Search results for: structural genes

Authors: Nandini B. Nagaraju, Punya D. Gowda, S. Aishwarya, Benjamin Rohit

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This paper attempts to understand the structural behavior of non-prismatic channel beams subjected to bending through finite element (FE) analysis. The present study aims at shedding some light on how tapered channel beams behave by studying the effect of taper ratio on structural behavior. As a weight reduction is always desired in aerospace structures beams are tapered in order to obtain highest structural efficiency. FE analysis has been performed to study the effect of taper ratio on linear deflection, lateral torsional buckling, non-linear parameters, stresses and dynamic parameters. Taper ratio tends to affect the mechanics of tapered beams innocuously and adversely. Consequently, it becomes important to understand and document the mechanics of channel tapered beams. Channel beams generally have low torsional rigidity due to the off-shear loading. The effect of loading type and location of applied load have been studied for flange taper, web taper and symmetric taper for different conditions. Among these, as the taper ratio is increased, the torsional angular deflection increases but begins to decrease when the beam is web tapered and symmetrically tapered for a mid web loaded beam. But when loaded through the shear center, an increase in the torsional angular deflection can be observed with increase in taper ratio. It should be considered which parameter is tapered to obtain the highest efficiency.

Keywords: channel beams, tapered beams, lateral torsional bucking, shear centre

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Authors: Freyedon Ahmadi

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Corporate citizenship is considered as one of the most discussed topics in the developed countries, in which a citizen considers a Corporate just like a usual citizen with every civil right as respectful for corporate as for actual citizens, and in return citizens expect that corporate would pay a reciprocal respect to them. The current study’s purpose is to identify the impact of the current state of corporate citizenship along effective factors on its condition on industrial producing units, in order to find an accession plane for corporate citizenship development. In this study corporate citizenship is studied in four dimensions like legal corporate, economical corporate, ethical corporate and voluntary corporate. Moreover, effective factors’ impact on corporate citizenship is explored based on threefold dimensional model: behavioral, structural, and content factors, as well. In this study, 50 corporate of Food industry and of petrochemical industry, along with 200 selected individuals from directors’ board on Tehran province’s scale with stratified random sampling method, are chosen as actuarial sample. If based on functional goal and compilation methods, the present study is a description of correlation type; questionnaire is used for accumulation of initial Data. For Instrument Validity expert’s opinion is used and structural equations and its reliability is qualified by using Cronbach Alpha. The results of this study indicate that close to 70 percent of under survey corporate have not a good condition in corporate citizenship. And all of structural factors, behavioral factors, contextual factors, have a great deal of impression and impact on the advent corporate citizenship behavior in the producing Units. Among the behavioral factors, social responsibility; among structural factors, organic structure and human centered orientation, medium size, high organizational capacity; and among the contextual factors, the clientele’s positive viewpoints toward corporate had the utmost importance in impression on under survey Producing units.

Keywords: corporate citizenship, structural factors, behavioral factors, contextual factors, producing units

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Authors: B. Grygalewicz, R. Woroniecka, J. Rygier, K. Borkowska, A. Labak, B. Nowakowska, B. Pienkowska-Grela

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Introduction: Chronic lymphocytic leukemia (CLL) is the most common form of adult leukemia in the Western world. Hemizygous and or homozygous loss at 13q14 occur in more than half of cases and constitute the most frequent chromosomal abnormality in CLL. It is believed that deletions 13q14 play a role in CLL pathogenesis. Two microRNA genes miR-15a and miR- 16-1 are targets of 13q14 deletions and plays a tumor suppressor role by targeting antiapoptotic BCL2 gene. Deletion size, as a single change detected in FISH analysis, has haprognostic significance. Patients with small deletions, without RB1 gene involvement, have the best prognosis and the longest overall survival time (OS 133 months). In patients with bigger deletion region, containing RB1 gene, prognosis drops to intermediate, like in patients with normal karyotype and without changes in FISH with overall survival 111 months. Aim: Precise delineation of 13q14 deletions regions in two groups of CLL patients, with mono- and biallelic deletions and qualifications of their prognostic significance. Methods: Detection of 13q14 deletions was performed by FISH analysis with CLL probe panel (D13S319, LAMP1, TP53, ATM, CEP-12). Accurate deletion size detection was performed by CGH Haematological Cancer and SNP array (8x60K). Results: Our investigated group of CLL patients with the 13q14 deletion, detected by FISH analysis, comprised two groups: 18 patients with monoallelic deletions and 18 patients with biallelic deletions. In FISH analysis, in the monoallelic group the range of cells with deletion, was 43% to 97%, while in biallelic group deletion was detected in 11% to 94% of cells. Microarray analysis revealed precise deletion regions. In the monoallelic group, the range of size was 348,12 Kb to 34,82 Mb, with median deletion size 7,93 Mb. In biallelic group discrepancy of total deletions, size was 135,27 Kb to 33,33 Mb, with median deletion size 2,52 Mb. The median size of smaller deletion regions on one copy chromosome 13 was 1,08 Mb while the average region of bigger deletion on the second chromosome 13 was 4,04 Mb. In the monoallelic group, in 8/18 deletion region covered RB1 gene. In the biallelic group, in 4/18 cases, revealed deletion on one copy of biallelic deletion and in 2/18 showed deletion of RB1 gene on both deleted 13q14 regions. All minimal deleted regions included miR-15a and miR-16-1 genes. Genetic results will be correlated with clinical data. Conclusions: Application of CGH microarrays technique in CLL allows accurately delineate the size of 13q14 deletion regions, what have a prognostic value. All deleted regions included miR15a and miR-16-1, what confirms the essential role of these genes in CLL pathogenesis. In our investigated groups of CLL patients with mono- and biallelic 13q14 deletions, patients with biallelic deletion presented smaller deletion sizes (2,52 Mb vs 7,93 Mb), what is connected with better prognosis.

Keywords: CLL, deletion 13q14, CGH microarrays, SNP array

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Authors: Babak Forouraghi

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A genetic circuit is a collection of interacting genes and proteins that enable individual cells to implement and perform vital biological functions such as cell division, growth, death, and signaling. In cell engineering, synthetic gene circuits are engineered networks of genes specifically designed to implement functionalities that are not evolved by nature. These engineered networks enable scientists to tackle complex problems such as engineering cells to produce therapeutics within the patient's body, altering T cells to target cancer-related antigens for treatment, improving antibody production using engineered cells, tissue engineering, and production of genetically modified plants and livestock. Construction of computational models to realize genetic circuits is an especially challenging task since it requires the discovery of flow of genetic information in complex biological systems. Building synthetic biological models is also a time-consuming process with relatively low prediction accuracy for highly complex genetic circuits. The primary goal of this study was to investigate the utility of a pre-trained bidirectional encoder transformer that can accurately predict gene expressions in genetic circuit designs. The main reason behind using transformers is their innate ability (attention mechanism) to take account of the semantic context present in long DNA chains that are heavily dependent on spatial representation of their constituent genes. Previous approaches to gene circuit design, such as CNN and RNN architectures, are unable to capture semantic dependencies in long contexts as required in most real-world applications of synthetic biology. For instance, RNN models (LSTM, GRU), although able to learn long-term dependencies, greatly suffer from vanishing gradient and low-efficiency problem when they sequentially process past states and compresses contextual information into a bottleneck with long input sequences. In other words, these architectures are not equipped with the necessary attention mechanisms to follow a long chain of genes with thousands of tokens. To address the above-mentioned limitations of previous approaches, a transformer model was built in this work as a variation to the existing DNA Bidirectional Encoder Representations from Transformers (DNABERT) model. It is shown that the proposed transformer is capable of capturing contextual information from long input sequences with attention mechanism. In a previous work on genetic circuit design, the traditional approaches to classification and regression, such as Random Forrest, Support Vector Machine, and Artificial Neural Networks, were able to achieve reasonably high R2 accuracy levels of 0.95 to 0.97. However, the transformer model utilized in this work with its attention-based mechanism, was able to achieve a perfect accuracy level of 100%. Further, it is demonstrated that the efficiency of the transformer-based gene expression classifier is not dependent on presence of large amounts of training examples, which may be difficult to compile in many real-world gene circuit designs.

Keywords: transformers, generative ai, gene expression design, classification

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Authors: Nguyen Lan, Le Tan Kien, Nguyen Pham Gia Bao

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The cable-stayed bridge belongs to the combined system, in which the cables is a major strutual element. Cable-stayed bridges with large spans are often arranged with structural health monitoring systems to collect data for bridge health diagnosis. Cables tension monitoring is a structural monitoring content. It is common to measure cable tension by a direct force sensor or cable vibration accelerometer sensor, thereby inferring the indirect cable tension through the cable vibration frequency. To translate cable-stayed vibration acceleration data to real-time tension requires some necessary calculations and programming. This paper introduces the algorithm, labview program that converts cable-stayed vibration acceleration data to real-time tension. The research results are applied to the monitoring system of Tran Thi Ly cable-stayed bridge and Song Hieu cable-stayed bridge in Vietnam.

Keywords: cable-stayed bridge, cable fore, structural heath monitoring (SHM), fast fourie transformed (FFT), real time, vibrations

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Authors: Juan Bojórquez, Henry E. Reyes, Edén Bojórquez, Alfredo Reyes-Salazar

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This paper addressed the use of Artificial Intelligence to obtain the structural reliability of reinforced concrete buildings. For this purpose, artificial neuronal networks (ANN) are developed to predict seismic demand hazard curves. In order to have enough input-output data to train the ANN, a set of reinforced concrete buildings (low, mid, and high rise) are designed, then a probabilistic seismic hazard analysis is made to obtain the seismic demand hazard curves. The results are then used as input-output data to train the ANN in a feedforward backpropagation model. The predicted values of the seismic demand hazard curves found by the ANN are then compared. Finally, it is concluded that the computer time analysis is significantly lower and the predictions obtained from the ANN were accurate in comparison to the values obtained from the conventional methods.

Keywords: structural reliability, seismic design, machine learning, artificial neural network, probabilistic seismic hazard analysis, seismic demand hazard curves

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Authors: Fangfang Wang, Fan Qu

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Polycystic ovary syndrome (PCOS), the most common endocrinopathy among women of reproductive age, is characterized by ovarian dysfunction, hyperandrogenism and reduced fecundity. The aim of this study is to investigate whether the circadian disruption is involved in pathogenesis of PCOS in androgen-induced animal model. We established a rat model of PCOS using single subcutaneous injection with testosterone propionate on the ninth day after birth, and confirmed their PCOS-like phenotypes with vaginal smears, ovarian hematoxylin and eosin (HE) staining and serum androgen measurement. The control group rats received the vehicle only. Gene expression was detected by real-time quantitative PCR. (1) Compared with control group, PCOS model rats of 10-week group showed persistently keratinized vaginal cells, while all the control rats showed at least two consecutive estrous cycles. (2) Ovarian HE staining and histological examination showed that PCOS model rats of 10-week group presented many cystic follicles with decreased numbers of granulosa cells and corpora lutea in their ovaries, while the control rats had follicles with normal layers of granulosa cells at various stages of development and several generations of corpora lutea. (3) In the 10-week group, serum free androgen index was notably higher in PCOS model rats than controls. (4) Disturbed mRNA expression patterns of core clock genes were found in ovaries of PCOS model rats of 10-week group. Abnormal expression of key genes associated with circadian rhythm in ovary may be one of the mechanisms for ovarian dysfunction in PCOS model rats induced by androgen.

Keywords: polycystic ovary syndrome, androgen, animal model, circadian disruption

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Authors: Jessica Pinheiro Silva, Brenda Rabello De Camargo, Daniel Gusmao De Morais, Eliane Ferreira Noronha

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The utilization of lignocellulosic biomass as source of polysaccharides for industrial applications requires an arsenal of enzymes with different mode of action able to hydrolyze its complex and recalcitrant structure. Clostridium thermocellum is gram-positive, thermophilic bacterium producing lignocellulosic hydrolyzing enzymes in the form of multi-enzyme complex, termed celulossomes. This complex has several hydrolytic enzymes attached to a large and enzymically inactive protein known as Cellulosome-integrating protein (CipA), which serves as a scaffolding protein for the complex produced. This attachment occurs through specific interactions between cohesin modules of CipA and dockerin modules in enzymes. The present work aims to construct celulosomes in vitro with the structural protein CipA, a xylanase called Xyn10D and a cellulose called CelJ from C.thermocellum. A mini-scafoldin was constructed from modules derived from CipA containing two cohesion modules. This was cloned and expressed in Escherichia coli. The other two genes were cloned under the control of the alcohol oxidase 1 promoter (AOX1) in the vector pPIC9 and integrated into the genome of the methylotrophic yeast Pichia pastoris GS115. Purification of each protein is being carried out. Further studies regarding enzymatic activity of the cellulosome is going to be evaluated. The cellulosome built in vitro and composed of mini-CipA, CelJ and Xyn10D, can be very interesting for application in industrial processes involving the degradation of plant biomass.

Keywords: cellulosome, CipA, Clostridium thermocellum, cohesin, dockerin, yeast

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Authors: André Furtado, Hugo Rodrigues, António Arêde, Humberto Varum

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Besides characterized as non-structural elements, infill masonry (IM) walls have an important contribute in the structural response of reinforced concrete structures as proved by the damages observed recent earthquakes. In particular, the out-of-plane (OOP) collapse has been one of the most observed failure mechanism. The aim of this research is to contribute to the increase of understanding regarding the OOP behaviour of full-scale infill panels considering different variables such as panel support width and axial load on the top of columns. For this, it was carried out in the Laboratory of Earthquake and Structural Engineering (LESE) an experimental campaign of five full-scale IM walls subjected to OOP distributed cyclic loadings. Specimens with different variables such as previous in-plane damage, support conditions, axial load on the top of the columns were studied. The results will be presented and discussed along the manuscript in terms of force-displacement hysteretic curves, cracking pattern, initial stiffness, stiffness degradation and accumulative energy dissipation.

Keywords: infill masonry walls, experimental testing, out-of-plane, full-scale

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Authors: Maru Chetan, Desai Abhilash

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The structural characteristics & application of TiO2 powder with different phases are study by various techniques in this paper. TTIP, EG and citric acid use as Ti source and catalyst respectively synthesis for sol gel synthesis of TiO2 powder. To replace sol gel method we develop the new method of making nano particle of TiO2 powder. It is two route method one is physical and second one is chemical route. Specific aim to this process is to minimize the production cost and the large scale production of nano particle The synthesis product work characterize by EDAX, SEM, XRD tests.

Keywords: mortal and pestle, nano particle , TiO2, TTIP

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Authors: Shu-Pin Huang, Pai-Chi Teng, Hao-Han Chang, Chia-Hsin Liu, Yung-Lun Lin, Shu-Chi Wang, Hsin-Chih Yeh, Chih-Pin Chuu, Jiun-Hung Geng, Li-Hsin Chang, Wei-Chung Cheng, Chia-Yang Li

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The emergence of immune checkpoint inhibitors (ICIs) targeting proteins like PD-1 and PD-L1 has changed the treatment paradigm of bladder cancer. However, not all patients benefit from ICIs, with some experiencing early death. There's a significant need for biomarkers associated with the PD-1 pathway in bladder cancer. Current biomarkers focus on tumor PD-L1 expression, but a more comprehensive understanding of PD-1-related biology is needed. Our study has developed a seven-gene risk score panel, employing a comprehensive bioinformatics strategy, which could serve as a potential prognostic and predictive biomarker for bladder cancer. This panel incorporates the FYN, GRAP2, TRIB3, MAP3K8, AKT3, CD274, and CD80 genes. Additionally, we examined the relationship between this panel and immune cell function, utilizing validated tools such as ESTIMATE, TIDE, and CIBERSORT. Our seven-genes panel has been found to be significantly associated with bladder cancer survival in two independent cohorts. The panel was also significantly correlated with tumor infiltration lymphocytes, immune scores, and tumor purity. These factors have been previously reported to have clinical implications on ICIs. The findings suggest the potential of a PD-1 pathway-based transcriptomic panel as a prognostic and predictive biomarker in bladder cancer, which could help optimize treatment strategies and improve patient outcomes.

Keywords: bladder cancer, programmed cell death protein 1, prognostic biomarker, immune checkpoint inhibitors, predictive biomarker

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Authors: Mengna Hu

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This paper examines the impact of an anti-speculation tax policy on the trading activities and home price movements in the housing market in Hong Kong. The study focuses on the secondary residential property market where transactions dominate. The policy intervention substantially raised the transaction cost to speculators as well as genuine homeowners who dispose their homes within a certain period. Through the demonstration of structural breaks, our empirical results show that the rise in transaction cost effectively reduced speculative trading activities. However, it accelerated price increase in the small-sized segment by vastly demotivating existing homeowners from trading up to better homes, causing congestion in the lower-end market where the demand from first-time buyers is still strong. Apart from that, by employing regime switching approach, we further show that the unintended consequences are likely to be persistent due to this policy together with other strengthened cooling measures.

Keywords: transaction costs, housing market, structural breaks, regime switching

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Authors: Abazar Ghorbani, W. M. Wishwajith W. Kandegama, Seyed Mehdi Razavi, Moxian Chen

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The roles of hydrogen sulfide (H₂S) and melatonin (MT) as gasotransmitters in plants are widely recognised. Nevertheless, the precise nature of their involvement in defensive reactions remains uncertain. This study investigates the impact of the ML-H2S interaction on tomato plants exposed to vanadium (V) toxicity, focusing on synthesising secondary metabolites and V metal sequestration. The treatments applied in this study included a control (T1), V stress (T2), MT+V (T3), MT+H2S+V (T4), MT+hypotaurine (HT)+V (T5), and MT+H2S+HT+V (T6). These treatments were administered: MT (150 µM) as a foliar spray pre-treatment (3X), HT treatment (0.1 mM, an H2S scavenger) as root immersion for 12 hours as pre-treatments, and H2S (NaHS, 0.2 mM) and V (40 mg/L) treatments added to the Hoagland solution for 2 weeks. Results demonstrate that ML and H2S+ML treatments alleviate V toxicity by promoting the transcription of key genes (ANS, F3H, CHS, DFR, PAL, and CHI) involved in phenolic and anthocyanin biosynthesis. Moreover, they decreased V uptake and accumulation and enhanced the transcription of genes involved in glutathione and phytochelatin synthesis (GSH1, PCS, and ABC1), leading to V sequestration in roots and protection against V-induced damage. Additionally, ML and H2S+ML treatments optimize chlorophyll metabolism, and increase internal H2S levels, thereby promoting tomato growth under V stress. The combined treatment of ML+H2S shows superior effects compared to ML alone, suggesting synergistic/interactive effects between these two substances. Furthermore, inhibition of the beneficial impact of ML+H2S and ML treatments by HT, an H2S scavenger, underscores the significant involvement of H₂S in the signaling pathway activated by ML during V toxicity. Overall, these findings suggest that ML requires the presence of endogenous H₂S to mitigate V-induced adverse effects on tomato seedlings.

Keywords: vanadium toxicity, secondary metabolites, vanadium sequestration, h2s-melatonin crosstalk

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Authors: Ammar Said Ahmed, M. Reissmann, R. Bortfeldt, G. A. Brockmann

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Milk protein genetic variants are of interest for characterizing domesticated mammalian species and breeds, and for studying associations with economic traits. The aim of this work was to analyze milk protein genetic variation in the Sudanese native cattle breeds, which have been gradually declining in numbers over the last years due to the breed substitution, and indiscriminate crossbreeding. The genetic variation at three milk protein genes αS1-casein (CSN1S1), αS2-casein (CSN1S2) and ƙ-casein (CSN3) was investigated in 250 animals belonging to five Bos indicus cattle breeds of Sudan (Butana, Kenana, White-nile, Erashy and Elgash). Allele specific primers were designed for five SNPs determine the CSN1S1 variants B and C, the CSN1S2 variants A and B, the CSN3 variants A, B and H. Allele, haplotype frequencies and genetic distances (D) were calculated and the phylogenetic tree was constructed. All breeds were found to be polymorphic for the studied genes. The CSN1S1*C variant was found very frequently (>0.63) in all analyzed breeds with highest frequency (0.82) in White-nile cattle. The CSN1S2*A variant (0.77) and CSN3*A variant (0.79) had highest frequency in Kenana cattle. Eleven haplotypes in casein gene cluster were inferred. Six of all haplotypes occurred in all breeds with remarkably deferent frequencies. The estimated D ranged from 0.004 to 0.049. The most distant breeds were White-nile and Kenana (D 0.0479). The results presented contribute to the genetic knowledge of indigenous cattle and can be used for proper definition and classification of the Sudanese cattle breeds as well as breeding, utilization, and potential development of conservation strategies for local breeds.

Keywords: milk protein, genetic variation, casein haplotype, Bos indicus

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Authors: Murat Gunduz, Mustafa Ozdemir

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In this research, a framework is to be proposed to model the safety performance in construction sites. Determinants of safety performance are to be defined through extensive literature review and a multidimensional safety performance model is to be developed. In this context, a questionnaire is to be administered to construction companies with sites. The collected data through questionnaires including linguistic terms are then to be defuzzified to get concrete numbers by using fuzzy set theory which provides strong and significant instruments for the measurement of ambiguities and provides the opportunity to meaningfully represent concepts expressed in the natural language. The validity of the proposed safety performance model, relationships between determinants of safety performance are to be analyzed using the structural equation modeling (SEM) which is a highly strong multi variable analysis technique that makes possible the evaluation of latent structures. After validation of the model, a safety performance index assessment tool is to be proposed by the help of software. The proposed safety performance assessment tool will be based on the empirically validated theoretical model.

Keywords: Fuzzy set theory, safety performance assessment, safety index, structural equation modeling (SEM), construction sites

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Authors: Arfan Ali, Idrees Ahmad Nasir

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The critical evaluation of tolerance in tomato plants against the induced saline soil were assessed by transcript analysis of genes coding for products potentially involved in stress tolerance. A reverse transcriptase PCR experiment was performed with Hsp90-1, MT2, and GR1like protein genes using RNA isolated from different tissues of tomato plants. Four strains of Bacillus magisterium were inoculated with 100 Mm & 200 Mm concentrations of salt. Eleven treatments each ten replica pots were installed in green house experiment and the parameters taken into account were morphological (length, weight, number of leaves, leaf surface area), chemical (anthocyanin, chlorophyll-a, chlorophyll-b, carotenoids) and biological (gene expression). Results bare a response i.e. highest response of MT2 like gene was at 24 hpi and the highest levels of GR1 like protein transcript accumulation were detected at 36 hpi. The chemical and morphological parameters at diverse salt concentrations bequeath superlative response amongst strains which candidly flank on Zm7 and Zm4. Therefore, Bacillus magisterium Zm7 strains and somehow Zm4 strain can be used in saline condition to make plants tolerant. The overall performance of strains Zm7, Zm6, and Zm4 was found better for all studied traits under salt stress conditions. Significant correlations among traits root length, shoot length, number of leaves, leaf surface area, carotenoids, anthocyanin, chlorophyll-a and chlorophyll-b were found and suggested that the salt tolerance in tomato may be improved through the use of PGPR strains.

Keywords: Bacillus magisterium, gene expression glutathione reductase, metallothionein, PGPR, Rhizobacteria, saline

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Authors: Yuriy A. Knirel

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Enteric bacteria Escherichia coli is the predominant facultative anaerobe of the colonic flora, and some specific serotypes are associated with enteritis, hemorrhagic colitis, and hemolytic uremic syndrome. Shigella spp. are human pathogens that cause diarrhea and bacillary dysentery (shigellosis). They are in effect E. coli with a specific mode of pathogenicity. Strains of Salmonella enterica are responsible for a food-borne infection (salmonellosis), and specific serotypes cause typhoid fever and paratyphoid fever. All these bacteria are closely related in respect to structure and genetics of the lipopolysaccharide, including the O-polysaccharide part (O‑antigen). Being exposed to the bacterial cell surface, the O antigen is subject to intense selection by the host immune system and bacteriophages giving rise to diverse O‑antigen forms and providing the basis for typing of bacteria. The O-antigen forms of many bacteria are unique, but some are structurally and genetically related to others. The sequenced O-antigen gene clusters between conserved galF and gnd genes were analyzed taking into account the O-antigen structures established by us and others for all S. enterica and Shigella and most E. coli O-serogroups. Multiple genetic mechanisms of diversification of the O-antigen forms, such as lateral gene transfer and mutations, were elucidated and are summarized in the present paper. They include acquisition or inactivation of genes for sugar synthesis or transfer or recombination of O-antigen gene clusters or their parts. The data obtained contribute to our understanding of the origins of the O‑antigen diversity, shed light on molecular evolutionary relationships between the O-antigens of enteric bacteria, and open a way for studies of the role of gene polymorphism in pathogenicity.

Keywords: enteric bacteria, O-antigen gene cluster, polysaccharide biosynthesis, polysaccharide structure

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Authors: N. Bekenova, A. Aitkaliyev, B. Kassiyeva, T. Vochshenkova

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Cardiac autonomic neuropathy is not always detected in diabetes, and its phenotypic manifestations may not be evident. Therefore, the study of genetic markers predisposing to the disease is gaining increasing relevance. Research Objective: The goal is to investigate the association of polymorphisms in the APOE and FTO genes with cardiac autonomic neuropathy among individuals of Kazakh nationality. Materials and Methods: A case-control study included 147 patients with cardiac autonomic neuropathy (cases) and 153 patients without cardiac autonomic neuropathy (controls). 300 individuals of Kazakh nationality were recruited from a hospital affiliated with the RSE ‘Medical Centre Hospital of the President's Affairs Administration of the Republic of Kazakhstan.’ Patients were genotyped for 5 FTO gene polymorphisms (rs17817449, rs1121980, rs11075995, rs9939609, rs12149832) and 2 APOE gene polymorphisms (rs429358, rs7412) using real-time PCR. Statistical analysis involved Chi-square methods and calculation of odds ratios (OR) with 95% confidence intervals (CI) and was performed using the Gen Expert genetic calculator. Results. Our research revealed an association between cardiac autonomic neuropathy and rs12149832 (FTO) and rs429358 (APOE). The AA genotype of the rs12149832 polymorphism was found to double the risk of neuropathy development, while the GA genotype decreased the risk of autonomic neuropathy (2.21 (1.38-3.52) and 0.61 (0.38-0.96), respectively, p=0.003). Additionally, we identified that the TC genotype of rs429358 predisposes individuals to the development of cardiac autonomic neuropathy, while the CC genotype decreases the risk (2.23 (1.18-4.22) and 0.26 (0.03-2.31), respectively). Conclusion. Thus, polymorphisms in the APOE and FTO genes (rs429358 and rs12149832) are associated with a predisposition to cardiac autonomic neuropathy and may play a significant role in the pathogenesis of the disease. Further research with a larger sample size and an assessment of their impact on the phenotype is necessary.

Keywords: polymorphisms, APOE gene, FTO gene, automatic neuropathy, Kazakh population.

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Authors: B. Bahloul, K. Babesse, A. Dkhira, Y. Bahloul, L. Amirouche

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Structural and electronic properties of the rock-salt BaxSr1−xS are calculated using the first-principles calculations based on the density functional theory (DFT) within the generalized gradient approximation (GGA), the local density approximation (LDA) and the virtual-crystal approximation (VCA). The calculated lattice parameters at equilibrium volume for x=0 and x=1 are in good agreement with the literature data. The BaxSr1−xS alloys are found to be an indirect band gap semiconductor. Moreoever, for the composition (x) ranging between [0-1], we think that our results are well discussed and well predicted.

Keywords: semiconductor, Ab initio calculations, rocksalt, band structure, BaxSr1−xS

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Authors: Ana Neves, John Leander, Ignacio Gonzalez, Raid Karoumi

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Systematic monitoring and inspection are needed to assess the present state of a structure and predict its future condition. If an irregularity is noticed, repair actions may take place and the adequate intervention will most probably reduce the future costs with maintenance, minimize downtime and increase safety by avoiding the failure of the structure as a whole or of one of its structural parts. For this to be possible decisions must be made at the right time, which implies using systems that can detect abnormalities in their early stage. In this sense, Structural Health Monitoring (SHM) is seen as an effective tool for improving the safety and reliability of infrastructures. This paper explores the decision-making problem in SHM regarding the maintenance of civil engineering structures. The aim is to assess the present condition of a bridge based exclusively on measurements using the suggested method in this paper, such that action is taken coherently with the information made available by the monitoring system. Artificial Neural Networks are trained and their ability to predict structural behavior is evaluated in the light of a case study where acceleration measurements are acquired from a bridge located in Stockholm, Sweden. This relatively old bridge is presently still in operation despite experiencing obvious problems already reported in previous inspections. The prediction errors provide a measure of the accuracy of the algorithm and are subjected to further investigation, which comprises concepts like clustering analysis and statistical hypothesis testing. These enable to interpret the obtained prediction errors, draw conclusions about the state of the structure and thus support decision making regarding its maintenance.

Keywords: artificial neural networks, clustering analysis, model-free damage detection, statistical hypothesis testing, structural health monitoring

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Authors: Mahmood Heshmati, Farhang Daneshmand

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Material scientists and engineers have introduced novel materials with complex geometries due to the recent technological advances and promotion of manufacturing methods. Among them, lattice structures with graded architectures denoted by functionally graded porous materials (FGPMs) have been developed to optimize the structural response. FGPMs are achieved by tailoring the size and density of the internal pores in one or more directions that lead to the desired mechanical properties and structural responses. Also, FGPMs provide more flexible transition and the possibility of designing and fabricating structural elements with complex and variable properties. In this paper, wave propagation in lattice structures with functionally graded (FG) porosity is investigated in order to examine the ability of shock absorbing effect. The behavior of FG porous beams with different porosity distributions under impact load and the effects of porosity distribution and porosity content on the wave speed are studied. Important conclusions are made, along with a discussion of the future scope of studies on FGPMs structures.

Keywords: functionally graded, porous materials, wave propagation, impact load, finite element

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Authors: Momita Das, Sofia Banu, Jibon Kotoky

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Environmental contamination of natural resources with persistent organic pollutants is of great world-wide apprehension. Polycyclic aromatic hydrocarbons (PAHs) are among the organic pollutants, released due to various anthropogenic activities. Due to their toxic, carcinogenic and mutagenic properties, PAHs are of environmental and human concern. Presently, bioremediation has evolved as the most promising biotechnology for cleanup of such contaminants because of its economical and less cost effectiveness. In the present study, distribution of 16 USEPA priority PAHs was determined in the soil samples collected from fifteen different sites of Guwahati City, the Gateway of the North East Region of India. The total concentrations of 16 PAHs (Σ16 PAHs) ranged from 42.7-742.3 µg/g. Higher concentration of total PAHs was found more in the Industrial areas compared to all the sites (742.3 µg/g and 628 µg/g). It is noted that among all the PAHs, Naphthalene, Acenaphthylene, Anthracene, Fluoranthene, Chrysene and Benzo(a)Pyrene were the most available and contain the higher concentration of all the PAHs. Since microbial activity has been deemed the most influential and significant cause of PAH removal; further, twenty-three bacteria were isolated from the most contaminated sites using the enrichment process. These strains were acclimatized to utilize naphthalene and anthracene, each at 100 µg/g concentration as sole carbon source. Among them, one Gram-positive strain (JMG-01) was selected, and biodegradation ability and initial catabolic genes of PAHs degradation were investigated. Based on 16S rDNA analysis, the isolate was identified as Bacillus cereus strain JMG-01. Topographic images obtained using Scanning Electron Microscope (SEM) and Atomic Force Microscope (AFM) at scheduled time intervals of 7, 14 and 21 days, determined the variation in cell morphology during the period of degradation. AFM and SEM micrograph of biomass showed high filamentous growth leading to aggregation of cells in the form of biofilm with reference to the incubation period. The percentage degradation analysis using gas chromatography and mass analyses (GC-MS) suggested that more than 95% of the PAHs degraded when the concentration was at 500 µg/g. Naphthalene, naphthalene-2-methy, benzaldehyde-4-propyl, 1, 2, benzene di-carboxylic acid and benzene acetic acid were the major metabolites produced after degradation. Moreover, PCR experiments with specific primers for catabolic genes, ndo B and Cat A suggested that JMG-01 possess genes for PAHs degradation. Thus, the study concludes that Bacillus cereus strain JMG-01 has efficient biodegrading ability and can trigger the clean-up of PAHs contaminated soil.

Keywords: AFM, Bacillus cereus strain JMG-01, degradation, polycyclic aromatic hydrocarbon, SEM

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Authors: Aishik Deb, Rituparna Sinha

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We have developed an algorithm to detect the abnormal segment/"structural variation in the genome across a number of samples. We have worked on simulated as well as real data from the BAM Files and have designed a segmentation algorithm where abnormal segments are detected. This algorithm aims to improve the accuracy and performance of the existing CNV-CH algorithm. The next-generation sequencing (NGS) approach is very fast and can generate large sequences in a reasonable time. So the huge volume of sequence information gives rise to the need for Big Data and parallel approaches of segmentation. Therefore, we have designed a map-reduce approach for the existing CNV-CH algorithm where a large amount of sequence data can be segmented and structural variations in the human genome can be detected. We have compared the efficiency of the traditional and map-reduce algorithms with respect to precision, sensitivity, and F-Score. The advantages of using our algorithm are that it is fast and has better accuracy. This algorithm can be applied to detect structural variations within a genome, which in turn can be used to detect various genetic disorders such as cancer, etc. The defects may be caused by new mutations or changes to the DNA and generally result in abnormally high or low base coverage and quantification values.

Keywords: cancer detection, convex hull segmentation, map reduce, next generation sequencing

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Authors: Rashad Al Araj, Adil K. Tamimi

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Concrete, despite being one of the most produced materials in the world, still has weaknesses and drawbacks. Significant concern of the cementitious materials in structural applications is their quasi-brittle behavior, which causes the material to crack and lose its durability. One of the very recently proposed mitigations for this problem is the implementation of nanotechnology in the concrete mix by adding carbon nanotubes (CNTs) to it. CNTs can enhance the critical mechanical properties of concrete as a structural material. Thus, this paper demonstrates a state-of-the-art review of reinforcing concrete with CNTs, emphasizing on the structural performance. It also goes over the properties of CNTs alone, the present methods and costs associated with producing them, the possible special applications of concretes reinforced with CNTs, the key challenges and drawbacks that this new technology still encounters, and the most reliable practices and methodologies to produce CNT-reinforced concrete in the lab. This work has shown that the addition of CNTs to the concrete mix in percentages as low as 0.25% weight of cement could increase the flexural strength and toughness of concrete by more than 45% and 25%, respectively, and enhance other durability-related properties, given that an effective dispersion of CNTs in the cementitious mix is achieved. Since nano reinforcement for cementitious materials is a new technology, many challenges have to be tackled before it becomes practiced at the mass level.

Keywords: sustainability, carbon nano tube, microsilica, concrete

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Authors: Chrysanthos Maraveas, Argiris Plesias, Garyfalia G. Triantafyllou, Konstantinos Petronikolos

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The current paper presents a structural assessment and proposals for retrofit of the National Youth Foundation Building, an existing reinforced concrete (RC) building in the city of Igoumenitsa, Greece. The building is scheduled to be renovated in order to create a Municipal Cultural Center. The bearing capacity and structural integrity have been investigated in relation to the provisions and requirements of the Greek Retrofitting Code (KAN.EPE.) and European Standards (Eurocodes). The capacity of the existing concrete structure that makes up the two central buildings in the complex (buildings II and IV) has been evaluated both in its present form and after including several proposed architectural interventions. The structural system consists of spatial frames of columns and beams that have been simulated using beam elements. Some RC elements of the buildings have been strengthened in the past by means of concrete jacketing and have had cracks sealed with epoxy injections. Static-nonlinear analysis (Pushover) has been used to assess the seismic performance of the two structures with regard to performance level B1 from KAN.EPE. Retrofitting scenarios are proposed for the two buildings, including type Λ steel bracings and placement of concrete shear walls in the transverse direction in order to achieve the design-specification deformation in each applicable situation, improve the seismic performance, and reduce the number of interventions required.

Keywords: earthquake resistance, pushover analysis, reinforced concrete, retrofit, strengthening

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Authors: Eman A. Alghamdi, A. M. Aldhafiri

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It was found that the induce an isolated dopant close to the middle of the bandgap by occupying the Cd position in the CdTe lattice structure is an efficient factor in reducing the nonradiative recombination rate and increasing the solar efficiency. According to our laboratory results, this work has been carried out to obtain the effect of substrate temperature on the CdTe0.6Sn0.4 prepared by thermal evaporation technique for photovoltaic application. Various substrate temperature (25°C, 100°C, 150°C, 200°C, 250°C and 300°C) was applied. Sn-doped CdTe thin films on a glass substrate at a different substrate temperature were made using CdTe and SnTe powders by the thermal evaporation technique. The structural properties of the prepared samples were determined using Raman, x-Ray Diffraction. Spectroscopic ellipsometry and spectrophotometric measurements were conducted to extract the optical constants as a function of substrate temperature. The structural properties of the grown films show hexagonal and cubic mixed structures and phase change has been reported. Scanning electron microscopy (SEM) reviled that a homogenous with a bigger grain size was obtained at 250°C substrate temperature. The conductivity measurements were recorded as a function of substrate temperatures. The open-circuit voltage was improved by controlling the substrate temperature due to the improvement of the fundamental material issues such as recombination and low carrier concentration. All the result was explained and discussed on the biases of the influences of the Sn dopant and the substrate temperature on the structural, optical and photovoltaic characteristics.

Keywords: CdTe, conductivity, photovoltaic, ellipsometry

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Authors: Omar Ali, Adesh Ramsubhag, Jayaraj Jayaraman

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Seaweed extracts have been reported as plant biostimulants which could be a safer, organic alternative to harsh pesticides. The incentive to use seaweed-based biostimulants is becoming paramount in sustainable agriculture. The current study, therefore, screened a commercial extract of A. nodosum in tomatoes, cultivated in Trinidad to showcase the multiple beneficial effects. Foliar treatment with an A. nodosum commercial extract led to significant increases in fruit yield and a significant reduction of incidence of bacterial spots and early blight diseases under both greenhouse and field conditions. Investigations were carried out to reveal the possible mechanisms of action of this biostimulant through defense enzyme assays and transcriptome profiling via RNA sequencing of tomato. Studies into disease control mechanisms by A. nodosum showed that the extract stimulated the activity of enzymes such as peroxidase, phenylalanine ammonia-lyase, chitinase, polyphenol oxidase, and β-1,3-glucanase. Additionally, the transcriptome survey revealed the upregulation and enrichment of genes responsible for the biosynthesis of growth hormones, defense enzymes, PR proteins and defense-related secondary metabolites, as well as genes involved in the nutrient mobilization, photosynthesis and primary and secondary metabolic pathways. The results of the transcriptome study also demonstrated the cross-talks between growth and defense responses, confirming the bioelicitor and biostimulant value of seaweed extracts in plants. These effects could potentially implicate the benefits of seaweed extract and validate its usage in sustainable crop production.

Keywords: A. nodosum, biostimulants, elicitor, enzymes, growth responses, seaweeds, tomato, transcriptome analysis

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Authors: Showkat Ahmad Bhat, Iqra Reyaz, Falaque ul Afshan, Ahmad Arif Reshi, Muneeb U. Rehman, Manzoor R. Mir, Sabhiya Majid, Sonallah, Sheikh Bilal, Ishraq Hussain

Abstract:

Background: Gastric cancer is the fourth most common cancer and the second leading cause of worldwide cancer-related deaths, with a wide variation in incidence rates across different geographical areas. The current view of cancer is that a malignancy arises from a transformation of the genetic material of a normal cell, followed by successive mutations and by chain of alterations in genes such as DNA repair genes, oncogenes, Tumor suppressor genes. Minerals are necessary for the functioning of several transcriptional factors, proteins that recognize certain DNA sequences and have been found to play a role in gastric cancer. Material Methods:The present work was a case control study and its aim was to ascertain the role of minerals and promoter hypermethylation of CpG islands of DAP-K gene in Gastric cancer patients among the Kashmiri population. Serum was extracted from all the samples and mineral estimation was done by AAS from serum, DNA was also extracted and was modified using bisulphite modification kit. Methylation-specific PCR was used for the analysis of the promoter hypermethylation status of DAP-K gene. The epigenetic analysis revealed that unlike other high risk regions, Kashmiri population has a different promoter hypermethylation profile of DAP-K gene and has different mineral profile. Results: In our study mean serum copper levels were significantly different for the two genders (p<0.05), while as no significant differences were observed for iron and zinc levels. In Methylation-specific PCR the methylation status of the promoter region of DAP-K gene was as 67.50% (27/40) of the gastric cancer tissues showed methylated DAP-K promoter and 32.50% (13/40) of the cases however showed unmethylated DAP-K promoter. Almost all 85% (17/20) of the histopathologically confirmed normal tissues showed unmethylated DAP-K promoter except only in 3 cases where DAP-K promoter was found to be methylated. The association of promoter hypermethylation with gastric cancer was evaluated by χ2 (Chi square) test and was found to be significant (P=0.0006). Occurrence of DAP-K methylation was found to be unequally distributed in males and females with more frequency in males than in females but the difference was not statistically significant (P =0.7635, Odds ratio=1.368 and 95% C.I=0.4197 to 4.456). When the frequency of DAP-K promoter methylation was compared with clinical staging of the disease, DAP-K promoter methylation was found to be certainly higher in Stage III/IV (85.71%) compared to Stage I/ II (57.69%) but the difference was not statistically significant (P =0.0673). These results suggest that DAP-K aberrant promoter hypermethylation in Kashmiri population contributes to the process of carcinogenesis in Gastric cancer and is reportedly one of the commonest epigenetic changes in the development of Gastric cancer.

Keywords: gastric cancer, minerals, AAS, hypermethylation, CpG islands, DAP-K gene

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Authors: K. C. Gayithri, S. K. Naveen Kumar

Abstract:

ZnO is one of the most important semiconductor materials, non toxic, biocompatible, antibacterial properties for research and it is used in many biomedical applications. MnxZn1-xO nano thin films were prepared by a spin coating sol-gel method on silicon substrate. The structural, optical, electrical properties of Mn Doped ZnO are studied by using X-rd, FESEM, UV-Visible spectrophotometer. The X-rd reveals that the sample shows hexagonal wurtzits structure. Surface morphology and thickness of the sample are characterized by field emission scanning electron microscopy. Absorption and transmission spectra are studied by UV-Visible spectrophotometer. The electrical properties are measured by TCR meter.

Keywords: transition metals, Mn doped ZnO, Sol-gel, x-ray diffraction

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Authors: Ricardo Alberto Chiong Zevallos, Eduardo Moraes Rego Reis

Abstract:

Pancreatic adenocarcinoma (PDAC) patients have a less than 10% 5-year survival rate. PDAC has no defined diagnostic and prognostic biomarkers. Gemcitabine is the first-line drug in PDAC and several other cancers. Long non-coding RNAs (lncRNAs) contribute to the tumorigenesis and are potential biomarkers for PDAC. Although lncRNAs aren’t translated into proteins, they have important functions. LncRNAs can decoy or recruit proteins from the epigenetic machinery, act as microRNA sponges, participate in protein translocation through different cellular compartments, and even promote chemoresistance. The chromatin remodeling enzyme EZH2 is a histone methyltransferase that catalyzes the methylation of histone 3 at lysine 27, silencing local expression. EZH2 is ambivalent, it can also activate gene expression independently of its histone methyltransferase activity. EZH2 is overexpressed in several cancers and interacts with lncRNAs, being recruited to a specific locus. EZH2 can be recruited to activate an oncogene or silence a tumor suppressor. The lncRNAs misregulation in cancer can result in the differential recruitment of EZH2 and in a distinct epigenetic landscape, promoting chemoresistance. The relevance of the EZH2-lncRNAs interaction to chemoresistant PDAC was assessed by Real Time quantitative PCR (RT-qPCR) and RNA Immunoprecipitation (RIP) experiments with naïve and gemcitabine-resistant PDAC cells. The expression of several lncRNAs and EZH2 gene targets was evaluated contrasting naïve and resistant cells. Selection of candidate genes was made by bioinformatic analysis and literature curation. Indeed, the resistant cell line showed higher expression of chemoresistant-associated lncRNAs and protein coding genes. RIP detected lncRNAs interacting with EZH2 with varying intensity levels in the cell lines. During RIP, the nuclear fraction of the cells was incubated with an antibody for EZH2 and with magnetic beads. The RNA precipitated with the beads-antibody-EZH2 complex was isolated and reverse transcribed. The presence of candidate lncRNAs was detected by RT-qPCR, and the enrichment was calculated relative to INPUT (total lysate control sample collected before RIP). The enrichment levels varied across the several lncRNAs and cell lines. The EZH2-lncRNA interaction might be responsible for the regulation of chemoresistance-associated genes in multiple cancers. The relevance of the lncRNA-EZH2 interaction to PDAC was assessed by siRNA knockdown of a lncRNA, followed by the analysis of the EZH2 target expression by RT-qPCR. The chromatin immunoprecipitation (ChIP) of EZH2 and H3K27me3 followed by RT-qPCR with primers for EZH2 targets also assess the specificity of the EZH2 recruitment by the lncRNA. This is the first report of the interaction of EZH2 and lncRNAs HOTTIP and PVT1 in chemoresistant PDAC. HOTTIP and PVT1 were described as promoting chemoresistance in several cancers, but the role of EZH2 is not clarified. For the first time, the lncRNA LINC01133 was detected in a chemoresistant cancer. The interaction of EZH2 with LINC02577, LINC00920, LINC00941, and LINC01559 have never been reported in any context. The novel lncRNAs-EZH2 interactions regulate chemoresistant-associated genes in PDAC and might be relevant to other cancers. Therapies targeting EZH2 alone weren’t successful, and a combinatorial approach also targeting the lncRNAs interacting with it might be key to overcome chemoresistance in several cancers.

Keywords: epigenetics, chemoresistance, long non-coding RNAs, pancreatic cancer, histone modification

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