Search results for: hepatitis delta virus

Authors: Thavasimuthu Citarasu, Mariavincent Michaelbabu, Vikram Vakharia

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The rhizome of Java grass, Cyperus rotundus was extracted different organic polar and non-polar solvents and performed the in vitro antiviral and immunostimulant activities against White Spot Syndrome Virus (WSSV) and Vibrio harveyi respectively. Based on the initial screening the ethyl acetate extract of C. rotundus was strong activities and further it was purified through silica column chromatography and the fractions were screened again for antiviral and immunostimulant activity. Among the different fractions screened against the WSSV and V. harveyi, the fractions, F-III to FV had strong activities. In order to study the in vivo influence of C. rotundus, the fractions (F-III to FV) were pooled and delivered to the F. indicus through artificial feed for 30 days. After the feeding trail the experimental and control diet fed F. indicus were challenged with virulent WSSV and studied the survival, molecular diagnosis, biochemical, haematological and immunological parameters. Surprisingly, the pooled fractions (F-III to FV) incorporated diets helped to significantly (P < 0.01) suppressed viral multiplication, showed significant (P < 0.01) differences in protein and glucose levels, improved total haemocyte count (THC), coagulase activity, significantly increased (P < =0.001) prophenol oxidase and intracellular superoxide anion production compared to the control shrimps. Based on the results, C. rotundus extracts effectively suppressed WSSV multiplication and improve the immune system in F. indicus against WSSV infection and this knowledge will helps to develop novel drugs from C. rotundus against WSSV.

Keywords: antiviral drugs, cyperus rotundus, fenneropenaeus indicus, WSSV

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Authors: Zainul A. Khan, Malik Z. Abdin, Jawaid A. Khan

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Begomoviruses belonging to the family Geminiviridae, have single-stranded circular DNA genomes that are monopartite or bipartite. The large intergenic region (LIR) of the monopartite and common region (CR) of bipartite begomoviruses possess promoter activity in their genomes. In this study, we have characterized novel bidirectional promoters from Cotton leaf curl Burewala virus (CLCuBuV) genome using high-throughput software and analyzed with PlantCARE, PLACE, Cister and PlantPAN databases. The promoters (Rep and CP promoters) were assayed both in stable and transient expression systems in tobacco as well as cotton plants. Rep and CP-based promoters from the LIR sequence of CLCuBuV and 35S promoter of Cauliflower mosaic virus (CaMV) were tagged with β-glucuronidase (GUS) and green fluorescent protein (GFP) reporter genes to check the efficacy of the promoters. Histochemical staining of GUS in transformed tobacco (Nicotiana tabacum cv. Xanthi) leaves showed higher GUS expression driven by CLCuBuV Rep (complimentary sense) promoter as compared to conventional CaMV 35S promoter and CLCuBuV CP (virion sense) promoter, respectively. GUS activity in individual plant cells driven by CLCuBuV Rep, CLCuBuV CP, and CaMV 35S promoter were quantified through fluorometric GUS assay and reverse transcription quantitative real-time PCR (RT-qPCR). The expression level of GUS tagged with CLCuBuV Rep promoter in the transformed tobacco plants was obtained 2 to 4 fold higher than CaMV 35S promoter. When CLCuBuV CP promoter was used, lower expression level was monitored than that by CaMV 35S promoter. The expression of GFP-tagged with CLCuBuV promoters was also investigated through agroinfiltration. The CLCuBuV Rep promoters showed stronger consistent transient expression in the leaves of N. benthamiana, N. tabacum and Gossypium hirsutum plants when compared with CaMV 35S and CLCuBuV CP promoter.

Keywords: Begmovirus, bidirectional promoter, CaMV 35S promoter, GFP, GUS, qPCR

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Authors: Mohammedi Ferhate

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This paper deals with the generalized the notion of the function of wave a micro particle moving free, the concept of the linear operator in the representation function delta of Dirac which is a generalization of the symbol of Kronecker to the case of a continuous variation of the sizes concerned with the condition of orthonormation of the Eigen functions the use of linear operators and their Eigen functions in connection with the solution of given differential equations, it is of interest to study the properties of the operators themselves and determine which of them follow purely from the nature of the operators, without reference to specific forms of Eigen functions. The models simulation examples are also presented.

Keywords: function, operator, simulation, wave

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Authors: Masoud Soltanialvar, Ali Bagherpour

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Documented cases of human infection with H9N2 avian influenza viruses, first detected in 1999 in Hong Kong and China, indicate that these viruses can be directly transmitted from birds to humans. In this study, we characterized the mutation in the Hemagglutinin (HA) genes and proteins that correlates with a shift in affinity of the Hemagglutinin (HA) protein from the “avian” type sialic receptors to the “human” type in 10 Iranian isolates. We delineated the genomes and receptor binding profile of HA gene of some field isolates and established their phylogenetic relationship to the other Asian H9N2 sub lineages. A total of 1200 tissue samples collected from 40 farms located in various states of Iran during 2008 – 2010 as part of a program to monitor Avian Influenza Viruses (AIV) infection. To determine the genetic relationship of Iranian viruses, the Hemagglutinin (HA) genes from ten isolates were amplified and sequenced (by RT-PCR method). Nucleotide sequences (orf) of the (HA) genes were used for phylogenetic tree construction. Deduced amino acid sequences showed the presence of L226 (234 in H9 numbering) in all ten Iranian isolates which indicates a preference to binding of α (2–6) sialic acid receptors, so these Iranian H9N2 viruses have the potential to infect human beings. These isolates showed high degree of homology with 2 human H9N2 isolates A/HK/1073/99, A/HK/1074/99. Phylogenetic analysis of showed that all the HA genes of the Iranian H9N2 viruses fall into a single group within a G1-like sublineage which had contributed as donor of six internal genes to H5N1 highly pathogenic avian influenza. The results of this study indicated that all Iranian viruses have the potential to emerge as highly pathogenic influenza virus, and considering the homology of these isolates with human H9N2 strains, it seems that the potential of these avian influenza isolates to infect human should not be overlooked.

Keywords: influenza virus, hemagglutinin, neuraminidase, Iran

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Authors: Wajad Nazeer, Saghir Ahmad, Khalid Mahmood, Altaf Hussain, Abid Mahmood, Baoliang Zhou

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MNH-886(Bt.) is a upland cotton cultivar (Gossypium hirsutum L.) developed through hybridization of three parents [(FH-207×MNH-770)×Bollgard-1] at Cotton Research Station Multan, Pakistan. It is resistant to CLCuVD with 16.25 % disease incidence (60 DAS, March sowing) whereas moderately susceptible to CLCuVD when planted in June with disease incidence 34 % (60 DAS). This disease reaction was lowest among 25 cotton advanced lines/varieties tested at hot spots of CLCuVD. Its performance was tested during 2009 to 2012 in various indigenous, provincial, and national varietal trials in comparison with the commercial variety IR-3701 and AA-802 & CIM-496. In PCCT trial during 2009-10; 2011-12, MNH-886 surpassed all the existing Bt. strains along with commercial varieties across the Punjab province with seed cotton yield production 2658 kg ha-1 and 2848 kg ha-1 which was 81.31 and 13% higher than checks, respectively. In National Coordinated Bt. Trial, MNH-886(Bt.) produced 3347 kg ha-1 seed cotton at CCRI, Multan; the hot spot of CLCuVD, in comparison to IR-3701 which gave 2556 kg ha-1. It possesses higher lint percentage (41.01%), along with the most desirable fibre traits (staple length 28.210mm, micronaire value 4.95 µg inch-1 and fibre strength 99.5 tppsi, and uniformity ratio 82.0%). The quantification of toxicity level of crystal protein was found positive for Cry1Ab/Ac protein with toxicity level 2.76µg g-1 and Mon 531 event was confirmed. Having tremendous yield potential, good fibre traits, and great tolerance to CLCuVD we can recommended this variety for cultivation in CLCuVD hotspots of Pakistan.

Keywords: cotton, cultivar, cotton leaf curl virus, CLCuVD hit districts

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Authors: Alessandro Poma, Kal Karim, Sergey Piletsky, Giuseppe Battaglia

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The recent increasing emergency threat to public health of infectious influenza diseases has prompted interest in the detection of avian influenza virus (AIV) H5N1 in humans as well as animals. A variety of technologies for diagnosing AIV infection have been developed. However, various disadvantages (costs, lengthy analyses, and need for high-containment facilities) make these methods less than ideal in their practical application. Molecularly Imprinted Polymeric Nanoparticles (MIP NPs) are suitable to overcome these limitations by having high affinity, selectivity, versatility, scalability and cost-effectiveness with the versatility of post-modification (labeling – fluorescent, magnetic, optical) opening the way to the potential introduction of improved diagnostic tests capable of providing rapid differential diagnosis. Here we present our first results in the production and testing of MIP NPs for the detection of AIV H5N1. Recent developments in the solid-phase synthesis of MIP NPs mean that for the first time a reliable supply of ‘soluble’ synthetic antibodies can be made available for testing as potential biological or diagnostic active molecules. The MIP NPs have the potential to detect viruses that are widely circulating in farm animals and indeed humans. Early and accurate identification of the infectious agent will expedite appropriate control measures. Thus, diagnosis at an early stage of infection of a herd or flock or individual maximizes the efficiency with which containment, prevention and possibly treatment strategies can be implemented. More importantly, substantiating the practicability’s of these novel reagents should lead to an initial reduction and eventually to a potential total replacement of animals, both large and small, to raise such specific serological materials.

Keywords: influenza virus, molecular imprinting, nanoparticles, polymers

Procedia PDF Downloads 362

Authors: Olga V. Chervyakova, Elmira T. Tailakova, Vitaliy M. Strochkov, Kulyaisan T. Sultankulova, Nurlan T. Sandybayev, Lev G. Nemchinov, Rosemarie W. Hammond

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Sheep pox is a highly contagious infection that OIE regards to be one of the most dangerous animal diseases. It causes enormous economic losses because of death and slaughter of infected animals, lower productivity, cost of veterinary and sanitary as well as quarantine measures. To control spread of sheep pox infection the attenuated vaccines are widely used in the Republic of Kazakhstan and other Former Soviet Union countries. In spite of high efficiency of live vaccines, the possible presence of the residual virulence, potential genetic instability restricts their use in disease-free areas that leads to necessity to exploit new approaches in vaccine development involving recombinant DNA technology. Vaccines on the basis of recombinant proteins are the newest generation of prophylactic preparations. The main advantage of these vaccines is their low reactogenicity and this fact makes them widely used in medical and veterinary practice for vaccination of humans and farm animals. The objective of the study is to produce recombinant immunogenic proteins for development of the high-performance means for sheep pox prophylaxis. The SPV proteins were chosen for their homology with the known immunogenic vaccinia virus proteins. Assay of nucleotide and amino acid sequences of the target SPV protein genes. It has been shown that four proteins SPPV060 (ortholog L1), SPPV074 (ortholog H3), SPPV122 (ortholog A33) and SPPV141 (ortholog B5) possess transmembrane domains at N- or C-terminus while in amino acid sequences of SPPV095 (ortholog А 4) and SPPV117 (ortholog А 27) proteins these domains were absent. On the basis of these findings the primers were constructed. Target genes were amplified and subsequently cloned into the expression vector рЕТ26b(+) or рЕТ28b(+). Six constructions (pSPPV060ΔТМ, pSPPV074ΔТМ, pSPPV095, pSPPV117, pSPPV122ΔТМ and pSPPV141ΔТМ) were obtained for expression of the SPV genes under control of T7 promoter in Escherichia coli. To purify and detect recombinant proteins the amino acid sequences were modified by adding six histidine molecules at C-terminus. Induction of gene expression by IPTG was resulted in production of the proteins with molecular weights corresponding to the estimated values for SPPV060, SPPV074, SPPV095, SPPV117, SPPV122 and SPPV141, i.e. 22, 30, 20, 19, 17 and 22 kDa respectively. Optimal protocol of expression for each gene that ensures high yield of the recombinant protein was identified. Assay of cellular lysates by western blotting confirmed expression of the target proteins. Recombinant proteins bind specifically with antibodies to polyhistidine. Moreover all produced proteins are specifically recognized by the serum from experimentally SPV-infected sheep. The recombinant proteins SPPV060, SPPV074, SPPV117, SPPV122 and SPPV141 were also shown to induce formation of antibodies with virus-neutralizing activity. The results of the research will help to develop a new-generation high-performance means for specific sheep pox prophylaxis that is one of key moments in animal health protection. The research was conducted under the International project ISTC # K-1704 “Development of methods to construct recombinant prophylactic means for sheep pox with use of transgenic plants” and under the Grant Project RK MES G.2015/0115RK01983 "Recombinant vaccine for sheep pox prophylaxis".

Keywords: prophylactic preparation, recombinant protein, sheep pox virus, subunit vaccine

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Authors: Aussara Panya, Nunghathai Sawasdee, Mutita Junking, Chatchawan Srisawat, Kiattawee Choowongkomon, Pa-Thai Yenchitsomanus

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Dengue virus (DENV) infection is a global public health problem with approximately 100 million infected cases a year. Presently, there is no approved vaccine or effective drug available; therefore, the development of anti-DENV drug is urgently needed. The clinical reports revealing the positive association between the disease severity and viral titer has been reported previously suggesting that the anti-DENV drug therapy can possibly ameliorate the disease severity. Although several anti-DENV agents showed inhibitory activities against DENV infection, to date none of them accomplishes clinical use in the patients. The surface envelope (E) protein of DENV is critical for the viral entry step, which includes attachment and membrane fusion; thus, the blocking of envelope protein is an attractive strategy for anti-DENV drug development. To search the safe anti-DENV agent, this study aimed to search for novel peptide inhibitors to counter DENV infection through the targeting of E protein using a structure-based in silico design. Two selected strategies has been used including to identify the peptide inhibitor which interfere the membrane fusion process whereby the hydrophobic pocket on the E protein was the target, the destabilization of virion structure organization through the disruption of the interaction between the envelope and membrane proteins, respectively. The molecular docking technique has been used in the first strategy to search for the peptide inhibitors that specifically bind to the hydrophobic pocket. The second strategy, the peptide inhibitor has been designed to mimic the ectodomain portion of membrane protein to disrupt the protein-protein interaction. The designed peptides were tested for the effects on cell viability to measure the toxic to peptide to the cells and their inhibitory assay to inhibit the DENV infection in Vero cells. Furthermore, their antiviral effects on viral replication, intracellular protein level and viral production have been observed by using the qPCR, cell-based flavivirus immunodetection and immunofluorescence assay. None of tested peptides showed the significant effect on cell viability. The small peptide inhibitors achieved from molecular docking, Glu-Phe (EF), effectively inhibited DENV infection in cell culture system. Its most potential effect was observed for DENV2 with a half maximal inhibition concentration (IC50) of 96 μM, but it partially inhibited other serotypes. Treatment of EF at 200 µM on infected cells also significantly reduced the viral genome and protein to 83.47% and 84.15%, respectively, corresponding to the reduction of infected cell numbers. An additional approach was carried out by using peptide mimicking membrane (M) protein, namely MLH40. Treatment of MLH40 caused the reduction of foci formation in four individual DENV serotype (DENV1-4) with IC50 of 24-31 μM. Further characterization suggested that the MLH40 specifically blocked viral attachment to host membrane, and treatment with 100 μM could diminish 80% of viral attachment. In summary, targeting the hydrophobic pocket and M-binding site on the E protein by using the peptide inhibitors could inhibit DENV infection. The results provide proof of-concept for the development of antiviral therapeutic peptide inhibitors to counter DENV infection through the use of a structure-based design targeting conserved viral protein.

Keywords: dengue virus, dengue virus infection, drug design, peptide inhibitor

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Authors: Aniekan Peter, ECS Naidu, Edidiong Akang, U. Offor, R. Kalhapure, A. A. Chuturgoon, T. Govender, O. O. Azu

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Introduction: Nano-drugs are novel innovations in the management of human immunodeficiency virus (HIV) pandemic, especially resistant strains of the virus in their sanctuary sites: testis and the brain. There are safety concerns to be addressed to achieve the full potential of this new drug delivery system. Aim of study: Our study was designed to investigate toxicity profile of Tenofovir Nanoparticle (TDF-N) synthesized by University of Kwazulu-Natal (UKZN) Nano-team for prevention and treatment of HIV infection. Methodology: Ten adult male Sprague-Dawley rats maintained at the Animal House of the Biomedical Resources Unit UKZN were used for the study. The animals were weighed and divided into two groups of 5 animal each. Control animals (A) were administered with normal saline. Therapeutic dose (4.3 mg/kg) of TDF-N was administered to group B. At the end of four weeks, animals were weighed and sacrificed. Liver and kidney were removed fixed in formal saline, processed and stained using H/E, PAS and MT stains for light microscopy. Serum was obtained for renal function test (RFT), liver function test (LFT) and full blood count (FBC) using appropriate analysers. Cellular measurements were done using ImageJ and Leica software 2.0. Data were analysed using graph pad 6, values < 0.05 were significant. Results: We reported no histological alterations in the liver, kidney, FBC, LFT and RFT between the TDF-N animals and saline control. There were no significant differences in weight, organo-somatic index and histological measurements in the treatment group when compared with saline control. Conclusion/recommendations: TDF-N is not toxic to the liver, kidney and blood cells in our study. More studies using human subjects is recommended.

Keywords: tenofovir nanoparticles, liver, kidney, blood cells

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Authors: Ibrahim Alreshidi, Aseel Albrekeit, Ruaa Alharthi

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Background: As a result of the spread of COVID-19 at the beginning of 2020, many governments, including Saudi Arabia, have suspended operations in many agencies. Most dermatologists have restricted their practice, including cosmetic procedures, to ensure social distancing. On the 7th of May 2020, Saudi authorities reduced the restriction of COVID-19 virus preventative measures, allowing clinics to start accepting patients following the ministry of health protocols. Objectives: Evaluation of the public's perception and willingness to undergo cosmetic procedures during COVID-19 outbreaks in Saudi Arabia. Materials and methods: A descriptive, cross-sectional, questionnaire-based study was carried out among the individuals who lack typical symptoms of COVID-19 infection in Saudi Arabia. A self-designed web-based questionnaire was developed; content face validity and a pilot study were done. The questionnaire was distributed electronically from the 8th of May until the 31st of May 2020. Results: A total of 656 individuals who lack typical symptoms of COVID-19 infection were included in this analysis. Only 10.5% of participants expressed their will to do cosmetic procedures during the COVID-19 pandemic. More than 90% of the participants believed that the COVID-19 pandemic was either somewhat serious (52.9%) or very serious (38.7%). The willingness to do cosmetic procedures during the COVID-19 pandemic remained unaltered when the price was discounted (p<0.001) and when infection control measures were ensured (p<0.001). Conclusion: The COVID-19 pandemic had a negative impact on the practice of cosmetic dermatology. Fear of transferring the infection to a beloved home member is the main reason to avoid these procedures. Generating well-structured safety guidelines to decrease the risk of this unusual virus transmission in dermatology practice and creating financial incentives may help increase the public willingness to do these cosmetic procedures during this pandemic.

Keywords: COVID-19 pandemic, cosmetic procedures, questionnaire, dermatology

Procedia PDF Downloads 182

Authors: Emanuel Guariglia

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In this paper we deal with Chebyshev wavelets. We analyze their properties computing their Fourier transform. Moreover, we discuss the differential properties of Chebyshev wavelets due the connection coefficients. The differential properties of Chebyshev wavelets, expressed by the connection coefficients (also called refinable integrals), are given by finite series in terms of the Kronecker delta. Moreover, we treat the p-order derivative of Chebyshev wavelets and compute its Fourier transform. Finally, we expand the mother wavelet in Taylor series with an application both in fractional calculus and fractal geometry.

Keywords: Chebyshev wavelets, Fourier transform, connection coefficients, Taylor series, local fractional derivative, Cantor set

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Authors: Wafa Toumi, Alessandro Ripalti, Luigi Ricciardiello, Dalila Gargouri, Jamel Kharrat, Abderraouf Cherif, Ahmed Bouhafa, Slim Jarboui, Mohamed Zili, Ridha Khelifa

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Background & aims: Colorectal cancer (CRC) is one of the most common malignancies throughout the world. Several risk factors, both genetic and environmental, including viral infections, have been linked to colorectal carcinogenesis. A few studies report the detection of human polyomavirus JC (JCV) DNA and transformation antigen (T-Ag) in a fraction of the colorectal tumors studied and suggest an association of this virus with CRC. In order to investigate whether such an association of JCV with CRC will hold in a different epidemiological setting, we looked for the presence of JCV DNA and T-Ag expression in a group of Tunisian CRC patients. Methods: Fresh colorectal mucosa biopsies were obtained from 17 healthy volunteers and from both colorectal tumors and adjacent normal tissues of 47 CRC patients. DNA was extracted from fresh biopsies or from formalin-fixed, paraffin-embedded tissue sections using the Invitrogen Purelink Genomic DNA mini Kit. A simple PCR and a nested PCR were used to amplify a region of the T-Ag gene. The obtained PCR products revealed a 154 bp and a 98 bp bands, respectively. Specificity was confirmed by sequencing of the PCR products. T-Ag expression was determined by immunohistochemical staining using a mouse monoclonal antibody (clone PAb416) directed against SV40 T-Ag that cross reacts with JCV T-Ag. Results: JCV DNA was found in 12 (25%) and 22 (46%) of the CRC tumors by simple PCR and by nested PCR, respectively. All paired adjacent normal mucosa biopsies were negative for viral DNA. Sequencing of the DNA amplicons obtained confirmed the authenticity of T-Ag sequences. Immunohistochemical staining showed nuclear T-Ag expression in all 22 JCV DNA- positive samples and in 3 additional tumor samples which appeared DNA-negative by PCR. Conclusions: These results suggest an association of JCV with a subpopulation of Tunisian colorectal tumors.

Keywords: colorectal cancer, immunohistochemistry, Polyomavirus JC, PCR

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Authors: Abhaydeep Pandey, Shweta Shukla, Saptamita Goswami, Bhaswati Bandyopadhyay, Vishnampettai Ramachandran, Sudhanshu Vrati, Arup Banerjee

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Background: Long non-coding RNAs (lncRNAs) are the important regulators of gene expression and play important role in viral replication and disease progression. The role of lncRNA genes in the pathogenesis of Dengue virus-mediated pathogenesis is currently unknown. Methods: To gain additional insights, we utilized an unbiased RNA sequencing followed by in silico analysis approach to identify the differentially expressed lncRNA and genes that are associated with dengue disease progression. Further, we focused our study on lncRNAs NEAT1 (Nuclear Paraspeckle Assembly Transcript 1) as it was found to be differentially expressed in PBMC of dengue infected patients. Results: The expression of lncRNAs NEAT1, as compared to dengue infection (DI), was significantly down-regulated as the patients developed the complication. Moreover, pairwise analysis on follow up patients confirmed that suppression of NEAT1 expression was associated with rapid fall in platelet count in dengue infected patients. Severe dengue patients (DS) (n=18; platelet count < 20K) when recovered from infection showing high NEAT1 expression as it observed in healthy donors. By co-expression network analysis and subsequent validation, we revealed that coding gene; IFI27 expression was significantly up-regulated in severe dengue cases and negatively correlated with NEAT1 expression. To discriminate DI from dengue severe, receiver operating characteristic (ROC) curve was calculated. It revealed sensitivity and specificity of 100% (95%CI: 85.69 – 97.22) and area under the curve (AUC) = 0.97 for NEAT1. Conclusions: Altogether, our first observations demonstrate that monitoring NEAT1and IFI27 expression in dengue patients could be useful in understanding dengue virus-induced disease progression and may be involved in pathophysiological processes.

Keywords: dengue, lncRNA, NEAT1, transcriptome

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Authors: Pradakshina Sharma, Jagriti Narang

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Due to the critical significance in the early identification of infectious diseases, electrochemical sensors have garnered considerable interest. Here, we develop a detection platform for the chikungunya virus by rationally implementing the extremely high charge-transfer efficiency of a ternary nanocomposite of graphene oxide, silver, and gold (G/Ag/Au) (CHIKV). Because paper is an inexpensive substrate and can be produced in large quantities, the use of electrochemical paper analytical device (EPAD) origami further enhances the sensor's appealing qualities. A cost-effective platform for point-of-care diagnostics is provided by paper-based testing. These types of sensors are referred to as eco-designed analytical tools due to their efficient production, usage of the eco-friendly substrate, and potential to reduce waste management after measuring by incinerating the sensor. In this research, the paper's foldability property has been used to develop and create 3D multifaceted biosensors that can specifically detect the CHIKVX-ray diffraction, scanning electron microscopy, UV-vis spectroscopy, and transmission electron microscopy (TEM) were used to characterize the produced nanoparticles. In this work, aptamers are used since they are thought to be a unique and sensitive tool for use in rapid diagnostic methods. Cyclic voltammetry (CV) and linear sweep voltammetry (LSV), which were both validated with a potentiostat, were used to measure the analytical response of the biosensor. The target CHIKV antigen was hybridized with using the aptamer-modified electrode as a signal modulation platform, and its presence was determined by a decline in the current produced by its interaction with an anionic mediator, Methylene Blue (MB). Additionally, a detection limit of 1ng/ml and a broad linear range of 1ng/ml-10µg/ml for the CHIKV antigen were reported.

Keywords: biosensors, ePAD, arboviral infections, point of care

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Authors: J. T. Koininga, J. E. Teigen, A. Wilkinson, D. Kanneh, F. Kanneh, M. Foday, D. S. Grant, M. Leach, L. M. Moses

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Lassa fever (LF) is a severe febrile illness endemic to West Africa. While human-to-human transmission occurs, evidence suggests most LF cases originate from exposure to rodents, particularly the Natal multimammate mouse, Mastomys natalensis. Within West Africa, LF occurs primarily in rural communities where agriculture is the main economic activity. Seasonality of LF has also been linked to agricultural cycles, with peak incidence occurring in the dry season when fields are burned and plowed. To investigate this pattern of seasonality, four agricultural communities were selected for this two-year longitudinal study. Each community was to be sampled four times each year, but this was interrupted by the Ebola virus disease outbreak. Agricultural land use, forested, and fallow areas were identified through participatory mapping. Transects were plotted in each area and Sherman traps were set for four nights. Captured small mammals were identified, ear tagged, and released. Mastomys natalensis abundance was found to be highest in areas of converted fallow land and rice swamps in the dry season and upland mixed crop areas toward the onset of the rainy season. All peak times were associated with heavy perturbation of soil. All ages and genders were present during these time points. These results suggest that peak abundance of the Mastomys natalensis in agricultural areas coincides with peak incidence of LF reported in this region. Although contact with rodents may be higher in villages, our study suggests human behaviors in agricultural areas may increase risk of transmission of Lassa virus.

Keywords: agriculture, land use, Lassa Fever, rodent abundance

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Authors: Saranya Ganapathy, Megha N. Parajulee, Michael San Francisco, Hong Zhang

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Insect pests are a serious threat to agricultural productivity. Use of chemical pesticides, the predominant control method thus far, has resulted in environmental damage, pest resurgence, and negative effects on non-target species. Genetically modified (GM) crops offer a promising alternative, and Bacillus thuringiensis endotoxin genes have played a major role in this respect. However, to overcome insect tolerance issues and to broaden the target range, it is critical to identify alternative-insecticidal toxins working through novel mechanisms. Our research group has identified a kinase from Chilo iridescent virus (CIV; Family Iridoviridae) that has insecticidal activity and designated it as ISTK (Iridovirus Serine/Threonine Kinase). A 35 kDa truncated form of ISTK, designated iridoptin, was obtained during expression and purification of ISTK in the yeast system. This yeast-expressed CIV toxin induced 50% mortality in cotton aphids and 100% mortality in green peach aphids (GPA). Optimized viral genes (o-ISTK and o-IRI) were stably transformed into the model plant, Arabidopsis. PCR analysis of genomic DNA confirmed the presence of the gene insert (oISTK/oIRI) in selected transgenic lines. The further screening was performed to identify the PCR positive lines that showed expression of respective toxins at the polypeptide level using Western blot analysis. The stable lines expressing either of these two toxins induced moderate to very high mortality in GPAs and significantly affected GPA development and fecundity. The aphicidal potential of these transgenic Arabidopsis lines will be presented.

Keywords: Chilo iridescent virus, insecticidal toxin, iridoviruses, plant-incorporated protectants, serine/threonine kinase

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Authors: Aman Ullah Khan, Muhammad Younus, Aqil Ijaz, Muti-Ur-Rehman Khan, Sayyed Aun Muhammad, Asif Idrees, Sanan Raza, Amar Nasir

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Dengue fever and malaria are important vector-borne diseases of public health significance affecting millions of people around the globe. Dengue fever is caused by Dengue virus while malaria is caused by plasmodium protozoan. Generally, the consequences of Malaria are less severe compared to dengue fever. This study was designed to differentiate dengue fever and malaria on the basis of clinical and laboratory findings and to compare the changes in both diseases having different causative agents transmitted by the common vector. A total of 200 patients of dengue viral infection (120 males, 80 females) were included in this prospective descriptive study. The blood samples of the individuals were first screened for malaria by blood smear examination and then the negative samples were tested by anti-dengue IgM strip. The strip positive cases were further screened by IgM capture ELISA and their complete blood count including hemoglobin estimation (Hb), total and differential leukocyte counts (TLC and DLC), erythrocyte sedimentation rate (ESR) and platelet counts were performed. On the basis of the severity of signs and symptoms, dengue virus infected patients were subdivided into dengue fever (DF) and dengue hemorrhagic fever (DHF) comprising 70 and 100 confirmed patients, respectively. On the other hand, 30 patients were found infected with Malaria while overall 120 patients showed thrombocytopenia. The patients of DHF were found to have more leucopenia, raised hemoglobin level and thrombocytopenia < 50,000/µl compared to the patients belonging to DF and malaria. On the basis of the outcomes of the study, it was concluded that patients affected by DF were at a lower risk of undergoing haematological disturbance than suffering from DHF. While, the patients infected by Malaria were found to have no significant change in their blood components.

Keywords: dengue fever, blood, serum, malaria, ELISA

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Authors: Dalia G. Aseel

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The potato (Solanum tubersum, L.) has become one of the major vegetable crops in Egypt and all over the world. Potato leafroll virus(PLRV) was observed on potato plants collected from different governorates in Egypt. Three cultivars, Spunta, Diamont, and Cara, infected with PLRV were collected; RNA was extracted and subjected to Real-Time PCR using the coat protein gene primers. The results showed that the expression of the coat protein was 39.6-fold, 12.45-fold, and 47.43-fold, respectively, for Spunta, Diamont, and Cara cultivars. Differential Display Polymerase Chain Reaction (DD-PCR) using pathogenesis-related protein 1 (PR-1), β-1,3-glucanases (PR-2), chitinase (PR-3), peroxidase (POD), and polyphenol oxidase (PPO) forward primers for pathogenesis-related proteins (PR). The obtained data revealed different banding patterns depending on the viral type and the region of infection. Regarding PLRV, 58 up-regulated and 19 down-regulated genes were detected. Sequence analysis of the up-and down-regulated genes revealed that infected plants were observed in comparison with the healthy control. Sequence analysis of the up-regulated gene was performed, and the encoding sequence analysis showed that the obtained genes include: induced stolen tip protein. On the other hand, two down-regulated genes were identified: disease resistance RPP-like protein and non-specific lipid-transfer protein. In this study, the expressions of PR-1, PR-2, PR-3, POD, and PPO genes in the infected leaves of three potato cultivars were estimated by quantitative real-time PCR. We can conclude that the PLRV-infection of potato plants inhibited the expression of the five PR genes. On the contrary, infected leaves by PLRV elevated the expression of some defense genes. This interaction may also induce and/or suppress the expression of some genes responsible for the plant's defense mechanisms.

Keywords: PLRV, pathogenesis-related proteins (PRs), DD-PCR, sequence, real-time PCR

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Authors: Chloé Kernaléguen, Laura Kundun, Tessie Lery, Ryan Laleg, Zhangyun Tan

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This study explores global disparities in respiratory syncytial virus (RSV) bronchiolitis incidence among children aged 0-2 years, focusing on the human development index (HDI) as a key determinant. RSV bronchiolitis poses a significant health risk to young children, influenced by factors, including socio-economic conditions captured by the HDI. Through a comprehensive systematic review and dataset selection (Switzerland, Brazil, United States of America), we formulated an HDI-SEIRS numerical model within the SEIRS framework. Results show variations in RSV bronchiolitis dynamics across countries, emphasizing the influence of HDI. Modelling reveals a correlation between higher HDI and increased bronchiolitis spread, notably in the USA and Switzerland. The ratios HDIcountry over HDImax strengthen this association, while climate disparities contribute to variations, especially in colder climates like the USA and Switzerland. The study raises the hypothesis of an indirect link between higher HDI and more frequent bronchiolitis, underlining the need for nuanced understanding. Factors like improved healthcare access, population density, mobility, and social behaviors in higher HDI countries might contribute to unexpected trends. Limitations include dataset quality and restricted RSV bronchiolitis data. Future research should encompass diverse HDI datasets to refine HDI's role in bronchiolitis dynamics. In conclusion, HDI-SEIRS models offer insights into factors influencing RSV bronchiolitis spread. While HDI is a significant indicator, its impact is indirect, necessitating a holistic approach to effective public health policies. This analysis sets the stage for further investigations into multifaceted interactions shaping bronchiolitis dynamics in diverse socio-economic contexts.

Keywords: bronchiolitis propagation, HDI influence, respiratory syncytial virus, SEIRS model

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Authors: Miriam Schiff, Hadas Rosenne, Ran Nir-Paz, Shiri Shinan Altman

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To examine (1) the level, predictors, and subjective perception of professional quality of life (PRoQL), posttraumatic growth, roles, task changes during the pandemic, and perceived preparedness for the next pandemic. These variables were added as part of an international study on social workers in healthcare stress, resilience, and perceived preparedness we took part in, along with Australia, Canada, China, Hong Kong, Singapore, and Taiwan. (2) The extent to which background variables, rate of exposure to the virus, working in COVID wards, profession, personal resilience, and resistance to organizational change predict posttraumatic growth, perceived preparedness, and PRoQL (the latter was examined among social workers only). (3) The teams' perceptions of how the pandemic impacted them at the personal, professional, and organizational levels and what assisted them. Methodologies: Mixed quantitative and qualitative methods were used. 1039 hospital healthcare workers from various professions participated in the quantitative study while 32 participated in in-depth interviews. The same methods were used in six other countries. Findings: The level of PRoQL was moderate, with higher burnout and secondary traumatization level than during routine times. Differences between countries in the level of PRoQL were found as well. Perceived preparedness for the next pandemic at the personal level was moderate and similar among the different health professions. Higher exposure to the virus was associated with lower perceived preparedness of the hospitals. Compared to other professions, doctors and nurses perceived hospitals as significantly less prepared for the next pandemic. The preparedness of the State of Israel for the next pandemic is perceived as low by all healthcare professionals. A moderate level of posttraumatic growth was found. Staff who worked at the COVID ward reported a greater level of growth. Doctors reported the lowest level of growth. The staff's resilience was high, with no differences among professions or levels of exposure. Working in the COVID ward and resilience predicted better preparedness, while resistance to organizational change predicted worse preparedness. Findings from the qualitative part of the study revealed that healthcare workers reported challenges at the personal, professional and organizational level during the different waves of the pandemic. They also report on internal and external resources they either owned or obtained during that period. Conclusion: Exposure to the COVID-19 virus is associated with secondary traumatization on one hand and personal posttraumatic growth on the other hand. Personal and professional discoveries and a sense of mission helped cope with the pandemic that was perceived as a historical event, war, or mass casualty event. Personal resilience, along with the support of colleagues, family, and direct management, were seen as significant components of coping. Hospitals should plan ahead and improve their preparedness to the next pandemic.

Keywords: covid-19, health-care, social workers, burnout, preparedness, international perspective

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Authors: Huynh Viet Khai, Mitsuyasu Yabe

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The study investigated the economic value of biodiversity attributes that could provide policy-makers reliable information to estimate welfare losses due to biodiversity reductions and analyse the trade-off between biodiversity and economics. In order to obtain the non-market benefits of biodiversity conservation, an indirect utility function and willingness to pay for biodiversity attributes were applied using the approach of choice modelling with the analysis of conditional logit model. The study found that Mekong Delta residents accepted their willingness to pay for VND 913 monthly for a one percent increase in healthy vegetation, VND 360 for an additional mammal species and VND 2,440 to avoid the welfare losses of 100 local farmers.

Keywords: choice modelling, genetic resources, wetland conservation, marginal willingness to pay

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Authors: Temple Probyne Abali

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Port Harcourt, Rivers State in the Niger Delta region of Nigeria is bedeviled by the phenomenon of climatechange, posing threat to food security and livelihood. This study examined a 4 decadel (1980-2020) trend of climate change as well as its socio-economic impact on food security in the region. Furthermore, to achieve sustainable food security and livelihood amidst the phenomenon, the study adopted the World Bank Assisted Third National Fadama Development Programme approach. The data source for climate change involved secondary data from Nigeria Meteorological Agency (NIMET). Consequently, the results for climate change over the 4decade period were displayed in tables, charts and maps for the expected changes. Data sources on socio-economic impact of food security and livelihood were acquired through questionnairedesign. A purposive random sampling technique was used in selecting 5 coastal communities inthe region known for viable economic potentials for agricultural development and the resultswere analyzed using Analysis of Variance (ANOVA). The Participatory Rural Appraisal (PRA) technique of the World Bank for needs assessment wasadopted in selecting 5 agricultural sub-project proposals/activities based on groups’ commoneconomic interest from a total of 1,000 farmers each drawn from the 5 communities of differentage groups including men, women, youths and the vulnerable. Based on the farmers’ sub-projectinterests, the various groups’ Strength, Weakness, Opportunities and Threats (SWOT), Problem Listing Matrix, Skill Gap Analysis as well as EIAson their sub-project proposals/activities were analyzed with substantialMonitoring and Evaluation (M & E), using the Specific, Measurable, Attribute, Reliable and Time bound (SMART)approach. Based on the findings from the PRA technique, the farmers recorded considerableincreaseinincomeofover200%withinthe5yearprojectplan(2008-2013).Thestudyrecommends capacity building and advisory services on this PRA innovation. By so doing, there would be a sustainable increase in agricultural production and assured food security in an environmental friendly manner, in line with the United Nation’s Sustainable Development Goals(SDGs).

Keywords: climate change, food security, fadama, world bank, agriculture, sdgs

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Authors: Jeni Stolow, Lina Moses, Carl Kendall

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Zika virus (ZIKV) reemerged as a global threat in 2015 with Brazil at its epicenter. Brazilians have a long history of combatting Aedes aegypti mosquitos as it is a common vector for dengue, chikungunya, and yellow fever. As a response to the epidemic, public health authorities promoted ZIKV prevention behaviors such as mosquito bite prevention, reproductive counseling for women who are pregnant or contemplating pregnancy, pregnancy avoidance, and condom use. Most prevention efforts from Brazil focused on the mosquito vector- utilizing recycled dengue approaches without acknowledging the context in which women were able to adhere to these prevention messages. This study used qualitative methods to explore how women in Fortaleza, Brazil perceive ZIKV, the Brazilian authorities’ ZIKV prevention recommendations, and the feasibility of adhering to these recommendations. A core study aim was to look at how women perceive their physical, social, and natural environment as it impacts women’s ability to adhere to ZIKV prevention behaviors. A Rapid Anthropological Assessment (RAA) containing observations, informational interviews, and semi-structured in-depth interviews were utilized for data collection. The study utilized Grounded Theory as the systematic inductive method of analyzing the data collected. Interviews were conducted with 35 women of reproductive age (15-39 years old), who primarily utilize the public health system. It was found that women’s self-identified economic class was associated with how strongly women felt they could prevent ZIKV. All women interviewed technically belong to the C-class, the middle economic class. Although all members of the same economic class, there was a divide amongst participants as to who perceived themselves as higher C-class versus lower C-class. How women saw their economic status was dictated by how they perceived their physical, social, and natural environment. Women further associated their environment and their economic class to their likelihood of contracting ZIKV, their options for preventing ZIKV, their ability to prevent ZIKV, and their willingness to attempt to prevent ZIKV. Women’s perceived economic status was found to relate to their structural environment (housing quality, sewage, and locations to supplies), social environment (family and peer norms), and natural environment (wetland areas, natural mosquito breeding sites, and cyclical nature of vectors). Findings from this study suggest that women’s perceived environment and economic status impact their perceived feasibility and desire to attempt behaviors to prevent ZIKV. Although ZIKV has depleted from epidemic to endemic status, it is suggested that the virus will return as cyclical outbreaks like that seen with similar arboviruses such as dengue and chikungunya. As the next ZIKV epidemic approaches it is essential to understand how women perceive themselves, their abilities, and their environments to best aid the prevention of ZIKV.

Keywords: Aedes aegypti, environment, prevention, qualitative, zika

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Authors: Lydia Tan, Philippe Lemey, Lieselot Houspie, Marco Viveen, Darren Martin, Frank Coenjaerts

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Introduction: Human respiratory syncytial virus (hRSV) is the leading cause of severe respiratory tract infections in infants under the age of two. Genomic substitutions and related evolutionary dynamics of hRSV are of great influence on virus transmission behavior. The evolutionary patterns formed are due to a precarious interplay between the host immune response and RSV, thereby selecting the most viable and less immunogenic strains. Studying genomic profiles can teach us which genes and consequent proteins play an important role in RSV survival and transmission dynamics. Study design: In this study, genetic diversity and evolutionary rate analysis were conducted on 36 RSV subgroup B whole genome sequences and 37 subgroup A genome sequences. Clinical RSV isolates were obtained from nasopharyngeal aspirates and swabs of children between 2 weeks and 5 years old of age. These strains, collected during epidemic seasons from 2001 to 2011 in the Netherlands and Belgium by either conventional or 454-sequencing. Sequences were analyzed for genetic diversity, recombination events, synonymous/non-synonymous substitution ratios, epistasis, and translational consequences of mutations were mapped to known 3D protein structures. We used Bayesian statistical inference to estimate the rate of RSV genome evolution and the rate of variability across the genome. Results: The A and B profiles were described in detail and compared to each other. Overall, the majority of the whole RSV genome is highly conserved among all strains. The attachment protein G was the most variable protein and its gene had, similar to the non-coding regions in RSV, more elevated (two-fold) substitution rates than other genes. In addition, the G gene has been identified as the major target for diversifying selection. Overall, less gene and protein variability was found within RSV-B compared to RSV-A and most protein variation between the subgroups was found in the F, G, SH and M2-2 proteins. For the F protein mutations and correlated amino acid changes are largely located in the F2 ligand-binding domain. The small hydrophobic phosphoprotein and nucleoprotein are the most conserved proteins. The evolutionary rates were similar in both subgroups (A: 6.47E-04, B: 7.76E-04 substitution/site/yr), but estimates of the time to the most recent common ancestor were much lower for RSV-B (B: 19, A: 46.8 yrs), indicating that there is more turnover in this subgroup. Conclusion: This study provides a detailed description of whole RSV genome mutations, the effect on translation products and the first estimate of the RSV genome evolution tempo. The immunogenic G protein seems to require high substitution rates in order to select less immunogenic strains and other conserved proteins are most likely essential to preserve RSV viability. The resulting G gene variability makes its protein a less interesting target for RSV intervention methods. The more conserved RSV F protein with less antigenic epitope shedding is, therefore, more suitable for developing therapeutic strategies or vaccines.

Keywords: drug target selection, epidemiology, respiratory syncytial virus, RSV

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Authors: Sadia Imran, Zenab Naseem

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Dengue fever is one of the most alarming mosquito-borne viral diseases. Dengue virus has been distributed over the years exponentially throughout the world be it tropical or sub-tropical regions of the world, particularly in the last ten years. Changing topography, climate change in terms of erratic seasonal trends, rainfall, untimely monsoon early or late and longer or shorter incidences of either summer or winter. Globalization, frequent travel throughout the world and viral evolution has lead to more severe forms of Dengue. Global incidence of dengue infections per year have ranged between 50 million and 200 million; however, recent estimates using cartographic approaches suggest this number is closer to almost 400 million. In recent years, Pakistan experienced a deadly outbreak of the disease. The reason could be that they have the maximum exposure outdoors. Public organizations have observed that changing climate, especially lower average summer temperature, and increased vegetation have created tropical-like conditions in the city, which are suitable for Dengue virus growth. We will conduct a time-series analysis to study the interrelationship between dengue incidence and diurnal ranges of temperature and humidity in Pakistan, Lahore being the main focus of our study. We have used annual data from 2005 to 2015. We have investigated the relationship between climatic variables and dengue incidence. We used time series analysis to describe temporal trends. The result shows rising trends of Dengue over the past 10 years along with the rise in temperature & rainfall in Lahore. Hence this seconds the popular statement that the world is suffering due to Climate change and Global warming at different levels. Disease outbreak is one of the most alarming indications of mankind heading towards destruction and we need to think of mitigating measures to control epidemic from spreading and enveloping the cities, countries and regions.

Keywords: Dengue, epidemic, globalization, climate change

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Authors: Mouna Baassi, Mohamed Moussaoui, Sanchaita Rajkhowa, Hatim Soufi, Said Belaaouad

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The objective of this paper is to address the challenging task of targeting Human Immunodeficiency Virus type 1 Reverse Transcriptase (HIV-1 RT) in the treatment of AIDS. Reverse Transcriptase inhibitors (RTIs) have limitations due to the development of Reverse Transcriptase mutations that lead to treatment resistance. In this study, a combination of statistical analysis and bioinformatics tools was adopted to develop a mathematical model that relates the structure of compounds to their inhibitory activities against HIV-1 Reverse Transcriptase. Our approach was based on a series of compounds recognized for their HIV-1 RT enzymatic inhibitory activities. These compounds were designed via software, with their descriptors computed using multiple tools. The most statistically promising model was chosen, and its domain of application was ascertained. Furthermore, compounds exhibiting comparable biological activity to existing drugs were identified as potential inhibitors of HIV-1 RT. The compounds underwent evaluation based on their chemical absorption, distribution, metabolism, excretion, toxicity properties, and adherence to Lipinski's rule. Molecular docking techniques were employed to examine the interaction between the Reverse Transcriptase (Wild Type and Mutant Type) and the ligands, including a known drug available in the market. Molecular dynamics simulations were also conducted to assess the stability of the RT-ligand complexes. Our results reveal some of the new compounds as promising candidates for effectively inhibiting HIV-1 Reverse Transcriptase, matching the potency of the established drug. This necessitates further experimental validation. This study, beyond its immediate results, provides a methodological foundation for future endeavors aiming to discover and design new inhibitors targeting HIV-1 Reverse Transcriptase.

Keywords: QSAR, ADMET properties, molecular docking, molecular dynamics simulation, reverse transcriptase inhibitors, HIV type 1

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Authors: Jun Won Kim

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Objective: Theta-phase gamma-amplitude coupling (TGC) was used as a novel evidence-based tool to reflect the dysfunctional cortico-thalamic interaction in patients with schizophrenia. However, to our best knowledge, no studies have reported the diagnostic utility of the TGC in the resting-state electroencephalographic (EEG) of neuroleptic-naive patients with schizophrenia compared to healthy controls. Thus, the purpose of this EEG study was to understand the underlying mechanisms in patients with schizophrenia by comparing the TGC at rest between two groups and to evaluate the diagnostic utility of TGC. Method: The subjects included 90 patients with schizophrenia and 90 healthy controls. All patients were diagnosed with schizophrenia according to the criteria of Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV) by two independent psychiatrists using semi-structured clinical interviews. Because patients were either drug-naïve (first episode) or had not been taking psychoactive drugs for one month before the study, we could exclude the influence of medications. Five frequency bands were defined for spectral analyses: delta (1–4 Hz), theta (4–8 Hz), slow alpha (8–10 Hz), fast alpha (10–13.5 Hz), beta (13.5–30 Hz), and gamma (30-80 Hz). The spectral power of the EEG data was calculated with fast Fourier Transformation using the 'spectrogram.m' function of the signal processing toolbox in Matlab. An analysis of covariance (ANCOVA) was performed to compare the TGC results between the groups, which were adjusted using a Bonferroni correction (P < 0.05/19 = 0.0026). Receiver operator characteristic (ROC) analysis was conducted to examine the discriminating ability of the TGC data for schizophrenia diagnosis. Results: The patients with schizophrenia showed a significant increase in the resting-state TGC at all electrodes. The delta, theta, slow alpha, fast alpha, and beta powers showed low accuracies of 62.2%, 58.4%, 56.9%, 60.9%, and 59.0%, respectively, in discriminating the patients with schizophrenia from the healthy controls. The ROC analysis performed on the TGC data generated the most accurate result among the EEG measures, displaying an overall classification accuracy of 92.5%. Conclusion: As TGC includes phase, which contains information about neuronal interactions from the EEG recording, TGC is expected to be useful for understanding the mechanisms the dysfunctional cortico-thalamic interaction in patients with schizophrenia. The resting-state TGC value was increased in the patients with schizophrenia compared to that in the healthy controls and had a higher discriminating ability than the other parameters. These findings may be related to the compensatory hyper-arousal patterns of the dysfunctional default-mode network (DMN) in schizophrenia. Further research exploring the association between TGC and medical or psychiatric conditions that may confound EEG signals will help clarify the potential utility of TGC.

Keywords: quantitative electroencephalography (QEEG), theta-phase gamma-amplitude coupling (TGC), schizophrenia, diagnostic utility

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Authors: Rasha Ahmadi

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In December 2019, a coronavirus, currently identified as SARS-CoV-2, produced a series of acute atypical respiratory illnesses in Wuhan, Hubei Province, China. The sickness induced by this virus was named COVID-19. The virus is transmittable between humans and has caused pandemics worldwide. The number of death tolls continues to climb and a huge number of countries have been obliged to perform social isolation and lockdown. Lack of focused therapy continues to be a problem. Epidemiological research showed that senior patients were more susceptible to severe diseases, whereas children tend to have milder symptoms. In this study, we focus on other possible side effects of COVID-19 and more detailed treatment strategies. Using bioinformatics analysis, we first isolated the gene expression profile of patients with severe COVID-19 from the GEO database. Patients' blood samples were used in the GSE183071 dataset. We then categorized the genes with high and low expression. In the next step, we uploaded the genes separately to the Enrichr database and evaluated our data for signs and symptoms as well as related medication regimens. The results showed that 138 genes with high expression and 108 genes with low expression were observed differentially in the severe COVID-19 VS control group. Symptoms and diseases such as embolism and thrombosis of the abdominal aorta, ankylosing spondylitis, suicidal ideation or attempt, regional enteritis were observed in genes with high expression and in genes with low expression of acute and subacute forms of ischemic heart, CNS infection and poliomyelitis, synovitis and tenosynovitis. Following the detection of diseases and possible signs and symptoms, Carmustine, Bithionol, Leflunomide were evaluated more significantly for high-expression genes and Chlorambucil, Ifosfamide, Hydroxyurea, Bisphenol for low-expression genes. In general, examining the different and invisible aspects of COVID-19 and identifying possible treatments can help us significantly in the emergency and hospitalization of patients.

Keywords: phenotypes, drug regimens, gene expression profiles, bioinformatics analysis, severe COVID-19

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Authors: Shahid Hussain Abro, Siamak Zohari, Lena H. M. Renström, Désirée S. Jansson, Faruk Otman, Karin Ullman, Claudia Baule

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Infectious bronchitis is an acute, highly contagious respiratory, nephropathogenic and reproductive disease of poultry that is caused by infectious bronchitis virus (IBV). The present study used a large data set of structural gene sequences, including newly generated ones and sequences available in the GenBank database to further analyze the diversity and to identify selective pressures and recombination spots. There were some deletions or insertions in the analyzed regions in isolates of the Italy-02 and D274 genotypes. Whereas, there were no insertions or deletions observed in the isolates of the Massachusetts and 4/91 genotype. The hypervariable nucleotide sequence regions spanned positions 152–239, 554–582, 686–737 and 802–912 in the S1 sub-unit of the all analyzed genotypes. The nucleotide sequence data of the E gene showed that this gene was comparatively unstable and subjected to a high frequency of mutations. The M gene showed substitutions consistently distributed except for a region between nucleotide positions 250–680 that remained conserved. The lowest variation in the nucleotide sequences of ORF5a was observed in the isolates of the D274 genotype. While, ORF5b and N gene sequences showed highly conserved regions and were less subjected to variation. Genes ORF3a, ORF3b, M, ORF5a, ORF5b and N presented negative selective pressure among the analyzed isolates. However, some regions of the ORFs showed favorable selective pressure(s). The S1 and E proteins were subjected to a high rate of mutational substitutions and non-synonymous amino acids. Strong signals of recombination breakpoints and ending break point were observed in the S and N genes. Overall, the results of this study revealed that very likely the strong selective pressures in E, M and the high frequency of substitutions in the S gene can probably be considered the main determinants in the evolution of IBV.

Keywords: IBV, avian infectious bronchitis, structural genes, genotypes, genetic diversity

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Authors: Yong-Hui Zheng

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Viruses hijack host machineries to propagate and spread, which disrupts cellular homeostasis and activates various counteractive mechanisms. Infection of enveloped viruses is dependent on their fusion proteins, which bind to viral receptors to allow virus entry into cells. Fusion proteins are glycoproteins and expressed in the endoplasmic reticulum (ER) by hijacking the secretory pathway. Previously, we reported that Zaire ebolavirus (EBOV)-glycoprotein (GP) expression induces ER stress, and EBOV-GP is targeted by the calnexin cycle to macro-ER-phagy for degradation. We now report that expression of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/SARS2)-spike (S) protein also causes ER stress, and its expression is strongly downregulated by mannosidase alpha class 1B member 1 (MAN1B1), a class I α-mannosidase from the ER. MAN1B1 co-localizes with SARS2-S in the ER, and its downregulation of SARS2-S is blocked by inhibitors targeting lysosomes and autophagy, but not proteasomes, indicating SARS2-S degradation by autolysosomes. Notably, the SARS2-S degradation does not require the core autophagy machinery including ATG3, ATG5, ATG7, and phosphatidylinositol 3-kinase catalytic subunit type 3 (PI3KC3)/vacuolar protein sorting 34 (VPS34), and instead, it requires Beclin 1 (BECN1), a core component in the PI3KC3 complex. In addition, MAN1B1 does not trigger SARS2-S polyubiquitination, and consistently, the SARS2-S degradation does not require the autophagy receptor sequestosome 1 (SQSTM1)/p62. MAN1B1 also downregulates EBOV-GP similarly, but this degradation does not require BECN1. Collectively, we conclude that MAN1B1 downregulates viral fusions by micro-ER-phagy, and importantly, we have identified BECN1-dependent and BECN1-independent mechanisms for micro-ER-phagy.

Keywords: Micro-ER-phagy, reticulophagy, fusion proteins, ER stress

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