Search results for: whole genome diversity

Authors: Bibi Alajmi, Israa Alshammari

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This study investigates diversity strands covered in courses offered by library and information sciences (LIS) graduate programs. It aims to identify the extent to which these programs prepare students to work in diverse communities. Information was collected from 17 ALA-accredited MLIS programs. Diversity-related topics were identified and categorized. The methodology consisted of content analysis of course syllabi. The findings show that coverage of diversity-related content in LIS graduate curricula is increasing at a slow but significant rate, and is often a low priority. Apart from LIS graduate courses for future librarians and information professionals in public libraries, school libraries, and museums providing services to young adults and children, there is not enough interest in the provision of services to diverse communities.

Keywords: diversity, multiculturalism, inclusion, equality, gender

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Authors: Yu Guang

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“Case studies are the preferred strategy when ‘how’ or ‘why’ questions are being posed.” Therefore, the study is based on two cases: strategy performed in JingNan War and by NIKE. The two samples are chosen as they are of comparability. Data are gathered and PEST and SWOT are used as analysis models to examine their strategic employment in order that the answer to brilliant strategies in variety is found. The niche strategy has been used in the past and present, in the battle fields and business. The homogeneity among diversity is the skill of performing strategies.

Keywords: challenger, homogeneity, managing diversity, niche strategy

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Authors: Farahnaz Sadat Golestan Hashemi, Mohd Razi Ismail, Mohd Y. Rafii

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Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system can facilitate targeted genome editing in organisms. Dual or single guide RNA (gRNA) can program the Cas9 nuclease to cut target DNA in particular areas; thus, introducing concise mutations either via error-prone non-homologous end-joining repairing or via incorporating foreign DNAs by homologous recombination between donor DNA and target area. In spite of high demand of such promising technology, developing a well-organized procedure in order for reliable mining of potential target sites for gRNAs in large genomic data is still challenging. Hence, we aimed to perform high-throughput detection of target sites by specific PAMs for not only common Streptococcus pyogenes (SpCas9) but also for Neisseria meningitides (NmCas9) CRISPR-Cas systems. Previous research confirmed the successful application of such RNA-guided Cas9 orthologs for effective gene targeting and subsequently genome manipulation. However, Cas9 orthologs need their particular PAM sequence for DNA cleavage activity. Activity levels are based on the sequence of the protospacer and specific combinations of favorable PAM bases. Therefore, based on the specific length and sequence of PAM followed by a constant length of the target site for the two orthogonals of Cas9 protein, we created a reliable procedure to explore possible gRNA sequences. To mine CRISPR target sites, four different searching modes of sgRNA binding to target DNA strand were applied. These searching modes are as follows i) coding strand searching, ii) anti-coding strand searching, iii) both strand searching, and iv) paired-gRNA searching. Finally, a complete list of all potential gRNAs along with their locations, strands, and PAMs sequence orientation can be provided for both SpCas9 as well as another potential Cas9 ortholog (NmCas9). The artificial design of potential gRNAs in a genome of interest can accelerate functional genomic studies. Consequently, the application of such novel genome editing tool (CRISPR/Cas technology) will enhance by presenting increased versatility and efficiency.

Keywords: CRISPR/Cas9 genome editing, gRNA mining, SpCas9, NmCas9

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Authors: Hyeondal Jeong, Yoonjung Baek

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This study was carried out a meta-analysis on team workforce diversity and team outcomes. Using data from 3,534 teams in 13 studies conducted in team-level settings, we examined whether contextual factors at research local and team-size, influenced team outcomes of team workforce diversity. This meta-analytic examines the team workforce diversity and team outcomes. 13 studies included in the analysis are studies published from 2009 to 2014. We first examined the correlations between all types of diversity and team performance, significant result (Fisher`s Z = .112, k = 32, 95% CI = 0.039 to 0.183). After the analysis was conducted to moderating effect of research local (Republic of Korea=1, other area=0) and team-size. As a result, research local moderating effect had a significant but team-size was not supported. Based on the above findings suggest implications and future research directions.

Keywords: team workforce diversity, team outcomes, meta- analytic, cross-cultural research

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Authors: Suikinai Nobre Santos, Ranko Gacesa, Paul F. Long, Itamar Soares de Melo

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Extremophilic microorganism are adapted to biotopes combining several stress factors (temperature, pressure, radiation, salinity and pH), which indicate the richness valuable resource for the exploitation of novel biotechnological processes and constitute unique models for investigations their biomolecules (1, 2). The above information encourages us investigate bioprospecting synthesized compounds by a noval actinomycete, designated thermotolerant Streptomyces caatingaensis CMAA 1322, isolated from sample soil tropical dry forest (Caatinga) in the Brazilian semiarid region (3-17°S and 35-45°W). This set of constrating physical and climatic factores provide the unique conditions and a diversity of well adapted species, interesting site for biotechnological purposes. Preliminary studies have shown the great potential in the production of cytotoxic, pesticidal and antimicrobial molecules (3). Thus, to extend knowledge of the genes clusters responsible for producing biosynthetic pathways of natural products in strain CMAA1322, whole-genome shotgun (WGS) DNA sequencing was performed using paired-end long sequencing with PacBio RS (Pacific Biosciences). Genomic DNA was extracted from a pure culture grown overnight on LB medium using the PureLink genomic DNA kit (Life Technologies). An approximately 3- to 20-kb-insert PacBio library was constructed and sequenced on an 8 single-molecule real-time (SMRT) cell, yielding 116,269 reads (average length, 7,446 bp), which were allocated into 18 contigs, with 142.11x coverage and N50 value of 20.548 bp (BioProject number PRJNA288757). The assembled data were analyzed by Rapid Annotations using Subsystems Technology (RAST) (4) the genome size was found to be 7.055.077 bp, comprising 6167 open reading frames (ORFs) and 413 subsystems. The G+C content was estimated to be 72 mol%. The closest-neighbors tool, available in RAST through functional comparison of the genome, revealed that strain CMAA1322 is more closely related to Streptomyces hygroscopicus ATCC 53653 (similarity score value, 537), S. violaceusniger Tu 4113 (score value, 483), S. avermitilis MA-4680 (score value, 475), S. albus J1074 (score value, 447). The Streptomyces sp. CMAA1322 genome contains 98 tRNA genes and 135 genes copies related to stress response, mainly osmotic stress (14), heat shock (16), oxidative stress (49). Functional annotation by antiSMASH version 3.0 (5) identified 41 clusters for secondary metabolites (including two clusters for lanthipeptides, ten clusters for nonribosomal peptide synthetases [NRPS], three clusters for siderophores, fourteen for polyketide synthetase [PKS], six clusters encoding a terpene, two clusters encoding a bacteriocin, and one cluster encoding a phenazine). Our work provide in comparative analyse of genome and extract produced (data no published) by lineage CMAA1322, revealing the potential of microorganisms accessed from extreme environments as Caatinga” to produce a wide range of biotechnological relevant compounds.

Keywords: caatinga, streptomyces, environmental stresses, biosynthetic pathways

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Authors: Ghulam Muhammad Ali

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Unveiling of genes involved in drought and root architecture using transcriptomic analyses remained fragmented for further improvement of wheat through genome editing. The purpose of this research endeavor was to unveil the variations in different genes implicated in drought tolerance and root architecture in wheat through RNA-seq data analysis. In this study seedlings of 8 days old, 6 cultivars of wheat namely, Batis, Blue Silver, Local White, UZ888, Chakwal 50 and Synthetic wheat S22 were subjected to transcriptomic analysis for root and shoot genes. Total of 12 RNA samples was sequenced by Illumina. Using updated wheat transcripts from Ensembl and IWGC references with 54,175 gene models, we found that 49,621 out of 54,175 (91.5%) genes are expressed at an RPKM of 0.1 or more (in at least 1 sample). The number of genes expressed was higher in Local White than Batis. Differentially expressed genes (DEG) were higher in Chakwal 50. Expression-based clustering indicated conserved function of DRO1and RPK1 between Arabidopsis and wheat. Dendrogram showed that Local White is sister to Chakwal 50 while Batis is closely related to Blue Silver. This study flaunts transcriptomic sequence variations in different cultivars that showed mutations in genes associated with drought that may directly contribute to drought tolerance. DRO1 and RPK1 genes were fetched/isolated for genome editing. These genes are being edited in wheat through CRISPR-Cas9 for yield enhancement.

Keywords: transcriptomic, wheat, genome editing, drought, CRISPR-Cas9, yield enhancement

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Authors: Titanilla Komenda, Viktorio Malisa

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In this paper, the influence of diversity-related factors on the design of collaborative scenarios is analysed. Based on the evaluation, a framework for simulating human-robot-collaboration is presented that considers both human factors as well as the overall system performance. The implementation of the model is shown on a real-life scenario from industry and validated in terms of traceability, safety and physical limitations. By comparing scenarios that consider diversity with those only meeting system performance, an overall understanding of individually adapted human-robot-collaborative workspaces is reached. A diversity-related guideline for human-robot-collaborations provides a summary of the research and aids in optimizing future applications. Finally, limitations and future amendments of the model are discussed.

Keywords: diversity, human-machine system, human-robot collaboration, simulation

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Authors: D. l. David, J. A. Wahedi, U. Buba, R. Zakariya

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Between January, 2004 to December, 2005, studies were carried out on the bird species diversity and relative abundance of two lakes, Kiri and Gyawana near Numan using the “Timed Species Count (TSC)” method. 163 species in 53 bird families and 160 species in 55 bird families were recorded at Kiri and Gyawana lakes respectively. There was no significant difference in species diversity within bird families between the two lakes (p > 0.05), whereas in Gyawana Lake, one of the sites qualified as Ramsar site, none strongly qualified as an Important Bird Area (IBA). The significance of these findingsare also discussed.

Keywords: conservation, diversity, lacustrine, wetlands

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Authors: Adel M. Zakri, Mohammed A. Al-Saleh, Judith. K. Brown, Ali M. Idris

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Betasatellites are small circular single stranded DNA molecules found associated with begomoviruses on field symptomatic plants. Their genome size is about half that of the helper begomovirus, ranging between 1.3 and 1.4 kb. The helper begomoviruses are usually members of the family Geminiviridae. Okra leaves showing vein thickening were collected from okra plants growing in Jazan, Saudi Arabia. Total DNA was extracted from leaves and used as a template to amplify circular DNA using rolling circle amplification (RCA) technology. Products were digested with PstI to linearize the helper viral genome(s), and associated DNA satellite(s), yielding a 2.8kbp and 1.4kbp fragment, respectively. The linearized fragments were cloned into the pGEM-5Zf (+) vector and subjected to DNA sequencing. The 2.8 kb fragment was identified as Cotton leaf curl Gezira virus genome, at 2780bp, an isolate closely related to strains reported previously from Saudi Arabia. A clone obtained from the 1.4 kb fragments he 1.4kb was blasted to GeneBank database found to be a betasatellite. The genome of betasatellite was 1357-bp in size. It was found to be a recombinant containing one fragment (877-bp) that shared 91% nt identity with Cotton leaf curl Gezira betasatellite [KM279620], and a smaller fragment [133--bp) that shared 86% nt identity with Tomato leaf curl Sudan virus [JX483708]. This satellite is thus a recombinant between a malvaceous-infecting satellite and a solanaceous-infecting begomovirus.

Keywords: begomovirus, betasatellites, cotton leaf curl Gezira virus, okra plants

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Authors: Bedilu Tafesse

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Conservation of crop genetic resources presents a challenge of identifying specific determinants driving maintenance of diversity at farm and agroecosystems. The objectives of this study were to identify socioeconomic, market and agroecological determinants of farmers’ maintenance of wheat diversity at the household level and derive implications for policies in designing on-farm conservation programs. We assess wheat diversity at farm level using household survey data. A household decision making model is conceptualized using microeconomic theory to assess and identify factors influencing on-farm rice diversity. The model is then tested econometrically by using various factors affecting farmers’ variety choice and diversity decisions. The findings show that household-specific socioeconomic, agroecological and market factors are important in determining on-farm wheat diversity. The significant variables in explaining richness and evenness of wheat diversity include distance to the nearest market, subsistence ratio, modern variety sold, land types and adult labour working in agriculture. The statistical signs of the factors determining wheat diversity are consistent in explaining the richness, dominance and evenness among rice varieties. Finally, the study implies that the cost-effective means of promoting and sustaining on-farm conservation programmes is to target them in market isolated geographic locations of high crop diversity where farm households have more heterogeneity of agroecological conditions and more active family adult labour working on-farm.

Keywords: diversity indices, dominance, evenness, on-farm conservation, wheat diversity, richness

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Authors: Xin Chen

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Pre-industrial old-world human cultural diversity and societal complexity exhibits remarkable geographic regularities. Along the latitudinal axis from the equator to the arctic, a descending trend of human ethno-cultural diversity is found to be in coincidence with a descending trend of biological diversity. Along the same latitudinal axis, the pre-industrial human societal complexity shows to peak at the intermediate latitude. It is postulated that human cultural diversity and societal complexity are strongly influenced by collective learning, and that collective learning is positively related to human population size, social interactions, and environmental challenges. Under such postulations the relationship between collective learning and important geographical-environmental factors, including climate and biodiversity/bio-productivity is examined. A hypothesis of intermediate bio-productivity is formulated to account for those latitudinal patterns of pre-industrial human societal complexity.

Keywords: cultural diversity, soetal complexity, latitudinal patterns, biodiversity, bio-productivity, collective learning

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Authors: Sushmita Chaudhuri, Parthiba Basu

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Urbanization leads to habitat degradation and is responsible for the fast disappearance of native butterfly species. Random sampling of rural, suburban and urban sites in an around Kolkata metropolis revealed the presence of 28 species of butterfly belonging to 5 different families in winter (February-March). Butterfly diversity, species richness and abundance decreased with increase in urbanization. Psyche (Leptosia nina of family Pieridae) was the most predominant butterfly species found everywhere in Kolkata during the winter period. The most dominant family was Nymphalidae (11species), followed by Pieridae (6 species), Lycaenidae (5 species), Papilionidae (4 species) and Hesperiidae (2 species). The rural and suburban sites had butterfly species that were unique to those sites. Vegetation cover and flowering shrub density were significantly related to butterfly diversity.

Keywords: butterfly, Kolkata metropolis, Shannon-Weiner diversity index, species diversity

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Authors: Sandra Thomas

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This study tries to analyse the level of food security and dietary diversity among households of different socio-economic classes in the urban centers of Thrissur. The study revealed that there is no much difference in purchasing patterns of food articles among the socio-economic classes indicating a very high level of both physical and economic accessibility of food. On analysing the dietary diversity of the households none of the households scored below five and fifty-three per cent of the households scored eleven or twelve indicating higher diversity in diet. It was also found that income and education are the two important factors that influence the level of household food security.

Keywords: food security, dietary diversity, household level, socio-economic classes

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Authors: Andra Vidyarini

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Adolescence is a transition period in which various changes occur, both biologically, intellectually and psychosocially. Changes in adolescents, one of which is a change in food consumption patterns that make adolescents vulnerable to nutritional problems that can affect their growth and health in the future. Nutritional problems in adolescents have increased from year to year and one of the causes is the low diversity and quality of consumption. The diversity and quality of consumption can be seen through the Individual Dietary Diversity Score and the Healthy Eating Index. Currently, in Indonesia, data on the diversity and quality of food consumption, especially among adolescents, are still scarce. In general, the purpose of this study is to describe the diversity and quality of adolescent food consumption and the relationship between the diversity and quality of food consumption with nutritional status. This study is a cross-sectional study by looking at the diversity and quality of consumption of adolescents aged 15-17 years. The total number of subjects in this study amounted to 70 teenagers. This research was conducted online via a google form. Data analysis in this study was univariate and bivariate. The results showed that the diversity of the subject's food consumption was in the diverse and very diverse category with an average of 6. However, the quality was still not good, whereas it was still in the bad and moderate categories with an average of 12.93. The nutritional status of the majority of the subjects was in the normal category and overweight to obese. The implementation of blended learning where there are still limited face-to-face meetings at school can be the reason why teenagers' food consumption is more diverse than when they are face-to-face schools. In addition, changes in people's diet during the pandemic also influenced the results of the study. The change in pattern is a change in eating habits to three times a day with menu choices ranging from rice, meat, fish, bean and vegetables. Analysis of the relationship between the diversity and quality of food consumption shows that the diversity of consumption has a significant relationship with the quality of food consumption with a p-value of 0.002 (p<0.05). Meanwhile, the diversity and quality of food consumption have no significant relationship with nutritional status, with p values 0.777 and 0.251 (>0.05), respectively. This shows that the diversity of food consumption is directly proportional to the quality of consumption, where if you have a variety of food consumption, the quality or in terms of portions and weight are also sufficient in accordance with the recommendations of PGRS.

Keywords: healthy eating index (HEI), food diversity, quality of consumption, adolescent

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Authors: Sintayehu W. Dejene, Ignas M. A. Heitkönig, Herbert H. T. Prins, Zewdu K. Tessema, Willem F. de Boer

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Current theories on diversity-disease relationships describe host species diversity and species identity as important factors influencing disease risk, either diluting or amplifying disease prevalence in a community. Whereas the simple term ‘diversity’ embodies a set of animal community characteristics, it is not clear how different measures of species diversity are correlated with disease risk. We, therefore, tested the effects of species richness, Pielou’s evenness and Shannon’s diversity on bTB risk in cattle in the Afar Region and Awash National Park between November 2013 and April 2015. We also analysed the identity effect of a particular species and the effect of host habitat use overlap on bTB risk. We used the comparative intradermal tuberculin test to assess the number of bTB infected cattle. Our results suggested a dilution effect through species evenness. We found that the identity effect of greater kudu - a maintenance host – confounded the dilution effect of species diversity on bTB risk. bTB infection was positively correlated with habitat use overlap between greater kudu and cattle. Different diversity indices have to be considered together for assessing diversity-disease relationships, for understanding the underlying causal mechanisms. We posit that unpacking diversity metrics is also relevant for formulating control strategies to manage cattle in ecosystems characterized by seasonally limited resources and intense wildlife-livestock interactions.

Keywords: evenness, diversity, greater kudu, identity effect, maintenance hosts, multi-host disease ecology, habitat use overlap

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Authors: Cedric Herring, Loren Henderson, Hayward Derrick Horton, Melvin Thomas

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This paper asks whether business startups benefit from having racially diverse founding ownership teams. Using nationally representative data from the Kauffman Firm Survey, the analysis examines the relationship between the racial diversity of the founding ownership teams of business startups and their net worth, revenue, debt, and profits. The analysis shows that, net of firm characteristics and human capital characteristics, startups with racially diverse founding teams have higher net worth, lower debt, and greater profits than their non-diverse counterparts. The racial diversity of ownership teams is not, however, related to startup firms’ revenues, net of other factors. The implications of these findings are explored.

Keywords: racial diversity, business startups, founding ownership teams, diversity and business performance

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Authors: Ahmed M. Debela, Mayreli Ortiz , Ciara K. O´Sullivan

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The completion of the human genome Project (HGP) has paved the way for mapping the diversity in the overall genome sequence which helps to understand the genetic causes of inherited diseases and susceptibility to drugs or environmental toxins. Arrayed primer extension (APEX) is a microarray based minisequencing strategy for screening disease causing mutations. It is derived from Sanger DNA sequencing and uses fluorescently dideoxynucleotides (ddNTPs) for termination of a growing DNA strand from a primer with its 3´- end designed immediately upstream of a site where single nucleotide polymorphism (SNP) occurs. The use of DNA polymerase offers a very high accuracy and specificity to APEX which in turn happens to be a method of choice for multiplex SNP detection. Coupling the high specificity of this method with the high sensitivity, low cost and compatibility for miniaturization of electrochemical techniques would offer an excellent platform for detection of mutation as well as sequencing of DNA templates. We are developing an electrochemical APEX for the analysis of SNPs found in the MYH7 gene for group of cardiomyopathy patients. ddNTPs were labeled with four different redox active compounds with four distinct potentials. Thiolated oligonucleotide probes were immobilised on gold and glassy carbon substrates which are followed by hybridisation with complementary target DNA just adjacent to the base to be extended by polymerase. Electrochemical interrogation was performed after the incorporation of the redox labelled dedioxynucleotide. The work involved the synthesis and characterisation of the redox labelled ddNTPs, optimisation and characterisation of surface functionalisation strategies and the nucleotide incorporation assays.

Keywords: array based primer extension, labelled ddNTPs, electrochemical, mutations

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Authors: Agostinho Antunes

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The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Keywords: adaptation, animals, evolution, genomics

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Authors: Payton Small

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In response to increasing demographic diversity, many U.S. organizations have implemented diversity initiatives to increase the representation of women and ethnic minorities. While these initiatives aim to promote more fair and positive outcomes for underrepresented minorities (URMs) widespread backlash against these policies can negatively impact the groups of individuals that are supposed to be supported by them. A recent theory-based analysis of best practices for instituting diversity policies proposes an "inclusion for all" approach that negotiates the oft-divergent goals and motivations of both marginalized and dominant group members in these contexts. Empirical work finds that "inclusion for all" strategies decrease White's tendency to implicitly associate diversity with exclusion and increased their personal endorsement of diversity initiatives. Similarly, Whites report higher belongingness when considering an inclusion for all approach to diversity versus a colorblind approach. While inclusion-for-all approaches may effectively increase Whites' responsiveness to diversity efforts, the downstream consequences of implementing these policies on URM's have yet to be explored. The current research investigated how inclusion-for-all diversity framing influences Whites' sensitivity to detecting discrimination against URM's as well as perceptions of reverse discrimination against Whites. Lastly, the current research looked at how URM's respond to inclusion-for-all diversity approaches. Three studies investigated the impact of inclusion-for-all diversity framing on perceptions of discrimination against Whites and URM's in a company setting. Two separate mechanisms by which exposure to an inclusion-for-all diversity statement might differentially influence perceptions of discrimination for URMs and Whites were also tested. In Studies 1 and 2, exposure to an inclusion-for-all diversity approach reduced Whites' concerns about reverse discrimination and heightened sensitivity to detecting discrimination against URM's. These effects were mediated by decreased concerns about zero-sum outcomes at the company. Study 3 found that racial minorities are concerned about increased discrimination at a company with an inclusion-for-all diversity statement and that this effect is mediated by decreased feelings of belonging at the company. In sum, companies that adopt an inclusion-for-all approach to diversity implementation reduce Whites' backlash and the negative downstream consequences associated with such backlash; however, racial minorities feel excluded and expect heightened experiences of discrimination at these same companies.

Keywords: diversity, intergroup relations, organizational social psychology, zero-sum

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Authors: Maryam Saeidi, Ehsan Motamedian, Seyed Abbas Shojaosadati

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Zymomonas mobilis is known as an example of the uncoupled growth phenomenon. This microorganism also has a unique metabolism that degrades glucose by the Entner–Doudoroff (ED) pathway. In this paper, a genome-scale metabolic model including 434 genes, 757 reactions and 691 metabolites was reconstructed to simulate uncoupled growth and study its effect on flux distribution in the central metabolism. The model properly predicted that ATPase was activated in experimental growth yields of Z. mobilis. Flux distribution obtained from model indicates that the major carbon flux passed through ED pathway that resulted in the production of ethanol. Small amounts of carbon source were entered into pentose phosphate pathway and TCA cycle to produce biomass precursors. Predicted flux distribution was in good agreement with experimental data. The model results also indicated that Z. mobilis metabolism is able to produce biomass with maximum growth yield of 123.7 g (mol glucose)-1 if ATP synthase is coupled with growth and produces 82 mmol ATP gDCW-1h-1. Coupling the growth and energy reduced ethanol secretion and changed the flux distribution to produce biomass precursors.

Keywords: genome-scale metabolic model, Zymomonas mobilis, uncoupled growth, flux distribution, ATP dissipation

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Authors: Mohammad Ahangari

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Schizophrenia is a psychiatric disorder with symptoms that include cognitive deficits and nicotine has been suggested to have an effect on cognition. In recent years, the advents of Genome-Wide Association Studies(GWAS) has evolved our understanding about the genetic causes of complex disorders such as schizophrenia and studying the role of genome-wide significant genes could potentially lead to the development of new therapeutic agents for treatment of cognitive deficits in schizophrenia. The current study identified six Single Nucleotide Polymorphisms (SNP) from schizophrenia and smoking GWAS that are located on or in close proximity to the nicotinic receptor gene cluster (CHRN) and studied their association with cognition in an Irish sample of 1297 cases and controls using linear regression analysis. Further on, the interaction between CHRN gene cluster and Dopamine receptor D2 gene (DRD2) during working memory was investigated. The effect of these polymorphisms on nicotinic and dopaminergic neurotransmission, which is disrupted in schizophrenia, have been characterized in terms of their effects on memory, attention, social cognition and IQ as measured by a neuropsychological test battery and significant effects in two polymorphisms were found across global IQ domain of the test battery.

Keywords: cognition, dopamine, GWAS, nicotine, schizophrenia, SNPs

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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

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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: Waqas Shafqat Chattha, Muhammad Iqbal, Amir Shakeel

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Transcriptional factors are proteins that play a vital role in regulating the transcription of target genes in different biological processes and are being widely studied in different plant species. In the current era of genomics, plant genomes sequencing has directed to the genome-wide identification, analyses and categorization of diverse transcription factor families and hence provide key insights into their structural as well as functional diversity. The DNA-binding with One Finger (DOF) proteins belongs to C2-C2-type zinc finger protein family. DOF proteins are plant-specific transcription factors implicated in diverse functions including seed maturation and germination, phytohormone signalling, light-mediated gene regulation, cotton-fiber elongation and responses of the plant to biotic as well as abiotic stresses. In this context, a genome-wide in-silico analysis of DOF TF family in diploid cotton species i.e. Gossypium raimondii has enabled us to identify 55 non-redundant genes encoding DOF proteins renamed as GrDofs (Gossypium raimondii Dof). Gene distribution studies have shown that all of the GrDof genes are unevenly distributed across 12 out of 13 G. raimondii chromosomes. The gene structure analysis illustrated that 34 out of 55 GrDof genes are intron-less while remaining 21 genes have a single intron. Protein sequence-based phylogenetic analysis of putative 55 GrDOFs has divided these proteins into 5 major groups with various paralogous gene pairs. Molecular evolutionary studies aided with the conserved domain as well as gene structure analysis suggested that segmental duplications were the principal contributors for the expansion of Dof genes in G. raimondii.

Keywords: diploid cotton , G. raimondii, phylogenetic analysis, transcription factor

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Authors: Argyro-Maria Skourmalla

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Today’s reality is characterized by diversity in different levels and aspects of everyday life. Focusing on the aspect of language and communication in Higher Education (HE), the present paper draws on the example of the University of Luxembourg as a multilingual and international setting. The University of Luxembourg, which is located between France, Germany, and Belgium, adopted its new multilingualism policy in 2020, establishing English, French, German, and Luxembourgish as the official languages of the Institution. In addition, with around 10.000 students and staff coming from various countries around the world, linguistic diversity in this university is seen as both a resource and a challenge that calls for an inclusive and multilingual approach. The present paper includes data derived from semi-structured interviews with lecturing staff from different disciplines and an online survey with undergraduate students at the University of Luxembourg. Participants shared their experiences and point of view regarding linguistic diversity in this context. Findings show that linguistic diversity in this university is seen as an asset but comes with challenges, and even though there is progress in the use of multilingual practices, a lot needs to be done towards the recognition of staff and students’ linguistic repertoires for inclusion and education equity.

Keywords: linguistic diversity, higher education, Luxembourg, multilingual practices, teaching, learning

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Authors: Guna Raj Dhungana, Roshan Nepal, Apshara Parajuli, , Archana Maharjan, Shyam K. Mishra, Pramod Aryal, Rajani Malla

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Introduction: Klebsiella pneumoniae is a well-known opportunistic human pathogen, primarily causing healthcare-associated infections. The global emergence of carbapenemase-producing K. pneumoniaeis a major public health burden, which is often extensively multidrug resistant.Thus, because of the difficulty to treat these ‘superbug’ and menace and some term as ‘apocalypse’ of post antibiotics era, an alternative approach to controlling this pathogen is prudent and one of the approaches is phage mediated control and/or treatment. Objective: In this study, we aimed to isolate novel bacteriophage against carbapenemase-producing K. pneumoniaeand characterize for potential use inphage therapy. Material and Methods: Twenty lytic phages were isolated from river water using double layer agar assay and purified. Biological features, physiochemical characters, burst size, host specificity and activity spectrum of phages were determined. One most potent phage: Phage TU_Kle10O was selected and characterized by electron microscopy. Whole genome sequences of the phage were analyzed for presence/absence of virulent factors, and other lysin genes. Results: Novel phage TU_Kle10O showed multiple host range within own genus and did not induce any BIM up to 5th generation of host’s life cycle. Electron microscopy confirmed that the phage was tailed and belonged to Caudovirales family. Next generation sequencing revealed its genome to be 166.2 Kb. bioinformatical analysis further confirmed that the phage genome ‘did not’ contain any ‘bacterial genes’ within phage genome, which ruled out the concern for transfer of virulent genes. Specific 'lysin’ enzyme was identified phages which could be used as 'antibiotics'. Conclusion: Extensively multidrug resistant bacteria like carbapenemase-producing K. pneumoniaecould be treated efficiently by phages.Absence of ‘virulent’ genes of bacterial origin and presence of lysin proteins within phage genome makes phages an excellent candidate for therapeutics.

Keywords: bacteriophage, Klebsiella pneumoniae, MDR, phage therapy, carbapenemase,

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Authors: Asma Afshari, Abdollah Jamshidi, Jamshid Razmyar, Mehrnaz Rad

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Clostridium perfringens is a serious pathogen which causes enteric diseases in domestic animals and food poisoning in humans. Spores can survive cooking processes and play an important role in the possible onset of disease. In this study RAPD-PCR and REP-PCR were used to examine the genetic diversity of 49isolates ofC. Perfringens type A from 3 different sources. The results of RAPD-PCR revealed the most genetic diversity among poultry isolates, while human isolates showed the least genetic diversity. Cluster analysis obtained from RAPD_PCR and based on the genetic distances split the 49 strains into five distinct major clusters (A, B, C, D, and E). Cluster A and C were composed of isolates from poultry meat, cluster B was composed of isolates from human feces, cluster D was composed of isolates from minced meat, poultry meat and human feces and cluster E was composed of isolates from minced meat. Further characterization of these strains by using (GTG) 5 fingerprint repetitive sequence-based PCR analysis did not show further differentiation between various types of strains. To our knowledge, this is the first study in which the genetic diversity of C. perfringens isolates from different types of meats and human feces has been investigated.

Keywords: C. perfringens, genetic diversity, RAPD-PCR, REP-PCR

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Authors: Abdul Musaweer Habib, Habibul Hasan Mazumder, Saiful Islam, Sohel Sikder, Omar Faruk Sikder

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The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1499 proteins of Fusobacterium nucleatum, which has no homolog in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the KEGG Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the 3-D structure of these three proteins. Finally, determination of ligand binding sites of the key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against Fusobacterium nucleatum.

Keywords: colorectal cancer, drug target, Fusobacterium nucleatum, homology modeling, ligands

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Authors: M. F. Miah, A. Chakrabarty

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Two popular and highly valued fish, Stinging catfish (Heteropneustes fossilis) and Asian catfish (Clarias batrachus) are considered for observing genetic enhancement. Cross breeding was performed considering wild and farmed fish through inducing agent. Five RAPD markers were used to assess genetic diversity among parents and offspring of these two catfish for evaluating genetic enhancement in F1 generation. Considering different genetic data such as banding pattern of DNA, polymorphic loci, polymorphic information content (PIC), inter individual pair wise similarity, Nei genetic similarity, genetic distance, phylogenetic relationships, allele frequency, genotype frequency, intra locus gene diversity and average gene diversity of parents and offspring of these two fish were analyzed and finally in both cases higher genetic diversity was found in F1 generation than the parents.

Keywords: Heteropneustes fossilis, Clarias batrachus, cross breeding, genetic enhancement

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Authors: Yanto Santosa, Rozza Tri Kwatrina

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High Conservation Value (HCV) is an area with conservation function within oil palm plantation. Despite the important role of HCV area in biodiversity conservation and various studies on HCV, there was a lack of research studying the factors determining its success. A preliminary study was conducted to identify the determinant factor of HCV that affected the diversity. Line transect method was used to calculate the species diversity of butterfly, birds, mammals, and herpetofauna species as well as their richness. Specifically for mammals, camera traps were also used. The research sites comprised of 12 HCV areas in 3 provinces of Indonesia (Central Kalimantan, Riau, and Palembang). The relationship between the HCV biophysical factor with the species number and species diversity for each wildlife class was identified using Chi-Square analysis with Cross tab (contingency table). Results of the study revealed that species diversity varied by research locations. Four factors determining the success of HCV area in relations to the number and diversity of wildlife species are land cover types for mammals, the width of area and distance to rivers for birds, and distance to settlements for butterflies.

Keywords: wildlife diversity, oil palm plantation, high conservation value area, ecological factors

Procedia PDF Downloads 124