Search results for: protein functional module

Authors: Wang Lin, Li Zhiqiang

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The purpose of this paper is to analyze the cooperative learning behavior pattern based on the data of students' movement. The study firstly reviewed the cooperative learning theory and its research status, and briefly introduced the k-means clustering algorithm. Then, it used clustering algorithm and mathematical statistics theory to analyze the activity rhythm of individual student and groups in different functional areas, according to the movement data provided by 10 first-year graduate students. It also focused on the analysis of students' behavior in the learning area and explored the law of cooperative learning behavior. The research result showed that the cooperative learning behavior analysis method based on movement data proposed in this paper is feasible. From the results of data analysis, the characteristics of behavior of students and their cooperative learning behavior patterns could be found.

Keywords: behavior pattern, cooperative learning, data analyze, k-means clustering algorithm

Procedia PDF Downloads 179

Authors: M. N. Hanina, M. Hairul Shahril, I. Ismatul Nurul Asyikin, A. K. Abdul Jalil, M. R. Salina, M. R. Maryam, M. Rosfarizan

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The extracellular proteins secreted by bacteria may be increased in stressful surroundings, such as in the presence of antibiotics. It appears that many antibiotics, when used at low concentrations, have in common the ability to activate or repress gene transcription, which is distinct from their inhibitory effect. There have been comparatively few studies on the potential of antibiotics as a specific chemical signal that can trigger a variety of biological functions. Therefore, this study was carried out to determine the effect of Streptomycin Sulfate in regulating extracellular proteins secreted by Bacillus subtilis ATCC21332. Results of Microdilution assay showed that the Minimum Inhibition Concentration (MIC) of Streptomycin Sulfate on B. subtilis ATCC21332 was 2.5 mg/ml. The bacteria cells were then exposed to Streptomycin Sulfate at concentration of 0.01 MIC before being further incubated for 48h to 72 h. The extracellular proteins secreted were then isolated and analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Proteins profile revealed that three additional bands with approximate sizes of 30 kDa, 22 kDa and 23 kDa were appeared for the treated bacteria with Streptomycin Sulfate. Thus, B. subtilis ATCC21332 in stressful condition with the presence of Streptomycin Sulfate at low concentration could induce the extracellular proteins secretion.

Keywords: Bacillus subtilis ATCC21332, streptomycin sulfate, extracellular proteins, antibiotics

Procedia PDF Downloads 277

Authors: Juliana Shimara Pires Ferrão, Letícia Palmeira Pinto, Francisco Palma Rennó, Francisco Javier Hernandez Blazquez

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The ruminant stomach is a complex and multi-chambered organ. Although the true stomach (abomasum) is fully differentiated and functional at birth, the same does not occur with the rumen chamber. At this moment, rumen papillae are small or nonexistent. The papillae only fully develop after weaning and during calf growth. Papillae development and ruminal epithelium specialization during the fetus growth and at birth must be two interdependent processes that will prepare the rumen to adapt to ruminant adult feeding. The microscopic study of rumen epithelium at these early phases of life is important to understand how this structure prepares the rumen to deal with the following weaning processes and its functional activation. Samples of ruminal mucosa of bovine fetuses (110- and 150 day-old) and newborn calves were collected (dorsal and ventral portions) and processed for light and electron microscopy and immunohistochemistry. The basal cell layer of the stratified pavimentous epithelium present in different ruminal portions of the fetuses was thicker than the same portions of newborn calves. The superficial and intermediate epithelial layers of 150 day-old fetuses were thicker than those found in the other 2 studied ages. At this age (150 days), dermal papillae begin to invade the intermediate epithelial layer which gradually disappears in newborn calves. At birth, the ruminal papillae project from the epithelial surface, probably by regression of the epithelial cells (transitory cells) surrounding the dermal papillae. The PCNA cell proliferation index (%) was calculated for all epithelial samples. Fetuses 150 day-old showed increased cell proliferation in basal cell layer (Dorsal Portion: 84.2%; Ventral Portion: 89.8%) compared to other ages studied. Newborn calves showed an intermediate index (Dorsal Portion: 65.1%; Ventral Portion: 48.9%), whereas 110 day-old fetuses had the lowest proliferation index (Dorsal Portion: 57.2%; Ventral Portion: 20.6%). Regarding the transitory epithelium, 110 day-old fetuses showed the lowest proliferation index (Dorsal Portion: 44.6%; Ventral Portion: 20.1%), 150 day-old fetuses showed an intermediate proliferation index (Dorsal Portion: 57.5%; Ventral Portion: 71.1%) and newborn calves presented a higher proliferation index (Dorsal Portion: 75.1%; Ventral Portion: 19.6%). Under TEM, the 110- and 150 day-old fetuses presented thicker and poorly organized basal cell layer, with large nuclei and dense cytoplasm. In newborn calves, the basal cell layer was more organized and with fewer layers, but typically similar in both regions of the rumen. For the transitory epithelium, fetuses displayed larger cells than those found in newborn calves with less electrondense cytoplasm than that found in the basal cells. The ruminal dorsal portion has an overall higher cell proliferation rate than the ventral portion. Thus we can infer that the dorsal portion may have a higher cell activity than the ventral portion during ruminal development. Moreover, the basal cell layer is thicker in the 110- and 150 day-old fetuses than in the newborn calves. The transitory epithelium, which is much reduced, at birth may have a structural support function of the developing dermal papillae. When it regresses or is sheared off, the papillae are “carved out” from the surrounding epithelial layer.

Keywords: bovine, calf, epithelium, fetus, hematoxylin-eosin, immunohistochemistry, TEM, Rumen

Procedia PDF Downloads 374

Authors: Esmeralda Hysenbelliu

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The aim of this paper is to present the QoE (Quality of Experience) IPTV SDN-based media streaming server enhanced architecture for configuring, controlling, management and provisioning the improved delivery of IPTV service application with low cost, low bandwidth, and high security. Furthermore, it is given a virtual QoE IPTV SDN-based topology to provide an improved IPTV service based on QoE Control and Management of multimedia services functionalities. Inside OpenFlow SDN Controller there are enabled in high flexibility and efficiency Service Load-Balancing Systems; based on the Loading-Balance module and based on GeoIP Service. This two Load-balancing system improve IPTV end-users Quality of Experience (QoE) with optimal management of resources greatly. Through the key functionalities of OpenFlow SDN controller, this approach produced several important features, opportunities for overcoming the critical QoE metrics for IPTV Service like achieving incredible Fast Zapping time (Channel Switching time) < 0.1 seconds. This approach enabled Easy and Powerful Transcoding system via FFMPEG encoder. It has the ability to customize streaming dimensions bitrates, latency management and maximum transfer rates ensuring delivering of IPTV streaming services (Audio and Video) in high flexibility, low bandwidth and required performance. This QoE IPTV SDN-based media streaming architecture unlike other architectures provides the possibility of Channel Exchanging between several IPTV service providers all over the word. This new functionality brings many benefits as increasing the number of TV channels received by end –users with low cost, decreasing stream failure time (Channel Failure time < 0.1 seconds) and improving the quality of streaming services.

Keywords: improved quality of experience (QoE), OpenFlow SDN controller, IPTV service application, softwarization

Procedia PDF Downloads 141

Authors: Rogelio Portillo Vélez, Eduardo Vázquez-Santacruz, Mariano Gamboa-Zúñiga

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In this paper a new mechanical architecture design of a multi functional robot bed, is presented. The importance of this design relies on the fact that in next years the need of assistive devices development will increase in such way that elderly patients will use this kind of devices. This mechanical design implies following specific mechanisms which attend Mexican hospital requirements. This design is the base of next step of this kind of development given that it shows all technical details of the mechanical systems which are needed in order to construct the bed. This is first hospital bed design which could responds to the Latin America hospital requirements. We have obtained these hospital requirements using our diagnosis methodology [14]. From these results we have designed the mechanical system. This is the mechanical base of the hospital robotic bed which is being developed in our robotics laboratory. It will be useful in different hospital environments for elderly and disabled patients.

Keywords: assistive robotics, methodology, feasibility analysis, robotics, operational feasibility, assistive technology, viability analysis matrix, social impact

Procedia PDF Downloads 390

Authors: Natina Yaduma, Allan Williams, Sangwon Park, Andrew Lockwood

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This paper analyses flexible working, and the employment of migrants, as determinants of productivity in hotels. Controlling for the institutional environment, by focussing on a single firm, it analyses data on actual hours worked and outputs, on a weekly basis, over an 8 year period. The unusually disaggregated data allows the paper to examine not only inter-establishment, but also intra-establishment (departmental) variations in productivity, and to compare financial versus physical measures. The findings emphasise the complexity of productivity findings, sometimes contrasting evidence for establishments versus departments, and the positive but scale and measure-specific contributions of both the employment of migrants and flexible working, especially the utilisation of zero hours contracts.

Keywords: labour productivity, physical productivity, financial productivity, numerical flexibility, functional flexibility, migrant employment, cero-contract employment

Procedia PDF Downloads 358

Authors: S. M. Satyam, K. L. Bairy, R. Pirasanthan, R. L. Vaishnav

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Zincovit tablets have been used as nutritional food supplement over a prolonged period of time. The aim of the present study was to investigate the cardio-protective effect of combined formulation of grape seed extract and Zincovit tablets (40, 80 and 160 mg/kg) using a Langendorff model of ischemia-reperfusion in Wistar rats. Following 21 days of pre-treatment, combined formulation of grape seed extract and Zincovit tablets significantly attenuated ischemia-reperfusion induced cardiac injury in terms of increased coronary flow rate (p < 0.01), decreased creatine kinase activity in coronary effluent (p < 0.05), decreased MDA (p < 0.001), 4-HNE (p < 0.001) and increased protein thiol content (p < 0.01) in comparison with the untreated (control) group. This study opens an avenue to clinical studies to demonstrate the validity of this paradigm as a nutritional food supplement, which could improve the clinical outcome of patients subjected to percutaneous angioplasty.

Keywords: grape seed extract, myocardial ischemia-reperfusion injury, oxidative stress, Zincovit tablets

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Authors: Khiem M. Nguyen, Ming C. Yang

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Chloroplast pigments are extremely important during photosynthesis since they play essential roles in light absorption and energy transfer. Therefore, understanding the efficiency of chlorophyll (Chl) biosynthesis could facilitate enhancement in photo-assimilates accumulation, and ultimately, in crop yield. The Chl-deficient mutants have been used extensively to study the Chl biosynthetic pathways and the biogenesis of the photosynthetic apparatus. Rice (Oryza sativa L.) is one of the most leading food crops, serving as staple food for many parts of the world. To author’s best knowledge, Chl b–lacking rice has been found; however the molecular mechanism of Chl biosynthesis still remains unclear compared to wild-type rice. In this study, the ultrastructure analysis, photosynthetic properties, and transcriptome profile of wild-type rice (Norin No.8, N8) and its Chl b-lacking mutant (Chlorina 1, C1) were examined. The finding concluded that total Chl content and Chl b content in the C1 leaves were strongly reduced compared to N8 leaves, suggesting that reduction in the total Chl content contributes to leaf color variation at the physiological level. Plastid ultrastructure of C1 possessed abnormal thylakoid membranes with loss of starch granule, large number of vesicles, and numerous plastoglobuli. The C1 rice also exhibited thinner stacked grana, which was caused by a reduction in the number of thylakoid membranes per granum. Thus, the different Chl a/b ratio of C1 may reflect the abnormal plastid development and function. Transcriptional analysis identified 23 differentially expressed genes (DEGs) and 671 transcription factors (TFs) that were involved in Chl metabolism, chloroplast development, cell division, and photosynthesis. The transcriptome profile and DEGs revealed that the gene encoding PsbR (PSII core protein) was down-regulated, therefore suggesting that the lower in light-harvesting complex proteins are responsible for the lower photosynthetic capacity in C1. In addition, expression level of cell division protein (FtsZ) genes were significantly reduced in C1, causing chloroplast division defect. A total of 19 DEGs were identified based on KEGG pathway assignment involving Chl biosynthesis pathway. Among these DEGs, the GluTR gene was down-regulated, whereas the UROD, CPOX, and MgCH genes were up-regulated. Observation through qPCR suggested that later stages of Chl biosynthesis were enhanced in C1, whereas the early stages were inhibited. Plastid structure analysis together with transcriptomic analysis suggested that the Chl a/b ratio was amplified both by the reduction in Chl contents accumulation, owning to abnormal chloroplast development, and by the enhanced conversion of Chl b to Chl a. Moreover, the results indicated the same Chl-cycle pattern in the wild-type and C1 rice, indicating another Chl b degradation pathway. Furthermore, the results demonstrated that normal grana stacking, along with the absence of Chl b and greatly reduced levels of Chl a in C1, provide evidence to support the conclusion that other factors along with LHCII proteins are involved in grana stacking. The findings of this study provide insight into the molecular mechanisms that underlie different Chl a/b ratios in rice.

Keywords: Chl-deficient mutant, grana stacked, photosynthesis, RNA-Seq, transcriptomic analysis

Procedia PDF Downloads 112

Authors: Mukhtar Raban

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Nelson Mandela University subscribes to a humanizing pedagogy (HP), as housed under broader critical pedagogy, that underpins and informs learning and teaching activities at the institution. The investigation sought to explore the implications of humanizing and critical pedagogical considerations for a technology-enhanced language learning (TELL) environment in a university course. The paper inquires into the design of a learning resource in an online learning environment of an English communication module, that applied HP principles. With an objective of creating agentive spaces for foregrounding identity, student voice, critical self-reflection, and recognition of others’ humanity; a flexible and open 'My Presence' feature was added to the TELL environment that allowed students and lecturers to share elements of their backgrounds in a ‘mutually vulnerable’ manner as a way of establishing digital identity and a more ‘human’ presence in the online language learning encounter, serving as a catalyst for the recognition of the ‘other’. Following a qualitative research design, the study adopted an auto-ethnographic approach, complementing the critical inquiry nature embedded into the activity’s practices. The study’s findings provide critical reflections and deductions on the possibilities of leveraging digital human expression within a humanizing pedagogical framework to advance the realization of HP-adoption in language learning and teaching encounters. It was found that the consideration of humanizing pedagogical principles in the design of online learning was more effective when the critical outcomes were explicated to students and lecturers prior to the completion of the activities. The integration of humanizing pedagogy also led to a contextual advancement of ‘affective’ language learning. Upon critical reflection and analysis, student identity and agency can flourish in a technology-enhanced learning environment when humanizing, and critical pedagogy influences the learning design.

Keywords: critical reflection, humanizing pedagogy, student identity, technology-enhanced language learning

Procedia PDF Downloads 122

Authors: A. M. Plante, F. O’Halloran, A. L. McCarthy

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By 2050 it is projected that 2 billion of the global population will be more than 60 years old. Older adults have unique dietary requirements and aging is associated with physiological changes that affect appetite, sensory perception, metabolism, and digestion. Therefore, it is essential that foods recommended and designed for older adults promote healthy aging. To assess cheese as a functional food for the elderly, a range of commercial cheese products were selected and compared for their antioxidant properties. Cheese from various milk sources (bovine, goats, sheep) with different textures and fat content, including cheddar, feta, goats, brie, roquefort, halloumi, wensleydale and gouda, were initially digested with two different simulated in vitro gastrointestinal digestion (SGID) models. One SGID model represented a validated in vitro adult digestion system and the second model, an elderly SGID, was designed to consider the physiological changes associated with aging. The antioxidant potential of all cheese digestates was investigated using in vitro chemical-based antioxidant assays, (2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, ferric reducing antioxidant power (FRAP) and total phenolic content (TPC)). All adult model digestates had high antioxidant activity across both DPPH ( > 70%) and FRAP ( > 700 µM Fe²⁺/kg.fw) assays. Following in vitro digestion using the elderly SGID model, full-fat red cheddar, low-fat white cheddar, roquefort, halloumi, wensleydale, and gouda digestates had significantly lower (p ≤ 0.05) DPPH radical scavenging properties compared to the adult model digestates. Full-fat white cheddar had higher DPPH radical scavenging activity following elderly SGID digestion compared to the adult model digestate, but the difference was not significant. All other cheese digestates from the elderly model were comparable to the digestates from the adult model in terms of radical scavenging activity. The FRAP of all elderly digestates were significantly lower (p ≤ 0.05) compared to the adult digestates. Goats cheese was significantly higher (p ≤ 0.05) in FRAP (718 µM Fe²/kg.fw) compared to all other digestates in the elderly model. TPC levels in the soft cheeses (feta, goats) and low-fat cheeses (red cheddar, white cheddar) were significantly lower (p ≤ 0.05) in the elderly digestates compared to the adult digestates. There was no significant difference in TPC levels, between the elderly and adult model for full-fat cheddar (red, white), roquefort, wensleydale, gouda, and brie digestates. Halloumi cheese was the only cheese that was significantly higher in TPC levels following elderly digestion compared to adult digestates. Low fat red cheddar had significantly higher (p ≤ 0.05) TPC levels compared to all other digestates for both adult and elderly digestive systems. Findings from this study demonstrate that aging has an impact on the bioactivity of cheese, as antioxidant activity and TPC levels were lower, following in vitro elderly digestion compared to the adult model. For older adults, soft cheese, particularly goats cheese, was associated with high radical scavenging and reducing power, while roquefort cheese had low antioxidant activity. Also, elderly digestates of halloumi and low-fat red cheddar were associated with high TPC levels. Cheese has potential as a functional food for the elderly, however, bioactivity can vary depending on the cheese matrix. Funding for this research was provided by the RISAM Scholarship Scheme, Cork Institute of Technology, Ireland.

Keywords: antioxidants, cheese, in-vitro digestion, older adults

Procedia PDF Downloads 221

Authors: Charalabos Antonatos, Mariza Panoutsopoulou, Georgios K. Georgakilas, Evangelos Evangelou, Yiannis Vasilopoulos

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The extended tissue damage and severe clinical outcomes of autoimmune diseases, accompanied by the high annual costs to the overall health care system, highlight the need for an efficient therapy. Increasing knowledge over the pathophysiology of specific chronic inflammatory diseases, namely Psoriasis (PsO), Inflammatory Bowel Diseases (IBD) consisting of Crohn’s disease (CD) and Ulcerative colitis (UC), and Rheumatoid Arthritis (RA), has provided insights into the underlying mechanisms that lead to the maintenance of the inflammation, such as Tumor Necrosis Factor alpha (TNF-α). Hence, the anti-TNFα biological agents pose as an ideal therapeutic approach. Despite the efficacy of anti-TNFα agents, several clinical trials have shown that 20-40% of patients do not respond to treatment. Nowadays, high-throughput technologies have been recruited in order to elucidate the complex interactions in multifactorial phenotypes, with the most ubiquitous ones referring to transcriptome quantification analyses. In this context, a random effects meta-analysis of available gene expression cDNA microarray datasets was performed between responders and non-responders to anti-TNFα therapy in patients with IBD, PsO, and RA. Publicly available datasets were systematically searched from inception to 10th of November 2020 and selected for further analysis if they assessed the response to anti-TNFα therapy with clinical score indexes from inflamed biopsies. Specifically, 4 IBD (79 responders/72 non-responders), 3 PsO (40 responders/11 non-responders) and 2 RA (16 responders/6 non-responders) datasetswere selected. After the separate pre-processing of each dataset, 4 separate meta-analyses were conducted; three disease-specific and a single combined meta-analysis on the disease-specific results. The MetaVolcano R package (v.1.8.0) was utilized for a random-effects meta-analysis through theRestricted Maximum Likelihood (RELM) method. The top 1% of the most consistently perturbed genes in the included datasets was highlighted through the TopConfects approach while maintaining a 5% False Discovery Rate (FDR). Genes were considered as Differentialy Expressed (DEGs) as those with P ≤ 0.05, |log2(FC)| ≥ log2(1.25) and perturbed in at least 75% of the included datasets. Over-representation analysis was performed using Gene Ontology and Reactome Pathways for both up- and down-regulated genes in all 4 performed meta-analyses. Protein-Protein interaction networks were also incorporated in the subsequentanalyses with STRING v11.5 and Cytoscape v3.9. Disease-specific meta-analyses detected multiple distinct pro-inflammatory and immune-related down-regulated genes for each disease, such asNFKBIA, IL36, and IRAK1, respectively. Pathway analyses revealed unique and shared pathways between each disease, such as Neutrophil Degranulation and Signaling by Interleukins. The combined meta-analysis unveiled 436 DEGs, 86 out of which were up- and 350 down-regulated, confirming the aforementioned shared pathways and genes, as well as uncovering genes that participate in anti-inflammatory pathways, namely IL-10 signaling. The identification of key biological pathways and regulatory elements is imperative for the accurate prediction of the patient’s response to biological drugs. Meta-analysis of such gene expression data could aid the challenging approach to unravel the complex interactions implicated in the response to anti-TNFα therapy in patients with PsO, IBD, and RA, as well as distinguish gene clusters and pathways that are altered through this heterogeneous phenotype.

Keywords: anti-TNFα, autoimmune, meta-analysis, microarrays

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Authors: Lotem Sarid, Meirav Trebicz-Geffen, Serge Ankri

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Queuosine (Q) is a naturally occurring modified nucleoside that occurs in the first position of transfer RNA anticodons such as Asp, Asn, His, and Tyr. As eukaryotes lack pathways to synthesize queuine, the nucleobase of queuosine, they must obtain it from their diet or gut microbiota. Our previous work investigated the effects of queuine on the physiology of the eukaryotic parasite Entamoeba histolytica and defined the enzyme EhTGT responsible for its incorporation into tRNA. To our best knowledge, it is unknown how E. histolytica salvages Q from gut bacteria. We used N-acryloyl-3-aminophenylboronic acid (APB) PAGE analysis to demonstrate that E. histolytica trophozoites can salvage queuine from Q or E. coli K12 but not from the modified E. coli QueC strain, which cannot produce queuine. Next, we examined the role of EhDUF2419, a protein with homology to DNA glycosylase, as a queuine salvage enzyme in E. histolytica. When EhDUF2419 expression is silenced, it inhibits Q's conversion to queuine, resulting in a decrease in Q-tRNA levels. We also observed that Q protects control trophozoites from oxidative stress (OS), but not siEhDUF2419 trophozoites. Overall, our data reveal that EhDUF2419 is central for the salvaging of queuine from bacteria and for the resistance of the parasite to OS.

Keywords: entamoeba histolytica, epitranscriptomics, gut microbiota, queuine, queuosine, response to oxidative stress, tRNA modification.

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Authors: Alexander A. Stakheev, Larisa V. Samokhvalova, Sergey K. Zavriev

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Fusarium fungi are among the most devastating plant pathogens distributed all over the world. Significant reduction of grain yield and quality caused by Fusarium leads to multi-billion dollar annual losses to the world agricultural production. These organisms can also cause infections in immunocompromised persons and produce the wide range of mycotoxins, such as trichothecenes, fumonisins, and zearalenone, which are hazardous to human and animal health. Identification of Fusarium fungi based on the morphology of spores and spore-forming structures, colony color and appearance on specific culture media is often very complicated due to the high similarity of these features for closely related species. Modern Fusarium taxonomy increasingly uses data of crossing experiments (biological species concept) and genetic polymorphism analysis (phylogenetic species concept). A number of novel Fusarium sibling species has been established using DNA barcoding techniques. Species recognition is best made with the combined phylogeny of intron-rich protein coding genes and ribosomal DNA sequences. However, the internal transcribed spacer of (ITS), which is considered to be universal DNA barcode for Fungi, is not suitable for genus Fusarium, because of its insufficient variability between closely related species and the presence of non-orthologous copies in the genome. Nowadays, the translation elongation factor 1 alpha (TEF1α) gene is the “gold standard” of Fusarium taxonomy, but the search for novel informative markers is still needed. In this study, we used two novel DNA markers, frataxin (FXN) and heat shock protein 90 (HSP90) to discover phylogenetic relationships between Fusarium species. Multilocus phylogenetic analysis based on partial sequences of TEF1α, FXN, HSP90, as well as intergenic spacer of ribosomal DNA (IGS), beta-tubulin (β-TUB) and phosphate permease (PHO) genes has been conducted for 120 isolates of 19 Fusarium species from different climatic zones of Russia and neighboring countries using maximum likelihood (ML) and maximum parsimony (MP) algorithms. Our analyses revealed that FXN and HSP90 genes could be considered as informative phylogenetic markers, suitable for evolutionary and taxonomic studies of Fusarium genus. It has been shown that PHO gene possesses more variable (22 %) and parsimony informative (19 %) characters than other markers, including TEF1α (12 % and 9 %, correspondingly) when used for elucidating phylogenetic relationships between F. avenaceum and its closest relatives – F. tricinctum, F. acuminatum, F. torulosum. Application of novel DNA barcodes confirmed the fact that F. arthrosporioides do not represent a separate species but only a subspecies of F. avenaceum. Phylogeny based on partial PHO and FXN sequences revealed the presence of separate cluster of four F. avenaceum strains which were closer to F. torulosum than to major F. avenaceum clade. The strain F-846 from Moldova, morphologically identified as F. poae, formed a separate lineage in all the constructed dendrograms, and could potentially be considered as a separate species, but more information is needed to confirm this conclusion. Variable sites in PHO sequences were used for the first-time development of specific qPCR-based diagnostic assays for F. acuminatum and F. torulosum. This work was supported by Russian Foundation for Basic Research (grant № 15-29-02527).

Keywords: DNA barcode, fusarium, identification, phylogenetics, taxonomy

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Authors: Tayeb Chihi, Messaoud Fatmi

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We present calculations of the structural, elastic and electronic properties of nonferrous Ti, Zr, and Hf pure metals in both parent and martensite phases in bcc and hcp structures respectively. They are based on the generalized gradient approximation (GGA) within the density functional theory (DFT). The shear modulus, Young's modulus and Poisson's ratio for Ti, Zr, and Hf metals have were calculated and compared with the corresponding experimental values. Using elastic constants obtained from calculations GGA, the bulk modulus along the crystallographic axes of single crystals was calculated. This is in good agreement with experiment for Ti and Zr, whereas the hcp structure for Hf is a prediction. At zero temperature and zero pressure, the bcc crystal structure is found to be mechanically unstable for Ti, Zr, and Hf. In our calculations the hcp structures is correctly found to be stable at the equilibrium volume. In the electronic density of states (DOS), the smaller n(EF) is, the more stable the compound is. Therefore, in agreement with the results obtained from the total energy minimum.

Keywords: Ti, Zr, Hf, pure metals, transformation, energy

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Authors: Ege Can Onal, Enver Ersen, Meltem Elitas

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Laparoscopy is a surgical operation, well known as keyhole surgery. The operation is performed through small holes, hence, scars of a patient become much smaller, patients can recover in a short time and the hospital stay becomes shorter in comparison to an open surgery. Several tools are used at laparoscopic operations; among them, the laparoscope has a crucial role. It provides the vision during the operation, which will be the main focus in here. Since the operation area is very small, motion of the surgical tools might be limited in laparoscopic operations compared to traditional surgeries. To overcome this limitation, most of the laparoscopic tools have become more precise, dexterous, multi-functional or automated. Here, we present a robotic-assisted laparoscope that is controlled with pedals directly by a surgeon. Thus, the movement of the laparoscope might be controlled better, so there will not be a need to calibrate the camera during the operation. The need for an assistant that controls the movement of the laparoscope will be eliminated. The duration of the laparoscopic operation might be shorter since the surgeon will directly operate the camera.

Keywords: laparoscope, laparoscopy, low-cost, minimally invasive surgery, robotic-assisted surgery

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Authors: Anuj Tyagi, Balwinder Singh, Naveen Kumar B. T., Niraj K. Singh

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Characterization of diverse microbial communities in specific environment plays a crucial role in the better understanding of their functional relationship with the ecosystem. It is now well established that gut microbiome of fish is not the simple replication of microbiota of surrounding local habitat, and extensive species, dietary, physiological and metabolic variations in fishes may have a significant impact on its composition. Moreover, overuse of antibiotics in human, veterinary and aquaculture medicine has led to rapid emergence and propagation of antibiotic resistance genes (ARGs) in the aquatic environment. Microbial communities harboring specific ARGs not only get a preferential edge during selective antibiotic exposure but also possess the significant risk of ARGs transfer to other non-resistance bacteria within the confined environments. This phenomenon may lead to the emergence of habitat-specific microbial resistomes and subsequent emergence of virulent antibiotic-resistant pathogens with severe fish and consumer health consequences. In this study, gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. Metagenomic DNA, extracted from the fish gut, was subjected to sequencing on Illumina NextSeq to generate paired-end (PE) 2 x 150 bp sequencing reads. After the QC of raw sequencing data by Trimmomatic, taxonomic analysis by Kraken2 taxonomic sequence classification system revealed the presence of 36 phyla, 326 families and 985 genera in the fish gut microbiome. At phylum level, Proteobacteria accounted for more than three-fourths of total bacterial populations followed by Actinobacteria (14%) and Cyanobacteria (3%). Commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) were found to be very less prevalent in fish gut. After sequencing data assembly by MEGAHIT v1.1.2 assembler and PROKKA automated analysis pipeline, pathway analysis revealed the presence of 1,608 Metacyc pathways in the fish gut microbiome. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy-metabolism (4%) and fermentation (2%). Almost one-third (33%) of biosynthesis pathways were involved in the synthesis of secondary metabolites. Metabolic pathways for the biosynthesis of 35 antibiotic types were also present, and these accounted for 5% of overall metabolic pathways in the fish gut microbiome. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. More than 90% ARGs in fish gut microbiome were against beta-lactams (penicillins, cephalosporins, penems, and monobactams). Resistance against tetracycline, macrolides, fluoroquinolones, and phenicols ranged from 0.7% to 1.3%. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment.

Keywords: antibiotic resistance, fish gut, metabolic pathways, microbial diversity

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Authors: Debajit Kalita, Macmillan Nongkhlaw, S. R. Joshi

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Mercury (Hg) is a highly toxic heavy metal released both from naturally occurring volcanoes and anthropogenic activities like alkali and mining industries as well as biomedical wastes. Exposure to mercury is known to affect the nervous, gastrointestinal and renal systems. In the present study, a bacterial isolate identified using 16S rRNA marker as Paenibacillus jamilae PKR1 isolated from India’s largest sandstone-type uranium deposits, containing an average of 0.1% U3O8, was found to be resistance to Hg contamination under culture conditions. It showed strong hydrophobicity as revealed by SAT, MATH, PAT, SAA adherence assays. The Fourier Transform Infrared (FTIR) spectra showed the presence of hydroxyl, amino and carboxylic functional groups on the cell surface EPS which are known to contribute in the binding of metals. It is proposed that the characterized isolate tolerating up to 4.0mM of mercury provides scope for its application in bioremediation of mercury from contaminated sites.

Keywords: mercury, Domiasiat, uranium, paenibacillus jamilae, hydrophobicity, FTIR

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Authors: Surjyakanta Rana, Sreekantha B. Jonnalagadda

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Synthesis of well distributed Pd nanoparticles (3 – 7 nm) on organo amine-functionalized graphene is reported, which demonstrated excellent catalytic activity towards Suzuki coupling reaction. The active material was characterized by X-ray diffraction (XRD), BET surface area, X-ray photoelectron spectra (XPS), Fourier-transfer infrared spectroscopy (FTIR), Raman spectra, Scanning electron microscope (SEM), Transmittance electron microscopy (TEM) analysis and HRTEM. FT-IR revealed that the organic amine functional group was successfully grafted onto the graphene oxide surface. The formation of palladium nanoparticles was confirmed by XPS, TEM and HRTEM techniques. The catalytic activity in the coupling reaction was superb with 100% conversion and 98 % yield and also activity remained almost unaltered up to six cycles. Typically, an extremely high turnover frequency of 185,078 h-1 is observed in the C-C Suzuki coupling reaction using organo di-amine functionalized graphene as catalyst.

Keywords: Di-amine, graphene, Pd nanoparticle, suzuki coupling

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Authors: Meghana Shankara, Priyadarshini Natarajan

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Infrared (IR) spectroscopy has revolutionized the way we look at materials around us. Unraveling the pattern in the molecular spectra of materials to analyze the composition and properties of it has been one of the most interesting challenges in modern science. Applications of the IR spectrometry are numerous in the field’s pharmaceuticals, health, food and nutrition, oils, agriculture, construction, polymers, beverage, fabrics and much more limited only by the curiosity of the people. Near Infrared (NIR) spectrometry is applied robustly in analyzing the solids and liquid substances because of its non-destructive analysis method. In this paper, we have reviewed the application of NIR spectrometry in milk quality analysis and have presented the modes of measurement applied in NIRS measurement setup, Design of Experiment (DoE), classification/quantification algorithms used in the case of milk composition prediction like Fat%, Protein%, Lactose%, Solids Not Fat (SNF%) along with different approaches for adulterant identification. We have also discussed the important NIR ranges for the chosen milk parameters. The performance metrics used in the comparison of the various Chemometric approaches include Root Mean Square Error (RMSE), R^2, slope, offset, sensitivity, specificity and accuracy

Keywords: chemometrics, design of experiment, milk quality analysis, NIRS measurement modes

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Authors: Baby Tabassum, Priya Bajaj

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Cadmium is the second most hazardous heavy metal occurring in both elemental as well as compound forms. It is a highly toxic metal with a very high bio-concentration factor (BCF>100). WHO permitted groundwater cadmium concentration is 0.005 mg/L only, but reality is far away from this limit. A number of natural and anthropogenic industrial activities contribute to the spread of cadmium into the environment. The present study had been designated to find out the renal changes at functional level after cadmium intoxication and protection against these changes offered by Mentha piperata. For the purpose, albino rats were selected as the model organism. Cadmium significantly increases the serum level of serum proteins and nitrogenous wastes showing reduced filtration rate of kidneys. Pretreatment with Mentha piperata leaf extract causes significant retention of these levels to normalcy. These findings conclude that Cadmium exposure affects renal functioning but Mentha could prevent it, proving its nephro-protective potential against heavy metal toxicity.

Keywords: albino rat, cadmium, Mentha piperata, nephrotoxicity

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Authors: Prosper Kudzanai Mushauri

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In issues of anomalous experiences commonly referred to as madness or mental illness, attempts have been made to deal with it so that people manage to live their lives in a more functional way. It is in this stance that psychiatry has sort of portraying itself as seeking to ameliorate perturbations which individuals live with via nosological systems and use of medicine to anomalous experiences. It is from this hegemony that has led to the untold harm which people living with madness have endured from antique to contemporary life. The paper reflects via a literature review on the history of psychiatry and argues that it is akin to contemporary psychiatry to be involved in iatrogenic acts. As antique psychiatry meddled with gory issues of inhumanity, deceit and mass murders which some of those the contemporary psychiatry has not weaned itself from such diabolical acts. The objective of the paper is to suggest to psychiatry that it has not comported to the mores of psychological ethics. In doing this, the paper hopes that psychiatry will reflect and reform its curricular and praxis so that it comports to ethical standards in psychological science in ameliorating anomalous experiences.

Keywords: nosology, psychiatry, madness, diagnosis, eugenics

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Authors: N. S. Okoro

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An experiment was conducted to determine the growth performance, blood parameters and reproductive characteristics of 8-week old male weaner rabbits fed 2% boiled pigeon pea seed meal. The study lasted for 16 weeks. Results showed that hematological parameters of the two groups of rabbit bucks were not significantly affected (p > 0.05) by the treatment, meaning that the PPSM was adequate for maintaining the blood parameters at the normal levels. The 20% boiled PPSM significantly affected (P < 0.05) serum Alanine Aminotransferase (ALT) (67.72±2.5 I.U/I) more than the ALT (57.50±2.02 I.U/I) of the control, which is an indication of liver problem. The globulin level (3.00 ± 0.23g/dl) of the 20% boiled PPSM group was significantly higher than that of the control (2.60±0.06 g/dl), indicating that the test diet did not alter protein metabolism in the rabbits. Boiled pigeon pea seed meal supported organ weight and testicular development in rabbit bucks, suggesting that boiling reduced the level of the anti-nutritional factors in pigeon pea seed meal. Thus, 20% boiled pigeon pea can be included in diets of rabbits without adverse effect on blood parameters and internal organs characteristics.

Keywords: hematology, internal organs, Pigeon pea, rabbits, serum biochemistry

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Authors: Tejeet Singh, Harmanjit Singh

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Creep behavior of thick-walled functionally graded cylinder consisting of AlSiC and subjected to internal pressure and high temperature has been analyzed. The functional relationship between strain rate with stress can be described by the well-known threshold stress based creep law with a stress exponent of five. The effect of imposing non-linear particle gradient on the distribution of creep stresses in the thick-walled functionally graded composite cylinder has been investigated. The study revealed that for the assumed non-linear particle distribution, the radial stress decreases throughout the cylinder, whereas the tangential, axial and effective stresses have averaging effect. The strain rates in the functionally graded composite cylinder could be reduced to significant extent by employing non-linear gradient in the distribution of reinforcement.

Keywords: functionally graded material, pressure, steady state creep, thick-cylinder

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Authors: Gu Sihao

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The coordinated development of "ecology-production-life" in cities has been highly concerned by the country, and the transformation development and sustainable development of resource-based cities have become a hot research topic at present. As an important part of China's resource-based cities, coal resource-based cities have the characteristics of large number and wide distribution. However, due to the adjustment of national energy structure and the gradual exhaustion of urban coal resources, the development vitality of coal resource-based cities is gradually reduced. In many studies, the deterioration of ecological environment in coal resource-based cities has become the main problem restricting their urban transformation and sustainable development due to the "emphasis on economy and neglect of ecology". Since the 18th National Congress of the Communist Party of China (CPC), the Central Government has been deepening territorial space planning and development. On the premise of optimizing territorial space development pattern, it has completed the demarcation of ecological protection red lines, carried out ecological zoning and ecosystem evaluation, which have become an important basis and scientific guarantee for ecological modernization and ecological civilization construction. Grasp the regional multiple ecosystem services is the precondition of the ecosystem management, and the relationship between the multiple ecosystem services study, ecosystem services cluster can identify the interactions between multiple ecosystem services, and on the basis of the characteristics of the clusters on regional ecological function zoning, to better Social-Ecological system management. Based on this cognition, this study optimizes the spatial function zoning of Gujiao, a coal resource-based city, in order to provide a new theoretical basis for its sustainable development. This study is based on the detailed analysis of characteristics and utilization of Gujiao city land space, using SOFM neural networks to identify local ecosystem service clusters, according to the cluster scope and function of ecological function zoning of space partition balance and coordination between different ecosystem services strength, establish a relationship between clusters and land use, and adjust the functions of territorial space within each zone. Then, according to the characteristics of coal resources city and national spatial function zoning characteristics, as the driving factors of land change, by cellular automata simulation program, such as simulation under different restoration strategy situation of urban future development trend, and provides relevant theories and technical methods for the "third-line" demarcations of Gujiao's territorial space planning, optimizes territorial space functions, and puts forward targeted strategies for the promotion of regional ecosystem services, providing theoretical support for the improvement of human well-being and sustainable development of resource-based cities.

Keywords: coal resource-based city, territorial spatial planning, ecosystem service cluster, gmop model, geosos-FLUS model, functional zoning optimization and upgrading

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Authors: L. C. Ansanelli, P. Alfredini

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The article presents the evaluation of the effectiveness of two groins located at Gonzaguinha and Milionários Beaches, situated on the southeast coast of Brazil. The effectiveness of these coastal defense structures is evaluated in terms of sedimentary dynamics, which is one of the most important environmental processes to be assessed in coastal engineering studies. The applied method is based on the implementation of the Delft3D numerical model system tools. Delft3D-WAVE module was used for waves modelling, Delft3D-FLOW for hydrodynamic modelling and Delft3D-SED for sediment transport modelling. The calibration of the models was carried out in a way that the simulations adequately represent the region studied, evaluating improvements in the model elements with the use of statistical comparisons of similarity between the results and waves, currents and tides data recorded in the study area. Analysis of the maximum wave heights was carried to select the months with higher accumulated energy to implement these conditions in the engineering scenarios. The engineering studies were performed for two scenarios: 1) numerical simulation of the area considering only the two existing groins; 2) conception of breakwaters coupled at the ends of the existing groins, resulting in two “T” shaped structures. The sediment model showed that, for the simulated period, the area is affected by erosive processes and that the existing groins have little effectiveness in defending the coast in question. The implemented T structures showed some effectiveness in protecting the beaches against erosion and provided the recovery of the portion directly covered by it on the Milionários Beach. In order to complement this study, it is suggested the conception of further engineering scenarios that might recover other areas of the studied region.

Keywords: coastal engineering, coastal erosion, Sao Vicente bay, Delft3D, coastal engineering works

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Authors: Osama Saber

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Cyanate is one such anion which is produced during protein poisoning in the body and has been studied extensively in the field of biochemistry because of its toxicity. The present work aims at confinement and storage of cyanate in the nano scale. It was achieved through the intercalation of cyanate anions into nanolayerd structures of Ni-Al LDH. In addition, the effect of aging time on the intercalation of cyanate was clarified using X-ray diffraction and scanning electron microscopy. Furthermore, the effect of cations on the affinity towards the intercalation of cyanate anions inside LDH structure was studied by replacement of tetra-valent cations Ti4+ instead of the tri-vallent cations Al3+ during the preparation of LDH structure. X-ray diffraction patterns of the Ni-Ti LDH showed that the interlayer spacing was 0.73 nm. This spacing was smaller than that of Ni-Al LDH suggesting that the interlayered anions into Ni-Ti LDH are different from those into Ni-Al LDH. Thermal analyses (TG, DTG, and DTA) and Infra-red spectra revealed the presence of only cyanate anions into Ni-Ti LDH while, in the case of Ni-Al LDH, both cyanate and carbonate anions were observed. SEM images showed plate-like morphology for both Ni-Ti and Ni-Al LDHs although the shapes of their plates are not similar. Our results suggested that the LDH structures containing titanium cations have higher affinity for cyanate anions than those containing aluminum cations. Therefore, this choice for cyanate in the interlayered spacing widens the applicability to study the effect of the confinement on the toxicity of cyanate by bio researchers.

Keywords: nanolayered structures, Ni-Al LDH, Ni-Ti LDH, intercalation of cyanate anions, urea hydrolysis

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Authors: Nguyen Thi Thanh Truc, Chi-Hyeon Lee, Srinivasa Reddy Mallampati, Byeong-Kyu Lee

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This study evaluated to facilitate separation of ABS plastics from other waste plastics by froth flotation after surface hydrophilization of ABS with heat treatment. The mild heat treatment at 100oC for 60s could selectively increase the hydrophilicity of the ABS plastics surface (i.e., ABS contact angle decreased from 79o to 65.8o) among other plastics mixture. The SEM and XPS results of plastic samples sufficiently supported the increase in hydrophilic functional groups and decrease contact angle on ABS surface, after heat treatment. As a result of the froth flotation (at mixing speed 150 rpm and airflow rate 0.3 L/min) after heat treatment, about 85% of ABS was selectively separated from other heavy plastics with 100% of purity. The effect of optimum treatment condition and detailed mechanism onto separation efficiency in the froth floatation was also investigated. This research is successful in giving a simple, effective, and inexpensive method for ABS separation from waste plastics.

Keywords: ABS, hydrophilic, heat treatment, froth flotation, contact angle

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Authors: Sirous Eydivandi

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Diacylglycerol-O-acyltransferase (DGAT1) gene encodes diacylglycerol transferase enzyme that plays an important role in glycerol lipid metabolism. DGAT1 is considered to be the key enzyme in controlling the synthesis of triglycerides in adipocytes. This enzyme catalyzes the final step of triglyceride synthesis (transform triacylglycerol (DAG) into triacylglycerol (TAG). A total of 20 DGAT1 gene sequences and corresponding amino acids belonging to 4 species include cattle, goats, sheep and yaks were analyzed, and the differentiation within and among the species was also studied. The length of the DGAT1 gene varies greatly, from 1527 to 1785 bp, due to deletion, insertion, and stop codon mutation resulting in elongation. Observed genetic diversity was higher among species than within species, and Goat had more polymorphisms than any other species. Novel amino acid variation sites were detected within several species which might be used to illustrate the functional variation. Differentiation of the DGAT1 gene was obvious among species, and the clustering result was consistent with the taxonomy in the National Center for Biotechnology Information.

Keywords: DGAT1gene, bioinformatic, ruminnants, biotechnology information

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Authors: Sundaram Arulmozhiraja, Kanade Shimizu, Yuta Yamamoto, Satoshi Ichikawa, Maenaka Katsumi, Hiroaki Tokiwa

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Drug discovery is shifting from small molecule based drugs targeting local active site to middle molecules (MM) targeting large, flat, and groove-shaped binding sites, for example, protein-protein interface because at least half of all targets assumed to be involved in human disease have been classified as “difficult to drug” with traditional small molecules. Hence, MMs such as peptides, natural products, glycans, nucleic acids with various high potent bioactivities become important targets for drug discovery programs in the recent years as they could be used for ‘undruggable” intracellular targets. Cell membrane permeability is one of the key properties of pharmacodynamically active MM drug compounds and so evaluating this property for the potential MMs is crucial. Computational prediction for cell membrane permeability of molecules is very challenging; however, recent advancement in the molecular dynamics simulations help to solve this issue partially. It is expected that MMs with high membrane permeability will enable drug discovery research to expand its borders towards intracellular targets. Further to understand the chemistry behind the permeability of MMs, it is necessary to investigate their conformational changes during the permeation through membrane and for that their interactions with the membrane field should be studied reliably because these interactions involve various non-bonding interactions such as hydrogen bonding, -stacking, charge-transfer, polarization dispersion, and non-classical weak hydrogen bonding. Therefore, parameters-based classical mechanics calculations are hardly sufficient to investigate these interactions rather, quantum mechanical (QM) calculations are essential. Fragment molecular orbital (FMO) method could be used for such purpose as it performs ab initio QM calculations by dividing the system into fragments. The present work is aimed to study the cell permeability of middle molecules using molecular dynamics simulations and FMO-QM calculations. For this purpose, a natural compound syringolin and its analogues were considered in this study. Molecular simulations were performed using NAMD and Gromacs programs with CHARMM force field. FMO calculations were performed using the PAICS program at the correlated Resolution-of-Identity second-order Moller Plesset (RI-MP2) level with the cc-pVDZ basis set. The simulations clearly show that while syringolin could not permeate the membrane, its selected analogues go through the medium in nano second scale. These correlates well with the existing experimental evidences that these syringolin analogues are membrane-permeable compounds. Further analyses indicate that intramolecular -stacking interactions in the syringolin analogues influenced their permeability positively. These intramolecular interactions reduce the polarity of these analogues so that they could permeate the lipophilic cell membrane. Conclusively, the cell membrane permeability of various middle molecules with potent bioactivities is efficiently studied using molecular dynamics simulations. Insight of this behavior is thoroughly investigated using FMO-QM calculations. Results obtained in the present study indicate that non-bonding intramolecular interactions such as hydrogen-bonding and -stacking along with the conformational flexibility of MMs are essential for amicable membrane permeation. These results are interesting and are nice example for this theoretical calculation approach that could be used to study the permeability of other middle molecules. This work was supported by Japan Agency for Medical Research and Development (AMED) under Grant Number 18ae0101047.

Keywords: fragment molecular orbital theory, membrane permeability, middle molecules, molecular dynamics simulation

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Authors: S. N. Derrar, M. Sekkal-Rahal

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The Nonlinear optics (NLO) technique is widely used in the field of biological imaging. In fact, grafting biological entities with a high NLO response on tissues and cells enhances the NLO responses of these latter, and ameliorates, consequently, their biological imaging quality. In this optics, we carried out a theoretical study, in the aim of analyzing the peptide bonds created between alanine amino acid and both unnatural amino acids: L-Dopa and Azatryptophan, respectively. Ramachandran plots have been performed for these systems, and their structural parameters have been analyzed. The NLO responses of these peptides have been reported by calculating the first hyperpolarizability values of all the minima found on the plots. The use of such unnatural amino acids as endogenous probing molecules has been investigated through this study. The Density Functional Theory (DFT) has been used for structural properties, while the Second-order Møller-Plesset Perturbation Theory (MP2) has been employed for the NLO calculations.

Keywords: biological imaging, hyperpolarizability, nonlinear optics, probing molecule

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