Search results for: encompassing nucleotide positions 37 to 340

Authors: Mariam Khaled, Noha Farag, Ghada Mohamed Abdel Salam, Khaled Abu-Aisha, Mohamed El-Azizi

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Gastric and colorectal cancers are among the most frequent causes of cancer-associated mortalities in Africa. They have been considered as a global public health concern, as nearly one million new cases are reported per year. IL-1β is a pro-inflammatory cytokine-produced by activated macrophages and monocytes- and a member of the IL-1 family. The inactive IL-1β precursor is cleaved and activated by caspase-1 enzyme, which itself is activated by the assembly of intracellular structures defined as NLRP3 (Nod Like receptor P3) inflammasomes. Activated IL-1β stimulates the Interleukin-1 receptor type-1 (IL-1R1), which is responsible for the initiation of a signal transduction pathway leading to cell proliferation. It has been proven that the IL-1β gene is a highly polymorphic gene in which single nucleotide polymorphisms (SNPs) may affect its expression. It has been previously reported that SNPs including base transitions between C and T at positions, -511 (C-T; dbSNP: rs16944) and -31 (C-T; dbSNP: rs1143627), from the transcriptional start site, contribute to the pathogenesis of gastric and colorectal cancers by affecting IL-1β levels. Altered production of IL-1β due to such polymorphisms is suspected to stimulate an amplified inflammatory response and promote Epithelial Mesenchymal Transition leading to malignancy. Allele frequency distribution of the IL-1β-31 and -511 SNPs, in different populations, and their correlation to the incidence of gastric and colorectal cancers, has been intriguing to researchers worldwide. The current study aims to investigate allele distributions of the IL-1β SNPs among gastric and colorectal cancers Egyptian patients. In order to achieve to that, 89 Biopsy and surgical specimens from the antrum and corpus mucosa of chronic gastritis subjects and gastric and colorectal carcinoma patients was collected for DNA extraction followed by restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR). The amplified PCR products of IL-1β-31C > T and IL-1β-511T > C were digested by incubation with the restriction endonuclease enzymes ALu1 and Ava1. Statistical analysis was carried out to determine the allele frequency distribution in the three studied groups. Also, the effect of the IL-1β -31 and -511 SNPs on nuclear factor binding was analyzed using Fluorescence Electrophoretic Mobility Shift Assay (EMSA), preceded by nuclear factor extraction from gastric and colorectal tissue samples and LPS stimulated monocytes. The results of this study showed that a significantly higher percentage of Egyptian gastric cancer patients have a homozygous CC genotype at the IL-1β-31 position and a heterozygous TC genotype at the IL-1β-511 position. Moreover, a significantly higher percentage of the colorectal cancer patients have a homozygous CC genotype at the IL-1β-31 and -511 positions as compared to the control group. In addition, the EMSA results showed that IL-1β-31C/T and IL-1β-511T/C SNPs do not affect nuclear factor binding. Results of this study suggest that the IL-1β-31 C/T and IL-1β-511 T/C may be correlated to the incidence of gastric cancer in Egyptian patients; however, similar findings couldn’t be proven in the colorectal cancer patients group for the IL-1β-511 T/C SNP. This is the first study to investigate IL-1β -31 and -511 SNPs in the Egyptian population.

Keywords: colorectal cancer, Egyptian patients, gastric cancer, interleukin-1β, single nucleotide polymorphisms

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Authors: Lorico D. S. Lapitan Jr., Yihan Xu, Yuan Guo, Dejian Zhou

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The ability of ultrasensitive detection of specific genes and discrimination of single nucleotide polymorphisms is important for clinical diagnosis and biomedical research. Herein, we report the development of a new ultrasensitive approach for label-free DNA detection using magnetic nanoparticle (MNP) assisted rapid target capture/separation in combination with signal amplification using poly-enzyme tagged polymer nanobead. The sensor uses an MNP linked capture DNA and a biotin modified signal DNA to sandwich bind the target followed by ligation to provide high single-nucleotide polymorphism discrimination. Only the presence of a perfect match target DNA yields a covalent linkage between the capture and signal DNAs for subsequent conjugation of a neutravidin-modified horseradish peroxidase (HRP) enzyme through the strong biotin-nuetravidin interaction. This converts each captured DNA target into an HRP which can convert millions of copies of a non-fluorescent substrate (amplex red) to a highly fluorescent product (resorufin), for great signal amplification. The use of polymer nanobead each tagged with thousands of copies of HRPs as the signal amplifier greatly improves the signal amplification power, leading to greatly improved sensitivity. We show our biosensing approach can specifically detect an unlabeled DNA target down to 10 aM with a wide dynamic range of 5 orders of magnitude (from 0.001 fM to 100.0 fM). Furthermore, our approach has a high discrimination between a perfectly matched gene and its cancer-related single-base mismatch targets (SNPs): It can positively detect the perfect match DNA target even in the presence of 100 fold excess of co-existing SNPs. This sensing approach also works robustly in clinical relevant media (e.g. 10% human serum) and gives almost the same SNP discrimination ratio as that in clean buffers. Therefore, this ultrasensitive SNP biosensor appears to be well-suited for potential diagnostic applications of genetic diseases.

Keywords: DNA detection, polymer beads, signal amplification, single nucleotide polymorphisms

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Authors: Venkat Garigapati

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To date, more than a dozen oligonucleotide products are approved as injectable products for clinical use. However, there is no single oligo nucleotide product approved for clinical use. Oral delivery of oligo nucleotides is patient friendly administration however, many challenges involved in the development of oral formulation. Over the course of last twenty plus years, the research in this space aimed to address these challenges. This paper describes the issues involved in solubility, stability, enzymatic (nuclease) induced degradation, and permeation of nucleotides in the Gastrointestinal (GI) and how to overcome these challenges. Also, the translation of in vitro data to in vivo models hinders the formulation development. This paper describes the challenges involved in the development of Oligo Nucleotide products for oral administration. It also discusses the chemistry and formulation strategies for oral administration of oligonucleotides.

Keywords: oral adminstration, oligo nucleotides, stability, permeation, gastrointestinal tract

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Authors: Eva Maleviti, Evan Stamoulis

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This paper is part of a wider research project, on environmental management in aviation and aerospace industries. The core elements of this research are the level of knowledge, awareness, applicability of environmental management systems, according to employees’ perspectives. This paper focuses at employees’ level of environmental awareness. The main scope of this research is to evaluate the level of environmental awareness and the adoption of environmental management practices. The primary scope of the research is to define a method to quantify the key indicators that would improve the implementation of environmental management. The opinion of people employed in aviation industry is considered, based on the versatility of their working positions. Up to this stage, 330 respondents have participated globally in the current research. This study uses a questionnaire survey to gain an understanding of the views and attitudes of aerospace staff toward environmental management. The results are analyzed through a quantitative approach using SPSS. The statistical significance shows that the data could follow the same distribution as the distribution of the total population that the sample belongs. As of the above, the number of respondents constitutes a representative sample of the total population. A descriptive analysis is presented. According to the responses given in the survey, the data are analyzed according to the working positions and the characteristics of each position that all the respondents hold. The results demonstrate that the level of environmental awareness is immediately linked with the employees’ positions. Managerial/post holder positions, as expected have, a higher level of environmental awareness. However, the level of applicability of environmental practices by the same group is considered low. The other working groups show variability in environmental awareness, which also depends on their operating task and the applicability or not of environmental practices. Flight operations and engineering/maintenance employees, that their tasks involve higher safety considerations, there are more reluctant in applying environmental practices in their positions. In the current paper an analysis of the data collection is presented, correlating them with the working positions and responsibilities of respondents.

Keywords: environmental awareness, environmental management, sustainability, sustainable aviation

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Authors: M. G. Gopisankar, A. Surendiran, M. Hemachandren

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The dose requirement of warfarin to achieve target INR range varies in patients with prosthetic heart valve. This variation in is affected by both genetic and non-genetic factors. Earlier studies have identified role of CYP2C9 and VKORC1 genetic polymorphisms on warfarin dose requirement. Warfarin being a substrate for drug transporter, P-glycoprotein coded by ABCB1 gene, may also be influenced by its genetic polymorphisms. This study was aimed to study the effect of single nucleotide polymorphism (SNP), ABCB1 2677G > T on warfarin maintenance dose requirement in patients with steady-state International Normalized Ratio (INR). The median dose requirement was significantly different between the genotype groups GG vs. GT (35 ± 20; 42.5 ± 18, p < 0.05), GG vs. TT (35 ± 20; 41.25 ± 25, p<0.05). There was no significant difference between GT vs. TT. In conclusion, patients with variant allele require a higher weekly maintenance dose of warfarin compared to patients without variant allele.

Keywords: warfarin pharamcogenetics, pharmacogenomics of warfarin, ABCB1 and warfarin, pglycoprotein and warfarin

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Authors: Roya Bakhtiar, Alireza Abdolmohammadi, Hadi Hajarian, Zahra Nikousefat, Davood, Kalantar-Neyestanaki

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The objective of the present study was to determine the polymorphism in the leptin (332G>A) and its association with biometric traits in Sanjabi sheep. For this purpose, blood samples from 96 rams were taken, and tail length, width tail, circumference tail, body length, body width, and height were simultaneously recorded. PCR was performed using specific primer to amplify 463 bp fragment including exon 3 of leptin gene, and PCR products were digested by Cail restriction enzymes. The 332G>A (at 332th nucleotide of exon 3 leptin gene) that caused an amino acid change from Arg to Gln was detected by Cail (CAGNNNCTG) endonuclease, as the endonuclease cannot cut this region if G nucleotide is located in this position. Three genotypes including GG (463), GA (463, 360and 103 bp) and GG (360 bp and 103 bp) were identified after digestion by enzyme. The estimated frequencies of three genotypes including GG, GA, and AA for 332G>A locus were 0.68, 0.29 and 0.03 and those were 0.18 and 0.82 for A and G alleles, respectively. In the current study, chi-square test indicated that 332G>A positions did not deviate from the Hardy–Weinberg (HW) equilibrium. The most important reason to show HW equation was that samples used in this study belong to three large local herds with a traditional breeding system having random mating and without selection. Shannon index amount was calculated which represent an average genetic variation in Sanjabi rams. Also, heterozygosity estimated by Nei index indicated that genetic diversity of mutation in the leptin gene is moderate. Leptin gene polymorphism in the 332G>A had significant effect on body length (P<0.05) trait, and individuals with GA genotype had significantly the higher body length compared to other individuals. Although animals with GA genotype had higher body width, this difference was not statistically significant (P>0.05). This non-synonymous SNP resulted in different amino acid changes at codon positions111(R/Q). As leptin activity is localized, at least in part, in domains between amino acid residues 106-1406, it is speculated that the detected SNP at position 332 may affect the activity of leptin and may lead to different biological functions. Based to our results, due to significant effect of leptin gene polymorphism on body size traits, this gene may be used a candidate gene for improving these traits.

Keywords: body size, Leptin gene, PCR-RFLP, Sanjabi sheep

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Authors: Tatiana Butkova, Nikolai Kibrik, Kristina Malsagova, Alexander Izotov, Alexander Stepanov, Anna Kaysheva

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Relevance. The genetic risk of developing schizophrenia is determined by two factors: single nucleotide polymorphisms and gene copy number variations. The search for serological markers for early diagnosis of schizophrenia is driven by the fact that the first five years of the disease are accompanied by significant biological, psychological, and social changes. It is during this period that pathological processes are most amenable to correction. The aim of this study was to analyze single nucleotide polymorphisms (SNPs) that are hypothesized to potentially influence the onset and development of the endogenous process. Materials and Methods It was analyzed 73 single nucleotide polymorphism variants. The study included 48 patients undergoing inpatient treatment at "Psychiatric Clinical Hospital No. 1" in Moscow, comprising 23 females and 25 males. Inclusion criteria: - Patients aged 18 and above. - Diagnosis according to ICD-10: F20.0, F20.2, F20.8, F21.8, F25.1, F25.2. - Voluntary informed consent from patients. Exclusion criteria included: - The presence of concurrent somatic or neurological pathology, neuroinfections, epilepsy, organic central nervous system damage of any etiology, and regular use of medication. - Substance abuse and alcohol dependence. - Women who were pregnant or breastfeeding. Clinical and psychopathological assessment was complemented by psychometric evaluation using the PANSS scale at the beginning and end of treatment. The duration of observation during therapy was 4-6 weeks. Total DNA extraction was performed using QIAamp DNA. Blood samples were processed on Illumina HiScan and genotyped for 652,297 markers on the Infinium Global Chips Screening Array-24v2.0 using the IMPUTE2 program with parameters Ne=20,000 and k=90. Additional filtration was performed based on INFO>0.5 and genotype probability>0.5. Quality control of the obtained DNA was conducted using agarose gel electrophoresis, with each tested sample having a volume of 100 µL. Results. It was observed that several SNPs exhibited gender dependence. We identified groups of single nucleotide polymorphisms with a membership of 80% or more in either the female or male gender. These SNPs included rs2661319, rs2842030, rs4606, rs11868035, rs518147, rs5993883, and rs6269.Another noteworthy finding was the limited combination of SNPs sufficient to manifest clinical symptoms leading to hospitalization. Among all 48 patients, each of whom was analyzed for deviations in 73 SNPs, it was discovered that the combination of involved SNPs in the manifestation of pronounced clinical symptoms of schizophrenia was 19±3 out of 73 possible. In study, the frequency of occurrence of single nucleotide polymorphisms also varied. The most frequently observed SNPs were rs4849127 (in 90% of cases), rs1150226 (86%), rs1414334 (75%), rs10170310 (73%), rs2857657, and rs4436578 (71%). Conclusion. Thus, the results of this study provide additional evidence that these genes may be associated with the development of schizophrenia spectrum disorders. However, it's impossible cannot rule out the hypothesis that these polymorphisms may be in linkage disequilibrium with other functionally significant polymorphisms that may actually be involved in schizophrenia spectrum disorders. It has been shown that missense SNPs by themselves are likely not causative of the disease but are in strong linkage disequilibrium with non-functional SNPs that may indeed contribute to disease predisposition.

Keywords: gene polymorphisms, genotyping, single nucleotide polymorphisms, schizophrenia.

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Authors: A. T. Adetunji, F. B. Lewu, R. Mundembe

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Plants require nitrogen (N) to support desired production levels. Nitrogen is available to plants in the form of nitrate or ammonium, which are transported into the cell with the aid of various transport proteins. Ammonium transporters (AMTs) play a role in the uptake of ammonium, the form in which nitrogen is preferentially absorbed by plants. Solanum tuberosum AMT1 (StAMT1) was characterized using molecular biology and bioinformatics methods. Nucleotide database sequences were used to design AMT1-specific primers which were used to amplify the AMT1 internal regions. Nucleotide sequencing, alignment and phylogenetic analysis assigned StAMT1 to the AMT1 family. The deduced amino acid sequences showed that StAMT1 is 92%, 83% and 76% similar to Solanum lycopersicum LeAMT1.1, Lotus japonicus LjAMT1.1 and Solanum lycopersicum LeAMT1.2 respectively. StAMT1 fragments were shown to correspond to the 5th - 10th trans-membrane domains. Residue StAMT1 D15 is predicted to be essential for ammonium transport, while mutations of StAMT1 S76A may further enhance ammonium transport.

Keywords: ammonium transporter, bioinformatics, nitrogen, primers, Solanum tuberosum

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Authors: U. Harel, E. Carmeli

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The Purpose was to measure differences in activity patterns between major league adult and U-21 soccer players. Four U-21 players and four adult team players were evaluated using a repeated measures technique. All eight players were affiliated with the Maccabi Haifa soccer club from the Israeli professional and U-21major leagues, depending on the player’s age. GPS sensors were attached to the players during five consecutive games to identify patterns regarding running distance and speed according to the field positions. There was no significant difference in the total running distances covered by two age groups. When measuring running speed, an advantage was observed in the adult group when comparing two players from different age groups that played the same position. Differences in activity patterns were evident between adult and U-21 major league soccer players. Furthermore, differences in within group activity pattern emerged between the positions under investigation. These findings provide valuable knowledge that may serve the principle of training specificity.

Keywords: physical fitness, soccer, positional differences, GPS, training specificity

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Authors: Malik SS, Masood N, Mubarik S, Khadim TM

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Introduction: Xeroderma pigmentosum group G (XPG) gene plays a crucial role in the correction of UV-induced DNA damage through nucleotide excision repair pathway. Single nucleotide polymorphisms in XPG gene have been reported to be associated with different cancers. Current case-control study was designed to evaluate the relationship between one of the most frequently found XPG (rs1047768 T>C) polymorphism and breast cancer risk. Methodology: A total of 200 individuals were screened for this polymorphism including 100 pathologically confirmed breast cancer cases and age-matched 100 controls. Genotyping was carried out using Tetra amplification-refractory mutation system (ARMS) PCR and results were confirmed by gel electrophoresis. Results: Conditional logistic regression analysis showed significant association between TC genotype (OR: 8.9, CI: 2.0 – 38.7) and increased breast cancer risk. Although homozygous CC genotype was more frequent in patients as compared to controls, but it was statistically non-significant (OR: 3.9, CI: 0.4 – 35.7). Conclusion: In conclusion, XPG (rs1047768 T>C) polymorphism may contribute towards increased risk of breast cancer but other polymorphisms may also be evaluated to elucidate their role in breast cancer.

Keywords: XPG, breast cancer, NER, ARMS-PCR

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Authors: M. Bazin, I. Bouguir, D. Combe, V. Germain, G. Lassade

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The problem of managing a fleet of quad-rotor drones in a completely unknown environment is analyzed in the present paper. This work is following the footsteps of other studies about how should be managed the movements of a swarm of elements that have to stay gathered throughout their activities. In this paper we aim to demonstrate the limitations of a system where absolutely all the calculations and physical movements of our elements are done by one single external element. The strategy of control is an adaptive approach which takes into account the explored environment. This is made possible thanks to a set of command rules which can guide the drones through various missions with defined goal. The result of the mission is independent of the nature of environment and the number of drones in the fleet. This strategy is based on a simultaneous usage of different data: obstacles positions, real-time positions of all drones and relative positions between the different drones. The present work is made with the Robot Operating System and used several open-source projects on localization and usage of drones.

Keywords: cooperative guidance, distributed control, unmanned aerial vehicle, obstacle avoidance

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Authors: Daniel Schwarz, Jan Fivaz, Alessia Neuroni

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Although digitization is a buzzword in almost every election campaign, the political parties leave voters largely in the dark about their specific positions on digital issues. In the run-up to the 2019 elections in Switzerland, the ‘Digitization Monitor’ project (DMP) was launched in order to change this situation. Within the framework of the DMP, all 4,736 candidates were surveyed about their digital policy positions and values. The DMP is designed as a digital policy supplement to the existing ‘smartvote’ voting advice application. This enabled a direct comparison of the digital policy attitudes according to the DMP with the topics of the ‘smartvote’ questionnaire which are comprehensive in content but mainly related to conventional policy areas. This paper’s main research goal is to analyze and visualize possible differences between conventional and digital policy areas in terms of response patterns between and within political parties. The analysis is based on dimensionality reduction methods (multidimensional scaling and principal component analysis) for the visualization of inter-party differences, and on standard deviation as a measure of variation for the evaluation of intra-party unity. The results reveal that digital issues show a lower degree of inter-party polarization compared to conventional policy areas. Thus, the parties have more common ground in issues on digitization than in conventional policy areas. In contrast, the study reveals a mixed picture regarding intra-party unity. Homogeneous parties show a lower degree of unity in digitization issues whereas parties with heterogeneous positions in conventional areas have more united positions in digital areas. All things considered, the findings are encouraging as less polarized conditions apply to the debate on digital development compared to conventional politics. For the future, it would be desirable if in further countries similar projects to the DMP could emerge to broaden the basis for conclusions.

Keywords: comparison of political issue dimensions, digital awareness of candidates, digital policy space, party positions on digital issues

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Authors: Noboru Abe, Yoshinori Amai, Toshinori Nakatake, Sumio Masuda, Kazuaki Yamaguchi

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We consider the problem of placing labels of the points on a plane. For each point, its position, the size of its label and a priority are given. Moreover, several candidates of its label positions are prespecified, and each of such label positions is assigned a priority. The objective of our problem is to maximize the total sum of priorities of placed labels and their points. By refining a labeling algorithm that can use these priorities, we propose a new heuristic algorithm which is more suitable for treating the assigned priorities.

Keywords: map labeling, greedy algorithm, heuristic algorithm, priority

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Authors: Amr A. El Hanafy, Muhammad I. Qureshi, Jamal Sabir, Mohamed Mutawakil, Mohamed M. Ahmed, Hassan El Ashmaoui, Hassan Ramadan, Mohamed Abou-Alsoud, Mahmoud Abdel Sadek

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β-Lactoglobulin (β-LG) is the dominant non-casein whey protein found in bovine milk and of most ruminants. The amino acid sequence of β-LG along with its 3-dimensional structure illustrates linkage with the lipocalin superfamily. Preliminary studies in goats indicated that milk yield can be influenced by polymorphism in genes coding for whey proteins. The aim of this study is to identify and evaluate the incidence of functional polymorphisms in the exonic and intronic portions of β-LG gene in native Saudi goat breeds (Ardi, Habsi, and Harri). Blood samples were collected from 300 animals (100 for each breed) and genomic DNA was extracted using QIAamp DNA extraction Kit. A fragment of the β-LG gene from exon 7 to 3’ flanking region was amplified with pairs of specific primers. Subsequent digestion with Sac II restriction endonuclease revealed two alleles (A and B) and three different banding patterns or genotypes i.e. AA, AB and BB. The statistical analysis showed that β-LG AA genotype had higher milk yield than β-LG AB and β-LG BB genotypes. Nucleotide sequencing of the selected β-LG fragments was done and submitted to GenBank NCBI (Accession No. KJ544248, KJ588275, KJ588276, KJ783455, KJ783456 and KJ874959). Two already established SNPs in exon 7 (+4601 and +4603) and one fresh SNP in the 3’ UTR region were detected in the β-LG fragments with designated AA genotype. The polymorphisms in exon 7 did not produce any amino acid change. Phylogenetic analysis on the basis of nucleotide sequences of native Saudi goats indicated evolutional similarity with the GenBank reference sequences of goat, Bubalus bubalis and Bos taurus.

Keywords: β-Lactoglobulin, Saudi goats, PCR-RFLP, functional polymorphism, nucleotide sequencing, phylogenetic analysis

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Authors: Stefanos Karanasios, Charkleia Koutri, Maria Moutzouri, Sofia A. Xergia, Vasiliki Sakellari, George Gioftsos

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The precise calculation of arterial occlusive pressure (AOP) is a critical step to accurately prescribe individualized pressures during blood flow restriction training (BFRT). AOP is usually measured in a supine position before training; however, previous reports suggested a significant influence in lower limb AOP across different body positions. The aim of the study was to investigate the effect of three different body positions on upper limb AOP and the reliability of the method for its standardization in clinical practice. Forty-two healthy participants (Mean age: 28.1, SD: ±7.7) underwent measurements of upper limb AOP in supine, seated, and standing positions by three blinded raters. A cuff with a manual pump and a pocket doppler ultrasound were used. A significantly higher upper limb AOP was found in seated compared with supine position (p < 0.031) and in supine compared with standing position (p < 0.031) by all raters. An excellent intraclass correlation coefficient (0.858- 0.984, p < 0.001) was found in all positions. Upper limb AOP is strongly dependent on body position changes. The appropriate measurement position should be selected to accurately calculate AOP before BFRT. The excellent inter-rater reliability and repeatability of the method suggest reliable and consistent results across repeated measurements.

Keywords: Kaatsu training, blood flow restriction training, arterial occlusion, reliability

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Authors: S. Dodd

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This presentation examines the gender gap in leadership positions at colleges and universities within the United States. Despite the fact that women now outnumber men in earning doctorate degrees, women continue to hold far fewer positions of educational leadership, and still, earn less money than men do at every level. Considering the lack of female representation in positions of leadership, there are clearly outside variables preventing women from attaining these positions, despite their educational attainment. Following this study, the American Council on Education (ACE) set a goal to achieve an equal percentage of females holding college presidency positions by the year 2030. This goal is particularly ambitious, especially when considering the gender disparity at all ranks in higher education. Men still hold nearly 70% of all full professorships at degree-granting institutions. Even when women are equally represented in numbers, men typically hold a higher rank and are more likely to be tenured. Across all four-year colleges and universities in the United States, men earn more money than women at every rank and in every discipline. There are over twice as many men than women represented on governing boards, who help formed and uphold campus policies. The fact that the low percentage of female presidents has remained static for many years deepens the challenge for the ACE. Although emphasizing the need to create greater opportunities for women in educational administration is admirable, it is difficult to simplify the social forces that create and uphold the status quo of male leadership. When aiming to ensure 'women' hold 50% of all college presidency positions, it is important to consider how the intersections of race, social class, and other factors also correlate with lower job status. This presentation explores how gendered notions of leadership begin in a child’s early years and are carried into future careers, and how these conceptualizations impact the creation and upholding of educational policies at every academic level. Current research that emphasizes the importance establishing a bottom-up approach to a gender equity infrastructure for children early in their educational careers will be discussed. A top-down approach starting with female college presidents is incomplete and insufficient if the mindsets of the youth who will one day be entering those institutions of higher education are not also taken into consideration. Although ACE has established this lofty goal for female college presidencies by the year 2030, a road map for this will ensue, has not yet been provided. The talent pool of women who are educated and experienced for such positions is vast, but acknowledging the social barriers existing for women in these positions will be crucial to making the changes necessary for these leadership opportunities to be long lasting and successful.

Keywords: equity, higher education, leadership, women

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Authors: Fulufhelo Amanda Doboro, Kgomotso Sebeko, Stephen Njiro, Moritz Van Vuuren

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Ovine herpesvirus 2 (OvHV-2) genome obtained from the lymphopblastoid cell line of a BJ1035 cow was recently sequenced in the United States of America (USA). Information on the sequences of OvHV-2 genes obtained from South African strains from bovine or other African countries and molecular characterization of OvHV-2 is not documented. Present investigation provides information on the nucleotide and derived amino acid sequences and genetic diversity of Ov 7, Ov 8 ex2, ORF 27 and ORF 73 genes, of these genes from OvHV-2 strains circulating in South Africa. Gene-specific primers were designed and used for PCR of DNA extracted from 42 bovine blood samples that previously tested positive for OvHV-2. The expected PCR products of 495 bp, 253 bp, 890 bp and 1632 bp respectively for Ov 7, Ov 8 ex2, ORF 27 and ORF 73 genes were sequenced and multiple sequence analysis done on the selected regions of the sequenced PCR products. Two genotypes for ORF 27 and ORF 73 gene sequences, and three genotypes for Ov 7 and Ov 8 ex2 gene sequences were identified, and similar groupings for the derived amino acid sequences were obtained for each gene. Nucleotide and amino acid sequence variations that led to the identification of the different genotypes included SNPs, deletions and insertions. Sequence analysis of Ov 7 and ORF 27 genes revealed variations that distinguished between sequences from SA and reference OvHV-2 strains. The implication of geographic origin among SA sequences was difficult to evaluate because of random distribution of genotypes in the different provinces, for each gene. However, socio-economic factors such as migration of people with animals, or transportation of animals for agricultural or business use from one province to another are most likely to be responsible for this observation. The sequence variations observed in this study have no impact on the antibody binding activities of glycoproteins encoded by Ov 7, Ov 8 ex2 and ORF 27 genes, as determined by prediction of the presence of B cell epitopes using BepiPred 1.0. The findings of this study will be used for selection of gene candidates for the development of diagnostic assays and vaccine development as well.

Keywords: amino acid, genetic diversity, genes, nucleotide

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Authors: Juliana Lukša, Bazilė Ravoitytė, Elena Servienė, Saulius Serva

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Totiviridae L-A virus is a persistent Saccharomyces cerevisiae dsRNA virus. It encodes the major structural capsid protein Gag and Gag-Pol fusion protein, responsible for virus replication and encapsulation. These features also enable the copying of satellite dsRNAs (called M dsRNAs) encoding a secreted toxin and immunity to it (known as killer toxin). Viral capsid pore presumably functions in nucleotide uptake and viral mRNA release. During cell division, sporogenesis, and cell fusion, the virions remain intracellular and are transferred to daughter cells. By employing high throughput RNA sequencing data analysis, we describe the influence of solely L-A virus on the expression of genes in three different S. cerevisiae hosts. We provide a new perception into Totiviridae L-A virus-related transcriptional regulation, encompassing multiple bioinformatics analyses. Transcriptional responses to L-A infection were similar to those induced upon stress or availability of nutrients. It also delves into the connection between the cell metabolism and L-A virus-conferred demands to the host transcriptome by uncovering host proteins that may be associated with intact virions. To better understand the virus-host interaction, we applied differential proteomic analysis of virus particle-enriched fractions of yeast strains that harboreither complete killer system (L-A-lus and M-2 virus), M-2 depleted orvirus-free. Our analysis resulted in the identification of host proteins, associated with structural proteins of the virus (Gag and Gag-Pol). This research was funded by the European Social Fund under the No.09.3.3-LMT-K-712-19-0157“Development of Competences of Scientists, other Researchers, and Students through Practical Research Activities” measure.

Keywords: totiviridae, killer virus, proteomics, transcriptomics

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Authors: Mostafa Shahriari, Theophile Chaumont-Frelet, David Pardo

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Resistivity measurements are used to characterize the Earth’s subsurface. They are categorized into two different groups: (a) those acquired on the Earth’s surface, for instance, controlled source electromagnetic (CSEM) and Magnetotellurics (MT), and (b) those recorded with borehole logging instruments such as Logging-While-Drilling (LWD) devices. LWD instruments are mostly used for geo-steering purposes, i.e., to adjust dip and azimuthal angles of a well trajectory to drill along a particular geological target. Modern LWD tools measure all nine components of the magnetic field corresponding to three orthogonal transmitter and receiver orientations. In order to map the Earth’s subsurface and perform geo-steering, we invert measurements using a gradient-based method that utilizes the derivatives of the recorded measurements with respect to the inversion variables. For resistivity measurements, these inversion variables are usually the constant resistivity value of each layer and the bed boundary positions. It is well-known how to compute derivatives with respect to the constant resistivity value of each layer using semi-analytic or numerical methods. However, similar formulas for computing the derivatives with respect to bed boundary positions are unavailable. The main contribution of this work is to provide an adjoint-based formulation for computing derivatives with respect to the bed boundary positions. The key idea to obtain the aforementioned adjoint state formulations for the derivatives is to separate the tangential and normal components of the field and treat them differently. This formulation allows us to compute the derivatives faster and more accurately than with traditional finite differences approximations. In the presentation, we shall first derive a formula for computing the derivatives with respect to the bed boundary positions for the potential equation. Then, we shall extend our formulation to 3D Maxwell’s equations. Finally, by considering a 1D domain and reducing the dimensionality of the problem, which is a common practice in the inversion of resistivity measurements, we shall derive a formulation to compute the derivatives of the measurements with respect to the bed boundary positions using a 1.5D variational formulation. Then, we shall illustrate the accuracy and convergence properties of our formulations by comparing numerical results with the analytical derivatives for the potential equation. For the 1.5D Maxwell’s system, we shall compare our numerical results based on the proposed adjoint-based formulation vs those obtained with a traditional finite difference approach. Numerical results shall show that our proposed adjoint-based technique produces enhanced accuracy solutions while its cost is negligible, as opposed to the finite difference approach that requires the solution of one additional problem per derivative.

Keywords: inverse problem, bed boundary positions, electromagnetism, potential equation

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Authors: Saima Suleman, Kalsoom Sughra, Naeem Mahmood Ashraf

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Mycobacterium tuberculosis is a communicable chronic illness. This disease is being highly focused by researchers as it is present approximately in one third of world population either in active or latent form. The genetic makeup of a person plays an important part in producing immunity against disease. And one important factor association is single nucleotide polymorphism of relevant gene. In this study, we have studied association between single nucleotide polymorphism of CD-209 gene (encode DC-SIGN receptor) and patients of tuberculosis. Dry lab (in silico) and wet lab (RFLP) analysis have been carried out. GWAS catalogue and GEO database have been searched to find out previous association data. No association study has been found related to CD-209 nsSNPs but role of CD-209 in pulmonary tuberculosis have been addressed in GEO database.Therefore, CD-209 has been selected for this study. Different databases like ENSEMBLE and 1000 Genome Project has been used to retrieve SNP data in form of VCF file which is further submitted to different software to sort SNPs into benign and deleterious. Selected SNPs are further annotated by using 3-D modeling techniques using I-TASSER online software. Furthermore, selected nsSNPs were checked in Gujrat and Faisalabad population through RFLP analysis. In this study population two SNPs are found to be associated with tuberculosis while one nsSNP is not found to be associated with the disease.

Keywords: association, CD209, DC-SIGN, tuberculosis

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Authors: Bahieh Mohajeri, Mohamad Sharif Mustaf, Mahani Mokhtar

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Purpose: This paper attempts to set the stage for the exploration of female participation in administrative positions within non-western countries by reviewing the studies on female in administrative positions within non-western countries and suggesting guidelines for future studies in this area in developing countries. Methodology: The paper is based on a systematic review of papers that have been published in journals. Findings: The review focuses on constraints to female’s participation in higher education of developing countries (e.g. strong family responsibility, low levels of women faculty members, social values and gendered cultural factors). Practical Implications: Further guidelines for future examination of this field of study are suggested (e.g. adopting a different theoretical view).Value: The article is an initial attempt to gather knowledge about constraints of female administrators in higher education of developing countries. The subject has received less attention in studies on administration and gender. In addition, the article provides suggestions for future studies in order to understand women administrators’ experiences in different educational and cultural settings.

Keywords: administrative position, female administrator, developing countries, participation

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Authors: Nefi Aris Ambar Asmara

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This paper discusses gender equality and career opportunities among female civil servants for better public services in a regency in West Java, Indonesia. Those two areas have not been considered comprehensively in terms of the goals of gender equality and career opportunities. The purposes of this paper are to describe (1) the number of available positions in relation to the number of female civil servants, (2) the socio-cultural outlook on female civil servants in relation to gender equality and career opportunities, and (3) socio-cultural views on gender equality and a career in politics. To achieve these three objectives, this paper used a qualitative approach with survey and interview techniques. The results showed that (1) only 37% of the official positions were presided by female civil servants. In contrast, male civil servants occupy 63% of the available positions, (2) the sociocultural view of female civil servants affirms that they are still regarded as male companions; (3) in addition, female civil servants do not need to compete with gender opponents, including the fact that women enter politics because the political world is considered dirty for women.

Keywords: gender equality, career opportunities, female civil servants, Indonesia

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Authors: Nefi Aris Ambar Asmara

Abstract:

This paper discusses gender equality and career opportunities among female civil servants for better public services in a regency in West Java, Indonesia. Those two areas have not been considered comprehensively in terms of the goals of gender equality and career opportunities. The purposes of this paper are to describe (1) the number of available positions in relation to the number of female civil servants, (2) the socio-cultural outlook on female civil servants in relation to gender equality and career opportunities and (3) socio-cultural views on gender equality and a career in politics. To achieve these three objectives, this paper used a qualitative approach with survey and interview techniques. The results showed that (1) only 37% of the official positions were presided by female civil servants. In contrast, male civil servants occupy 63% of the available positions, (2) the sociocultural view of female civil servants affirms that they are still regarded as male companions; (3) in addition, female civil servants do not need to compete with gender opponents, including the fact that women enter politics because the political world is considered dirty for women.

Keywords: gender equality, career opportunities, female civil servants, indonesia

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Authors: Fakhrosadat Sajjadian, Ramin Ghasemi Shayan

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The tumor microenvironment plays an fundamental part in tumor start, movement, metastasis, and treatment resistance. It varies from ordinary tissue in terms of its extracellular network, vascular and lymphatic arrange, as well as physiological conditions. The clinical application of atomic cancer imaging is regularly prevented by the tall commercialization costs of focused on imaging operators as well as the constrained clinical applications and little showcase measure of a few operators. . Since numerous cancer types share comparable characteristics of the tumor microenvironment, the capacity to target these biomarkers has the potential to supply clinically translatable atomic imaging advances for numerous types encompassing cancer and broad clinical applications. Noteworthy advance has been made in focusing on the tumor microenvironment for atomic cancer imaging. In this survey, we summarize the standards and methodologies of later progresses in atomic imaging of the tumor microenvironment, utilizing distinctive imaging modalities for early discovery and conclusion of cancer. To conclude, The tumor microenvironment (TME) encompassing tumor cells could be a profoundly energetic and heterogeneous composition of safe cells, fibroblasts, forerunner cells, endothelial cells, flagging atoms and extracellular network (ECM) components.

Keywords: molecular, imaging, TME, medicine

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Authors: Donatella Cimini, Sergio D’ambrosio, Saba Sadiq, Chiara Schiraldi

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Chondroitin sulfate (CS), as well as modified CS, and unsulfated chondroitin, are largely applied in research today. CS is a linear glycosaminoglycan normally present in cartilage-rich tissues and bones in the form of proteoglycans decorated with sulfate groups in different positions. CS is used as an effective non-pharmacological alternative for the treatment of osteoarthritis, and other potential applications in the biomedical field are being investigated. Some bacteria, such as E. coli K4, produce a polysaccharide that is a precursor of CS (unsulfated chondroitin). This work focused on the construction of integrative E. coli K4 recombinant strains overexpressing genes (kfoA, kfoF, pgm and galU in different combinations) involved in the biosynthesis of the nucleotide sugars necessary for polysaccharide synthesis. Strain growth and polymer production were evaluated using renewable waste materials as substrates in shake flasks and small-scale batch fermentation processes. Results demonstrated the potential to replace pure sugars with cheaper medium components to establish environmentally sustainable and cost-effective production routes for potential industrial development. In fact, although excellent fermentation results have been described so far by employing strains that naturally produce chondroitin-like polysaccharides on semi-defined media, there is still the need to reduce manufacturing costs by providing a cost-effective biotechnological alternative to currently used animal-based extraction procedures.

Keywords: E. coli K4, chondroitin, microbial cell factories, glycosaminoglycans, renewable resources

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Authors: Eisha Vienna M. Fernandez, Cristan Q. Cabanilla, Hiyasmin Lim, John Donnie A. Ramos

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Allergy is a multifactorial disease affecting a significant proportion of the population. It is developed through the interaction of allergens and the presence of certain polymorphisms in various susceptibility genes. In this study, the correlation of the 105A/C single nucleotide polymorphism (SNP) of the IL-18 gene and house dust mite-specific IgE among Filipino allergic and non-allergic population was investigated. Atopic status was defined by serum total IgE concentration of ≥100 IU/mL, while house dust mite allergy was defined by specific IgE value ≥ +1SD of IgE of nonatopic participants. Two hundred twenty match-paired Filipino cases and controls aged 6-60 were the subjects of this investigation. The level of total IgE and Specific IgE were measured using Enzyme-Linked Immunosorbent Assay (ELISA) while Polymerase Chain Reaction – Restriction Fragment Length Polymorphism (PCR-RFLP) analysis was used in the SNP detection. Sensitization profiles of the allergic patients revealed that 97.3% were sensitized to Blomia tropicalis, 40.0% to Dermatophagoides farinae, and 29.1% to Dermatophagoides pteronyssinus. Multiple sensitization to HDMs was also observed among the 47.27% of the atopic participants. Any of the allergy classes of the atopic triad were exhibited by the cases (allergic asthma: 48.18%; allergic rhinitis: 62.73%; atopic dermatitis: 19.09%), and two or all of these atopic states are concurrently occurring in 26.36% of the cases. A greater proportion of the atopic participants with allergic asthma and allergic rhinitis were sensitized to D. farinae, and D. pteronyssinus, while more of those with atopic dermatitis were sensitized to D. pteronyssinus than D. farinae. Results show that there is overrepresentation of the allele “A” of the 105A/C IL-18 gene SNP in both cases and control groups of the population. The genotype that predominate the population is the heterozygous “AC”, followed by the homozygous wild “AA”, and the homozygous variant “CC” being the least. The study confirmed a positive association between serum specific IgE against B. tropicalis and D. pteronyssinus and the allele “C” (Bt P=0.021, Dp P=0.027) and “AC” (Bt P=0.003, Dp P=0.026) genotype. Findings also revealed that the genotypes “AA” (OR:1.217; 95% CI: 0.701-2.113) and “CC” (OR, 3.5; 95% CI: 0.727-16.849) increase the risk of developing allergy. This indicates that the 105A/C IL-18 gene SNP is a candidate genetic marker for HDM allergy among Filipino patients.

Keywords: house dust mite allergy, interleukin-18 (IL-18), single nucleotide polymorphism,

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Authors: Ameen Alahdal

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This paper investigates copular constructions in Raimi Yemeni Arabic (RYA). The aim of the paper is actually twofold. First it explores the types of copular constructions in Raimi Yemeni Arabic, a variety of Arabic that has not attracted a lot of attention. In this connection, the paper shows that RYA manifests ‘bare’, verbal and pronominal/PRON copular constructions, just like other varieties of Arabic and indeed other Semitic languages like Hebrew. The sentences below from RYA represent the three constructions, respectively. (1) a. nada Hilwah Nada pretty.3sf ‘Nada is pretty’ b. kan al-banat hina was the-girls here ‘The girls were here c. ali hu-l mudiir Ali he-the manager ‘Ali is the manager’ Interestingly, in addition to these common types of copular constructions, RYA seems to exhibit dual copula sentences, a construction that features both a pronominal copula and a verbal copula. Such a construction is attested neither in Standard Arabic nor in other modern varieties of Arabic such as Lebanese, Moroccan, Egyptian, Jordanian. Remarkably, dual copular sentences do not appear even in other dialects of Yemeni Arabic such as Sanaani, Adeni and Tehami. (2) is an example. (2) maha kan-ih mudarrisah maha was-she teacher.3sf ‘Maha was a teacehr’ Second, the paper considers the cartography of subject positions in copular constructions proposed by Shlonsky and Rizzi (2018). Different copular constructions seem to involve different subject positions (which might eventually correlate with different interpretations – not our concern in this paper). Here, it is argued that in a bare copular sentence, as in (1a), RYA might exploit two criterial subject positions (in Rizzi’s sense), in addition to the canonical Spec,TP position. Under mainstream minimalist assumption, a copular sentence is analyzed as a PredP. Thus, in addition to the PredP-related thematic subject position, a criterial subject position is posited outside of PredP. (3) below represents the cartography of subject positions in a bare copular construction. (3) [……..DP subj PredP DP Pred DP/AP/PP ] In PRON sentences, as exemplified in (1c), another two subject positions are postulated high in the clause, particularly above PolP. (4) illustrates the hierarchy of the subject positions in a PRON copular construction. The subject resides in Spec,SUBJ2P. (4) …DP SUBJ2 …DP SUBJ1 … Pol … DP subj PredP Another related phenomenon in RYA which sets it apart from other languages like Hebrew is that of negative bare copular construction. This construction involves a PRON, which is not found in its affirmative counterpart. PRON, however, is hosted neither by SUBJ20 nor by SUBJ10. Rather, PRON occurs below Neg0 (Pol0 in the hierarchy). This situation raises interesting issues for the hierarchy of subjects in copular constructions as well as to the syntax of the left periphery in general. With regard to what causes the subject to move, there are different potential triggers. For instance, movement of the subject at the base, i.e., out of PredP is triggered by a labeling failure. Other movements of the subject can be driven by a formal feature like EPP, or a criterial feature like [subj].

Keywords: Yemeni Arabic, copular constructions, cartography of subjects, labeling, criterial positions

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Authors: R. H. Bustos, L. Martinez, J. García, F. Suárez

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MRP1 (Multi-drug resistance associated protein 1) and MRP2 (Multi-drug resistance associated protein 2) are two proteins belonging to the transporters of ABC (ATP-Binding Cassette). These transporter proteins are involved in the efflux of several biological drugs and xenobiotic and also in multiple physiological, pathological and pharmacological processes. Evidence has been found that there is a correlation among different polymorphisms found and their clinical implication in the resistance to antiepileptic, chemotherapy and anti-infectious drugs. In our study, exonic regions of MRP1/ABCC1 y MRP2/ABCC2 were studied in the Colombian population, specifically in the region of the central Savannah (Cundinamarca) to determinate SNP (Single Nucleotide Polymorphisms) and determinate its allele frequency and its genomics frequency. Results showed that for our population, SNP are found that have been previously reported for MRP1/ABCC1 (rs200647436, rs200624910, rs150214567) as well as for MRP2/ABCC2 (rs2273697, rs3740066, rs142573385, rs17216212). In addition, 13 new SNP were identified. Evidences show an important clinic correlation for polymorphisms rs3740066 and rs2273697. The study object population displays genetic variability as compared to the one reported in other populations.

Keywords: ATP-binding cassette (ABCC), Colombian population, multidrug-resistance protein (MRP), pharmacogenetic, single nucleotide polymorphism (SNP)

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Authors: Sakina Fatima, Joseph-Patrick W. E. Clarke, Patricia A. Thibault, Subha Kalyaanamoorthy, Michael Levin, Aravindhan Ganesan

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Heteronuclear ribonucleoprotein (hnRNPA1 or A1) is associated with the pathology of different diseases, including neurological disorders and cancers. In particular, the aggregation and dysfunction of A1 have been identified as a critical driver for neurodegeneration (NDG) in Multiple Sclerosis (MS). Structurally, A1 includes a low-complexity domain (LCD) and two RNA-recognition motifs (RRMs), and their interdomain coordination may play a crucial role in A1 aggregation. Previous studies propose that RNA-inhibitors or nucleoside analogs that bind to RRMs can potentially prevent A1 self-association. Therefore, molecular-level understanding of the structures, dynamics, and nucleotide interactions with A1 RRMs can be useful for developing therapeutics for NDG in MS. In this work, a combination of computational modelling and biochemical experiments were employed to analyze a set of RNA-A1 RRM complexes. Initially, the atomistic models of RNA-RRM complexes were constructed by modifying known crystal structures (e.g., PDBs: 4YOE and 5MPG), and through molecular docking calculations. The complexes were optimized using molecular dynamics simulations (200-400 ns), and their binding free energies were computed. The binding affinities of the selected complexes were validated using a thermal shift assay. Further, the most important molecular interactions that contributed to the overall stability of the RNA-A1 RRM complexes were deduced. The results highlight that adenine and guanine are the most suitable nucleotides for high-affinity binding with A1. These insights will be useful in the rational design of nucleotide-analogs for targeting A1 RRMs.

Keywords: hnRNPA1, molecular docking, molecular dynamics, RNA-binding proteins

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Authors: M. Suwaibah, S. W. Tan, I. Aiini, K. Yusoff, A. R. Omar

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Respiratory diseases are the most important infectious diseases affecting poultry worldwide. One of the avian respiratory virus of global importance causing significant economic losses is Infectious Bronchitis Virus (IBV). The virus causes a wide spectrum disease known as Infectious Bronchitis (IB), affecting not only the respiratory system but also the kidney and the reproductive system, depending on its strain. IB and Newcastle disease are two of the most prevalent diseases affecting poultry in Malaysia. However, a study on the molecular characterization of Malaysian IBV is lacking. In this study, an IBV strain IBS130 which was isolated in 2015 was fully sequenced using next-gene sequencing approach. Sequence analysis of IBS130 based on the complete genome, polyprotein 1ab and S1 genes were compared with other IBV sequences available in Genbank, National Center for Biotechnology Information (NCBI). IBV strain IBS130 is characterised as QX-like strain based on whole genome and S1 gene sequence analysis. Comparisons of the virus with other IBV strains showed that the nucleotide identity ranged from 67% to 99.2%, depending on the region analysed. The similarity in whole genome nucleotide ranging from 84.9% to 90.7% with the least similar was from Singapore strains (84.9%) and highly similar with China QX-like strains. Meanwhile, the similarity in polyprotein 1ab ranging from 85.3% to 89.9% with the least similar to Singapore strains (85.3%) and highly similar with Mass strains from USA.

Keywords: infectious bronchitis virus, phylogenetic analysis, chicken, Malaysia

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