide association studies (GWAS) have made considerable progress lately referred to the post-GWAS era. Annotation of the genes to the GWAS and fine-mapped functional variants, and understanding their biological pathway/gene networks enrichments is expected to give rich dividend by elucidating the mechanisms underlying prostate cancer. To this aim, we compiled and analysed currently available post-GWAS data on genes identified through GWAS and validated through experimental studies in prostate cancer to investigate molecular biological pathways enriched for assigned functional genes. The results highlight some well-known cancer signalling pathways, antigen presentation process and enrichment in cell growth and development gene networks suggesting prostate cancer may result from the accumulation of the effects of functional variants through multiple gene sets and pathways. The upstream analysis identifies critical transcription factors, which supplements the results regarding the regulatory role of the post-GWAS genes. We also identified the common genes between post-GWAS and three well-annotated prostate cancer Oncomine data in patient samples in order to uncover possible main genes in prostate cancer development/progression. Post-GWAS generated knowledge of gene networks and pathways, if analysed further and targeted appropriately, will have an important impact on clinical management of the disease.
ARTICLE | doi:10.20944/preprints201802.0013.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: pancreatic cancer; proteomics; PI3K pathway; precision medicine; predictor of therapeutic response
Online: 2 February 2018 (06:57:47 CET)
In metastatic pancreatic cancer patients non eligible to surgery, signal-targeted therapies so far failed to show a significant amelioration of survival. These therapeutic options were tested in Phase II/III clinical trials mostly in combination with the reference treatment Gemcitabine. These innovative therapies aim at annihilating the oncogene dependency; they also aim at renormalizing the tumoral stroma to allow immune cell function or re-vascularisation. Transcriptomics and genomics large scale analysis show the great heterogeneity of pancreatic cancers and failed to clearly delineate specific oncogene dependency besides oncogenic Kras. In this review, we will describe the most recent proteomic data in pancreatic tumors and its metastasis, which could help at identifying their major signalling dependencies, as well as explain why they are intrinsically resistant to signal-targeted therapies. We will also discuss why PI3K signalling, as a paradigm of pro-tumorigenic cell signalling and of tumoral adaptative resistance to drugs, is a relevant target in this context.
REVIEW | doi:10.20944/preprints201802.0011.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Pancreatic cancer, proteomics, PI3K pathway, precision medicine, predictor of therapeutic response
Online: 1 February 2018 (17:16:04 CET)
In metastatic pancreatic cancer patients non eligible to surgery, signal-targeted therapies so far failed to show a significant amelioration of survival. These therapeutic options were tested in Phase II/III clinical trials mostly in combination with the reference treatment Gemcitabine. These innovative therapies aim at annihilating the oncogene dependency; they also aim at renormalizing the tumoral stroma to allow immune cell function or re-vascularisation. Transcriptomics and genomics large scale analysis show the great heterogeneity of pancreatic cancers and failed to clearly delineate specific oncogene dependency besides oncogenic Kras. In this review, we will describe the most recent proteomic data in pancreatic tumors and its metastasis, which could help at identifying their major signalling dependencies, as well as explain why they are intrinsically resistant to signal-targeted therapies. We will also discuss why PI3K signalling, as a paradigm of pro-tumorigenic cell signalling and of tumoral adaptative resistance to drugs, is a relevant target in this context.
ARTICLE | doi:10.20944/preprints201706.0120.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: sinulariolide; human bladder cancer; migration; invasion; PI3K/AKT/mTOR signaling pathway
Online: 27 June 2017 (06:23:44 CEST)
Sinulariolide, a natural product extracted from cultured-type soft coral Sinularia flexibilis, possesses bioactivity against the movement of several types of cancer cell. However, the molecular pathway of its effects on human bladder cancer remain poorly understood. Using a human bladder cancer cell line as an in vitro model, this study investigated the underlying mechanism of sinulariolide against cell migration/invasion in TSGH-8301 cells. We found that sinulariolide inhibited TSGH-8301 cell migration/invasion, and the effect was concentration-dependent. Furthermore, the protein expressions of matrix metalloproteinases (MMPs) MMP-2 and MMP-9, as well as urokinase, were significantly decreased after 24-h sinulariolide treatment. Meanwhile, the increased expressions of tissue inhibitors of metalloproteinases (TIMPs) TIMP-1 and TIMP-2 were in parallel with an increased concentration of sinulariolide. Finally, the expressions of several key phosphorylated proteins in the mTOR signaling pathway were also downregulated by sinulariolide treatment. Our results demonstrated that sinulariolide has significant effects against TSGH-8301 cell migration/invasion, and its effects were associated with decreased levels of MMP-2/-9 and urokinase expression, as well as increased TIMP-1/TIMP-2 expression. The inhibitory effects were mediated by reducing phosphorylation proteins of the PI3K, AKT and mTOR signaling pathway. The findings suggested that sinulariolide is a good candidate for advanced investigation with the aim of developing a new drug for the treatment of human bladder cancer.
ARTICLE | doi:10.20944/preprints201609.0074.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: hepatocellular carcinoma; hepatitis B virus X protein; Notch1 pathway; ERK; AKT
Online: 21 September 2016 (09:49:13 CEST)
Hepatitis B virus (HBV) is the dominant risk factor for hepatocellular carcinoma (HCC). HBV X protein (HBx) plays crucial roles in HCC carcinogenesis. HBx interferes with several signaling pathways including Notch1 pathway in HCC. In our study, we found that Notch1 was highly expressed in HCC especially in large HCC. Notch1 and HBx co-localized in HCC and their levels were positively correlated with each other. Notch1 expression was more elevated in HepG2.2.15 than that in HepG2. HBx activated Notch1 pathway in HepG2.2.15. Repression of HBx and Notch1 pathway attenuated the growth of HepG2.2.15. Notch1, ERK and AKT pathways were inhibited after a γ-secretase inhibitor treatment. Dual-specificity phosphatase 1 (DUSP1) and phosphatase and tensin homolog (PTEN) were up-regulated after the γ-secretase inhibitor treatment and Hes1 inhibition. Luciferase reporter assays showed that Hes1 repressed the promoters of DUSP1 and PTEN and this was reverted by γ-secretase inhibitor treatment. Western blotting demonstrated that DUSP1 dephosphorylated pERK and PTEN dephosphorylated pAKT. Collectively, we reported a link among HBx, Notch1 pathway, DUSP1/PTEN, and ERK/AKT pathways, which influenced HCC cell survival and could be a therapeutic target for HCC.
ARTICLE | doi:10.20944/preprints202207.0378.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: FHB; plant metabolomic; plant-pathogen interaction; barley; wheat; Brachypodium distachyon; pathway enrichment
Online: 26 July 2022 (03:22:55 CEST)
Background: Fusarium head blight (FHB) is a serious fungal disease of crop plants due to substantial yield reduction and production of mycotoxins in the infected grains. The breeding progress in increasing resistance with maintaining a high yield is not possible without a thorough examination of the molecular basis of plant immunity responses; Methods: LC-MS based metabolomics approaches powered by three-way ANOVA and differentially accumulated metabolites (DAMs) selection, correlation network and functional enrichment were conducted on grains of resistant and susceptible to FHB genotypes of barley and wheat as well as model grass Brachypodium distachyon (Bd) still poorly known at metabolomic level; Results: We selected common and genotype-specific DAMs in response to F. culmorum inoculation. Immunological reaction at metabolomic level was strongly diversified between resistant and susceptible genotypes. DAMs common for all tested species from porphyrins, flavonoids and phenylpropanoids metabolic pathways were highly correlated and reflects conservativeness in FHB response in Poaceae family. Resistant related DAMs belonged to different structural classes including tryptophan derived metabolites, pirimidines, amino acids proline and serine as well as phenylpropanoids and flavonoids. Physiological response to F. culmorum of Bd was close to barley and wheat genotypes however, metabolomic changes were strongly diversified. Conclusions: Combined targeted and untargeted metabolomics provides comprehensive knowledge about significant elements of plant immunity with potential of being molecular biomarkers of enhance resistance to FHB in grass family. Thorough examination of Bd21 metabolome in juxtaposition with barley and wheat diversified genotypes facilitate their setting as model grass for plant-microbe interaction.
ARTICLE | doi:10.20944/preprints202207.0375.v1
Subject: Life Sciences, Virology Keywords: Enterovirus; vemurafenib; RAF; MAPK signaling pathway; genome replication; virus assembly; VP0 cleavage
Online: 25 July 2022 (12:25:13 CEST)
Enterovirus A71 (EV-A71) infection is a major cause of hand, foot and mouth disease (HFMD) which may be occasionally associated with severe neurological complications. There are currently a lack of treatment options for EV-A71 infection. The Raf-MEK-ERK signaling pathway, in addition to its critical importance in the regulation of cell growth, differentiation and survival, has been shown to be essential for virus replication. In this study, we investigated the anti-EV-A71 activity of vemurafenib, a clinically approved B-Raf inhibitor used in the treatment of late stage melanoma. Vemurafenib exhibits potent anti-EV-A71 effect in cytopathic effect inhibition and viral load reduction assays, with half maximal effective concentration (EC50) at nanomolar concentration. Mechanistically, vemurafenib interrupts both EV-A71 genome replication and assembly. These findings expand the list of potential antiviral candidates of anti-EV-A71 therapeutics.
ARTICLE | doi:10.20944/preprints202108.0019.v1
Subject: Medicine & Pharmacology, Allergology Keywords: leptin; JAK/STAT pathway; myocardial infarction; hemodynamics; arrhythmias; dyslipidaemia; inflammation; cardiac remodeling
Online: 2 August 2021 (11:24:57 CEST)
Hyperleptinemia potentiates the effects of many atherogenic factors, such as inflammation, platelet aggregation, migration, hypertrophy, proliferation of vascular smooth muscle cells, and endothelial cell dysfunction. The present study analysed the eﬀects of long-term hyperleptinemia in an in vivo myocardial ischemia-reperfusion model to demonstrate whether the in vivo deleterious effect also affects cardiac structure and function. Rats by were subcutaneously administered leptin for 8 days to estimate the involvement of the JAK/STAT pathway. Data from 58 male Wistar rats were included in the final analysis. Myocardial infarction (MI) was modelled by the 30-minute ligation of the main left coronary artery followed by 120-minute reperfusion. Hemodynamic measurements, electrocardiography monitoring, echocardiography, myocardial infarct size and area at risk, blood biochemical parameters, leptin, IL-6, TNF-alpha, FGF-21, and cardiomyocyte morphology were measured. Statistical analyses were performed using IBM SPSS Statistics v.26. Seven-day hyperleptinemia in rats led to increased an blood pressure and heart rate, myocardial hypertrophy, impaired LV function, an increased frequency of ischemic arrhythmias, dyslipidaemia, systemic inflammation, and an increased size of induced myocardial infarction. The blockade of the JAK/STAT signalling pathway effectively reversed the negative effects of leptin, including increased blood pressure and total cholesterol.
Subject: Physical Sciences, Acoustics Keywords: thermonuclear function; pathway model; reaction rate probability integral; H-function; Mellin transform
Online: 6 May 2021 (12:33:07 CEST)
The closed forms of the non-resonant thermonuclear function in the Maxwell-Boltzmann and Tsallis case with depleted tail are obtained in generalized special functions. The results are written in terms of H-function of two variables. The importance of the results in this paper lies in the fact that the reaction rate probability integrals in Maxwell-Boltzmann and Tsallis cases are not obtained by the conventional method of approximation or by means of a single variable transform technique but by means of a two variable transform method. The Behaviour of the depleted non-resonant thermonuclear functions are examined using graphs. The results in the paper are of much interest to astrophysicists and statisticians in their further work in this area.
ARTICLE | doi:10.20944/preprints202105.0064.v1
Subject: Life Sciences, Biochemistry Keywords: pancreas; tissue slices; beta cells; calcium imaging; amplifying pathway; forskolin; Epac2A KO
Online: 5 May 2021 (13:34:10 CEST)
Beta cells couple stimulation by glucose with insulin secretion and impairments in this coupling play a central role in diabetes mellitus. To clarify the effect of cAMP and the role of Epac2A in intracellular calcium signals and intercellular coupling, we performed functional multicellular calcium imaging in beta cells in mouse pancreas tissue slices after stimulation with glucose and forskolin in wild-type and Epac2A knock-out mice. Increased cAMP evoked calcium signals in otherwise sub-stimulatory glucose and beta cells from Epac2A knock-out mice displayed a faster activation. During the plateau phase, beta cells from Epac2A knock-out mice displayed a slightly higher active time in response to glucose compared with wild-type littermates, and increased cAMP increased the active time via a large increase in oscillation frequency and small decrease in oscillation duration in both Epac2A knock-out and wild-type mice. Functional network properties during stimulation with glucose did not differ in Epac2A knock-out mice, but the presence of Epac2A was crucial for the protective effect of increased cAMP in preventing a decline in beta cell functional connectivity with time. Finally, increased cAMP prolonged beta cell activity during deactivation in an Epac2A-independent manner.
ARTICLE | doi:10.20944/preprints202012.0496.v1
Subject: Life Sciences, Biochemistry Keywords: Hungateiclostridium thermocellum; adaptive laboratory evolution; RNA-seq; cellulosomal genes; EMP pathway; monosaccharides
Online: 21 December 2020 (10:36:00 CET)
Hungateiclostridium thermocellum ATCC 27405 is a promising bacterium with a robust ability to degrade lignocellulosic biomass complexes, including crystalline cellulose components, through a multienzyme cellulosomal system. In contrast, it exhibits poor growth on simple monosaccharides such as fructose and glucose. This phenomenon raises many important questions concerning its glycolytic pathways and sugar transport systems. Until now, the detailed mechanisms of H. thermocellum adaptation to growth on monosaccharides have been poorly explored. In this study, adaptive laboratory evolution was applied to train the bacterium on monosaccharides, and genome resequencing was used to detect the genes that had mutated during adaptation. RNA-seq data of the 1st-generation culture growing on either fructose or glucose revealed that several glycolytic genes in the EMP pathway were expressed at lower levels in these cells than in cellobiose-grown cells. After 8 generations of culture on fructose and glucose, the evolved H. thermocellum strains grew faster and yielded greater biomass than the nonadapted strains. Genomic screening also revealed several mutation events in the genomes of the evolved strains, especially in genes responsible for sugar transport and central carbon metabolism. Consequently, these genes could be applied as targets for further metabolic engineering to improve this bacterium for bioindustrial usage.
REVIEW | doi:10.20944/preprints202008.0369.v2
Subject: Life Sciences, Other Keywords: Extreme capsule; uncinate fasciculus; IFOF; ventral pathway of language; bottle neck; DTI
Online: 7 September 2020 (10:26:24 CEST)
On review of neuroscience literature extreme capsule considered as a whiter matter tract. Nevertheless it is not clear that extreme capsule itself is a association fiber pathway or is o bottleneck for passing other association fiber. By a systematic search with investigating anatomical position, dissection, connectivity and cognitive role of extreme capsule it can be argued that extreme capsule probably is a bottleneck for passing uncinated fasciculus (UF) and inferior fronto – occipital fasciculus(IFOF), And its different role of language processing is duo to different tract that passing it.
Subject: Medicine & Pharmacology, Ophthalmology Keywords: HLA; Uveitis; Birdshot; Antigen Presentation Pathway; Autoimmune Disease; Inflammation; ERAP1 and ERAP2
Online: 30 August 2020 (17:39:55 CEST)
HLA class I alleles constitute established risk factors for non-infectious uveitis and preemptive genotyping of HLA class I alleles is standard practice in the diagnostic work-up. The HLA-A29 serotype is indispensable to Birdshot Uveitis (BU) and renders this enigmatic eye condition a unique model to better understand how the antigen processing and presentation machinery contributes to non-infectious uveitis or chronic inflammatory conditions in general. This review will discuss salient points regarding the protein structure of HLA-A29 using and how key amino acid positions impact the peptide binding preference and interaction with T cells. We discuss to what extent the risk genes ERAP1 and ERAP2 uniquely affect HLA-A29 and how the discovery of a HLA-A29-specific submotif may impact autoantigen discovery. We further provide a compelling argument to solve the long-standing question why BU only affects HLA-A29-positive individuals from Western-European ancestry by exploiting data from the 1000 Genomes Project. We combine novel insights from structural and immunopeptidomic studies and discuss the functional implications of genetic associations across the HLA class I antigen presentation pathway to refine the etiological basis of Birdshot Uveitis.
Subject: Life Sciences, Biotechnology Keywords: pathway optimization; machine learning tools; enzyme activity prediction; promoter classification; expression tuning
Online: 26 August 2020 (04:05:47 CEST)
Successful engineering of a microbial host for efficient production of a target product from a given substrate can be viewed as an extensive optimization task. Such a task involves the selection of high activity enzymes as well as their gene expression regulatory control elements (i.e., promoters and ribosome binding sites). Finally, there is also the need to tune expression of multiple genes along a heterologous pathway to relieve constraints from rate-limiting step and help reduce metabolic burden on cells from unnecessary over-expression of high activity enzymes. While the aforementioned tasks could be performed through combinatorial experiments, such an approach incurs significant cost, time and effort, which is a handicap that can be relieved by application of modern machine learning tools. Such tools could attempt to predict high activity enzymes from sequence, but they are currently most usefully applied in classifying strong promoters from weaker ones as well as combinatorial tuning of expression of multiple genes. This perspective reviews the application of machine learning tools to aid metabolic pathway optimization through identifying challenges in metabolic engineering that could be overcome with the help of machine learning tools.
HYPOTHESIS | doi:10.20944/preprints202004.0171.v1
Subject: Life Sciences, Virology Keywords: Coronavirus; COVID-19 outbreak; SARS-CoV; ESCRT pathway; FGI-104 quinolone; chloroquine;
Online: 10 April 2020 (13:22:27 CEST)
Although phylogenetic analysis shows coronaviruses (CoV) share similar genome sequences, CoVs encode different number of proteins (5 to 14). The newly isolated viruses harbour more proteins than the old ones. Therefore, identifying the functional protein unites will benefits to understand the molecular interactions of the virus, and then identify molecular targets for antiviral drug. Here, the comparative in-silico analysis of 33 coronavirus proteomes show that coronaviruses harbour diverse number of protein functional motifs. Coronaviruses harbour wide-range of motifs including those involved in integrin-binding and ESCRT pathway before virus budding. For example, SARS-CoV-2, but not SARS-CoV-1, encodes PPxY motif, which is required for virus entry and budding of HIV, influenza and adenoviruses. The quinolone inulding the antiviral FGI-104 is able to block ESCRT pathway and viral budding and has been used against HIV, HCV and Ebola virus.
ARTICLE | doi:10.20944/preprints201910.0154.v1
Subject: Life Sciences, Genetics Keywords: papillary thyroid cancer; germline mutations; whole genome sequencing; predisposition markers; pathway analysis
Online: 13 October 2019 (17:07:34 CEST)
Evidence of familial inheritance in non-medullary thyroid cancer (NMTC) has accumulated over the last few decades. However, known variants account for a very small percentage of the genetic burden. Here, we focused on the identification of common pathways and networks enriched in NMTC families to better understand its pathogenesis with the final aim of identifying one novel high/moderate-penetrance germline predisposition variant segregating with the disease in each studied family. We performed whole genome sequencing on 23 affected and 3 unaffected family members from five NMTC-prone families and prioritized the identified variants using our Familial Cancer Variant Prioritization Pipeline (FCVPPv2). In total, 31 coding variants and 39 variants located in upstream, downstream, 5′ or 3′ untranslated regions passed FCVPPv2 filtering. Altogether, 210 genes affected by variants that passed the first three steps of the FCVPPv2 were analyzed using Ingenuity Pathway Analysis software. These genes were enriched in tumorigenic signaling pathways mediated by receptor tyrosine kinases and G-protein coupled receptors, implicating a central role of PI3K/AKT and MAPK/ERK signaling in familial NMTC. Our approach can facilitate the identification and functional validation of causal variants in each family as well as the screening and genetic counseling of other individuals at risk of developing NMTC.
ARTICLE | doi:10.20944/preprints201907.0018.v1
Subject: Medicine & Pharmacology, Dermatology Keywords: atopic dermatitis; AD; dermatology; target identification; pathway identification; bioinformatics; protein-protein networks
Online: 1 July 2019 (12:47:49 CEST)
The exploration and identification of targets and pathways for Atopic dermatitis (AD) treatment and diagnosis are critical for AD control. The conventional target exploration approach such as the literature review is not satisfying in terms of efficiency and accuracy. Recently, the bioinformatic approach is drawing attention for its unique advantage of high-volume data analysis for target and pathway exploration; Open Targets Platform is the targets source for this study to extract top 200 high-rank proteins from 3122 AD associated proteins. STRING, Cytoscape, CytoHubba, ClueGo, and CluePedia function had been applied for data analysis. The KEGG Mapper search & colour pathway was the pathway map resource for identified pathways; 23 key hub genes (VDR, KIT, BCL2L11, NFKBIA, KRAS, IL13, JAK2, STAT3, IL21, IL4R, REL, PDGFRB, FOXP3, RARA, RELB, EGFR, IL21R, MYC, CREBBP, NR3C1, IL2, JAK1, and KITLG). Additionally, 8 correlated pathways and the biological process had been identified; Through this study, a viable approach for target and pathway exploration had been presented. The identified AD targets and pathways will be tested for upcoming research for traditional Chinese medicinal herb interactions
ARTICLE | doi:10.20944/preprints201703.0237.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: valproic acid; doxorubicin; reactive oxygen species; autophagy; cell death; caveolae endocytosis pathway
Online: 31 March 2017 (12:08:53 CEST)
We evaluated the mono- and combination-therapy effects of valproic acid (VPA) and doxorubicin (DOX) in hepatocellular carcinoma (HCC) and identified a specific and efficient, synergistic anti-proliferative effect of the VPA and DOX combination in HCC cells, especially HepG2 cells; this effect was not apparent in MIHA cells, a normal hepatocyte cell line. The calculation of the coefficient of drug interaction confirmed the significant synergistic effect of the combination treatment. Concurrently, the synergistic apoptotic cell death caused by the VPA and DOX combination treatment was confirmed by Hoechst nuclear staining and western blot analysis of caspase-3 and poly (ADP-ribose) polymerase (PARP) activation. Co-treatment with VPA and DOX enhanced reactive oxygen species (ROS) generation and autophagy, which were clearly attenuated by ROS and autophagy inhibitors, respectively. Furthermore, as an indication of the mechanism underlying the synergistic effect, we observed that DOX internalization, which was induced in the VPA and DOX combination-treated group, occurred via by the caveolae-mediated endocytosis pathway. Taken together, our study uncovered the potential effect of the VPA and DOX combination treatment with regard to cell death, including induction of cellular ROS, autophagy, and the caveolae-mediated endocytosis pathway. Therefore, these results present novel implications in drug delivery research for the treatment of HCC.
ARTICLE | doi:10.20944/preprints202103.0336.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Myalgic Encephalomyelitis/chronic fatigue syndrome; Wnt pathway; inflammation; neuro-immune; oxidative stress; biomarkers
Online: 12 March 2021 (08:46:45 CET)
End-stage renal disease (ESRD) is associated with fatigue and physio-somatic symptoms. The aims of this study are to delineate the associations between severity of fatigue and physio-somatic symptoms and glomerular filtration rate, inflammatory biomarkers, and Wnt/catenin-pathway proteins. The Wnt-pathway related proteins β-catenin, Dickkopf-related protein 1 (DKK1), R-spondin-1, and sclerostin were measured by ELISA technique in 60 ESRD patients and 30 controls. The Fibromyalgia and Chronic Fatigue Syndrome (FF) Rating Scale was used to assess severity of FF symptoms. ESRD is characterized by a significant increase in the total FF score, muscle tension, fatigue, sadness, sleep disorders, GI symptoms, and a flu-like malaise. The total FF score was significantly correlated with serum levels of urea, creatinine, phosphate, and copper (positively), and β-catenin, eGFR, hemoglobin, albumin, and zinc (inversely). The total FF score was associated with the number of total dialysis and weekly dialysis sessions, and these dialysis characteristics were more important in predicting FF scores than eGFR measurements. Partial Least Squares analysis showed that the FF score comprised two factors which are differently associated with biomarkers: a) 43.0% of the variance in fatigue, GI symptoms, muscle tension, sadness, and insomnia is explained by hemoglobin, albumin, zinc, β-catenin, and R-spondin-1; and b) 22.3% of the variance in irritability, concentration and memory impairments by increased copper and cations/chloride ratio, and male sex. ESRD patients show high levels of fatigue and physio-somatic symptoms which are associated with hemodialysis and mediated by dialysis-induced changes in inflammatory pathways, the Wnt/catenin pathway, and copper.
ARTICLE | doi:10.20944/preprints202004.0016.v2
Subject: Life Sciences, Biochemistry Keywords: glaucoma; retina ganglion cell degeneration; microarray; genes coordination; notch signaling pathway; complement cascade
Online: 23 February 2021 (12:44:20 CET)
Glaucoma is a multifactorial neurodegenerative disease, characterized by degeneration of the retinal ganglion cells (RGCs). There has been little progress in developing efficient strategies for neuroprotection in glaucoma. We profiled the retina transcriptome of Lister Hooded rats at 2 weeks after optic nerve crush (ONC) and analyzed the data from the Genomic Fabric Paradigm (GFP) to bring additional insights into the molecular mechanisms of the retinal remodeling after induction of RGC degeneration. GFP considers for the expression of each gene 3 independent characteristics: level, variability and correlation with each other gene. Thus, the 17,657 quantified genes our study generated a total of 155,911,310 values to analyze. This represents 8,830x more data per condition than a traditional transcriptomic analysis. ONC led to a 57% reduction in RGC numbers as detected by retrograde labeling with DiI. We observed a higher Relative Expression Variability after ONC. Gene expression stability was used as a measure of transcription control and disclosed a robust reduction in the number of very stably expressed genes. Predicted Protein-Protein interaction (PPI) analysis with STRING revealed axon and neuron projection as mostly decreased processes, consistent with RGC degeneration. Conversely, immune response PPIs were found among up-regulated genes. Enrichment analysis showed that Complement Cascade and Notch Signaling Pathway, as well as Oxidative Stress and Kit Receptor Pathway were affected after ONC. To expand our studies of altered molecular pathways, we examined the pair-wise coordination of gene expressions within each pathway and within the entire transcriptome using Pearson correlations. ONC increased the number of synergistically coordinated pairs of genes and the number of similar profiles mainly in Complement Cascade and Notch Signaling Pathway. This deep bioinformatic study provides novel insights beyond the regulation of individual gene expression and discloses changes in the control of expression of Complement Cascade and Notch Signaling functional pathways that may be relevant for both RGC degeneration and remodeling of the retinal tissue after ONC.
ARTICLE | doi:10.20944/preprints202008.0322.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: TAP1; transcriptional expression; methylation analysis; survival analysis; co-expression; pathway analysis; health informatics
Online: 14 August 2020 (11:17:29 CEST)
Transporter associated with antigen processing 1 (TAP1) gene codes for a transporter protein, which is responsible for tumor antigen presentation in the MHC I or HLA complex. A defect in the gene results in an inadequate tumor tracking. TAP1 may also influence multi drug resistance, which is an extreme threat in providing treatment by drugs which are chemotherapeutic. The gene of TAP1 was analyzed bioinformatically. It gave us prognostic data as a confirmation of whether it should be used as a biomarker. The expression level and pattern analysis were conducted using ONCOMINE, GENT2 and GEPIA2 online platforms. Samples with different clinical outcomes were investigated for expression and promoter methylation analysis was done in cancer vs normal tissues using UALCAN. The copy number alteration and mutation frequency and expression in different cancer studies were analyzed using cBioPortal. The PrognoScan and KM plotter survival analysis of significant data (p-value<0.05) was representing graphically. Pathway and Gene ontology analysis of gene correlated to TAP1 gene was presented using bar charts. After arranging the data in a single panel and correlating expression to prognosis, understanding mutational and alterations and comparing pathways, TAP1 may be a potential novel target to evade a threat against chemotherapy and the study gives new aspects to consider for immunotherapy in human breast, lung, liver and ovarian cancer.
REVIEW | doi:10.20944/preprints201912.0165.v2
Subject: Medicine & Pharmacology, Nutrition Keywords: glucose; pentose phosphate pathway; NADPH; redox balance; glycogen; glycolysis; stress resistance; insulin resistance
Online: 30 January 2020 (12:49:19 CET)
A human organism depends on stable glucose blood levels in order to maintain the metabolic needs. Glucose is considered as the most important energy source and glycolysis is postulated as a backbone pathway. However, when glucose supply is limited, ketone bodies and amino acids can be used to produce enough ATP. In contrast, for the functioning of pentose phosphate pathway (PPP) glucose is essential and cannot be substituted by other metabolites. PPP generates and maintains levels of NADPH needed for reduction of oxidized glutathione and protein thiols, synthesis of lipids and DNA as well as for xenobiotic detoxification, regulatory redox signaling and counteracting infections. Flux of glucose into a PPP, particularly under extreme oxidative and toxic challenges is critical for survival, whereas the glycolytic pathway is primarily activated when glucose is abundant, and there is lack of NADP+ that is required for activation of glucose-6 phosphate dehydrogenase. An important role of glycogen stores in resistance to oxidative challenges is discussed. Current evidences explain disruptive metabolic effects and detrimental health consequences of chronic nutritional carbohydrate overload and provides new insights into positive metabolic effects of intermittent fasting, caloric restriction, exercise, and ketogenic diet through modulation of redox homeostasis.
ARTICLE | doi:10.20944/preprints201809.0525.v1
Subject: Life Sciences, Virology Keywords: hepatitis E virus; innate immunity; interferon response; JAK/STAT pathway; zoonosis; emerging pathogen
Online: 27 September 2018 (03:34:49 CEST)
Hepatitis E virus (HEV) is responsible for large waterborne epidemics of hepatitis in endemic countries and is an emerging zoonotic pathogen worldwide. In endemic regions, HEV-1 or HEV-2 genotypes are frequently associated with fulminant hepatitis in pregnant women, while with zoonotic HEV (HEV-3 and HEV-4), chronic cases of hepatitis and severe neurological disorders are reported. Hence, it is important to characterize the interactions between HEV and its host. Here, we investigated the ability of the non-structural polyprotein encoded by the first open reading frame (ORF1) of HEV to modulate the host early antiviral response and in particular the type I interferon (IFN-I) system. We found that the amino-terminal region of HEV-3 ORF1 (MetPCP), containing a putative methyltransferase (Met) and a papain-like cysteine protease (PCP) functional domain, inhibited IFN-stimulated response element (ISRE) promoter activation and the expression of several IFN-stimulated genes (ISGs) in response to IFN-I. We showed that the MetPCP domain interfered with the Janus kinase (JAK)/signal transducer and activator of transcription protein (STAT) signalling pathway by inhibiting STAT1 nuclear translocation and phosphorylation after IFN-I treatment. By contrast, MetPCP had no effect on STAT2 phosphorylation and a limited impact on the activation of the JAK/STAT pathway after IFN-II stimulation. This inhibitory function seemed to be genotype-dependent as MetPCP from HEV-1 had no significant effect on the JAK/STAT pathway. Overall, this study provides evidence that the predicted MetPCP domain of HEV ORF1 antagonises STAT1 activation to modulate the IFN response.
ARTICLE | doi:10.20944/preprints202001.0295.v1
Subject: Life Sciences, Virology Keywords: Hepatitis B virus; hepatocyte nuclear factor 4 alpha; long-term infection; ERK signaling pathway
Online: 25 January 2020 (15:25:57 CET)
Hepatitis B virus (HBV) infection is a major factor in development of various liver diseases such as hepatocellular carcinoma (HCC). Among HBV encoded proteins, HBV X protein (HBx) is known to play key role in development of HCC. Hepatocyte nuclear factor 4α (HNF4α) is a nuclear transcription factor which is critical for hepatocyte differentiation. However, the expression level as well as its regulatory mechanism in HBV infection have yet to be clarified. Here, we observed the suppression of HNF4α in cells which stably express HBV whole genome or HBx protein alone, while transient transfection of HBV replicon or HBx plasmid had no effect on the HNF4α level. Importantly, in the stable HBV- or HBx-expressing hepatocytes, the downregulated level of HNF4α was restored by inhibiting ERK signaling pathway. Our data showed that HNF4α was suppressed during long-term HBV infection in cultured HepG2-NTCP cells as well as in mouse model following hydrodynamic injection of pAAV-HBV or in mice intravenously infected with rAAV-HBV. Importantly, HNF4α downregulation increased cell proliferation which contributed to the formation and development of tumor in xenograft nude mice. The data presented here provided several proofs for the effect of HBV infection in manipulating HNF4α regulatory pathway in HCC development.
REVIEW | doi:10.20944/preprints201908.0271.v1
Subject: Life Sciences, Biophysics Keywords: GPCRs; membrane protein; molecular dynamics; protein structure; drug design; biased-signaling pathway; allosteric sites
Online: 26 August 2019 (15:34:57 CEST)
G protein-coupled receptors (GPCRs) are critical drug targets. GPCRs convey signals from the extracellular to the intracellular environment through G proteins. There is evidence that some ligands that bind to the GPCRs activate different downstream signaling pathways. G protein activation or -arrestin biased signaling involves ligands binding to receptors and stabilizing conformations that trigger a specific pathway. Molecular dynamics (MD) simulations are especially valuable for obtaining detailed mechanistic information, including identification of allosteric sites and understanding modulators' interactions between receptors and ligands. Here, we highlight recent simulation studies and methods used to study biased G protein-coupled receptor signaling and their conformational dynamics. We also highlight applications of MD simulations to drug discovery.
ARTICLE | doi:10.20944/preprints201809.0058.v1
Subject: Biology, Plant Sciences Keywords: Gossypium hirsutum L.; Adelphocoris suturalis (Jakovlev); alpha-linolenic acid pathway; tryptophan metabolism; plant defence
Online: 4 September 2018 (06:29:16 CEST)
Cotton (Gossypium hirsutum Linn.) is widely cultivated in China. The polyphagous insect Adelphocoris suturalis (Jakovlev) is a serious insect pest in cotton growing regions. Plants have evolved sophisticated systems to cope with herbivore attacks. However, the cotton defense mechanisms induced by A. suturalis feeding have lagged behind. We carried out untargeted proteomic analysis using the iTARQ technique and metabolomics based on LC-MS/MS analysis of cotton leaves fed upon by A. suturalis. Proteomic analysis identified 775 upregulated proteins and 477 downregulated proteins in plants that were infested by A. sututralis compared to the controls. Metabolomic analysis identified 50 differentially expressed metabolites in the positive ion mode and 14 in the negative ion mode compared to the controls. The tryptophan metabolism pathway was significantly changed in both the positive and negative ion mode in the metabolomics analysis. The alpha-linolenic acid pathway was significantly changed in both the proteomic and metabolomics analyses. Furthermore, the result was validated by RT-qPCR analysis of 5 related genes involved in alpha-linolenic acid pathway. These results indicate that tryptophan metabolism and the alpha-linolenic acid pathway may be important in cotton defense against herbivores and would enhance our understanding of plant defenses induced by A. sututrali feeding.
ARTICLE | doi:10.20944/preprints202108.0023.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Nicotine toxicity; Wnt1 pathway; spinal cord injury; locomotor networks; excitotoxicity; fictive locomotion; postnatal; rat; mice
Online: 2 August 2021 (11:52:54 CEST)
The postnatal rodent spinal cord in-vitro is a useful model to investigate early pathophysiological changes after injury. While low dose nicotine (1µM) induces neuroprotection, how higher doses affect spinal networks is unknown. Using spinal preparations of postnatal wild-type Wistar rat and Wnt1Cre2:Rosa26Tom double-transgenic mouse, we studied the effect of nicotine (0.5-10µM) on locomotor networks in-vitro. Nicotine 10µM induced motoneuron depolarization, suppressed monosynaptic reflexes, and decreased fictive locomotion in rat spinal cord. Delayed fall in neuronal numbers (including motoneurons) of central and ventral regions emerged without loss of dorsal neurons. Conversely, nicotine (0.5-1µM) preserved neurons throughout the spinal cord and strongly activated the Wnt1 signaling pathway. High-dose nicotine enhanced expression of S100 and GFAP in astrocytes suggesting their response to stress. Excitotoxicity induced by kainate was contrasted by nicotine (10µM) in the dorsal area and persisted in central and ventral regions with no change basal Wnt signaling. When combining nicotine with kainate, the activation of Wnt1 was reduced compared to kainate/sham. The present results suggest that high dose nicotine was neurotoxic to central and ventral spinal neurons as the neuroprotective role of Wnt signaling became attenuated. This also corroborates the risk of cigarette smoking for the foetus/newborn since tobacco contains nicotine.
REVIEW | doi:10.20944/preprints202011.0147.v1
Subject: Medicine & Pharmacology, Allergology Keywords: antineuronal autoantibodies; autoimmune diseases; autoimmune encephalitis; food antigens; kynurenine pathway; microbiota; prolactin; cytokines; schizophrenia; stress
Online: 3 November 2020 (12:53:38 CET)
The review analyzes a possible role of autoimmune processes in the pathogenesis of schizophrenia and evolution of concepts on this issue from its origin to present. Risks of autoimmune processes causing schizophrenia are associated with several factors: an impaired functioning of dopaminergic and glutamatergic systems in the brain, kynurenine pathway disorder with overproduction of quinolinic, anthranilic and kynurenic acids (possibly altering both neurons and T-regulators), increased intestinal permeability, as well as food antigens’ effects, stress and infections with various pathogens at different stages of ontogenesis. An increase in the levels of proinflammatory cytokines and chemokines as well as a decrease in the levels of anti-inflammatory ones also may contribute to schizophrenia risks. Schizophrenia often occurs in those patients having various autoimmune diseases and their first-degree relatives. Cases of schizophrenia resulted from autoimmune pathogenesis (including autoimmune encephalitis caused by autoantibodies against various neuronal antigens) are characterized by quite severe cognitive and psychotic symptoms and less favorable prognosis. This severe course may result from the chronic immune damage of the neuronal receptors such as NMDA, GABA, and others and depend on hyperprolactinemia, induced by antipsychotics, but aggravating autoimmune processes [with 2 tables, 4 figures, bibliography: 99 references].
ARTICLE | doi:10.20944/preprints202005.0389.v1
Subject: Life Sciences, Virology Keywords: Asian citrus psyllid; citrus greening bacterium; huanglongbing; transcriptomics; virus-vector relationship; vitellogenin; cytoskeleton; endocytotic pathway
Online: 24 May 2020 (17:03:45 CEST)
Citrus greening disease or huanglongbing (HLB) caused by Candidatus Liberibacter asiaticus (CLas) limits the citrus production worldwide. CLas is transmitted by the Asian citrus psyllid (ACP), Diaphorina citri (Hemiptera: Psyllidae) in a persistent-propagative manner. Application of insecticides to manage the psyllid vectors and disease is the most common practice. Understanding the molecular interaction between CLas and ACP and interrupting the interrelationship can provide an alternative to insecticides for managing citrus greening disease. Transcriptome analysis of ACP in response to CLas showed differential expression of 3911 genes (2196 up-regulated, and 1715 down-regulated) including the key genes of ACP involved in cytoskeleton synthesis and nutrition-related proteins. Majority of the differentially expressed genes were categorized under molecular function followed by cellular components and biological processes. KEGG pathway analysis showed differential regulation of carbohydrate, nucleotide and energy metabolic pathways, the endocytotic pathway and the defense-related pathways. Differential regulation of genes associated with the key pathways might favors CLas to become systemic and propagate in its insect vector. The study provides an understanding of genes involved in circulation of CLas in ACP. The candidate genes involved in key physiological processes and CLas transmission by ACP would be potential targets for sustainable management of ACP and CLas.
ARTICLE | doi:10.20944/preprints202002.0019.v1
Subject: Life Sciences, Endocrinology & Metabolomics Keywords: metabolomics; LC-MS; mass spectrometry; metabolic profiling; computational; statistical; unsupervised learning; supervised learning; pathway analysis
Online: 3 February 2020 (05:54:14 CET)
Metabolomics analysis generates vast arrays of data, necessitating comprehensive workflows involving expertise in analytics, biochemistry and bioinformatics, in order to provide coherent and high-quality data that enables discovery of robust and biologically significant metabolic findings. In this protocol article, we introduce NoTaMe, an analytical workflow for non-targeted metabolic profiling approaches utilizing liquid chromatography–mass spectrometry analysis. We provide an overview of lab protocols and statistical methods that we commonly practice for the analysis of nutritional metabolomics data. The paper is divided into three main sections: the first and second sections introducing the background and the study designs available for metabolomics research, and the third section describing in detail the steps of the main methods and protocols used to produce, preprocess and statistically analyze metabolomics data, and finally to identify and interpret the compounds that have emerged as interesting.
ARTICLE | doi:10.20944/preprints201912.0092.v2
Subject: Earth Sciences, Environmental Sciences Keywords: climate change; warming levels; river runoff; extremes; emission pathway; LISFLOOD; Europe; PESETA project; climate adaptation
Online: 16 January 2020 (02:56:30 CET)
The outcomes of the 2015 Paris Agreement triggered a number of climate impact assessments, such as for floods and droughts, to focus on future time frames corresponding to the years of reaching specific levels of global warming. Yet, the links between the timing of the warming levels and the corresponding greenhouse gas concentration pathways to reach them, remain poorly understood. To address this gap, we compare projected changes of annual mean, extreme high and extreme low river discharges in Europe at 1.5°C and 2°C under scenarios RCP8.5 and RCP4.5 from an ensemble of Regional Climate Model (RCM) simulations. The statistical significance of the difference between the two scenarios for both warming levels is then evaluated. Results show that in the majority of Europe (>95% of the surface area for the annual mean discharge, >98% for high and low extremes), the changes projected in the two pathways are statistically indistinguishable. These results suggest that in studies of changes at specific warming levels the projections of the two pathways can be merged into a single ensemble without major loss of information. With regard to the uncertainty of the unified ensemble, findings show that the projected changes of annual mean, extreme high and extreme low river discharge are statistically significant in large portions of Europe.
HYPOTHESIS | doi:10.20944/preprints201908.0087.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: Hox genes; collinearity; segmental identity; chromatin modifications; vertebral malformations; vertebrae; Hox synteny; somitogenesis; Notch pathway
Online: 7 August 2019 (03:51:41 CEST)
It is not understood how the numbers and identities of vertebrae are controlled during mammalian development. The remarkable robustness and conservation of segmental numbers may suggest a digital nature of the underlying process. Here I propose a mechanism that allows cells to obtain and store the segmental information in digital form, and to produce a pattern of chromatin accessibility that in turn regulates Hox gene expression specific to the metameric segment. The model requires that a regulatory element be present such that the number of occurrences of the motif between two consecutive Hox genes equals the number of segments under the control of the anterior gene. This is true for the recently discovered HRC3 motif, associated with histone modifications and developmental genes. The finding not only allows correctly predicting the numbers of segments using only sequence information, but also resolves the 40-year-old enigma of the function of temporal and spatial collinearity of Hox genes. The logic of the mechanism is illustrated in an animated video: https://youtu.be/4a3XOQ7Lz28. I also discuss how different aspects of the proposed mechanism can be tested experimentally.
ARTICLE | doi:10.20944/preprints201803.0219.v1
Subject: Medicine & Pharmacology, Ophthalmology Keywords: pigmentary glaucoma; pigment dispersion; intraocular pressure; trabecular meshwork; cytoskeleton; phagocytosis; gene expression microarray; signal pathway
Online: 27 March 2018 (05:22:15 CEST)
Pigment dispersion can lead to pigmentary glaucoma, a poorly understood condition of younger myopic eyes with fluctuating high intraocular pressure. It has been difficult to investigate its pathogenesis without a model similar to human eyes in size and behavior. Here we present a porcine ex vivo model that recreates several features of pigmentary glaucoma, including intraocular hypertension, accumulation of pigment in the trabecular meshwork, and declining phagocytosis. We found that trabecular meshwork cells regulate outflow, form actin stress fibers, and have a decreased phagocytic activity. Gene expression microarrays and a pathway analysis of TM monolayers as well as ex vivo anterior segment perfusion cultures indicated that RhoA plays a central role in regulating the cytoskeleton, motility, and phagocytosis in the trabecular meshwork, providing new insights and targets to investigate in pigmentary glaucoma.
ARTICLE | doi:10.20944/preprints202108.0506.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: NF-kB; non-canonical NF-κB pathway; sTNFR2; sTNFSF8; sTNFSF13; mitochondrial dynamics; fission and fusion; TFAM
Online: 26 August 2021 (11:46:14 CEST)
Interactions between receptors and ligands of the tumor necrosis factor superfamily (TNFSF) provide costimulatory signals that control the survival, proliferation, differentiation, and effector function of immune cells. All components of the TNF superfamily are associated with NF-kB functions that are not limited to cell death and may promote survival in the face of adipose tissue inflammation in obesity. Inflammation and pro-inflammatory dysfunction of mitochondria are key factors associated with insulin resistance in obesity. The aim of the study was to analyze the relationship of soluble forms of receptors and ligands of the TNF superfam-ily in blood plasma with mitochondrial dynamics in adipose tissue (greater omentum (GO) and subcutaneous adipose tissue (Sat)) of obese patients with and without type 2 diabetes mellitus (T2DM). Increased plasma sTNF-R1, sTNF-R2, sTNFRSF8 receptors and ligands TNFSF12, TNFSF13, TNFSF13B are characteristic of obese patients without T2DM. Increases in TNFSF12, TNFSF13B, and sTNF-R1 levels are associated with decreased glucose concentration and decreased BMI in obese patients. The gene expression levels responsible for regulating mitochondrial dynamics were increased in obese patients without T2DM and were unbalanced in patients with obesity and T2DM.
ARTICLE | doi:10.20944/preprints201907.0051.v1
Subject: Life Sciences, Genetics Keywords: lung cancer; molecular signature; molecular pathway; differentially expressed genes; protein-protein interaction; reporter biomolecules and bioinformatics
Online: 3 July 2019 (08:54:37 CEST)
Lung cancer is one of the most important health risks worldwide for human. Non-small cell lung cancer (NSCLC) is the most common cause of premature death from malignant disease. This study provides in-depth insights from systems biology analyses to identify molecular to inform systemic drug targeting in NSCLC. Gene expression profiles from non small cell lung cancer were analyzed with genome-scale biomolecular networks (I,e., protein-protein interaction, transcriptional and post transcriptional regulatory networks). The aim of the study was to determine the pathways and expression profile of the genes to discover molecular signature at RNA and protein levels which could serve as potential drug targets for therapeutics innovation and the identification of novel targets. Eight proteins, six TFs and seven miRNAs came into prominence as potential drug targets. The differential expression profiles of these reporter biomolecules were cross-validated by independent RNA-Seq and miRNA-Seq. Risk discrimination performance of the reporter biomolecules NPR3, JUN, PPARG, TP53, CKMT1A, SP3 and TFAP2A were also evaluated. Total 213 drugs and 7 proteins were found for non small cell lung cancer through dgidb. Among these identified drugs seven drugs such as- Gemcitabine, Carboplatin, paclitaxel, Docetaxel, Crizotinib, Bevacizumab and Gemcitabine is used for NSCLC which is approved by National Cancer Institute. The molecular signatures and repurposed drugs presented here permit further attention for experimental studies which are offer significant potential as biomarkers and candidate therapeutics for precision medicine approaches to clinical management of NSCLC.
ARTICLE | doi:10.20944/preprints201804.0007.v1
Subject: Medicine & Pharmacology, Ophthalmology Keywords: pigment dispersion syndrome; pigmentary glaucoma; trabecular meshwork; phagocytosis; migration; contraction; cytoskeleton; gene microarray; Rho signaling pathway
Online: 2 April 2018 (07:00:45 CEST)
Purpose: To investigate the effect of pigment dispersion on trabecular meshwork (TM) cells. Methods: Porcine TM cells from ab interno trabeculectomy specimens were exposed to pigment dispersion, then analyzed for changes in morphology, immunostaining, and ultrastructure. Their abilities to phagocytose, migrate, and contract were quantified. An expression microarray, using 23,937 probes, and a pathway analysis were performed. Results: TM cells readily phagocytosed pigment granules. Pigment induced stress fiber formation (pigment (P): 60.1 ± 0.3%, n = 10, control (C): 38.4 ± 2.5%, n = 11, P < 0.001) and contraction at 24 hours onward (P < 0.01). Phagocytosis declined (P: 68.7 ± 1.3%, C: 37.0 ± 1.1%, n = 3, P < 0.001) and migration was reduced after 6 hours (P: 28.0.1 ± 2.3, n = 12, C: 40.6 ± 3.3, n = 13, P < 0.01). Microarray analysis revealed that Rho, IGF-1, and TGFβ signaling cascades were central to these responses. Conclusions: TM cell exposure to pigment dispersion resulted in reduced phagocytosis and migration, as well as increased stress fiber formation and cell contraction. The Rho signaling pathway played a central and early role, suggesting that its inhibitors could be used as a specific intervention in treatment of pigmentary glaucoma.
REVIEW | doi:10.20944/preprints202110.0447.v1
Subject: Life Sciences, Biochemistry Keywords: UPR; IRE1; PERK; ATF6; lipid bilayer stress; ER stress; secretory pathway; hydrophobic mismatch; membrane thickness; membrane stiffness
Online: 29 October 2021 (07:57:29 CEST)
The endoplasmic reticulum (ER) is the major site of membrane biogenesis in most eukaryotic cells. As the entry point to the secretory pathway, it handles more than 10.000 different secretory and membrane proteins. The membrane insertion of proteins, their folding, and ER exit are affected by the lipid composition of the ER membrane and its collective membrane stiffness. The ER is also a hotspot of lipid metabolism for membrane lipids including sterols, glycerophospholipids, ceramides and neural storage lipids. The unfolded protein response (UPR) bears an evolutionary conserved, dual sensitivity to both protein folding-imbalances in the ER lumen and aberrant compositions of the ER membrane, referred to as lipid bilayer stress (LBS). Through transcriptional and non-transcriptional mechanisms, the UPR upregulates the protein folding capacity of the ER and balances the production of proteins and lipids to maintain a functional secretory pathway. In this review, we discuss how UPR transducers sense unfolded proteins and LBS with a particular focus on their role as guardians of the secretory pathway.
COMMUNICATION | doi:10.20944/preprints202104.0291.v1
Subject: Biology, Anatomy & Morphology Keywords: phosphorelay; high osmolarity glycerol (HOG) pathway; alternative splicing; signaling; histidine kinases; Magnaporthe oryzae; YPD1; phosphotransfer; signal transduction
Online: 12 April 2021 (12:34:48 CEST)
Different external stimuli are perceived by multiple sensor histidine kinases and transmitted by phosphorylation via the phosphotransfer protein Ypd1p in the multistep phosphorelay system of the high osmolarity glycerol signaling pathway of filamentous fungi. How the signal propagation takes place is still not known in detail, since multiple sensor histidine kinase genes in most filamentous fungi are coded in the genome, whereas only one gene for Ypd1 exists. That raises the hypothesis that various Ypd1 isoforms are produced from a single gene sequence, perhaps by alternative splicing, facilitating a higher variability in signal transduction. We found that the mRNA of MoYPD1 in the rice blast fungus Magnaporthe oryzae is subjected to an increased structural variation and amplified putative isoforms on a cDNA level. We then generated mutant strains overexpressing these isoforms, purified the products and present here one previously unknown MoYpd1 isoform on a proteome level. Alternative splicing was found to be a valid molecular mechanism to increase the signal diversity in eukaryotic multistep phosphorelay systems.
ARTICLE | doi:10.20944/preprints202103.0242.v1
Subject: Life Sciences, Biochemistry Keywords: apoptosis; evading apoptosis; expression variability; cancer functional pathway; prostate cancer phenotype; immortality; proliferation; P53 signaling; transcriptomic network
Online: 9 March 2021 (08:44:15 CET)
Prostate cancer is a leading cause of death among men but its genomic characterization and best therapeutic strategy are still under debate. The Genomic Fabric Paradigm (GFP) considers the transcriptome as a multi-dimensional mathematical object subjected to a dynamic set of expression correlations among the genes. Here, GFP is applied to gene expression profiles of three (one primary, and two secondary) cancer nodules and the surrounding normal tissue from a surgically removed prostate tumor. GFP was used to determine the regulation and rewiring of the P53 signaling, apoptosis, prostate cancer and several other pathways involved in survival and proliferation of the cancer cells. Genes responsible for the block of differentiation, evading apoptosis, immortality, insensitivity to anti-growth signals, proliferation, resistance to chemotherapy and sustained angiogenesis were found as differently regulated in the three cancer nodules with respect to the normal tissue. The analysis indicates that even histo-pathologically equally graded cancer nodules from the same tumor have substantially different transcriptomic organizations, raising legitimate questions about the validity of meta-analyses comparing large populations of healthy and cancer humans. The study suggests that GFP may provide a personalized alternative to the biomarkers’ approach of cancer genomics.
ARTICLE | doi:10.20944/preprints202008.0112.v1
Subject: Chemistry, Medicinal Chemistry Keywords: AKT/PI3K signaling pathway; apoptosis; human hepatocarcinoma HepG2 cells; migration activity; proliferation; oxidative stress; ROS level; uvaol
Online: 5 August 2020 (05:58:26 CEST)
Natural products have a significant role in the development of new drugs, being relevant the pentacyclic triterpenes extracted from Olea europaea. Anticancer effect of uvaol, a natural triterpene, has been scarcely studied. The aim of this study was to understand the anticancer mechanism of uvaol in HepG2 cell line. Cytotoxicity results showed a selectivity effect of uvaol with higher influence in HepG2 than WRL68 cells used as control. Uvaol presented anti-migratory capacity in HepG2, supported by the morphological changes and higher HSP-60 expression. This compound also induced arrest in G0/G1 phase and an increase in apoptosis rate. These results are supported by decreased Bcl-2 expression and down-regulation of AKT/PI3K signaling pathway. A reduction in reactive oxygen species levels in HepG2 cells was observed. Altogether, results showed anti-proliferative and pro-apoptotic effect of uvaol on hepatocellular carcinoma, constituting an interesting challenge in the development of new treatments against this type of cancer.
ARTICLE | doi:10.20944/preprints202004.0108.v1
Subject: Medicine & Pharmacology, Nutrition Keywords: prebiotics; oligosaccharides; GOS; FOS; RNA-seq; transcriptome; differential gene expression; functional pathway analysis; Caco-2; polarized monolayers
Online: 7 April 2020 (13:37:18 CEST)
Prebiotic oligosaccharides are widely used as human and animal feed additives for their beneficial effects on the gut microbiota. However, there are limited data to assess the direct effect of such functional foods on the transcriptome of intestinal epithelial cells. The purpose of this study is to describe the differential transcriptomes and cellular pathways of colonic cells directly exposed to galacto-oligosaccharides (GOS) and fructo-oligosaccharides (FOS). We have examined the differential gene expression of polarized Caco-2 cells treated with GOS or FOS and their respective mock-treated cells using mRNA sequencing (RNA-seq). A total of 89 significant differentially expressed genes were identified between GOS and mock-treated groups. For FOS treatment, a reduced number of 12 significant genes were observed to be differentially expressed relative to the control group. KEGG and Gene Ontology functional analysis revealed that genes up-regulated in the presence of GOS were involved in digestion and absorption processes, fatty acids and steroids metabolism, potential antimicrobial proteins, energy-dependent and -independent transmembrane trafficking of solutes and amino acids. Using our data, we have established complementary non-prebiotic modes of action for these frequently used dietary fibers.
ARTICLE | doi:10.20944/preprints201904.0254.v3
Subject: Life Sciences, Molecular Biology Keywords: Microprocessor, miRNA, Drosha, Pasha, miRNA biogenesis pathway, Holozoa, Metazoa, RNA interference, bona fide miRNA, canonical eumetazoan miRNA
Online: 23 September 2019 (10:16:40 CEST)
It is standard to identify and compare predicted protein sequence of the Drosha and Pasha genes subsidiary to detection and identification of novel microRNAs in newly sequenced taxa or review of previous deep sequencing data. Drosha and Pasha proteins are the key, conserved members of the ‘microprocessor’ protein complex which facilitates nuclear nuclear localized, pri to pre miRNA processing miRNAs of the canonical eumetazoan complement. Because of the necessity of the microprocessor for production of c anonical eumetazoan miRNA, the detection of both (1) bona fide microRNAs and (2) presence of Drosha/Pasha orthologs (or homologs) is often presented as sufficient to represent a functional canonical eumetazoan microRNA biogenesis pathway. However, the fun ctional role of the Drosha and Pasha homologs sometimes, though not always experimentally validated in non model taxa. Differentiation of ‘bona fide miRNAs’, opposed to ‘non bona fide’ small RNAs of similar size, are also necessary for miRNA identificatio n projects. Recent rubrics are based on structural and sequence elements of the miRNAs themselves, however these inclusion criteria include paraphyletic groupings of miRNAs, for example eumetazoan miRNAs and S treptophyte (green plant) miRNAs which are not produced by the Drosha/Pasha microprocessor mechanism. Therefore, a dichotomy exists between the structural definitions for miRNAs and understanding of the evolutionarily conserved function of the microprocessor and its components. In this article, I re view literature in the context of this topic and discuss philosophical significance for understanding the importance of the microprocessor in understanding the evolutionary and molecular origins of miRNA.
ARTICLE | doi:10.20944/preprints201811.0321.v1
Subject: Medicine & Pharmacology, Nutrition Keywords: Theaflavins; Hepatocyte; Insulin resistance; Insulin signaling pathway; Mitochondrial biogenesis; Peroxisome proliferator-activated receptor coactivator-1 (PGC-1)
Online: 13 November 2018 (15:16:30 CET)
Theaflavins, the characteristic and bioactive polyphenols in black tea, possess the potential improvement effects on insulin resistance-associated metabolic abnormalities including obesity and type 2 diebetes. However, the molecular mechanisms of theaflavins improving insulin sensitivity are still not clear. In this study, we investigated the protective effects and mechanisms of theaflavins on palmitic acid-induced insulin resistance in HepG2 cells. Theaflavins could significantly increase glucose uptake of insulin-resistant cells at noncytotoxic doses. This activity was mediated by upregulating the glucose transporter 4 protein expression, increasing the phosphorylation of IRS-1 at Ser307, and reduced the phosphor-Akt (Ser473) level. Moreover, theaflavins were found to enhance mitochondrial DNA copy number through down-regulate the PGC-1β mRNA level and up-regulate PRC mRNA expression in insulin-resistant HepG2 cells. These results indicated that theaflavins could improve free fatty acid-induced hepatic insulin resistance by promoting mitochondrial biogenesis, and were promising functional food and medicines for insulin resistance-related disorders.
ARTICLE | doi:10.20944/preprints201709.0119.v1
Subject: Life Sciences, Molecular Biology Keywords: lentinula edodes; Lp16-PSP; acute promyeloid leukemia; extrinsic and lntrinsic apoptotic pathway; G1 phase cell cycle arrest
Online: 25 September 2017 (08:53:12 CEST)
Lp16-PSP from Lentinula edodes strain C91-3 has been reported previously in our laboratory to have selective cytotoxic activity against a panel of human cell lines. Herein, we have used several parameters in order to characterize the Lp16-PSP-induced cell death using HL-60 as model cancer. The results of phase contrast microscopy, nuclear examination, DNA fragmentation detection and flow cytometry revealed that high doses of Lp16-PSP resulted in the induction of apoptosis in HL-60 cells. The colorimetric assay showed the activation of caspase-8, -9 and -3 cascade highlighting the involvement of Fas/FasL-related pathway. Whereas, western blot revealed the cleavage of caspase-3, increased expression of Bax, the release of cytochrome c and decreased expression of Bcl-2 in a dose-dependent manner, suggesting the intrinsic pathway might be involved in Lp16-PSP-induced apoptosis either. Low doses of Lp16-PSP resulted in the anchorage-independent growth inhibition, induction of G1 phase arrest accompanied by the increased expression of p21WAF1/CIP1 along with the decreased expression of cyclin D, E, and cdk6. Our findings suggest that induction of apoptosis and p21WAF1/CIP1 mediated G1 arrest might be one of the mechanisms of the action of Lp16-PSP, however, further investigations on multiple leukemia cell lines and in vivo models are of ultimate need.
REVIEW | doi:10.20944/preprints202004.0540.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: cholinergic anti-inflammatory pathway; novel coronavirus; SARS-CoV-2; COVID-19; meta-analysis; Cytokine Release Syndrome; nicotine; smokers
Online: 30 April 2020 (17:01:38 CEST)
SARS-CoV-2 is a new coronavirus that has caused a worldwide pandemic. It produces severe acute respiratory disease (COVID-19), which is fatal in many cases, characterised by cytokine release syndrome (CRS). According to the World Health Organization (WHO), those who smoke are likely to be more vulnerable to infection. Here, in order to clarify the epidemiologic relationship between smoking and COVID-19, we present a systematic literature review until 28 April 2020 and a meta-analysis. It includes 18 recent COVID-19 clinical and epidemiological studies based on smoking patient status from 720 initial studies in China, USA, and Italy. The percentage of hospitalised current smokers was 7.7% (95%CI: 6.9-8.4) in China, 2.3% (95%CI: 1.7-2.9) in the USA and 7.6% (95%CI: 4.2-11.0) in Italy. These percentages were compared to the smoking prevalence of each country and statistically significant differences were found in them all (p <0.0001). By means of the meta-analysis, we offer epidemiological evidence showing that smokers were statistically less likely to be hospitalised (OR=0.18, 95%CI: 0.14-0.23, p<0.01). CRS and exacerbated inflammatory response are associated with aggravation of hospitalise patients. In this scenario, we hypothesise that nicotine, not smoking, could ameliorate the cytokine storm and severe related inflammatory response through the cholinergic-mediated anti-inflammatory pathway.
ARTICLE | doi:10.20944/preprints201910.0333.v1
Subject: Engineering, Biomedical & Chemical Engineering Keywords: metabolic engineering; lycopene; MEP pathway; 1-deoxy-D-xylulose-5-phosphate synthase; farnesyl diphosphate synthase; Vibrio sp. dhg
Online: 29 October 2019 (10:40:18 CET)
Microbial production is a promising method that can overcome major limitations in conventional methods of lycopene production, such as low yields and variations in product quality. Significant efforts have been made to improve lycopene production by engineering either the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway or mevalonate (MVA) pathway in microorganisms. To further improve lycopene production, it is critical to utilize metabolic enzymes with high specific activities. Two enzymes, 1-deoxy-D-xylulose-5-phosphate synthase (Dxs) and farnesyl diphosphate synthase (IspA), are required in lycopene production using MEP pathway. Here, we evaluated the activities of Dxs and IspA of Vibrio sp. dhg, a newly isolated and fast-growing microorganism. Considering that the MEP pathway is closely related to the cell membrane and electron transport chain, the activities of the two enzymes of Vibrio sp. dhg were expected to be higher than the enzymes of E. coli. We found that Dxs and IspA in Vibrio sp. dhg exhibited 1.08-fold and 1.38-fold higher catalytic efficiencies, respectively. Consequently, the heterologous overexpression improved the specific lycopene production by 1.88-fold. Our findings could be widely utilized to enhance production of lycopene and other carotenoids.
ARTICLE | doi:10.20944/preprints201907.0140.v1
Subject: Life Sciences, Molecular Biology Keywords: PlGF; PGF; blood-retinal barrier; RNA Seq; HREC; gene ontology; fastQC; Trimmomatic; KEGG; pentose phosphate pathway; TGF-β
Online: 10 July 2019 (07:48:20 CEST)
Placental growth factor (PlGF or PGF) is a member of the VEGF family, which is known to play a critical role in pathological angiogenesis, inflammation, and endothelial cell barrier function. However, the molecular mechanisms by which PlGF mediates its effects in non-proliferative diabetic retinopathy (DR) remain elusive. In this study, we performed transcriptome-wide profiling of differential gene expression for human retinal endothelial cells (HRECs) treated with PlGF antibody. The effect of antibody treatment on the samples was validated using trans-endothelial electric resistance (TEER), and western blot. A total of 3760 genes (1750 upregulated and 2010 downregulated) were found to be differentially expressed between the control and PlGF antibody treatment group. These differentially expressed genes (DEGs) were used for gene ontology and enrichment analysis to identify gene function, signal pathway, and interaction networks. The gene ontology results revealed that catalytic activity (GO:0003824) of molecular function, cell (GO:0005623) of the cellular component, and cellular process (GO:0009987) were among the most enriched biological processes. Pathways such as TGF-β, VEGF-VEGFR2, p53, apoptosis, pentose phosphate pathway, and ubiquitin-proteasome pathway, were among the most enriched, and TGF-β1 was identified as a primary upstream regulator. These data provide new insights into the underlying molecular mechanisms of PlGF in mediating biological functions, in relation to DR.
REVIEW | doi:10.20944/preprints201711.0015.v1
Subject: Biology, Plant Sciences Keywords: RGSV; movement proteins; gene silencing; transgenic mechanism; virus-induced small interfering RNA; RNA silencing pathway; antiviral plant defenses
Online: 2 November 2017 (03:05:04 CET)
Rice grassy stunt virus (RGSV) a member of Tenuivirus family, is very potent and destructive which effects rice crop in many countries, particularly China. Non coding RNAs have important functions in development and epigenetic regulation of gene expression in numerous organsisms. There is three type of small non coding RNAs have been found in eukaryotes, which are small interferring RNAs (siRNAs), microRNAs (miRNAs) and piwi interacting RNAs (piRNAs). Small RNAs (sRNAs) origination is from the infecting virus which is known as virus-derived small interfering RNAs (vsiRNAs), has responsibility for RNA silencing in plants. Virus-induced gene silencing (VIGS) is mainly dependent on RNA silencing (RNAi). Interestingly, RNA silencing happens in plants during viral infections. RNAi technique showed significant results in Nephotettix cincticeps. RNAi technique demonstrated the gene silencing of planthopper Nilaparvata lugens. The proteins P5, pcf4, Dnj, psn5, and pn6 act as potential movement proteins and serve as silencing suppressors for RGSV. VsiRNAs originate from dsRNA molecules which require Dicer-like (DCL) proteins, RNA dependent RNA polymerase (RdRP) proteins, and Argonaute (AGO) proteins. RdRP uses ssRNA for perfect RNA amplification process and can also be used for DCL dependent secondary vsiRNA formation. VSRs interfere with the movement of signals during silencing mechanism. Moreover, intercellular movement of viruses is facilitated by virus-encoded movement protein. RNAi is found in many eukaryotes which are related to transcriptional or post-transcriptional regulation by gene suppression. Transcription is bidirectional in ssDNA viruses which are originated from dsRNA molecules. In this review, we highlighted the biology of Rice grassy stunt virus and its insect vector and its silencing suppressors. This work will be helpful for plant virologists to understand the whole biogenesis mechanism for rice viruses especially RGSV.
ARTICLE | doi:10.20944/preprints201612.0042.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: acute lung injury; mycelium of Sanghuangporus sanghuang; lipopolysaccharide; KAP1/Nrf2 pathway; PI3K/Akt/mTOR pathways; HO-1; HNGB1
Online: 7 December 2016 (11:15:30 CET)
Acute lung injury (ALI) is characterized by inflammation of the lung tissue and oxidative injury caused by excessive accumulation of reactive oxygen species. Studies have suggested that anti-inflammatory or antioxidant agents could be used for the treatment of ALI with a good outcome. Therefore, our study aimed to test whether the mycelium extract of Sanghuangporus sanghuang (SS-1), believed to exhibit antioxidant and anti-inflammatory properties, could be used against the excessive inflammatory response associated with LPS-induced ALI in mice and to investigate its possible mechanism of action. The experimental results showed that the administration of SS-1 could inhibit LPS-induced inflammation. SS-1 could reduce the number of inflammatory cells, inhibit MPO activity, regulate the TLR4/PI3K/Akt/mTOR pathway and the signal transduction of NF-κB and MAPK pathways in the lung tissue, and inhibit HNGB1 activity in BALF. In addition, SS-1 could affect the synthesis of antioxidant enzymes HO-1 and Trx-1 in the lung tissue and regulate signal transduction in the KAP1/Nrf2/Keap1 pathway. Histological results showed that administration of SS-1 prior to induction could inhibit the large-scale LPS-induced neutrophil infiltration of the lung tissue. Therefore, based on all experimental results, we propose that SS-1 exhibits a protective effect against LPS-induced (ALI) in mice. The mycelium of S. sanghuang can potentially be used for the treatment or prevention of inflammation-related diseases
ARTICLE | doi:10.20944/preprints201609.0001.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: protein-disulfide isomerase-associated 3; osteoarthritis; extracorporeal shockwave therapy; 1α,25-Dihydroxyvitamin D3 signaling pathway; two dimensional electrophoresis
Online: 1 September 2016 (10:47:39 CEST)
Dysregulation of cartilage homeostasis and the changes in the density and the architecture of the subchondral bone were postulated as a potent mechanically pathological activity contributing to osteoarthritis (OA) pathogenesis. Extracorporeal shockwave therapy (ESWT) is a new, none invasive and effective method in the treatment of animal OA model. In the current study, we demonstrated that shockwave induced the expression of protein-disulfide isomerase-associated 3 (Pdia-3) which is a multifunctional protein hypothesized to be a significant mediator for 1α,25-Dihydroxyvitamin D3 (1α,25(OH)2D3) signaling pathway using two-dimensional electrophoresis. Histological analysis and quantitative polymerase chain reaction (qPCR) were verified and observed that the expression of Pdia-3 at 2 weeks was significantly higher than that of any other group at 4 weeks, 8 weeks, and 12 weeks post-shockwave treatment in early OA knee of rat. The other factors of the 1α,25(OH)2D3 rapid membrane signaling pathway including extracellular signal-regulated protein kinases 1 (ERK1), osteopontin (OPG), alkaline phosphatase (ALP), and matrix metallopeptidase 13 (MMP13) were measured and significantly increased by qPCR at 2 weeks post-shockwave treatment in early OA knee. Our proteomic data revealed significant Pdia-3 expression in microenvironments of joint tissue that could be actively responded to ESWT, which may potentially regulate biological function of chondrocytes and osteoblasts in the treatment of OA knee.
ARTICLE | doi:10.20944/preprints202209.0207.v1
Subject: Earth Sciences, Environmental Sciences Keywords: SSP (Shared Socio-economic Pathway) scenarios; air quality; WRF-CAMx; numerical modelling; urban areas; health impact assessment; premature deaths
Online: 14 September 2022 (11:57:03 CEST)
The World Health Organization estimates that every year air pollution kills seven million people worldwide. As it is expected that climate change will affect future air quality patterns, the full understanding of the links between air pollution and climate change, and how they affect human health, are challenges of future research. In this scope, a methodology to assess the air quality impacts on health was developed. The WRF-CAMx modelling framework was applied for the medium-term future climate (considering the SSP24.5 scenario) and for the recent past (considered as baseline). Following the WHO recommendations, mortality health indicators were used to estimate health impacts of long-term exposures. For that, the Aveiro Region, in Portugal, was considered as a case study. Future climate results indicate the occurrence of higher temperatures, and lower total precipitation. Despite that, improvements in the main pollutants’ concentrations, and consequently in the reduction of the related premature deaths are foreseen, mainly due to the reduction of pollutants emissions imposed by the European legislation for the upcoming years. The applied approach constitutes an added value in this research field, being crucial to anticipate the effects of climate change on air quality and evaluate their impacts on human health.
ARTICLE | doi:10.20944/preprints202105.0527.v1
Subject: Biology, Anatomy & Morphology Keywords: Phenylpropanoid pathway; Caffeoylquinic acid; BAHDs; hydroxycinnamoyl-coenzyme A: quinate hydroxycinnamoyl transferase; hydroxycinnamoyl-coenzyme A: shikimate/quinate hy droxycinnamoyl transferase;
Online: 21 May 2021 (15:13:15 CEST)
The phenylpropanoid pathway is a major secondary metabolite pathway that helps plants overcome biotic and abiotic stress and produces various by-products that promote human health. Its byproduct, chloroquinic acid (CQA), is a soluble phenolic compound present in many angiosperms. Hy-droxycinnamate-CoA shikimate/quinate transferase(BAHDs superfamily enzyme) is a significant en-zyme that plays a role in accumulating CQA biosynthesis. This study analyzed transcriptome-wide identification of the phenylpropanoid to chloroquinic acid biosynthesis candidate genes in A. spathulifolius flowers and leaves. Transcriptomic analyses of the flowers and leaves showed a differential expression of the PPP and CQA biosynthesis regulated unigenes. An analysis of PPP captive unigenes revealed the following: the major duplication of the key enzyme, PAL, 120 unigenes in leaves and 76 in flowers; the gene encoding C3’H, 169 unigenes in leaves and 140 unigenes in flowers; duplicated unigenes of 4CL, 41 in leaves and 27 in flowers. In addition, C4H unigenes had 12 unigenes in the leaves of A. spathulifolius and four in the flowers. The characterization of the BAHDs superfamily members identified 82 in leaves and 72 in flowers. Among them, phylogenetic analysis showed that five unigenes encoded HQT and three en-coded HCT in A. spathulifolius. The three HQT are common to both leaves and flowers, whereas the two HQT were specialized for leaves. The pattern of HQT synthesis was upregulated in flowers, whereas HCT was expressed strongly in the leaves of A. spathulifolius. Overall, 4CL, C4H, and HQT are expressed strongly in flowers, and caffeic acid and HCT show more expression in leaves. Therefore, CQA biosynthesis occurs in the flowers of A. spathulifolius rather than leaves.
COMMUNICATION | doi:10.20944/preprints202104.0275.v1
Subject: Biology, Anatomy & Morphology Keywords: fludioxonil; fungicide; mode of action; high osmolarity glycerol (HOG) pathway; Magnaporthe oryzae; signal transduction; histidine kinase; MoHIK1; HIK1; phenylpyrrole
Online: 12 April 2021 (09:38:33 CEST)
The group III two-component hybrid histidine kinase MoHik1p in the filamentous fungus Magnaporthe oryzae is known to be a sensor for external osmotic stress and essential for the fungicidal activity of the phenylpyrrole fludioxonil. The mode of action of fludioxonil has not yet been completely clarified but rather assumed to hyperactivate the high osmolarity glycerol (HOG) signaling pathway. To date, not much is known about the detailed molecular mechanism of how osmotic stress is detected or fungicidal activity is initiated within the HOG pathway. The molecular mechanism of signaling was studied using a mutant strain in which the HisKA signaling domain was modified by an amino acid change of histidine H736 to alanine A736. We found that MoHik1pH736A is as resistant to fludioxonil but not as sensitive to osmotic stress as the null mutant ∆Mohik1. H736 is required for fludioxonil action but is not essential for sensing sorbitol stress. Consequently, this report provides evidence of the difference in the molecular mechanism of fludioxonil action and the perception of osmotic stress. This is an excellent basis to understand the successful phenylpyrrole-fungicides’ mode of action better and will give new ideas to decipher cellular signaling mechanisms.
ARTICLE | doi:10.20944/preprints202008.0048.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: 8505C cell line; apoptosis; BCPAP cell line; CFLAR; DDX19B; IL6; oxidative phosphorylation; SPINT2; thyroid hormone synthesis; weighted pathway regulation
Online: 2 August 2020 (17:32:47 CEST)
Publically available (own) transcriptomic data were re-analyzed to quantify the alteration of functional pathways in the thyroid cancer, establish the gene hierarchy, identify potential gene targets and predict the effects of their manipulation. The expression data were generated from one case of papillary thyroid carcinoma (PTC) and from genetically manipulated BCPAP (papillary) and 8505C (anaplastic) human thyroid cancer cell lines. The study used the genomic fabric perspective that considers the transcriptome as a multi-dimensional mathematical object based on the three independent characteristics that can be derived for each gene from the expression data. We found remarkable remodeling of the thyroid hormone synthesis, cell cycle, oxidative phosphorylation and apoptosis pathways. Serine peptidase inhibitor, Kunitz type, 2 (SPINT2) was identified as the Gene Master Regulator of the investigated PTC. The substantial increase of the expression synergism of SPINT2 with apoptosis genes in the cancer nodule with respect to the surrounding normal tissue (NOR) suggests that its experimental overexpression may force the PTC cells into apoptosis with negligible effect on the NOR cells. The predictive value of the expression coordination for the expression regulation was validated with data from 8505C and BCPAP cells before and after lentiviral transfection with DDX19B.
CASE REPORT | doi:10.20944/preprints202002.0280.v1
Subject: Medicine & Pharmacology, Veterinary Medicine Keywords: spinal disc herniation, dog, NADPH diaphorase, the aging-related NADPH diaphorase body, megaloneurite, homogeneous formazan globule, intermedial collateral pathway
Online: 19 February 2020 (11:47:26 CET)
Neuronal lesion or injury is a traditional approach to investigate neural circuit. Is any new neural pathway or new neurodegeneration related central nerve system injury? Spinal disc herniation can cause the spinal cord injury. However, the histological examination is still lack. It happened that a case of spinal disc herniation of a 10-year old dog was examined with NADPH diaphorase (N-d) histology. We did not find the N-d neurodegenerative aberrant in the tissue of the mid-rostral lumber segment besides the metamorphoses by the compression of the disc herniation. However, the severe neuropathological changes majorly occurred in the lumbosacral spinal cord. We found more diverse neurodegenerative alterations: the aging-related N-d body (ANB), megaloneurite and N-d homogeneous formazan globule in the lumbosacral spinal cord. We also found that a new circuit pathway (intermedial collateral pathway) showed by a megaloneurite between the lateral collateral pathway and the medial collateral pathway. The enormous notch caused by spinal disc herniation located at the mid-rostral lumber segments. The aging-related neurodegeneration occurred the specific lumbosacral segments. The homogeneous formazan globule was round or oval homogeneous N-d positivity which distributed in the gray matter and dorsal column. In the medulla oblongata, ANBs were revealed in the gracile nucleus, nucleus reticularis lateralis (ventrolateral spinal trigeminal nucleus) and middle of the spinal trigeminal nucleus.