Search results for: De Novo

Authors: Romasa Qasim, G. M. Sayedur Rahman, Nahid Hasan, M. Shazzad Hosain

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Millions of people worldwide suffer from Hepatitis C, one of the fatal diseases. Interferon (IFN) and ribavirin are the available treatments for patients with Hepatitis C, but these treatments have their own side-effects. Our research focused on the development of an orally taken small molecule drug targeting the proteins in Hepatitis C Virus (HCV), which has lesser side effects. Our current study aims to the Pharmacophore based drug development of a specific small molecule anti-viral drug for Hepatitis C Virus (HCV). Drug designing using lab experimentation is not only costly but also it takes a lot of time to conduct such experimentation. Instead in this in silico study, we have used computer-aided techniques to propose a Pharmacophore-based anti-viral drug specific for the protein domains of the polyprotein present in the Hepatitis C Virus. This study has used homology modeling and ab initio modeling for protein 3D structure generation followed by pocket identification in the proteins. Drug-able ligands for the pockets were designed using de novo drug design method. For ligand design, pocket geometry is taken into account. Out of several generated ligands, a new Pharmacophore is proposed, specific for each of the protein domains of HCV.

Keywords: pharmacophore-based drug design, anti-viral drug, in-silico drug design, Hepatitis C virus (HCV)

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Authors: Ashish Kumar Pathak, Ritika Sharma, Vishal Nath, Sudhir Pratap Singh, Rakesh Tuli

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Litchi is a sub-tropical fruit crop with genotypes bearing delicious juicy fruits with variable seed size (bold to rudimentary size). Small seed size is a desirable trait in litchi, as it increases consumer acceptance and fruit processing. The biochemical activities in mid- stage ovules (e.g. 16, 20, 24 and 28 days after anthesis) determine the fate of seed and fruit development in litchi. Comprehensive ovule-specific transcriptome analysis was performed in two litchi genotypes with contrasting seed size to gain molecular insight on determinants of seed fates in litchi fruits. The transcriptomic data was de-novo assembled in 1,39,608 trinity transcripts, out of which 6,325 trinity transcripts were differentially expressed between the two contrasting genotypes. Differential transcriptional pattern was found among ovule development stages in contrasting litchi genotypes. The putative genes for salicylic acid, jasmonic acid and brassinosteroid pathway were down-regulated in ovules of small-seeded litchi. Embryogenesis, cell expansion, seed size and stress related trinity transcripts exhibited altered expression in small-seeded genotype. The putative regulators of seed maturation and seed storage were down-regulated in small-seed genotype.

Keywords: Litchi, seed, transcriptome, defence

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Authors: Ji Hye Im, Nguyen T. T. Phuong, Keon Wook Kang

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Estrogens are important for the development and growth of estrogen receptor (ER)-positive breast cancer, for which anti-estrogen therapy is one of the most effective treatments. However, its efficacy can be limited by either de novo or acquired resistance. Aromatase is a key enzyme for the biosynthesis of estrogens, and inhibition of this enzyme leads to profound hypoestrogenism. Here, we found that the basal expression and activity of aromatase were significantly increased in tamoxifen (TAM)-resistant human breast cancer (TAMR-MCF-7) cells compared to control MCF-7 cells. We further revealed that aromatase immunoreactivity in tumor tissues was increased in recurrence group after TAM therapy compared to non-recurrence group after TAM therapy. Phosphorylation of Akt, extracellular signal-regulated kinase (ERK), and p38 kinase were all increased in TAMR-MCF-7 cells. Inhibition of phosphoinositide 3-kinase (PI3K) suppressed the transactivation of the aromatase gene and its enzyme activity. Furthermore, we have also shown that PI3K/Akt-dependent cAMP-response element binding protein (CREB) activation was required for the enhanced expression of aromatase in TAMR-MCF-7 cells. Our findings suggest that aromatase expression is up-regulated in TAM-resistant breast cancer via PI3K/Akt-dependent CREB activation.

Keywords: TAMR-MCF-7, CREB, estrogen receptor, aromatase

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Authors: Vignesh Ratnaraj, Daniel Marascia, Kelly Ruecker

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Purpose: Pulmonary embolism (PE) is a major cause of morbidity and mortality in trauma patients. Data suggests PE is occurring earlier in trauma patients, with attention being turned to possible de novo events. Here, we examine the incidence of early PE at a level 1 trauma center and examine the relationship with a chest injury. Method: A retrospective analysis was performed from a prospective trauma registry at a level 1 trauma center. All patients admitted from 1 January 2010 to 30 June 2019 diagnosed with PE following trauma were included. Early PE was considered a diagnosis within 72 hours of admission. The severity of the chest injury was determined by the Abbreviated Injury Score (AIS). Analysis of severe chest injury and incidence of early PE was performed using chi-square analysis. Sub-analysis on the timing of PE and PE location was also performed using chi-square analysis. Results: Chest injury was present in 125 of 184 patients diagnosed with PE. Early PE occurred in 28% (n=35) of patients with a chest injury, including 24.39% (n=10) with a severe chest injury. Neither chest injury nor severe chest injury determined the presence of early PE (p= > 0.05). Sub-analysis showed a trend toward central clots in early PE (37.14%, n=13) compared to late (27.78%, n=25); however, this was not found to be significant (p= > 0.05). Conclusion: PE occurs early in trauma patients, with almost one-third being diagnosed before 72 hours. This analysis does not support the paradigm that chest injury, nor severe chest injury, results in statistically significant higher rates of early PE. Interestingly, a trend toward early central PE was noted in those suffering chest trauma.

Keywords: trauma, PE, chest injury, anticoagulation

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Authors: Saroj Poudel, Joshua Mancini, Douglas Pike, Jennifer Timm, Alexei Tyryshkin, Vikas Nanda, Paul Falkowski

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On the early Earth, protein-metal complexes likely harvested energy from a reduced environment. These complexes would have been precursors to the metabolic enzymes of ancient organisms. Hydrogenase is an essential enzyme in most anaerobic organisms for the reduction and oxidation of hydrogen in the environment and is likely one of the earliest evolved enzymes. To attempt to reinvent a precursor to modern hydrogenase, we computationally designed a short thirteen amino acid peptide that binds the often-required catalytic transition metal Nickel in hydrogenase. This simple complex can achieve hundreds of hydrogen evolution cycles using light energy in a broad range of temperature and pH. Biophysical and structural investigations strongly indicate the peptide forms a di-nickel active site analogous to Acetyl-CoA synthase, an ancient protein central to carbon reduction in the Wood-Ljungdahl pathway and capable of hydrogen evolution. This work demonstrates that prior to the complex evolution of multidomain enzymes, early peptide-metal complexes could have catalyzed energy transfer from the environment on the early Earth and enabled the evolution of modern metabolism

Keywords: hydrogenase, prebiotic enzyme, metalloenzyme, computational design

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Authors: Hulya Ilyasoglu Buyukkestelli, Sedef Nehir El

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Lutein is a member of xanthophyll group of carotenoids found in fruits and vegetables. Lutein accumulates in the macula region of the retina and known as macular pigment which absorbs damaging light in the blue wavelengths. The presence of lutein in retina has been related to decreased risk of two common eye diseases, age-related macular degeneration, and cataract. Being a strong antioxidant, it may also have effects on prevention some types of cancer, cardiovascular disease, cognitive dysfunction. Humans are not capable of synthesizing lutein de novo; therefore it must be provided naturally by the diet, fortified foods, and beverages or nutritional supplement. However, poor bioavailability and physicochemical stability limit its usage in the food industry. Poor solubility in digestive fluids and sensitivity to heat, light, and oxygen are both affect the stability and bioavailability of lutein. In this context, new technologies, delivery systems and formulations have been applied to improve stability and solubility of lutein. Nanotechnology, including nanoemulsion, nanocrystal, nanoencapsulation technology and microencapsulation by complex coacervation, spray drying are promising ways of increasing solubilization of lutein and stability of it in different conditions. Bioavailability of lutein is also dependent on formulations used, starch formulations and milk proteins, especially sodium caseinate are found effective in improving the bioavailability of lutein. Designing foods with highly bioavailable and stabile lutein needs knowledge about current technologies, formulations, and further needs. This review provides an overview of the new technologies and formulations used to improve bioavailability of lutein and also gives a future outlook to food researches.

Keywords: bioavailability, formulation, lutein, nanotechnology

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Authors: Zeeshan Khan, Faisal Nouroz, Shumaila Noureen

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European or common rabbit (Oryctolagus cuniculus) belongs to class Mammalia, order Lagomorpha of family Leporidae. They are distributed worldwide and are native to Europe (France, Spain and Portugal) and Africa (Morocco and Algeria). LTR retrotransposons are major Class I mobile genetic elements of eukaryotic genomes and play a crucial role in genome expansion, evolution and diversification. They were mostly annotated in various genomes by conventional approaches of homology searches, which restricted the annotation of novel elements. Present work involved de novo identification of LTR retrotransposons by LTR_FINDER in haploid genome of rabbit (2247.74 Mb) distributed in 22 chromosomes, of which 7,933 putative full-length or partial copies were identified containing 69.38 Mb of elements, accounting 3.08% of the genome. Highest copy numbers (731) were found on chromosome 7, followed by chromosome 12 (705), while the lowest copy numbers (27) were detected in chromosome 19 with no elements identified from chromosome 21 due to partially sequenced chromosome, unidentified nucleotides (N) and repeated simple sequence repeats (SSRs). The identified elements ranged in sizes from 1.2 - 25.8 Kb with average sizes between 2-10 Kb. Highest percentage (4.77%) of elements was found in chromosome 15, while lowest (0.55%) in chromosome 19. The most frequent tRNA type was Arginine present in majority of the elements. Based on gained results, it was estimated that rabbit exhibits 15,866 copies having 137.73 Mb of elements accounting 6.16% of diploid genome (44 chromosomes). Further molecular analyses will be helpful in chromosomal localization and distribution of these elements on chromosomes.

Keywords: rabbit, LTR retrotransposons, genome, chromosome

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Authors: Navodit Goel, Prabir K. Paul

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Tomato (Solanum lycopersicum) is attacked by Pseudomonas syringae pv. tomato causing speck lesions on the leaves leading to severe economic casualty. In the present study, aqueous fruit extracts of Azadirachta indica (neem) were sprayed on a single node of tomato plants grown under controlled contamination-free conditions. The treatment of plants was performed with neem fruit extract either alone or along with the pathogen. The parameters of observation were activities of polyphenol oxidase (PPO) and lysozyme, and isoform analysis of PPO; both at the treated leaves as well as untreated leaves away from the site of extract application. Polyphenol oxidase initiates phenylpropanoid pathway resulting in the synthesis of quinines from cytoplasmic phenols and production of reactive oxygen species toxic to broad spectrum microbes. Lysozyme is responsible for the breakdown of bacterial cell wall. The results indicate the upregulation of PPO and lysozyme activities in both the treated and untreated leaves along with de novo expression of newer PPO isoenzymes (which were absent in control samples). The appearance of additional PPO isoenzymes in bioelicitor-treated plants indicates that either the isoenzymes were expressed after bioelicitor application or the already expressed but inactive isoenzymes were activated by it. Lysozyme activity was significantly increased in the plants when treated with the bioelicitor or the pathogen alone. However, no new isoenzymes of lysozyme were expressed upon application of the extract. Induction of resistance by neem fruit extract could be a potent weapon in eco-friendly plant protection strategies.

Keywords: Azadirachta indica, lysozyme, polyphenol oxidase, Solanum lycopersicum

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Authors: Namwinwelbere Dabire, Eugene C. Ezin, Adandedji M. Firmin

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The prediction of hydrological flows (rainfall-depth or rainfall-discharge) is becoming increasingly important in the management of hydrological risks such as floods. In this study, the Long Short-Term Memory (LSTM) network, a state-of-the-art algorithm dedicated to time series, is applied to predict the daily water level of Nokoue Lake in Benin. This paper aims to provide an effective and reliable method enable of reproducing the future daily water level of Nokoue Lake, which is influenced by a combination of two phenomena: rainfall and river flow (runoff from the Ouémé River, the Sô River, the Porto-Novo lagoon, and the Atlantic Ocean). Performance analysis based on the forecasting horizon indicates that LSTM can predict the water level of Nokoué Lake up to a forecast horizon of t+10 days. Performance metrics such as Root Mean Square Error (RMSE), coefficient of correlation (R²), Nash-Sutcliffe Efficiency (NSE), and Mean Absolute Error (MAE) agree on a forecast horizon of up to t+3 days. The values of these metrics remain stable for forecast horizons of t+1 days, t+2 days, and t+3 days. The values of R² and NSE are greater than 0.97 during the training and testing phases in the Nokoué Lake basin. Based on the evaluation indices used to assess the model's performance for the appropriate forecast horizon of water level in the Nokoué Lake basin, the forecast horizon of t+3 days is chosen for predicting future daily water levels.

Keywords: forecasting, long short-term memory cell, recurrent artificial neural network, Nokoué lake

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Authors: Sachin K. Samuchiwal, Barbara Balestrieri, Amanda Paskavitz, Hannah Raff, Joshua A. Boyce

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IL-33, a recently discovered member of the IL-1 cytokine family, binds to the TLR/IL1R super family receptor ST2 and induces type 2 immune responses. IL-33 is constitutively expressed in structural cells at barrier sites such as skin, lung, and intestine, and also inducibly expressed by hematopoietic cells including macrophages. Stimulation of macrophages by Lipopolysaccharide (LPS) can induce de novo IL-33 expression, and also causes the production of prostaglandin-E2 (PGE2) via cyclooxygenase (COX)-2 and microsomal PGE2 synthase-1 (mPGES-1). Because PGE2 can regulate macrophage functions through both autocrine and paracrine mechanisms, the potential interplay of endogenous PGE2 on IL-33 production was explored. Bone-marrow derived murine macrophages (bmMF) that lack either mPGES-1 or EP2 receptor expression were stimulated with LPS in the absence or presence of exogenous PGE2 along with pharmacological agonists and antagonists. The study results demonstrate that endogenous PGE2 markedly enhances LPS-induced IL-33 production by bmMFs via EP2 receptors. Moreover, exogenous PGE2 can amplify LPS-induced IL-33 expression dominantly by EP2 and partly by EP4 receptors by a pathway involving cAMP and exchange protein activated by cAMP (EPAC), but not protein kinase A (PKA). Though both IL-33 production and PGE2 generation in response to LPS require activation of both p38 MAPK and NF-κB, PGE2 did not influence this activation. In conclusion, it is demonstrated that endogenous PGE2 signaling through EP2 and EP4 receptors is a prerequisite for LPS-induced IL-33 production in bmMFs and the underlying cAMP mediated pathway involves EPAC. Since IL-33 is a critical pro-inflammatory cytokine in various pathological disorders, this PGE2-EP2/EP4-cAMP mediated pathway can be exploited to intervene in IL-33 driven pathologies.

Keywords: bone marrow macrophages, EPAC, IL-33, PGE2

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Authors: Raquel Mateo Mendaza, Carmen Novo Urraca

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The current paper presents the elaboration of a corpus database that aligns two different corpora in order to simplify the search of information both for researchers and students of Old English. This database comprises the information contained in two main reference corpora, namely the Dictionary of Old English Corpus (DOEC), compiled at the University of Toronto, and the York-Toronto-Helsinki Parsed Corpus of Old English (YCOE). The first one provides information on all surviving texts written in the Old English language. The latter offers the syntactical and morphological annotation of several texts included in the DOEC. Although both corpora are closely related, as the YCOE includes the DOE source text identifier, the main problem detected is that there is not an alignment of texts that allows for the search of whole fragments to be further analysed in terms of morphology and syntax. The database proposed in this paper gathers all this information and presents it in a simple, more accessible, visual, and educational way. The alignment of fragments has been done in an automatized way. However, some problems have emerged during the creating process particularly related to the lack of correspondence in the division of fragments. For this reason, it has been necessary to revise the whole entries manually to obtain a truthful high-quality product and to carefully indicate the gaps encountered in these corpora. All in all, this database contains more than 60,000 entries corresponding with the DOE fragments annotated by the YCOE. The main strength of the resulting product is its research and teaching implications in the study of Old English. The use of this database will help researchers and students in the study of different aspects of the language, such as inflectional morphology, syntactic behaviour of given words, or translation studies, among others. By means of the search of words or fragments, the annotated information on morphology and syntax will be automatically displayed, automatizing, and speeding up the search of data.

Keywords: alignment, corpus database, morphosyntactic analysis, Old English

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Authors: C. A. Ologunde

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Escherichia coli have been a major microorganisms associated with, and isolated from feacal samples either in adult or children all over the world. Strains of these organisms are resistant to cephalosporins and fluoroquinolone (FQ) antimicrobial agents among hospitalized patients and FQs are the most frequently prescribed antimicrobial class in hospitals, and the level of resistant of E. coli to these antimicrobial agents is a risk factor that should be assessed. Hence, this study was conducted to determine the prevalence and risk factors for colonization with fluoroquinolone (FQ)-resistant E. coli in hospitalized patients in Ado-Ekiti. Rectal swabs were obtained from patients in hospitals in the study area and FQ-resistant E. coli were isolated and identified by means of Nalidixic acid multi-disk and a 1-step screening procedure. Species identification and FQ resistance were confirmed by automated testing (Vitek, bioMerieux, USA). Individual colonies were subjected to pulse-field gel electrophoresis (PAGE) to determine macro-restriction polymorphism after digestion of chromosomal DNA. FQ-resistant E. coli was detected in the stool sample of 37(62%) hospitalized patient. With multivariable analyses, the use of FQ before hospitalization was the only independent risk factor for FQ-resistant E. coli carriage and was consistent for FQ exposures for the 3-12 months of study. Pulsed-field gel electrophoresis of FQ-resistant E. coli identified conal spread of 1(one) strain among 18 patients. Loss (9 patients) or acquisition (10 residents) of FQ-resistant E. coli was documented and was associated with de novo colonization with genetically distinct strains. It was concluded that FQ-resistant E. coli carriage was associated with clonal spread. The differential effects of individual fluoroquinolone on antimicrobial drug resistance are an important area for future study, as hospitals manipulate their formularies with regard to use of individual fluoroquinolone, often for economic reasons.

Keywords: E. coli, fluoroquinolone, risk factors, feacal carriage, hospitalized patients, Ado-Ekiti

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Authors: Masaaki Ii, Takashi Saito, Yasuhiko Tabata, Shintaro Nemoto

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Background: Clinical trials of autologous adipose-derived stem cell (AdSC) therapy for ischemic heart diseases (IHD) are now on-going. We have investigated the hypothesis that combination of AdSCs and statin, an agent with pleiotropic effects, could augment the therapeutic effect on myocardial infarction (MI). Methods and Results: Human AdSC functions with different doses of simvastatin-conjugated nanoparticle (STNP) uptake were evaluated by in vitro assays. STNP promoted the migration activity without changing the proliferation activity, and also up-regulated growth factors. Next, MI was induced by LAD ligation in nude mice, and the mice were assigned in the following groups 3 days after MI: 1) PBS (control), 2) NP-AdSCs (50000 cells), 3) STNP, and 4) STNP-AdSCs (50000 cells). Cardiac functional recovery assessed by echocardiography was improved at 4 weeks after surgery in STNP-AdSC group. Masson’s trichrome-stained sections revealed that LV fibrosis length was reduced, and the number of TUNEL-positive cardiomyocytes was less in STNP-AdSC group. Surprisingly, a number of de novo endogenous Nkx-2.5/GATA4 positive immature cardiomyocytes as well as massive vascular formation were observed in outer layer of infarcted myocardium despite of a few recruited/retained transfused STNP-AdSCs 4 weeks after MI in STNP-AdSC group. Finally, massive myocardial regeneration was observed 8 weeks after MI. Conclusions: Intravenously injected small number of statin nanoparticle-loaded hAdSCs exhibited a potent therapeutic effect inducing endogenous cardiac tissue regeneration.

Keywords: statin, drug delivery system, stem cells, cardiac regeneration

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Authors: Sakeh N. Mohd, Bahari M. N. Abdul, Abdullah S. N. Akmar

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Oil palm production generates high export earnings to many countries especially in Southeast Asian region. Infection by necrotrophic fungus, Ganoderma boninense on oil palm results in basal stem rot which compromises oil palm production leading to significant economic loss. There are no reliable disease treatments nor promising resistant oil palm variety has been cultivated to eradicate the disease up to date. Thus, understanding molecular mechanisms underlying early interactions of oil palm with Ganoderma boninense may be vital to promote preventive or control measure of the disease. In the present study, four months old oil palm seedlings were infected via artificial inoculation of Ganoderma boninense on rubber wood blocks. Roots of six biological replicates of treated and untreated oil palm seedlings were harvested at 0, 3, 7 and 11 days post inoculation. Next-generation sequencing was performed to generate high-throughput RNA-Seq data and identify differentially expressed genes (DEGs) during early oil palm-Ganoderma boninense interaction. Based on de novo transcriptome assembly, a total of 427,122,605 paired-end clean reads were assembled into 30,654 unigenes. DEGs analysis revealed upregulation of 173 transcription factors on Ganoderma boninense-treated oil palm seedlings. Sixty-one transcription factors were categorized as DEGs according to stringent cut-off values of genes with log2 ratio [Number of treated oil palm seedlings/ Number of untreated oil palm seedlings] ≥ |1.0| (corresponding to 2-fold or more upregulation) and P-value ≤ 0.01. Transcription factors in response to biotic stress will be screened out from abiotic stress using reverse transcriptase polymerase chain reaction. Transcription factors unique to biotic stress will be verified using real-time polymerase chain reaction. The findings will help researchers to pinpoint defense response mechanism specific against Ganoderma boninense.

Keywords: Ganoderma boninense, necrotrophic, next-generation sequencing, transcription factors

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Authors: Mohammad-Javad Eslami, Mahtab Zargham, Farshad Gholipour, Mohammadreza Hajian, Katayoun Bakhtiari, Sakineh Hajebrahimi, Melina Eghbal, Ziba Farajzadegan

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Introduction: To study the mid-term safety and functional outcomes of transvaginal anterior vaginal wall prolapse repair using polyvinylidene fluoride (PVDF) mesh (DynaMesh®-PR4) by the double trans-obturator technique (TOT). Methods: Between 2015 and 2020, we prospectively included women with symptomatic high-stage anterior vaginal wall prolapse with or without uterine prolapse or stress urinary incontinence (SUI) in the study. The patients underwent transvaginal repair of the prolapse using PVDF mesh in two medical centers. We followed all patients for at least 12 months. We recorded the characteristics of vaginal and sexual symptoms, urinary incontinence, and prolapse stage pre- and postoperatively using International Consultation on Incontinence Questionnaire-Vaginal Symptoms (ICIQ-VS), International Consultation on Incontinence Questionnaire-Urinary Incontinence-Short Form (ICIQ-UI-SF), and Pelvic Organ Prolapse Quantification (POP-Q) system, respectively. Results: One hundred eight women were included in the final analysis with a mean follow-up time of 34.5 ± 18.6 months. The anatomical success was achieved in 103 (95.4%) patients. There was a significant improvement in patients’ vaginal symptoms, urinary incontinence, and quality of life scores postoperatively (p < 0.0001). Only six patients (5.5%) had mesh extrusion, five of whom were managed successfully. The total rates of complications and de novo urinary symptoms were 21.3% and 7.4%, respectively. Significant pain was reported in 17 cases (15.7%). Conclusion: Our findings show that using PVDF mesh in the double TOT technique for anterior vaginal wall prolapse repair is a safe procedure with high anatomic and functional success rates and acceptable complication rates in mid-term follow-up.

Keywords: stress urinary incontinence (SU, incontinence questionnaire-vaginal symptoms (ICIQ-VS), polyvinylidene fluoride (PVDF) mes, double trans-obturator technique (TOT)

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Authors: Wadha Alqahtani

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In recent times, polymers have seen a great surge in interest in the field of medicine, particularly chemotherapeutics. One recent innovation is the conversion of polymeric materials into “polymeric nanoparticles”. These nanoparticles can be designed and modified to encapsulate and transport drugs selectively to cancer cells, minimizing collateral damage to surrounding healthy tissues, and improve patient quality of life. In this study, we have synthesized pseudo-branched polyester polymers from bio-based small molecules, including sorbitol, glutaric acid and a propargylic acid derivative to further modify the polymer to make it “click-able" with an azide-modified target ligand. Melt polymerization technique was used for this polymerization reaction, using lipase enzyme catalyst NOVO 435. This reaction was conducted between 90- 95 °C for 72 hours. The polymer samples were collected in 24-hour increments for characterization and to monitor reaction progress. The resulting polymer was purified with the help of methanol dissolving and filtering with filter paper then characterized via NMR, GPC, FTIR, DSC, TGA and MALDI-TOF. Following characterization, these polymers were converted to a polymeric nanoparticle drug delivery system using solvent diffusion method, wherein DiI optical dye and chemotherapeutic drug Taxol can be encapsulated simultaneously. The efficacy of the nanoparticle’s apoptotic effects were analyzed in-vitro by incubation with prostate cancer (LNCaP) and healthy (CHO) cells. MTT assays and fluorescence microscopy were used to assess the cellular uptake and viability of the cells after 24 hours at 37 °C and 5% CO2 atmosphere. Results of the assays and fluorescence imaging confirmed that the nanoparticles were successful in both selectively targeting and inducing apoptosis in 80% of the LNCaP cells within 24 hours without affecting the viability of the CHO cells. These results show the potential of using biodegradable polymers as a vehicle for receptor-specific drug delivery and a potential alternative for traditional systemic chemotherapy. Detailed experimental results will be discussed in the e-poster.

Keywords: chemotherapeutic drug, click chemistry, nanoparticle, prostat cancer

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Authors: Rossana Taravella, Gilberto M. Cellura, Giuseppe Cirrincione, Salvatore Asciutto, Marco Caruso, Massimo Benedetto, Renato Ciofalo, Giuliana Pace, Salvatore Novo

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Objectives: This retrospective analysis sought to evaluate 1-month outcomes and therapy effectiveness of a population of patients treated with MitraClip therapy. We describe in this article the preliminary results of primary effectiveness endpoint. Background: Percutaneous Mitral Repair is being developed to treat severe mitral regurgitation (MR), with increasing real-world cases of functional MR (FMR). In the EVEREST (Endovascular Valve Edge-to-Edge Repair Study)II trial, the percutaneous device showed superior safety but less reduction in MR at 1year. 4-year outcomes from EVEREST II trial showed no difference in the prevalence of moderate-severe and severe MR or mortality at 4years between surgical mitral repair and percutaneous approach. Methods: We analysed retrospectively collected data from one center experience in Italy enrolled from January 2011 to December 2016. The study included 62 patients [mean age 74±11years, 43 men (69%)] with MR of at least grade3+. Most of the patients had functional MR, were in New York Heart Association (NYHA) functional class III or IV, with a large portion (78%) of mild-to-moderate Tricuspid Regurgitation (TR). One or more clips were implanted in 67 procedures (62 patients). Results and Conclusions: Severity of MR was reduced in all successfully treated patients,54(90%) were discharged with MR≤2+ (primary effectiveness endpoint). Clinical 1-month follow-up data showed an improvement in NYHA functional class (42 patients (70%) in NYHA class I-II). 60 of 62 (97 %) successfully treated patients were free from death and mitral valve surgery at 1-month follow-up. MitraClip therapy reduces functional MR with acute MR reduction to <2+ in the great majority of patients, with a large freedom from death, surgery or recurrent MR in a great portion of patients.

Keywords: MitraClip, mitral regurgitation, heart valves, catheter-based therapy

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Authors: Vivian A. Panes, Raymond John S. Rebong, Miel Q. Diaz

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Moringa oleifera Lam. is known mainly for its high nutritional value and medicinal properties contributing to its popular reputation as a 'miracle plant' in the tropical climates where it usually grows. The main objective of this study is to discover the genes and gene products involved in abiotic stress-induced activity that may impact the M. oleifera Lam. mature seeds as well as their corresponding functions. In this study, RNA-sequencing and de novo transcriptome assembly were performed using two assemblers, Trinity and Oases, which produced 177,417 and 120,818 contigs respectively. These transcripts were then subjected to various bioinformatics tools such as Blast2GO, UniProt, KEGG, and COG for gene annotation and the analysis of relevant metabolic pathways. Furthermore, FPKM analysis was performed to identify gene expression levels. The sequences were filtered according to the 'response to stress' GO term since this study dealt with stress response. Clustered Orthologous Groups (COG) showed that the highest frequencies of stress response gene functions were those of cytoskeleton which make up approximately 14% and 23% of stress-related sequences under Trinity and Oases respectively, recombination, repair and replication at 11% and 14% respectively, carbohydrate transport and metabolism at 23% and 9% respectively and defense mechanisms 16% and 12% respectively. KEGG pathway analysis determined the most abundant stress-response genes in the phenylpropanoid biosynthesis at counts of 187 and 166 pathways for Oases and Trinity respectively, purine metabolism at 123 and 230 pathways, and biosynthesis of antibiotics at 105 and 102. Unique and cumulative GO term counts revealed that majority of the stress response genes belonged to the category of cellular response to stress at cumulative counts of 1,487 to 2,187 for Oases and Trinity respectively, defense response at 754 and 1,255, and response to heat at 213 and 208, response to water deprivation at 229 and 228, and oxidative stress at 508 and 488. Lastly, FPKM was used to determine the levels of expression of each stress response gene. The most upregulated gene encodes for thiamine thiazole synthase chloroplastic-like enzyme which plays a significant role in DNA damage tolerance. Data analysis implies that M. oleifera stress response genes are directed towards the effects of climate change more than other stresses indicating the potential of M. oleifera for cultivation in harsh environments because it is resistant to climate change, pathogens, and foreign invaders.

Keywords: stress response, genes, Moringa oleifera, transcriptomics

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Authors: Yasser Ahmed Mahmoud Ali Helal

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The use of CAD (Computer Aided Design) technology is ubiquitous in the architecture, engineering and construction (AEC) industry. This has led to its inclusion in the curriculum of architecture schools in Nigeria as an important part of the training module. This article examines the ethical issues involved in implementing CAD (Computer Aided Design) content into the architectural education curriculum. Using existing literature, this study begins with the benefits of integrating CAD into architectural education and the responsibilities of different stakeholders in the implementation process. It also examines issues related to the negative use of information technology and the perceived negative impact of CAD use on design creativity. Using a survey method, data from the architecture department of University was collected to serve as a case study on how the issues raised were being addressed. The article draws conclusions on what ensures successful ethical implementation. Millions of people around the world suffer from hepatitis C, one of the world's deadliest diseases. Interferon (IFN) is treatment options for patients with hepatitis C, but these treatments have their side effects. Our research focused on developing an oral small molecule drug that targets hepatitis C virus (HCV) proteins and has fewer side effects. Our current study aims to develop a drug based on a small molecule antiviral drug specific for the hepatitis C virus (HCV). Drug development using laboratory experiments is not only expensive, but also time-consuming to conduct these experiments. Instead, in this in silicon study, we used computational techniques to propose a specific antiviral drug for the protein domains of found in the hepatitis C virus. This study used homology modeling and abs initio modeling to generate the 3D structure of the proteins, then identifying pockets in the proteins. Acceptable lagans for pocket drugs have been developed using the de novo drug design method. Pocket geometry is taken into account when designing ligands. Among the various lagans generated, a new specific for each of the HCV protein domains has been proposed.

Keywords: drug design, anti-viral drug, in-silicon drug design, hepatitis C virus (HCV) CAD (Computer Aided Design), CAD education, education improvement, small-size contractor automatic pharmacy, PLC, control system, management system, communication

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Authors: A. Díaz-Roa, P. I. Silva Junior, F. J. Bello

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Sarconesiopsis magellanica (Diptera: Calliphoridae) is a medically important necrophagous fly which is used for establishing the post-mortem interval. Dipterous maggots release diverse proteins and peptides contained in larval excretion and secretion (ES) products playing a key role in digestion. The most important mechanism for combating infection using larval therapy depends on larval ES. These larvae are protected against infection by a diverse spectrum of antimicrobial peptides (AMPs), one already known like lucifensin. Special interest in these peptides has also been aroused regarding understanding their role in wound healing since they degrade necrotic tissue and kill different bacteria during larval therapy. The action of larvae on wounds occurs through 3 mechanisms of action: removal of necrotic tissue, stimulation of granulation tissue, and antibacterial action of larval ES. Some components of the ES include calcium, urea, allantoin ammonium bicarbonate and reducing the viability of Gram positive and Gram negative bacteria. The Lucilia sericata fly larvae have been the most used, however, we need to evaluate new species that could potentially be similar or more effective than fly above. This study was thus aimed at identifying and characterizing S. magellanica AMPs contained in ES products for the first time and compared them with the common fly used L. sericata. These products were obtained from third-instar larvae taken from a previously established colony. For the first analysis, ES fractions were separate by Sep-Pak C18 disposable columns (first step). The material obtained was fractionated by RP-HPLC by using Júpiter C18 semi-preparative column. The products were then lyophilized and their antimicrobial activity was characterized by incubation with different bacterial strains. The first chromatographic analysis of ES from L. sericata gives 6 fractions with antimicrobial activity against Gram-positive bacteria Micrococus luteus, and 3 fractions with activity against Gram-negative bacteria Pseudomonae aeruginosa while the one from S. magellanica gaves 1 fraction against M. luteus and 4 against P. aeruginosa. Maybe one of these fractions could correspond to the peptide already known from L. sericata. These results show the first work for supporting further experiments aimed at validating S. magellanica use in larval therapy. We still need to search if we find some new molecules, by making mass spectrometry and ‘de novo sequencing’. Further studies are necessary to identify and characterize them to better understand their functioning.

Keywords: antimicrobial peptides, larval therapy, Lucilia sericata, Sarconesiopsis magellanica

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Authors: Peter Edwar Mortada Nasif

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The use of CAD (Computer Aided Design) technology is ubiquitous in the architecture, engineering and construction (AEC) industry. This has led to its inclusion in the curriculum of architecture schools in Nigeria as an important part of the training module. This article examines the ethical issues involved in implementing CAD (Computer Aided Design) content into the architectural education curriculum. Using existing literature, this study begins with the benefits of integrating CAD into architectural education and the responsibilities of different stakeholders in the implementation process. It also examines issues related to the negative use of information technology and the perceived negative impact of CAD use on design creativity. Using a survey method, data from the architecture department of Chukwuemeka Odumegwu Ojukwu Uli University was collected to serve as a case study on how the issues raised were being addressed. The article draws conclusions on what ensures successful ethical implementation. Millions of people around the world suffer from hepatitis C, one of the world's deadliest diseases. Interferon (IFN) is treatment options for patients with hepatitis C, but these treatments have their side effects. Our research focused on developing an oral small molecule drug that targets hepatitis C virus (HCV) proteins and has fewer side effects. Our current study aims to develop a drug based on a small molecule antiviral drug specific for the hepatitis C virus (HCV). Drug development using laboratory experiments is not only expensive, but also time-consuming to conduct these experiments. Instead, in this in silicon study, we used computational techniques to propose a specific antiviral drug for the protein domains of found in the hepatitis C virus. This study used homology modeling and abs initio modeling to generate the 3D structure of the proteins, then identifying pockets in the proteins. Acceptable lagans for pocket drugs have been developed using the de novo drug design method. Pocket geometry is taken into account when designing ligands. Among the various lagans generated, a new specific for each of the HCV protein domains has been proposed.

Keywords: drug design, anti-viral drug, in-silicon drug design, hepatitis C virus, computer aided design, CAD education, education improvement, small-size contractor automatic pharmacy, PLC, control system, management system, communication

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Authors: Kamil Ganaev, Elina Vlasova, Andrei Shiryaev, Renat Akchurin

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De novo atrial fibrillation (AF) after coronary artery bypass grafting (CABG) is a common complication. To date, there are no data on the possible effect of diffuse lesions of coronary arteries on the incidence of postoperative AF complications. Methods. Patients operated on-pump under hypothermic conditions during the calendar year (2020) were studied. Inclusion criteria - isolated CABG and achievement of complete myocardial revascularization. Patients with a history of AF moderate and severe valve dysfunction, hormonal thyroid pathology, initial CHF(Congestive heart failure), as well as patients with developed perioperative complications (IM, acute heart failure, massive blood loss) and deceased were excluded. Thus 227 patients were included; mean age 65±9 years; 69% were men. 89% of patients had a 3-vessel lesion of the coronary artery; the remainder had a 2-vessel lesion. Mean LV size: 3.9±0.3 cm, indexed LV volume: 29.4±5.3 mL/m2. Two groups were considered: D (n=98), patients with diffuse coronary heart disease, and L (n=129), patients with local coronary heart disease. Clinical and demographic characteristics in the groups were comparable. Rhythm assessment: continuous bedside ECG monitoring up to 5 days; ECG CT at 5-7 days after CABG; daily routine ECG registration. Follow-up period - postoperative hospital period. Results. The Median follow-up period was 9 (7;11) days. POFP (Postoperative atrial fibrillation) was detected in 61/227 (27%) patients: 34/98 (35%) in group D versus 27/129 (21%) in group L; p<0.05. Moreover, the values of revascularization index in groups D and L (3.9±0.7 and 3.8±0.5, respectively) were equal, and the mean time Cardiopulmonary bypass (CPB) (107±27 and 80±13min), as well as the mean ischemic time (67±17 and 55±11min) were significantly longer in group D (p<0.05). However, a separate analysis of these parameters in patients with and without developed AF did not reveal any significant differences in group D (CPB time 99±21.2 min, ischemic time 63±12.2 min), or in group L (CPB time 88±13.1 min, ischemic time 58.7±13.2 min). Conclusion. With the diffuse nature of coronary lesions, the incidence of AF in the hospital period after isolated CABG definitely increases. To better understand the role of severe coronary atherosclerosis in the development of POAF, it is necessary to distinguish the influence of organic features of atrial and ventricular myocardium (as a consequence of chronic coronary disease) from the features of surgical correction in diffuse coronary lesions.

Keywords: atrial fibrillation, diffuse coronary artery disease, coronary artery bypass grafting, local coronary artery disease

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Authors: Aswini M. S.

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Tomato (Solanum lycopersicum L.) is one of the most significant vegetable crops in terms of its economic benefits. Both fresh and processed tomatoes are consumed. Tomatoes have a limited genetic base, which makes breeding extremely challenging. Plant breeding has become much simpler and more effective with genome editing tools of CRISPR and CRISPR-associated 9 protein (CRISPR/Cas9), which address the problems with traditional breeding, chemical/physical mutagenesis, and transgenics. With the use of CRISPR/Cas9, a number of tomato traits have been functionally distinguished and edited. These traits include plant architecture as well as flower characters (leaf, flower, male sterility, and parthenocarpy), fruit ripening, quality and nutrition (lycopene, carotenoid, GABA, TSS, and shelf-life), disease resistance (late blight, TYLCV, and powdery mildew), tolerance to abiotic stress (heat, drought, and salinity) and resistance to herbicides. This study explores the potential of CRISPR/Cas9 genome editing for enhancing yield in tomato plants. The study utilized the CRISPR/Cas9 genome editing technology to functionally edit various traits in tomatoes. The de novo domestication of elite features from wild cousins to cultivated tomatoes and vice versa has been demonstrated by the introgression of CRISPR/Cas9. The CycB (Lycopene beta someri) gene-mediated Cas9 editing increased the lycopene content in tomato. Also, Cas9-mediated editing of the AGL6 (Agamous-like 6) gene resulted in parthenocarpic fruit development under heat-stress conditions. The advent of CRISPR/Cas has rendered it possible to use digital resources for single guide RNA design and multiplexing, cloning (such as Golden Gate cloning, GoldenBraid, etc.), creating robust CRISPR/Cas constructs, and implementing effective transformation protocols like the Agrobacterium and DNA free protoplast method for Cas9-gRNAs ribonucleoproteins (RNPs) complex. Additionally, homologous recombination (HR)-based gene knock-in (HKI) via geminivirus replicon and base/prime editing (Target-AID technology) remains possible. Hence, CRISPR/Cas facilitates fast and efficient breeding in the improvement of tomatoes.

Keywords: CRISPR-Cas, biotic and abiotic stress, flower and fruit traits, genome editing, polygenic trait, tomato and trait introgression

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Authors: Selisha A. Sooklal, Phelelani Mpangase, Shaun Aron, Karl Rumbold

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Organically bound fluorine (C-F bond) is extremely rare in nature. Despite this, the first fluorinated secondary metabolite, fluoroacetate, was isolated from the plant Dichapetalum cymosum (commonly known as Gifblaar). However, the enzyme responsible for fluorination (fluorinase) in Gifblaar was never isolated and very little progress has been achieved in understanding this process in higher plants. Fluorinated compounds have vast applications in the pharmaceutical, agrochemical and fine chemicals industries. Consequently, an enzyme capable of catalysing a C-F bond has great potential as a biocatalyst in the industry considering that the field of fluorination is virtually synthetic. As with any biocatalyst, a range of these enzymes are required. Therefore, it is imperative to expand the exploration for novel fluorinases. This study aimed to gain molecular insights into secondary metabolite biosynthesis in Gifblaar using a high-throughput sequencing-based approach. Mechanical wounding studies were performed using Gifblaar leaf tissue in order to induce expression of the fluorinase. The transcriptome of the wounded and unwounded plant was then sequenced on the Illumina HiSeq platform. A total of 26.4 million short sequence reads were assembled into 77 845 transcripts using Trinity. Overall, 68.6 % of transcripts were annotated with gene identities using public databases (SwissProt, TrEMBL, GO, COG, Pfam, EC) with an E-value threshold of 1E-05. Sequences exhibited the greatest homology to the model plant, Arabidopsis thaliana (27 %). A total of 244 annotated transcripts were found to be differentially expressed between the wounded and unwounded plant. In addition, secondary metabolic pathways present in Gifblaar were successfully reconstructed using Pathway tools. Due to lack of genetic information for plant fluorinases, a transcript failed to be annotated as a fluorinating enzyme. Thus, a local database containing the 5 existing bacterial fluorinases was created. Fifteen transcripts having homology to partial regions of existing fluorinases were found. In efforts to obtain the full coding sequence of the Gifblaar fluorinase, primers were designed targeting the regions of homology and genome walking will be performed to amplify the unknown regions. This is the first genetic data available for Gifblaar. It has provided novel insights into the mechanisms of metabolite biosynthesis and will allow for the discovery of the first eukaryotic fluorinase.

Keywords: biocatalyst, fluorinase, gifblaar, transcriptome

Procedia PDF Downloads 273

Authors: Mario Hanna Louis Hanna

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The use of CAD (pc Aided layout) generation is ubiquitous inside the structure, engineering and construction (AEC) industry. This has led to its inclusion in the curriculum of structure faculties in Nigeria as an important part of the training module. This newsletter examines the moral troubles involved in implementing CAD (pc Aided layout) content into the architectural training curriculum. Using current literature, this study begins with the advantages of integrating CAD into architectural education and the responsibilities of various stakeholders in the implementation process. It also examines issues related to the terrible use of records generation and the perceived bad effect of CAD use on design creativity. The use of a survey technique, information from the architecture department of Chukwuemeka Odumegwu Ojukwu Uli college changed into accumulated to serve as a case observe on how the problems raised have been being addressed. The object draws conclusions on what guarantees a hit moral implementation. Tens of millions of human beings around the sector suffer from hepatitis C, one of the international's deadliest sicknesses. Interferon (IFN) is a remedy alternative for patients with hepatitis C, but these treatments have their aspect outcomes. Our research targeted growing an oral small molecule drug that goals hepatitis C virus (HCV) proteins and has fewer facet effects. Our contemporary study targets to broaden a drug primarily based on a small molecule antiviral drug precise for the hepatitis C virus (HCV). Drug improvement and the use of laboratory experiments isn't always best high-priced, however also time-eating to behavior those experiments. instead, on this in silicon have a look at, we used computational strategies to recommend a particular antiviral drug for the protein domain names of discovered in the hepatitis C virus. This examines used homology modeling and abs initio modeling to generate the 3-D shape of the proteins, then figuring out pockets within the proteins. Proper lagans for pocket pills were advanced the usage of the de novo drug design method. Pocket geometry is taken into consideration while designing ligands. A few of the various lagans generated, a different for each of the HCV protein domains has been proposed.

Keywords: drug design, anti-viral drug, in-silicon drug design, Hepatitis C virus (HCV) CAD (Computer Aided Design), CAD education, education improvement, small-size contractor automatic pharmacy, PLC, control system, management system, communication.

Procedia PDF Downloads 27

Authors: M. L. W. P. De Silva, R. A. C. Rabel, N. Smith, L. McIntyre, T. J Parkinson, K. A. N. Wijayawardhane

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Curricular integration is an important concept in medical education for developing students’ ability to create connections between different medical disciplines. Problem-Based Learning (PBL) is one of the vehicles through which such integration can be achieved. During the recent review of the veterinary curriculum at the University of Peradeniya, a series of courses in Integrative Veterinary Science (IVS) were introduced, in which PBL was the primary teaching methodology. The objectives of this study were to evaluate students’ opinions on PBL as a teaching method: it should be noted that, within the context of secondary and tertiary education in Sri Lanka, this would be an entirely novel learning experience for the students. Opinions were sought at the conclusion of IVS sessions where students of semesters 2, 4, 6, and 7 (of an 8-semester program) were exposed to a two, 2-hour PBL-based case scenario. The PBL-based case scenario in semesters 2, 4, and 7 were delivered using material previously developed by an experienced PBL practitioner, whilst material for semester 6 was prepared de novo by a less experienced practitioner. Each student (semesters 2: n=38, 4: n=37, 6: n=55, and 7: n=40) completed a questionnaire which asked whether: (i) the course had improved their critical thinking skills; (ii) the learning environment was sufficiently comfortable to express/share student’s opinion; (iii) there was sufficient facilitator guidance; (iv) the online study environment enhanced learning; and (v) the students were overall satisfied with the PBL approach and IVS concept. Responses were given on a 5-point Likert-scale (strongly agree (SA), agree (A), neutral (N), disagree (D), and strongly disagree (SD)). SA and A responses were summed to provide an overall ‘satisfactory’ response. Results were subjected to frequency-distribution statistical analysis. A total of 88.5% of students gave SA+A scores to their overall satisfaction. The proportion of SA+A scores differed between different semesters, such that 95% of semester 2, 4, and 7 students gave SA+A scores, whereas only 69% of semester 6 students did so for their respective sessions. Overall, 96% of the students gave SA+A scores to the question relating to the improvement of critical thinking skills: semester 6 students’ scores were marginally, but not significantly, lower (91% SA+A) than those in other semesters. The difference of scores between semester 6 and the other semesters may be attributed to the different PBL-material used and/or the different experience levels of the practitioners that developed the study material. The use of PBL as a means of teaching IVS curriculum-integration courses was well-received by the students in terms of their overall satisfaction and their perceptions of improved critical thinking skills. Importantly, this was achieved in the face of a methodology that was entirely novel to the students. Finally, the delivery of the PBL medium was readily mastered by the practitioner to whom it was also a novel methodology.

Keywords: critical thinking skills, integration, problem based learning, veterinary education

Procedia PDF Downloads 133

Authors: Ante Turudic, Filip Varga, Zlatko Liber, Jernej Jakse, Zlatko Satovic, Ivan Radosavljevic, Martina Grdisa

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Microsatellites (SSRs) are highly informative repetitive sequences of 2-6 base pairs, which are the most used molecular markers in assessing the genetic diversity of plant species. Dalmatian pyrethrum (Tanacetum cinerariifolium /Trevir./ Sch. Bip) is an outcrossing diploid (2n = 18) endemic to the eastern Adriatic coast and source of the natural insecticide pyrethrin. Due to the high repetitiveness and large size of the genome (haploid genome size of 9,58 pg), previous attempts to develop microsatellite markers using the standard methods were unsuccessful. A next-generation sequencing (NGS) approach was applied on genomic DNA extracted from fresh leaves of Dalmatian pyrethrum. The sequencing was conducted using NovaSeq6000 Illumina sequencer, after which almost 400 million high-quality paired-end reads were obtained, with a read length of 150 base pairs. Short reads were assembled by combining two approaches; (1) de-novo assembly and (2) joining of overlapped pair-end reads. In total, 6.909.675 contigs were obtained, with the contig average length of 249 base pairs. Of the resulting contigs, 31.380 contained one or multiple microsatellite sequences, in total 35.556 microsatellite loci were identified. Out of detected microsatellites, dinucleotide repeats were the most frequent, accounting for more than half of all microsatellites identifies (21,212; 59.7%), followed by trinucleotide repeats (9,204; 25.9%). Tetra-, penta- and hexanucleotides had similar frequency of 1,822 (5.1%), 1,472 (4.1%), and 1,846 (5.2%), respectively. Contigs containing microsatellites were further filtered by SSR pattern type, transposon occurrences, assembly characteristics, GC content, and the number of occurrences against the draft genome of T. cinerariifolium published previously. After the selection process, 50 microsatellite loci were used for primer design. Designed primers were tested on samples from five distinct populations, and 25 of them showed a high degree of polymorphism. The selected loci were then genotyped on 20 samples belonging to one population resulting in 17 microsatellite markers. Availability of codominant SSR markers will significantly improve the knowledge on population genetic diversity and structure as well as complex genetics and biochemistry of this species. Acknowledgment: This work has been fully supported by the Croatian Science Foundation under the project ‘Genetic background of Dalmatian pyrethrum (Tanacetum cinerariifolium /Trevir/ Sch. Bip.) insecticidal potential’ - (PyrDiv) (IP-06-2016-9034).

Keywords: genome assembly, NGS, SSR, Tanacetum cinerariifolium

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Authors: Yew Mun Yip, Dawei Zhang

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Proteins are the biological machinery that executes specific vital functions in every cell of the human body by folding into their 3D structures. When a protein misfolds from its native structure, the machinery will malfunction and lead to misfolding diseases. Although in vitro experiments are able to conclude that the mutations of the amino acid sequence lead to incorrectly folded protein structures, these experiments are unable to decipher the folding process. Therefore, molecular dynamic (MD) simulations are employed to simulate the folding process so that our improved understanding of the folding process will enable us to contemplate better treatments for misfolding diseases. MD simulations make use of force fields to simulate the folding process of peptides. Secondary structures are formed via the hydrogen bonds formed between the backbone atoms (C, O, N, H). It is important that the hydrogen bond energy computed during the MD simulation is accurate in order to direct the folding process to the native structure. Since the atoms involved in a hydrogen bond possess very dissimilar electronegativities, the more electronegative atom will attract greater electron density from the less electronegative atom towards itself. This is known as the polarization effect. Since the polarization effect changes the electron density of the two atoms in close proximity, the atomic charges of the two atoms should also vary based on the strength of the polarization effect. However, the fixed atomic charge scheme in force fields does not account for the polarization effect. In this study, we introduce the polarized structure-specific backbone charge (PSBC) model. The PSBC model accounts for the polarization effect in MD simulation by updating the atomic charges of the backbone hydrogen bond atoms according to equations derived between the amount of charge transferred to the atom and the length of the hydrogen bond, which are calculated from quantum-mechanical calculations. Compared to other polarizable models, the PSBC model does not require quantum-mechanical calculations of the peptide simulated at every time-step of the simulation and maintains the dynamic update of atomic charges, thereby reducing the computational cost and time while accounting for the polarization effect dynamically at the same time. The PSBC model is applied to two different β-peptides, namely the Beta3s/GS peptide, a de novo designed three-stranded β-sheet whose structure is folded in vitro and studied by NMR, and the trpzip peptides, a double-stranded β-sheet where a correlation is found between the type of amino acids that constitute the β-turn and the β-propensity.

Keywords: hydrogen bond, polarization effect, protein folding, PSBC

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Authors: Mohit Kumar, Beklashwar Salona, Shiv Murti, Mukesh Singh

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We report here a case of five-months old male baby, born as second child of non-consanguineous parents with no considerable history of genetic abnormality which was referred to our cytogenetic laboratory for chromosomal analysis. Physical dysmorphic facial features including mongoloid face, cleft palate, simian crease, and developmental delay were observed. We present this case with unique balanced autosomal translocation of t(3;10)(p21;p13). The risk of phenotypic abnormalities based on de novo balanced translocation was estimated to be 7%. The association of balanced chromosomal rearrangement with Down syndrome features such as multiple congenital anomalies, facial dysmorphism and congenital heart anomalies are very rare in a 5-months old male child. Trisomy-21 is not uncommon in chromosomal abnormality with the birth defect and balanced translocations are frequently observed in patients with secondary infertility or recurrent spontaneous abortion (RSA). Two ml heparinized peripheral blood cells cultured in RPMI-1640 for 72 hours supplemented with 20% fetal bovine serum, phytohemagglutinin (PHA), and antibiotics were used for chromosomal analysis. A total 30 metaphases images were captured using Olympus-BX51 microscope and analyzed using Bio-view karyotyping software through GTG-banding (G bands by trypsin and Giemsa) according to International System for Human Cytogenetic Nomenclature 2016. The results showed balanced translocation between short arm of chromosome # 3 and short arm of chromosome # 10. The karyotype of the child was found to be 46,XY,t(3;10)(p21; p13). Chromosomal abnormalities are one of the major causes of birth defect in new born babies. Also, balanced translocations are frequently observed in patients with secondary infertility or recurrent spontaneous abortion. The index case presented with dysmorphic facial features and had a balanced translocation 46,XY,t(3;10)(p21;p13). This translocation with break points at (p21; p13) has not been reported in the literature in a child with facial dysmorphism. To the best of our knowledge, this is the first report of novel balanced translocation t(3;10) with break points in a child with dysmorphic features. We found balanced chromosomal translocation instead of any trisomy or unbalanced aberrations along with some phenotypic abnormalities. Therefore, we suggest that such novel balanced translocation with abnormal phenotype should be reported in order to enable the pathologist, pediatrician, and gynecologist to have a better insight into the intricacies of chromosomal abnormalities and their associated phenotypic features. We hypothesized that dysmorphic features as seen in this case may be the result of change in the pattern of genes located at the breakpoint area in balanced translocations or may be due to deletion or mutation of genes located on the p-arm of chromosome # 3 and p-arm of chromosome # 10.

Keywords: balanced translocation, karyotyping, phenotypic abnormalities, facial dimorphisms

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Authors: Domingos Viegas, Miguel Almeida, Carmen Rocha, Ilda Novo, Yolanda Luna

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Forest fires along the more than 1200km of the Spanish-Portuguese border are more and more frequent, currently achieving around 2000 fire events per year. Some of these events develop to large international wildfire requiring concerted operations based on shared information between the two countries. The fire event of Valencia de Alcantara (2003) causing several fatalities and more than 13000ha burnt, is a reference example of these international events. Currently, Portugal and Spain have a specific cross-border cooperation protocol on wildfires response for a strip of about 30km (15 km for each side). It is recognized by public authorities the successfulness of this collaboration however it is also assumed that this cooperation should include more functionalities such as the development of a common risk information system for transboundary fire events. Since Portuguese and Spanish authorities use different approaches to determine the fire risk indexes inputs and different methodologies to assess the fire risk, sometimes the conjoint firefighting operations are jeopardized since the information is not harmonized and the understanding of the situation by the civil protection agents from both countries is not unique. Thus, a methodology aiming the harmonization of the fire risk calculation and perception by Portuguese and Spanish Civil protection authorities is hereby presented. The final results are presented as well. The fire risk index used in this work is the Canadian Fire Weather Index (FWI), which is based on meteorological data. The FWI is limited on its application as it does not take into account other important factors with great effect on the fire appearance and development. The combination of these factors is very complex since, besides the meteorology, it addresses several parameters of different topics, namely: sociology, topography, vegetation and soil cover. Therefore, the meaning of FWI values is different from region to region, according the specific characteristics of each region. In this work, a methodology for FWI calibration based on the number of fire occurrences and on the burnt area in the transboundary regions of Portugal and Spain, in order to assess the fire risk based on calibrated FWI values, is proposed. As previously mentioned, the cooperative firefighting operations require a common perception of the information shared. Therefore, a common classification of the fire risk for the fire events occurred in the transboundary strip is proposed with the objective of harmonizing this type of information. This work is integrated in the ECHO project SpitFire - Spanish-Portuguese Meteorological Information System for Transboundary Operations in Forest Fires, which aims the development of a web platform for the sharing of information and supporting decision tools to be used in international fire events involving Portugal and Spain.

Keywords: data harmonization, FWI, international collaboration, transboundary wildfires

Procedia PDF Downloads 252