Search results for: adhesion gene

Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

Procedia PDF Downloads 159

Authors: Chin-Tsu Ma, Yi-Jhen Wu, Hsia Ying Cheng, Han Hsiang Huang, Shyh Ming Kuo

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The use of specific molecules including nutrients and pharmacological agents has been tried in modulation of stem cells differentiation (MSCs) to insulin producing cells. The aim of this study is to investigate the ability of nano collagen molecules (nutrient or scaffold) to enhance the MSCs differentiation into insulin-producing cells in combination with nicotinamide and exendin-4 (pharmacological agents) in vitro and in vivo. The results demonstrated that the cells exhibit morphologically islet-like clusters after treatment with nano collagen molecules, nicotinamide and exendin-4. MSCs extra treated with nano collagen molecules showed significant increases in Nkx6.1 and insulin mRNA expression at 14-d and 21-d culture compared with those merely treated with nicotinamide and exendin-4. Early 7-day elevation in PDX-1 mRNA expression was observed. Furthermore, the MSCs exposed to nano collagen molecules produced the highest secretion of insulin (p ＜ 0.05). Type-2 diabetes induced by high-fat diet and low dose of streptozotocin in rat model was built in this study. This rat exhibited higher food intake, water intake, lower glucose tolerance, lower-insulin tolerance, and higher HbA1C (significant increases, p ＜ 0.01) as compared with the normal rat that demonstrated the model of type-2 diabetes was successfully built. Biopsy examinations also showed that obvious destruction of islet. After injection of differentiated MSCs into the destructed pancreas of diabetes rat, more regenerated islet were observed at the rats that treated with nano collagen molecules and exhibited much lower HbA1C as compared with the normal rat and diabetes rat after 4 weeks (significant deceases, p ＜ 0.001). These results indicate that the culturing MSCs with nano collagen molecules, nicotinamide, and exendin-4 are beneficial for MSCs differentiation into islet-like cells. These nano collagen molecules may lead to alternations or up-regulation of gene expression and influence the differentiated outcomes induced by nicotinamide and exendin-4.

Keywords: nano collagen molecules, nicotinamide, MSCs, diabetes

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Authors: Marjan Moradi fard, Hossein Rassi, Masoud Houshmand

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Aim: Breast cancer is one of the most common cancers affecting the morbidity and mortality of Iranian women. This disease is a result of collective alterations of oncogenes and tumor suppressor genes. Studies have produced conflicting results concerning the role of p53 codon 72 polymorphism (G>C) and miR-146a rs2910164 polymorphism (G>C) on the risk of several cancers; therefore, a research was performed to estimate the association between the p53 codon 72 polymorphism and miR-146a rs2910164 polymorphism in breast cancer. Methods and Materials: A total of 45 archival breast cancer samples from Khatam hospital and 40 healthy samples were collected. Verification of each cancer reported in a relative was sought through the pathology reports of the hospital records. Then, DNA extracted from all samples by standard methods and p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes were analyzed using multiplex PCR. The tubules, mitotic activity, necrosis, polymorphism and grade of breast cancer were staged by Nottingham histological grading and immunohistochemical staining of the sections from the paraffin wax embedded tissues for the expression of ER, PR and p53 was carried out using a standard method. Finally, data analysis was performed using the 7 version of the Epi Info(TM) 2012 software and test chi-square(x2) for trend. Results: Successful DNA extraction was assessed by PCR amplification of b-actin gene (99 bp). According to the results, p53 GG genotype and miR-146a rs2910164 CC genotype was significantly associated with increased risk of breast cancer in the study population. In this study, we established that tumors of p53 GG genotype and miR-146a rs2910164 CC genotype exhibited higher mitotic activity, higher polymorphism, lower necrosis, lower tubules, higher ER- and PR-negatives and lower TP53-positives than the other genotypes. Conclusion: The present study provided preliminary evidence that a p53 GG genotype may effect breast cancer risk in the study population, interacting synergistically with miR-146a rs2910164 CC genotype. Our results demonstrate that the testing of p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes in combination with clinical parameters can serve as major risk factors in the early identification of breast cancers.

Keywords: breast cancer, miR-146a rs2910164 polymorphism, p53 codon 72 polymorphism, tumors, pathology reports

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Authors: Zeina Bourhane, Anders Lanzen, Christine Cagnon, Olfa Ben Said, Cristiana Cravo-Laureau, Robert Duran

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The anthropogenic pressure in coastal areas increases dramatically with the exploitation of environmental resources. Biomonitoring coastal areas are crucial to determine the impact of pollutants on bacterial communities in soils and sediments since they provide important ecosystem services. However, relevant biomonitoring tools allowing fast determination of the ecological status are yet to be defined. Microbial ecology approaches provide useful information for developing such microbial monitoring tools reporting on the effect of environmental stressors. Chemical and microbial molecular approaches were combined in order to determine microbial bioindicators for assessing the ecological status of soil and river ecosystems around the Ichkeul Lake (Tunisia), an area highly impacted by human activities. Samples were collected along soil/river/lake continuums in three stations around the Ichkeul Lake influenced by different human activities at two seasons (summer and winter). Contaminant pressure indexes (PI), including PAHs (Polycyclic aromatic hydrocarbons), alkanes, and OCPs (Organochlorine pesticides) contents, showed significant differences in the contamination level between the stations with seasonal variation. Bacterial communities were characterized by 16S ribosomal RNAs (rRNA) gene metabarcoding. Although microgAMBI indexes, determined from the sequencing data, were in accordance with contaminant contents, they were not sufficient to fully explain the PI. Therefore, further microbial indicators are still to be defined. The comparison of bacterial communities revealed the specific microbial assemblage for soil, river, and lake sediments, which were significantly correlated with contaminant contents and PI. Such observation offers the possibility to define a relevant set of bioindicators for reporting the effects of human activities on the microbial community structure. Such bioindicators might constitute useful monitoring tools for the management of microbial communities in coastal areas.

Keywords: bacterial communities, biomonitoring, contamination, human impacts, microbial bioindicators

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Authors: Jin-Hyeong Park, Hong-Seok Kim, Jin-Hyeok Yim, Young-Ji Kim, Dong-Hyeon Kim, Jung-Whan Chon, Kun-Ho Seo

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Salmonella contamination in chicken samples can cause major health problems in humans. However, not only the effects of antibiotic treatment during growth but also the impacts of poultry slaughter line on the prevalence of Salmonella in final chicken meat sold to consumers are unknown. In this study, we compared the isolation rates and antimicrobial resistance of Salmonella between antibiotic-free, conventional, conventional Korean native retail chicken meat samples and clonal divergence of Salmonella isolates by multilocus sequence typing. In addition, the distribution of extended-spectrum β-lactamase (ESBL) genes in ESBL-producing Salmonella isolates was analyzed. A total of 72 retail chicken meat samples (n = 24 antibiotic-free broiler [AFB] chickens, n = 24 conventional broiler [CB] chickens, and n = 24 conventional Korean native [CK] chickens) were collected from local retail markets in Seoul, South Korea. The isolation rates of Salmonella were 66.6% in AFB chickens, 45.8% in CB chickens, and 25% in CK chickens. By analyzing the minimum inhibitory concentrations of β -lactam antibiotics with the disc-diffusion test, we found that 81.2% of Salmonella isolates from AFB chickens, 63.6% of isolates from CB chickens, and 50% of isolates from CK chickens were ESBL producers; all ESBL-positive isolates had the CTX-M-15 genotype. Interestingly, all ESBL-producing Salmonella were revealed as ST16 by multilocus sequence typing. In addition, all CTX-M-15-positive isolates had the genetic platform of blaCTX-M gene (IS26-ISEcp1-blaCTX-M-15-IS903), to the best of our knowledge, this is the first report in Salmonella around the world. The Salmonella ST33 strain (S. Hadar) isolated in this study has never been reported in South Korea. In conclusion, our findings showed that antibiotic-free retail chicken meat products were also largely contaminated with ESBL-producing Salmonella and that their ESBL genes and genetic platforms were the same as those isolated from conventional retail chicken meat products.

Keywords: antibiotic-free poultry, conventional poultry, multilocus sequence typing, extended-spectrum β-lactamase, antimicrobial resistance

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Authors: Sheraz Gul

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The requirements for progressing a compound to clinical trials is well established and relies on the results from in-vitro and in-vivo animal tests to indicate that it is likely to be safe and efficacious when testing in humans. The typical data package required will include demonstrating compound safety, toxicity, bioavailability, pharmacodynamics (potential effects of the compound on body systems) and pharmacokinetics (how the compound is potentially absorbed, distributed, metabolised and eliminated after dosing in humans). If the desired criteria are met and the compound meets the clinical Candidate criteria and is deemed worthy of further development, a submission to regulatory bodies such as the US Food & Drug Administration for an exploratory Investigational New Drug Study can be made. The purpose of this study is to collect data to establish that the compound will not expose humans to unreasonable risks when used in limited, early-stage clinical studies in patients or normal volunteer subjects (Phase I). These studies are also designed to determine the metabolism and pharmacologic actions of the drug in humans, the side effects associated with increasing doses, and, if possible, to gain early evidence on their effectiveness. In order to reach the above goals, we have developed a pre-clinical high throughput Absorption, Distribution, Metabolism and Excretion–Toxicity (ADME–Toxicity) panel of assays to identify compounds that are likely to meet the Lead and Candidate compound acceptance criteria. This panel includes solubility studies in a range of biological fluids, cell viability studies in cancer and primary cell-lines, mitochondrial toxicity, off-target effects (across the kinase, protease, histone deacetylase, phosphodiesterase and GPCR protein families), CYP450 inhibition (5 different CYP450 enzymes), CYP450 induction, cardio-toxicity (hERG) and gene-toxicity. This panel of assays has been applied to multiple compound series developed in a number of projects delivering Lead and clinical Candidates and examples from these will be presented.

Keywords: absorption, distribution, metabolism and excretion–toxicity , drug discovery, food and drug administration , pharmacodynamics

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Authors: Wenfa Yu, Thuva Gnanasampanthan, John Finlay, Jessica Clarke, Charlotte Anderson, Tony Clare, Axel Rosenhahn

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Marine biofouling is a worldwide problem at vast economic and ecological costs. Historically it was combated with toxic coatings such as tributyltin. As those coatings being banned nowadays, finding environmental friendly antifouling solution has become an urgent topic. In this study antifouling coatings consisted of natural occurring polysaccharides hyaluronic acid (HA), alginic acid (AA), chitosan (Ch) and polyelectrolyte polyethylenimine (PEI) are constructed into polyelectrolyte multilayers (PEMs) in a Layer-by-Layer (LbL) method. LbL PEM construction is a straightforward way to assemble biomacromolecular coatings on surfaces. Advantages about PEM include ease of handling, highly diverse PEM composition, precise control over the thickness and so on. PEMs have been widely employed in medical application and there are numerous studies regarding their protein adsorption, elasticity and cell adhesive properties. With the adjustment of coating composition, termination layer charge, coating morphology and cross-linking method, it is possible to prepare low marine biofouling coatings with PEMs. In this study, using spin coating technology, PEM construction was achieved at smooth multilayers with roughness as low as 2nm rms and highly reproducible thickness around 50nm. To obtain stability in sea water, the multilayers were covalently cross-linked either thermally or chemically. The cross-linking method affected surface energy, which was reflected in water contact angle, thermal cross-linking led to hydrophobic surfaces and chemical cross-linking generated hydrophilic surfaces. The coatings were then evaluated regarding its protein resistance and biological species resistance. While the hydrophobic thermally cross-linked PEM had low resistance towards proteins, the resistance of chemically cross-linked PEM strongly depended on the PEM termination layer and the charge of the protein, opposite charge caused high adsorption and same charge low adsorption, indicating electrostatic interaction plays a crucial role in the protein adsorption processes. Ulva linza was chosen as the biological species for antifouling performance evaluation. Despite of the poor resistance towards protein adsorption, thermally cross-linked PEM showed good resistance against Ulva spores settlement, the chemically cross-linked multilayers showed poor resistance regardless of the termination layer. Marine species adhesion is a complex process, although it involves proteins as bioadhesives, protein resistance its own is not a fully indicator for its antifouling performance. The species will pre select the surface, responding to cues like surface energy, chemistry, or charge and so on. Thus making it difficult for one single factors to determine its antifouling performance. Preparing PEM coating is a comprehensive work involving choosing polyelectrolyte combination, determining termination layer and the method for cross-linking. These decisions will affect PEM properties such as surface energy, charge, which is crucial, since biofouling is a process responding to surface properties in a highly sensitive and dynamic way.

Keywords: hyaluronic acid, polyelectrolyte multilayers, protein resistance, Ulva linza zoospores

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Authors: Irena Maus, Katharina Gabriella Cibis, Andreas Bremges, Yvonne Stolze, Geizecler Tomazetto, Daniel Wibberg, Helmut König, Alfred Pühler, Andreas Schlüter

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Within the agricultural sector, the production of biogas from organic substrates represents an economically attractive technology to generate bioenergy. Complex consortia of microorganisms are responsible for biomass decomposition and biogas production. Recently, species belonging to the phylum Thermotogae were detected in thermophilic biogas-production plants utilizing renewable primary products for biomethanation. To analyze adaptive genome features of representative Thermotogae strains, Defluviitoga tunisiensis L3 was isolated from a rural thermophilic biogas plant (54°C) and completely sequenced on an Illumina MiSeq system. Sequencing and assembly of the D. tunisiensis L3 genome yielded a circular chromosome with a size of 2,053,097 bp and a mean GC content of 31.38%. Functional annotation of the complete genome sequence revealed that the thermophilic strain L3 encodes several genes predicted to facilitate growth of this microorganism on arabinose, galactose, maltose, mannose, fructose, raffinose, ribose, cellobiose, lactose, xylose, xylan, lactate and mannitol. Acetate, hydrogen (H2) and carbon dioxide (CO2) are supposed to be end products of the fermentation process. The latter gene products are metabolites for methanogenic archaea, the key players in the final step of the anaerobic digestion process. To determine the degree of relatedness of dominant biogas community members within selected digester systems to D. tunisiensis L3, metagenome sequences from corresponding communities were mapped on the L3 genome. These fragment recruitments revealed that metagenome reads originating from a thermophilic biogas plant covered 95% of D. tunisiensis L3 genome sequence. In conclusion, availability of the D. tunisiensis L3 genome sequence and insights into its metabolic capabilities provide the basis for biotechnological exploitation of genome features involved in thermophilic fermentation processes utilizing renewable primary products.

Keywords: genome sequence, thermophilic biogas plant, Thermotogae, Defluviitoga tunisiensis

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Authors: Hilal Turkoglu Sasmazel, Ozan Ozkan, Seda Surucu

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Tissue engineering is the field of treating defects caused by injuries, trauma or acute/chronic diseases by using artificial scaffolds that mimic the extracellular matrix (ECM), the natural biological support for the tissues and cells within the body. The main aspects of a successful artificial scaffold are (i) large surface area in order to provide multiple anchorage points for cells to attach, (ii) suitable porosity in order to achieve 3 dimensional growth of the cells within the scaffold as well as proper transport of nutrition, biosignals and waste and (iii) physical, chemical and biological compatibility of the material in order to obtain viability throughout the healing process. By hybrid scaffolds where two or more different materials were combined with advanced fabrication techniques into complex structures, it is possible to combine the advantages of individual materials into one single structure while eliminating the disadvantages of each. Adding this to the complex structure provided by advanced fabrication techniques enables obtaining the desired aspects of a successful artificial tissue scaffold. In this study, fibroblast compatibility of poly(ε-caprolactone) (PCL)/chitosan core-shell electrospun hybrid scaffolds with proper mechanical, chemical and physical properties successfully developed in our previous study was investigated. Standard 7-day cell culture was carried out with L929 fibroblast cell line. The viability of the cells cultured with the scaffolds was monitored with 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) viability assay for every 48 h starting with 24 h after the initial seeding. In this assay, blank commercial tissue culture polystyrene (TCPS) Petri dishes, single electrospun PCL and single electrospun chitosan mats were used as control in order to compare and contrast the performance of the hybrid scaffolds. The adhesion, proliferation, spread and growth of the cells on/within the scaffolds were observed visually on the 3rd and the 7th days of the culture period with confocal laser scanning microscopy (CSLM) and scanning electron microscopy (SEM). The viability assay showed that the hybrid scaffolds caused no toxicity for fibroblast cells and provided a steady increase in cell viability, effectively doubling the cell density for every 48 h for the course of 7 days, as compared to TCPS, single electrospun PCL or chitosan mats. The cell viability on the hybrid scaffold was ~2 fold better compared to TCPS because of its 3D ECM-like structure compared to 2D flat surface of commercially cell compatible TCPS, and the performance was ~2 fold and ~10 fold better compared to single PCL and single chitosan mats, respectively, even though both fabricated similarly with electrospinning as non-woven fibrous structures, because single PCL and chitosan mats were either too hydrophobic or too hydrophilic to maintain cell attachment points. The viability results were verified with visual images obtained with CSLM and SEM, in which cells found to achieve characteristic spindle-like fibroblast shape and spread on the surface as well within the pores successfully at high densities.

Keywords: chitosan, core-shell, fibroblast, electrospinning, PCL

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Authors: Vitor Rafael Regiani, Carlos Henrique Viesi Do Nascimento Filho, Patricia Matos Biselli-Chicote, Claudia Aparecida Rainho, Luiz Sergio Raposo, José Victor Maniglia, Eny Maria Goloni-Bertollo, Erika Cristina Pavarino

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Promoter hypermethylation of tumor-related genes has been associated with prognosis in early-stage head-and-neck cancers, providing strong evidence that these hypermethylated genes are valuable biomarkers for prognostic evaluation. Hence, we selected the MGMT and RASSF1A genes to examine the methylation status in head and neck squamous cell carcinomas (HNSCC) samples matched with non-tumor tissues (tumor-surrounding tissues or peripheral blood samples). DNA methylation analysis was based on Methylation-Sensitive High Resolution Melting, and the methylation status was correlated with clinic-pathological characteristics of the patients. RASSF1A and MGMT promoter methylation was detected in 43.24% (16/37) and in 44.44% (16/36) of the tumors, respectively. RASSF1A and MGMT methylation was significantly more frequent in tumor tissue than non-tumor tissues, as well as, simultaneous methylation of RASSF1A and MGMT also was higher in tumor tissue than non-tumor tissues. In relation to anatomic site, larynx cancer presented significant methylation of MGMT gene compared to tumor-surrounding tissue. The frequency of RASSF1A and MGMT promoter methylated was higher in tumor tissues in relation to peripheral blood from the same patient. No association was found between methylation and the variables analyzed, including gender, age, smoking or alcohol drinking habits. Clinic-pathological characteristics also showed no association in the presence of methylation. The Kaplan–Meier's method showed no association of methylation and both disease-free and overall survival. In conclusion, the presence of epigenetic abnormalities in normal-appearing tissue corroborates the hypothesis of the ‘field cancerization', or it can reflect preneoplastic and/or preinvasive. Moreover, MGMT methylation may serve as an important laryngeal cancer biomarker because it showed significant difference between laryngeal cancer and surrounding tumor tissues.

Keywords: head and neck cancer, DNA methylation, MGMT promoter methylation, RASSF1A promoter methylation

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Authors: Nefzi Ahlem, Aydi Ben Abdallah Rania, Jabnoun-Khiareddine Hayfa, Ammar Nawaim, Mejda Daami-Remadi

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Fusarium Crown and Root Rot (FCRR) caused by Fusarium oxysporum f. sp. radicis-lycopersici (FORL) is a serious tomato (Solanum lycopersicum L.) disease in Tunisia. Its management is very difficult due to the long survival of its resting structures and to the luck of genetic resistance. In this work, we explored the wild Solanaceae species Withania somnifera, growing in the Tunisian Centre-East, as a potential source of biocontrol agents effective in FCRR suppression and tomato growth promotion. Seven fungal isolates were shown able to colonize tomato roots, crowns, and stems. Used as conidial suspensions or cell-free culture filtrates, all tested fungal treatments significantly enhanced tomato growth parameters by 21.5-90.3% over FORL-free control and by 27.6-93.5% over pathogen-inoculated control. All treatments significantly decreased the leaf and root damage index by 28.5-92.8 and the vascular browning extent 9.7-86.4% over FORL-inoculated and untreated control. The highest disease suppression ability (decrease by 86.4-92.8% in FCRR severity) over pathogen-inoculated control and by 81.3-88.8 over hymexazol-treated control) was expressed by I6 based treatments. This endophytic fungus was morphologically characterized and identified using rDNA sequencing gene as Fusarium sp. I6 (MG835371). This fungus was shown able to reduce FORL radial growth by 58.5–83.2% using its conidial suspension or cell-free culture filtrate. Fusarium sp. I6 showed chitinolytic, proteolytic and amylase activities. The current study clearly demonstrated that Fusarium sp. (I6) is a promising biocontrol candidate for suppressing FCRR severity and promoting tomato growth. Further investigations are required for elucidating its mechanism of action involved in disease suppression and plant growth promotion.

Keywords: antifungal activity, associated fungi, Fusarium oxysporum f. sp. radicis-lycopersici, Withania somnifera, tomato growth

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Authors: Mohammed H. Abu-Dieyeh, Mohammad M. Zalloum

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Plant growth-promoting rhizobacteria (PGPR) are known to enhance plant growth and/or reduce plant damage due to soil-borne pathogens. Tomato is the highest consumable vegetable world-wide including Jordan. Fusarium oxysporum is a pathogen that causes well-known damages and losses to many vegetable crops including tomato. In this study, purification of 112 isolates of PGPR strains from rhizosphere environment of different regions in Jordan was accomplished. All bacterial isolates were In-vitro screened for antagonistic effects against F. oxysporum. The eleven most effective isolates that caused 30%-50% in-vitro growth reduction of F. oxysporum were selected. 8 out of 11 of these isolates were collected from Al-Halabat (arid-land). 7 isolates of Al-Halabat exerted 40-54% In-vitro growth reduction of F. oxysporum. Four-week-old seedlings of tomato cultivar (Anjara, the most susceptible indigenous cultivar to F. oxysporum) treated with PGPR5 (Bacillus amyloliquefaciens), and exposed to F. oxysporum, showed no disease symptoms and no significant changes in biomasses or chlorophyll contents indicating a non-direct mechanism of action of PGPR on tomato plants. However PGPR3 (Bacillus sp.), PGPR4 (Bacillus cereus), and PGPR38 (Paenibacillus sp.) treated plants or PGPR treated and exposed to F. oxysporum showed a significant increasing growth of shoot and root biomasses as well as chlorophyll contents of leaves compared to control untreated plants or plants exposed to the fungus without PGPR treatment. A significant increase in number of flowers per plant was also recorded in all PGPR treated plants. The characterization of rhizobacterial strains were accomplished using 16S rRNA gene sequence analysis in addition to microscopic characterization. Further research is necessary to explore the potentiality of other collected PGPR isolates on tomato plants in addition to investigate the efficacy of the identified isolates on other plant pathogens and then finding a proper and effective methods of formulation and application of the successful isolates on selected crops.

Keywords: antagonism, arid land, growth promoting, rhizobacteria, tomato

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Authors: Mohamed Shafi Bin Mahboob Ali

Abstract:

Introduction: Synchronous tumor is defined as the presence of more than one primary malignant lesion in the same patient at the indexed diagnosis. It is a rare occurrence, especially in the spectrum of colorectal cancer, which accounts for less than 4%. The underlying pathology of a synchronous tumor is thought to be due to a genomic factor, which is microsatellite instability (MIS) with the involvement of BRAF, KRAS, and the GSRM1 gene. There are no specific sites of occurrence for the synchronous colorectal tumor, but many studies have shown that a synchronous tumor has about 43% predominance in the ascending colon with rarity in the sigmoid colon. Case Report: We reported a case of a young lady in the middle of her 30's with no family history of colorectal cancer that was diagnosed with a synchronous adenocarcinoma at the descending colon and rectosigmoid region. The lady's presentation was quite perplexing as she presented to the district hospital initially with simple, uncomplicated hemorrhoids and constipation. She was then referred to our center for further management as she developed a 'football' sized right gluteal swelling with a complete intestinal obstruction and bilateral lower-limb paralysis. We performed a CT scan and biopsy of the lesion, which found that the tumor engulfed the sacrococcygeal region with more than one primary lesion in the colon as well as secondaries in the liver. The patient was operated on after a multidisciplinary meeting was held. Pelvic exenteration with tumor debulking and anterior resection were performed. Postoperatively, she was referred to the oncology team for chemotherapy. She had a tremendous recovery in eight months' time with a partial regain of her lower limb power. The patient is still under our follow-up with an improved quality of life post-intervention. Discussion: Synchronous colon cancer is rare, with an incidence of 2.4% to 12.4%. It has male predominance and is pathologically more advanced compared to a single colon lesion. Down staging the disease by means of chemoradiotherapy has shown to be effective in managing this tumor. It is seen commonly on the right colon, but in our case, we found it on the left colon and the rectosigmoid. Conclusion: Managing a synchronous colon tumor could be challenging to surgeons, especially in deciding the extent of resection and postoperative functional outcomes of the bowel; thus, individual treatment strategies are needed to tackle this pathology.

Keywords: synchronous, colon, tumor, adenocarcinoma

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Authors: Yassir Adam Shuaib, Stefan Niemann, Eltahir Awad Khalil, Ulrich Schaible, Lothar Heinz Wieler, Mohammed Ahmed Bakhiet, Abbashar Osman Mohammed, Mohamed Abdelsalam Abdalla, Elvira Richter

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Tuberculosis (TB) is a chronic bacterial disease of humans and animals and it is characterized by the progressive development of specific granulomatous tubercle lesions in affected tissues. In a six-month study, from June to November 2014, a total of 2,304 carcasses of cattle, camel, sheep, and goats slaughtered at East and West Gaash slaughterhouses, Kassala, were investigated during postmortem, in parallel, 101 sputum samples from TB suspected patients at Kassala and El-Gadarif Teaching Hospitals were collected in order to investigate tuberculosis in animals and humans. Only 0.1% carcasses were found with suspected TB lesions in the liver and lung and peritoneal cavity of two sheep and no tuberculous lesions were found in the carcasses of cattle, goats or camels. All samples, tissue lesions and sputum, were decontaminated by the NALC-NaOH method and cultured for mycobacterial growth at the NRZ for Mycobacteria, Research Center Borstel, Germany. Genotyping and molecular characterization of the grown strains were done by line probe assay (GenoType CM and MTBC) and 16S rDNA, rpoB gene, and ITS sequencing, spoligotyping, MIRU-VNTR typing and next generation sequencing (NGS). Culture of the specimens revealed growth of organisms from 81.6% of all samples. Mycobacterium tuberculosis (76.2%), M. intracellulare (14.2%), mixed infection with M. tuberculosis and M. intracellulare (6.0%) and mixed infection with M. tuberculosis and M. fortuitum and with M. intracellulare and unknown species (1.2%) were detected in the sputum samples and unknown species (1.2%) were detected in the samples of one of the animals tissues. From the 69 M. tuberculosis strains, 25 (36.2%) were showing either mono-drug-resistant or multi-drug-resistant or poly-drug-resistant but none was extensively drug-resistant. In conclusion, the prevalence of TB in animals was very low while in humans M. tuberculosis-Delhi/CAS lineage was responsible for most cases and there was an evidence of MDR transmission and acquisition.

Keywords: animal, human, slaughterhouse, Sudan, tuberculosis

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Authors: Suchithra V., Shreedhanya, Kavya Menon, Vidya Niranjan

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Skin metagenomics has a wide range of applications with direct relevance to the health of the organism. It gives us insight to the diverse community of microorganisms (the microbiome) harbored on the skin. In the recent years, it has become increasingly apparent that the interaction between skin microbiome and the human body plays a prominent role in immune system development, cancer development, disease pathology, and many other biological implications. Next Generation Sequencing has led to faster and better understanding of environmental organisms and their mutual interactions. This project is studying the human skin microbiome of different individuals having varied skin conditions. Bacterial 16S rRNA data of skin microbiome is downloaded from SRA toolkit provided by NCBI to perform metagenomics analysis. Twelve samples are selected with two controls, and 3 different categories, i.e., sex (male/female), skin type (moist/intermittently moist/sebaceous) and occlusion (occluded/intermittently occluded/exposed). Quality of the data is increased using Cutadapt, and its analysis is done using FastQC. USearch, a tool used to analyze an NGS data, provides a suitable platform to obtain taxonomy classification and abundance of bacteria from the metagenome data. The statistical tool used for analyzing the USearch result is METAGENassist. The results revealed that the top three abundant organisms found were: Prevotella, Corynebacterium, and Anaerococcus. Prevotella is known to be an infectious bacterium found on wound, tooth cavity, etc. Corynebacterium and Anaerococcus are opportunist bacteria responsible for skin odor. This result infers that Prevotella thrives easily in sebaceous skin conditions. Therefore it is better to undergo intermittently occluded treatment such as applying ointments, creams, etc. to treat wound for sebaceous skin type. Exposing the wound should be avoided as it leads to an increase in Prevotella abundance. Moist skin type individuals can opt for occluded or intermittently occluded treatment as they have shown to decrease the abundance of bacteria during treatment.

Keywords: bacterial 16S rRNA , next generation sequencing, skin metagenomics, skin microbiome, taxonomy

Procedia PDF Downloads 172

Authors: Mukolwe D. Lubembe, Odongo O. David, Githaka Naftali, Kanduma Esther, Marinda Oosthuizen, Kgomotso P. Sibeko

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Theileriosis is a tick-borne disease of cattle caused by an apicomplexan protozoan parasite of the genus Theileria. In eastern and southern Africa, Theileria infections in cattle are caused by the species Theileria parva whose natural reservoir is the African buffalo (Syncerus caffer). Currently, East Coast Fever (ECF) caused by the cattle-derived Theileria parva is still a major problem in eastern Africa and some parts of southern Africa but not in South Africa following its eradication in the 1950s. However, Corridor disease (CD) caused by the buffalo-derived Theileria parva still remains a concern in South Africa. The diversity of Theileria parva in South Africa in comparison to other affected countries is poorly defined yet its known to be the survival strategy of this parasite. We assessed the antigenic diversity of Theileria parva isolates from Buffalo and cattle at the wildlife-livestock interface comparing samples from South Africa, Zimbabwe, Kenya, Tanzania, and Uganda. Antigenic epitopes of eight schizont antigen genes (Tp1, Tp3, Tp4, Tp5, Tp6, Tp7, Tp8 and Tp10) were amplified by PCR from genomic DNA extracted from blood samples collected from cattle and buffalo at the wildlife-livestock interface. Amplicons were purified and then sequenced on NGS platform. Full length open reading frames (ORFs) of two schizont antigen genes (Tp2 and Tp9) and one sporozoite antigen gene, p67 were also amplified from genomic DNA. Amplicons were then purified and cloned for sequencing. Analysis was based on sequence differences in the genes. Preliminary results show an extensively diverse population of Theileria parva circulating in buffalo and cattle populations at the wildlife-livestock interface. Diversity of the antigen genes contributes to the evasion of the immune system of the host by Theileria parva. This possess a concern in that, some of the Theileria parva populations may re-assort and become adapted to cattle to cause a form of theileriosis that is as fatal as ECF in areas where ECF was eradicated or is absent

Keywords: Theileria parva, east coast fever, corridor diseases, antigen genes, diversity

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Authors: Shih-Ping Liu, Cheng-Hsuan Chang, Yu-Chuen Huang, Shih-Yin Chen, Woei-Cherng Shyu

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Embryonic stem cells (ES) and induced pluripotnet stem cells (iPS) are both pluripotent stem cells. For mouse stem cells culture technology, leukemia inhibitory factor (LIF) was used to maintain the pluripotency of stem cells in vitro. However, LIF is an expensive reagent. The goal of this study was to find out a pure compound extracted from Chinese herbal medicine that could maintain stem cells pluripotency to replace LIF and improve the iPS generation efficiency. From 20 candidates traditional Chinese medicine we found that Cordycepsmilitaris triggered the up-regulation of stem cells activating genes (Oct4 and Sox2) expression levels in MEF cells. Cordycepin, a major active component of Cordycepsmilitaris, also could up-regulate Oct4 and Sox2 gene expression. Furthermore, we used ES and iPS cells and treated them with different concentrations of Cordycepin (replaced LIF in the culture medium) to test whether it was useful to maintain the pluripotency. The results showed higher expression levels of several stem cells markers in 10 μM Cordycepin-treated ES and iPS cells compared to controls that did not contain LIF, including alkaline phosphatase, SSEA1, and Nanog. Embryonic body formation and differentiation confirmed that 10 μM Cordycepin-containing medium was capable to maintain stem cells pluripotency after four times passages. For mechanism analysis, microarray analysis indicated extracellular matrix and Jak/Stat signaling pathway as the top two deregulated pathways. In ECM pathway, we determined that the integrin αVβ5 expression levels and phosphorylated Src levels increased after Cordycepin treatment. In addition, the phosphorylated Jak2 and phosphorylated Sat3 protein levels were increased after Cordycepin treatment and suppressed with the Jak2 inhibitor, AG490. The expression of cytokines associated with Jak2/Stat3 signaling pathway were also up-regulated by Q-PCR and ELISA assay. Lastly, we used Oct4-GFP MEF cells to test iPS generation efficiency following Cordycepin treatment. We observed that 10 Μm Cordycepin significantly increased the iPS generation efficiency in day 21. In conclusion, we demonstrated Cordycepin could maintain the pluripotency of stem cells through both of ECM and Jak2/Stat3 signaling pathway and improved iPS generation efficiency.

Keywords: cordycepin, iPS cells, Jak2/Stat3 signaling pathway, molecular biology

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Authors: Feixiong Chen, Naoufel Haddour, Marie Frenea-Robin, Yves MéRieux, Yann Chevolot, Virginie Monnier

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Neonatal thrombopenia occurs when the mother generates antibodies against her baby’s platelet antigens. It is particularly critical for newborns because it can cause coagulation troubles leading to intracranial hemorrhage. In this case, diagnosis must be done quickly to make platelets transfusion immediately after birth. Before transfusion, platelet antigens must be tested carefully to avoid rejection. The majority of thrombopenia (95 %) are caused by antibodies directed against Human Platelet Antigen 1a (HPA-1a) or 5b (HPA-5b). The common method for antigen platelets detection is polymerase chain reaction allowing for identification of gene sequence. However, it is expensive, time-consuming and requires significant blood volume which is not suitable for newborns. We propose to develop a point-of-care device based on double functionalized magnetic colloids with 1) antibodies specific to antigen platelets and 2) highly sensitive electroactive molecules in order to be detected by an electrochemical microsensor. These magnetic colloids will be used first to isolate platelets from other blood components, then to capture specifically platelets bearing HPA-1a and HPA-5b antigens and finally to attract them close to sensor working electrode for improved electrochemical signal. The expected advantages are an assay time lower than 20 min starting from blood volume smaller than 100 µL. Our functionalization procedure based on amine dendrimers and NHS-ester modification of initial carboxyl colloids will be presented. Functionalization efficiency was evaluated by colorimetric titration of surface chemical groups, zeta potential measurements, infrared spectroscopy, fluorescence scanning and cyclic voltammetry. Our results showed that electroactive molecules and antibodies can be immobilized successfully onto magnetic colloids. Application of a magnetic field onto working electrode increased the detected electrochemical signal. Magnetic colloids were able to capture specific purified antigens extracted from platelets.

Keywords: Magnetic Nanoparticles , Electroactive Molecules, Antibody, Platelet

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Authors: Esam Mohammed Al-shaebi

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One of the most crucial approaches for treating human diseases, particularly parasite infections, is nanomedicine. One of the most significant protozoan diseases that impact farm and domestic animals is coccidiosis. While, amprolium is one of the traditional anticoccidial medication, the advent of drug-resistant strains of Eimeria necessitates the development of novel treatments. The goal of the current investigation was to determine whether biosynthesized selenium nanoparticles (Bio-SeNPs) using Azadirachta indica leaves extract might treat mice with Eimeria papillata infection in the jejunal tissue. Five groups of seven mice each were used, as follows: Group 1: Non-infected-non-treated (negative control). Group 2: Non-infected treated group with Bio-SeNPs (0.5 mg/kg of body weight). Groups 3-5 were orally inoculated with 1×103 sporulated oocysts of E. papillata. Group 3: Infected-non-treated (positive control). Group 4: Infected and treated group with Bio-SeNPs (0.5 mg/kg). Group 5: Infected and treated group with the Amprolium. Groups 4 and 5 daily received oral administration (for 5 days) of Bio-SeNPs and anticoccidial medication, respectively, after infection. Bio-SeNPs caused a considerable reduction in oocyst output in mice feces (97.21%). This was also accompanied by a significant reduction in the number of developmental parasitic stages in the jejunal tissues. Glutathione reduced (GSH), glutathione peroxidase (GPx), and superoxide dismutase (SOD) levels were dramatically reduced by the Eimeria parasite, whereas, nitric oxide (NO) and malonaldehyde (MDA) levels were markedly elevated. The amount of goblet cells and MUC2 gene expression were used as apoptotic indicators, and both were considerably downregulated by infection. However, infection markedly increased the expression of inflammatory cytokines (IL-6 and TNF-α) and the apoptotic genes (Caspase-3 and BCL2). Bio-SeNPs were administrated to mice to drastically lower body weight, oxidative stress, and inflammatory and apoptotic indicators in the jejunal tissue. Our research thus showed the involvement of Bio-SeNPs in protecting mice with E. papillata infections against jejunal damage.

Keywords: coccidiosis, nanoparticles, azadirachta indica, oxidative stress

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Authors: Anyimc, C. J. Aneke, J. O. Orji, O. Nworie, U. C. C. Egbule

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The microbial examination and antimicrobial susceptibility profile of microorganism isolated from the salt mining site in Ebonyi state were evaluated in the present study using a standard microbiological technique. A total of 300 samples were randomly collected in three sample groups (A, B, and C) of 100 each. Isolation, Identification and characterization of organization present on the soil samples were determined by culturing, gram-staining and biochemical technique. The result showed the following organisms were isolated with their frequency as follow: Bacillus species (37.3%) and Staphylococcus species(23.5%) had the highest frequency in the whole Sample group A and B while Klebsiella specie (15.7%), Pseudomonas species(13.7%), and Erwinia species (9.8%) had the least. Rhizopus species (42.0%) and Aspergillus species (26.0%) were the highest fungi isolated, followed by Penicillum species (20.0%) while Mucor species (4.0%), and Fusarium species (8.0%) recorded the least. Sample group C showed high microbial population of all the microbial isolates when compared to sample group A and B. Disc diffusion method was used to determine the susceptibility of isolated bacteria to various antibiotics (oxfloxacin, pefloxacin, ciprorex, augumentin, gentamycin, ciproflox, septrin, ampicillin), while agar well diffusion method was used to determine the susceptibility of isolated fungi to some antifungal drugs (metronidazole, ketoconazole, itraconazole fluconazole). The antibacterial activity of the antibiotics used showed that ciproflux has the best inhibitory effect on all the test bacteria. Ketoconazole showed the highest inhibitory effect on the fungal isolates, followed by itraconazole, while metronidazole and fluconazole showed the least inhibitory effect on the entire test fungal isolates. Hence, the multiple drug resistance of most isolates to appropriate drugs of choice are of great public health concern and cells for periodic monitoring of antibiograms to detect possible changing patterns. Microbes isolated in the salt mining site can also be used as a source of gene(s) that can increase salt tolerance in different crop species through genetic engineering.

Keywords: microorganisms, antibacterial, antifungal, resistance, salt mining site, Ebonyi State

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Authors: Patarasuda Chaisupa, R. Clay Wright

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The selection of appropriate biomolecular targets is a crucial aspect of biopharmaceutical development. The Auxin-Inducible Degron Degradation (AID) technology has demonstrated remarkable potential in efficiently and rapidly degrading target proteins, thereby enabling the identification and acquisition of drug targets. The AID system also offers a viable method to deplete specific proteins, particularly in cases where the degradation pathway has not been exploited or when the adaptation of proteins, including the cell environment, occurs to compensate for the mutation or gene knockout. In this study, we have engineered an improved AID system tailored to deplete proteins of interest. This AID construct combines the auxin-responsive E3 ubiquitin ligase binding domain, AFB2, and the substrate degron, IAA17, fused to the target genes. Essential genes of fungi with the lowest percent amino acid similarity to human and plant orthologs, according to the Basic Local Alignment Search Tool (BLAST), were cloned into the AID construct in S. cerevisiae (AID-tagged strains) using a modular yeast cloning toolkit for multipart assembly and direct genetic modification. Each E3 ubiquitin ligase and IAA17 degron was fused to a fluorescence protein, allowing for real-time monitoring of protein levels in response to different auxin doses via cytometry. Our AID system exhibited high sensitivity, with an EC50 value of 0.040 µM (SE = 0.016) for AFB2, enabling the specific promotion of IAA17::target protein degradation. Furthermore, we demonstrate how this improved AID system enhances quantitative functional studies of various proteins in fungi. The advancements made in auxin-inducible protein degradation in this study offer a powerful approach to investigating critical target protein viability in fungi, screening protein targets for drugs, and regulating intracellular protein abundance, thus revolutionizing the study of protein function underlying a diverse range of biological processes.

Keywords: synthetic biology, bioengineering, molecular biology, biotechnology

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Authors: Liaqat Ali, Hubert E. Blum, Türkân Sakinc

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Enterococcus faecium is an emerging multidrug-resistant nosocomial pathogen increased dramatically worldwide and causing bacteremia, endocarditis, urinary tract and surgical site infections in immunocomprised patients. The capsular polysaccharides that contribute to pathogenesis through evasion of the host innate immune system are also involved in hindering leukocyte killing of enterococci. The gene cluster (enterococcal polysaccharide antigen) of E. faecalis encoding homologues of many genes involved in polysaccharide biosynthesis. We identified two putative loci with 22 kb and 19 kb which contained 11 genes encoding for glycosyltransferases (GTFs); this was confirmed by using genome comparison of already sequenced strains that has no homology to known capsule genes and the epa-locus. The polysaccharide-conjugate vaccines have rapidly emerged as a suitable strategy to combat different pathogenic bacteria, therefore, we investigated a polysaccharide biosynthesis CapD protein in E. faecium contains 336 amino acids and had putative function for N-linked glycosylation. The deletion/knock-out capD mutant was constructed and complemented by homologues recombination method and confirmed by using PCR and sequencing. For further characterization and functional analysis, in-vitro cell culture and in-vivo a mouse infection models were used. Our ΔcapD mutant shows a strong hydrophobicity and all strains exhibited biofilm production. Subsequently, the opsonic activity was tested in an opsonophagocytic assay which shows increased in mutant compared complemented and wild type strains but more than two fold decreased in colonization and adherence was seen on surface of uroepithelial cells. However, a significant higher bacterial colonialization was observed in capD mutant during animal bacteremia infection. Unlike other polysaccharides biosynthesis proteins, CapD does not seems to be a major virulence factor in enterococci but further experiments and attention is needed to clarify its function, exact mechanism and involvement in pathogenesis of enteroccocal nosocomial infections eventually to develop a vaccine/ or targeted therapy.

Keywords: E. faecium, pathogenesis, polysaccharides, biofilm formation

Procedia PDF Downloads 333

Authors: Maha Z. Rizk, Sami A. Fattah, Heba M. Darwish, Sanaa A. Ali, Mai O. Kadry

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Although it is known that nano-TiO2 and other nanoparticles can induce liver toxicity, the mechanisms and the molecular pathogenesis are still unclear. The present study investigated some biochemical indices of nano-sized Titanium dioxide (TiO2 NPS) toxicity in mice liver and the ameliorative efficacy of individual and combined doses of idebenone, carnosine and vitamin E. Nano-anatase TiO2 (21 nm) was administered as a total oral dose of 2.2 gm/Kg daily for 2 weeks followed by the afore-mentioned antioxidants daily either individually or in combination for 1month. TiO2-NPS induced a significant elevation in serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST) and hepatic oxidative stress biomarkers [lipid peroxides (LP), and nitric oxide levels (NOX), while it significantly reduced glutathione reductase (GR), reduced glutathione (GSH) and glutathione peroxidase(GPX) levels. Moreover the quantitative RT-PCR analysis showed that nano-anatase TiO2 can significantly alter the mRNA and protein expressions of the fibrotic factors TGF-B1, VEGFand Smad-2. Histopathological examination of hepatic tissue reinforced the previous biochemical results. Our results also implied that inflammatory responses and liver injury may be involved in nano-anatase TiO2-induced liver toxicity Tumor necrosis factor-α (TNF-α) and Interleukin -6 (IL-6) and increased the percent of DNA damage which was assessed by COMET assay in addition to the apoptotic marker Caspase-3. Moreover mRNA gene expression observed by RT-PCR showed a significant overexpression in nuclear factor relation -2 (Nrf2), nuclear factor kappa beta (NF-Kβ) and the apoptotic factor (bax), and a significant down regulation in the antiapoptotic factor (bcl2) level. In conclusion idebenone, carnosine and vitamin E ameliorated the deviated previously mentioned parameters with variable degrees with the most pronounced role in alleviating the hazardous effect of TiO2 NPS toxicity following the combination regimen.

Keywords: Nano-anatase TiO2, TGF-B1, SMAD-2

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Authors: Karol Rodriguez-Peña, Martha L. Macias-Rubalcava, Leticia Rocha-Zavaleta, Sergio Sanchez

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A bioassay-guided study for anti-cancer compounds from endophytes of the Mexican medicinal plant Amphipteryygium adstringens resulted in the isolation of a streptomycete capable of producing a group of compounds with high cytotoxic activity. Microorganisms from surface sterilized samples of various sections of the plant were isolated and all the actinomycetes found were evaluated for their potential to produce compounds with cytotoxic activity against cancer cell lines MCF7 (breast cancer) and HeLa (cervical cancer) as well as the non-tumoural cell line HaCaT (keratinocyte). The most active microorganism was picked for further evaluation. The identification of the microorganism was carried out by 16S rDNA gene sequencing, finding the closest proximity to Streptomyces scabrisporus, but with the additional characteristic that the strain isolated in this study was capable of producing colorful compounds never described for this species. Crude extracts of dichloromethane and ethyl acetate showed IC50 values of 0.29 and 0.96 μg/mL for MCF7, 0.51 and 1.98 μg/mL for HeLa and 0.96 and 2.7 μg/mL for HaCaT. Scaling the fermentation to 10 L in a bioreactor generated 1 g of total crude extract, which was fractionated by silica gel open column to yield 14 fractions. Nine of the fractions showed cytotoxic activity. Fraction 4 was chosen for subsequent purification because of its high activity against cancerous cell lines, lower activity against keratinocytes. HPLC-UV-MS/ESI was used for the evaluation of this fraction, finding at least 10 different compounds with high values of m/z (≈588). Purification of the compounds was carried out by preparative thin-layer chromatography. The prevalent compound was Steffimycin B, a molecule known for its antibiotic and cytotoxic activities and also for its low solubility in aqueous solutions. Along with steffimycin B, another five compounds belonging to the steffimycin family were isolated and at this moment their structures are being elucidated, some of which display better solubility in water: an attractive property for the pharmaceutical industry. As a conclusion to this study, the isolation of endophytes resulted in the discovery of a strain capable of producing compounds with high cytotoxic activity that need to be studied for their possible utilization.

Keywords: amphipterygium adstringens, cytotoxicity, streptomyces scabrisporus, steffimycin

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Authors: Vijaya Madhuri Devraj, Swarnalatha Guditi, Kiran Kumar Bokara, Gangadhar Taduri

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Cell-based strategies may open therapeutic approaches that promote tolerance through manipulation of macrophages to increase long-term transplant survival rates and minimize side effects of the current immune suppressive regimens. The aim of the present study was, therefore, to test and compare the therapeutic potential of MSC and Tregs on macrophage polarization to develop an alternate cell-based treatment option in kidney transplantation. In the current protocol, macrophages from kidney transplant recipients with graft dysfunction were co-cultured with MSCs and Treg cells with and without cell-cell contact on transwell plates, further to quantitatively assess macrophage polarization in response to MSC and Treg treatment over time, M1 and M2 cell surface markers were used. Additionally, multiple soluble analytes were analyzed in cell supernatant by using bead-based immunoassays. Furthermore, to confirm our findings, gene expression analysis was done. MSCs induced the formation of M2 macrophages more than Tregs when macrophages M0 were cultured in transwell without cell contact. From this, we deduced the mechanism that soluble factors present in the MSCs condition media are involved in skewing of macrophages towards type 2 macrophages; similarly, in co-culture with cell-cell contact, MSCs resulted in more M2 type macrophages than Tregs. And an important finding of this study is the combination of both MSC-Treg showed significantly effective and consistent results in both with and without cell contact setups. Hence, it is suggestive to prefer MSCs over Tregs for secretome-based therapy and a combination of both for either therapy for effective transplantation outcomes. Our findings underline a key role of Tregs and MSCs in promoting macrophage polarization towards anti-inflammatory type. The study has great importance in prolongation of allograft and patient survival without any rejection by cell-based therapy, which induce self-tolerance and controlling infection.

Keywords: graft rejection, graft tolerance, macrophage polarization, mesenchymal stem cells, regulatory T cells, transplant immunology

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Authors: Ali Bahkali, Rayan Yousef Booq, Mohammad Khiyami

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Soil samples were collected from five different regions in the Kingdom of Saudi Arabia. Microbiological methods included dilution methods and pour plates to isolate and purify bacteria soil. The ability of isolates to develop biopolymer was investigated on petri dishes containing elements and substance concentrations stimulating developing biopolymer. Fluorescent stains, Nile red and Nile blue were used to stain the bacterial cells developing biopolymers. In addition, Sudan black was used to detect biopolymers in bacterial cells. The isolates which developed biopolymers were identified based on their gene sequence of 1 6sRNA and their ability to grow and synthesize PHAs on mineral medium supplemented with 1% dates molasses as the only carbon source under nitrogen limitation. During the study 293 bacterial isolates were isolated and detected. Through the initial survey on the petri dishes, 84 isolates showed the ability to develop biopolymers. These bacterial colonies developed a pink color due to accumulation of the biopolymers in the cells. Twenty-three isolates were able to grow on dates molasses, three strains of which showed the ability to accumulate biopolymers. These strains included Bacillus sp., Ralstonia sp. and Microbacterium sp. They were detected by Nile blue A stain with fluorescence microscopy (OLYMPUS IX 51). Among the isolated strains Ralstonia sp. was selected after its ability to grow on molasses dates in the presence of a limited nitrogen source was detected. The optimum conditions for formation of biopolymers by isolated strains were investigated. Conditions studied included, best incubation duration (2 days), temperature (30°C) and pH (7-8). The maximum PHB production was raised by 1% (v1v) when using concentrations of dates molasses 1, 2, 3, 4 and 5% in MSM. The best inoculated with 1% old inoculum (1= OD). The ideal extraction method of PHA and PHB proved to be 0.4% sodium hypochlorite solution, producing a quantity of polymer 98.79% of the cell's dry weight. The maximum PHB production was 1.79 g/L recorded by Ralstonia sp. after 48 h, while it was 1.40 g/L produced by R.eutropha ATCC 17697 after 48 h.

Keywords: bacteria forming polyhydroxyalkanoate, detection, molecular, Saudi Arabia

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Authors: F. Iberraken, R. Medjoudj, D. Aissani

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The development of the smart grids concept is built around two separate definitions, namely: The European one oriented towards sustainable development and the American one oriented towards reliability and security of supply. In this paper, we have investigated reliability merits enabling decision-makers to provide a high quality of service. It is based on system behavior using interruptions and failures modeling and forecasting from one hand and on the contribution of information and communication technologies (ICT) to mitigate catastrophic ones such as blackouts from the other hand. It was found that this concept has been adopted by developing and emerging countries in short and medium terms followed by sustainability concept at long term planning. This work has highlighted the reliability merits such as: Benefits, opportunities, costs and risks considered as consistent units of measuring power customer satisfaction. From the decision making point of view, we have used the analytic hierarchy process (AHP) to achieve customer satisfaction, based on the reliability merits and the contribution of such energy resources. Certainly nowadays, fossil and nuclear ones are dominating energy production but great advances are already made to jump into cleaner ones. It was demonstrated that theses resources are not only environmentally but also economically and socially sustainable. The paper is organized as follows: Section one is devoted to the introduction, where an implicit review of smart grids development is given for the two main concepts (for USA and Europeans countries). The AHP method and the BOCR developments of reliability merits against power customer satisfaction are developed in section two. The benefits where expressed by the high level of availability, maintenance actions applicability and power quality. Opportunities were highlighted by the implementation of ICT in data transfer and processing, the mastering of peak demand control, the decentralization of the production and the power system management in default conditions. Costs were evaluated using cost-benefit analysis, including the investment expenditures in network security, becoming a target to hackers and terrorists, and the profits of operating as decentralized systems, with a reduced energy not supplied, thanks to the availability of storage units issued from renewable resources and to the current power lines (CPL) enabling the power dispatcher to manage optimally the load shedding. For risks, we have razed the adhesion of citizens to contribute financially to the system and to the utility restructuring. What is the degree of their agreement compared to the guarantees proposed by the managers about the information integrity? From technical point of view, have they sufficient information and knowledge to meet a smart home and a smart system? In section three, an application of AHP method is made to achieve power customer satisfaction based on the main energy resources as alternatives, using knowledge issued from a country that has a great advance in energy mutation. Results and discussions are given in section four. It was given us to conclude that the option to a given resource depends on the attitude of the decision maker (prudent, optimistic or pessimistic), and that status quo is neither sustainable nor satisfactory.

Keywords: reliability, AHP, renewable energy resources, smart grids

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Authors: Mikaela Kutrolli, Noah S. Pereira, Vanessa Scanlon, Mohamadmahdi Samandari, Ali Tamayol

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Bone tissue engineering has drawn significant attention and various biomaterials have been tested. Polymers such as polycaprolactone (PCL) offer excellent biocompatibility, reasonable mechanical properties, and biodegradability. However, PCL scaffolds suffer a critical drawback: a lack of micro/mesoporosity, affecting cell attachment, tissue integration, and mineralization. It also results in a slow degradation rate. While 3D-printing has addressed the issue of macroporosity through CAD-guided fabrication, PCL scaffolds still exhibit poor smaller-scale porosity. To overcome this, we generated composites of PCL, hydroxyapatite (HA), and powdered sucrose (PS). The latter serves as a sacrificial material to generate porous particles after sucrose dissolution. Additionally, we have incorporated dexamethasone (DEX) to boost the PCL osteogenic properties. The resulting scaffolds maintain controlled macroporosity from the lattice print structure but also develop micro/mesoporosity within PCL fibers when exposed to aqueous environments. The study involved mixing PS into solvent-dissolved PCL in different weight ratios of PS to PCL (70:30, 50:50, and 30:70 wt%). The resulting composite was used for 3D printing of scaffolds at room temperature. Printability was optimized by adjusting pressure, speed, and layer height through filament collapse and fusion test. Enzymatic degradation, porogen leaching, and DEX release profiles were characterized. Physical properties were assessed using wettability, SEM, and micro-CT to quantify the porosity (percentage, pore size, and interconnectivity). Raman spectroscopy was used to verify the absence of sugar after leaching. Mechanical characteristics were evaluated via compression testing before and after porogen leaching. Bone marrow stromal cells (BMSCs) behavior in the printed scaffolds was studied by assessing viability, metabolic activity, osteo-differentiation, and mineralization. The scaffolds with a 70% sugar concentration exhibited superior printability and reached the highest porosity of 80%, but performed poorly during mechanical testing. A 50% PS concentration demonstrated a 70% porosity, with an average pore size of 25 µm, favoring cell attachment. No trace of sucrose was found in Raman after leaching the sugar for 8 hours. Water contact angle results show improved hydrophilicity as the sugar concentration increased, making the scaffolds more conductive to cell adhesion. The behavior of bone marrow stromal cells (BMSCs) showed positive viability and proliferation results with an increasing trend of mineralization and osteo-differentiation as the sucrose concentration increased. The addition of HA and DEX also promoted mineralization and osteo-differentiation in the cultures. The integration of PS as porogen at a concentration of 50%wt within PCL scaffolds presents a promising approach to address the poor cell attachment and tissue integration issues of PCL in bone tissue engineering. The method allows for the fabrication of scaffolds with tunable porosity and mechanical properties, suitable for various applications. The addition of HA and DEX further enhanced the scaffolds. Future studies will apply the scaffolds in an in-vivo model to thoroughly investigate their performance.

Keywords: bone, PCL, 3D printing, tissue engineering

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Authors: Michael P. Mannino, Gerald W. Hart

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The majority of glucose metabolism proceeds through glycolytic pathways such as glycolysis or pentose phosphate pathway, however, about 5% is shunted through the hexosamine biosynthetic pathway, producing uridine diphosphate N-acetyl glucosamine (UDP-GlcNAc). This precursor can then be incorporated into complex oligosaccharides decorating the cell surface or remain as an intracellular post-translational-modification (PTM) of serine/threonine residues (O-GlcNAcylation, OGN), which has been identified on over 4,000 cytosolic or nuclear proteins. Intracellular OGN has major implications on cellularprocesses, typically by modulating protein localization, protein-protein interactions, protein degradation, and gene expression. Additionally, OGN is known to have an extensive cross-talk with phosphorylation, be in a competitive or cooperative manner. Unlike other PTMs there are only two cycling enzymes that are capable of adding or removing the GlcNAc moiety, O-linked N-aceytl glucosamine Transferase (OGT) and O-linked N-acetyl glucoamidase (OGA), respectively. The activity of OGT has been shown to be sensitive to cellular UDP-GlcNAc levels, even changing substrate affinity. Owing to this and that the concentration of UDP-GlcNAc is related to the metabolisms of glucose, amino acid, fatty acid, and nucleotides, O-GlcNAc is often referred to as a nutrient sensing rheostat. Indeed OGN is known to regulate several signaling pathways as a result of nutrient levels, such as insulin signaling. Dysregulation of OGN is associated with several disease states such as cancer, diabetes, and neurodegeneration. Improvements in glycomics over the past 10-15 years has significantly increased the OGT substrate pool, suggesting O-GlcNAc’s involvement in a wide variety of signaling pathways. However, O-GlcNAc’s role at the receptor level has only been identified in a case-by-case basis of known pathways. Examining the OGN of the plasma membrane (PM) may better focus our understanding of O-GlcNAc-effected signaling pathways. In this current study, PM fractions were isolated from several cell types via ultracentrifugation, followed by purification and MS/MS analysis in several cell lines. This process was repeated with or without OGT/OGA inhibitors or with increased/decreased glucose levels in media to ascertain the importance of OGN. Various pathways are followed up on in more detailed studies employing methods to localize OGN at the PM specifically.

Keywords: GlcNAc, nutrient sensitive, post-translational-modification, receptor

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