Search results for: gene diversity

Authors: P. Sindhumole, K. Soumya, R. Renjimol

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Rice (Oryza sativa L.) is the major staple food crop over the world. It is prone to a number of biotic and abiotic stresses, out of which Bacterial Leaf Blight (BLB), caused by Xanthomonas oryzae pv. oryzae, is the most rampant. Management of this disease through chemicals or any other means is very difficult. The best way to control BLB is by the development of Host Plant Resistance. BLB resistance is not an activity of a single gene but it involves a cluster of more than thirty genes reported. Among these, Xa5 and Xa13 genes are two important ones, which can be diagnosed through marker assisted selection using closely linked molecular markers. During 2014, the first phase of field screening using forty traditional rice genotypes was carried out and twenty resistant symptomless genotypes were identified. Molecular characterisation of these genotypes using RM 122 SSR marker revealed the presence of Xa5 gene in thirteen genotypes. Forty-two traditional rice genotypes were used for the second phase of field screening for BLB resistance. Among these, sixteen resistant genotypes were identified. These genotypes, along with two susceptible check genotypes, were subjected to marker assisted selection for Xa13 gene, using the linked STS marker RG-136. During this process, presence of Xa13 gene could be detected in ten resistant genotypes. In future, these selected genotypes can be directly utilised as donors in Marker assisted breeding programmes for BLB resistance in rice.

Keywords: oryza sativa, SSR, STS, marker, disease, breeding

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Authors: Yunfeng Shan, Xiaoliang Wang, Youjun Zhou

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Whole-genome data from two lungfish species, along with other species, present a valuable opportunity to re-investigate the longstanding debate regarding the evolutionary relationships among tetrapods, lungfishes, and coelacanths. However, the use of bootstrap support has become outdated for large-scale phylogenomic data. Without robust phylogenetic support, the phylogenetic trees become meaningless. Therefore, it is necessary to re-evaluate the phylogenies of tetrapods, lungfishes, and coelacanths using novel measures of phylogenetic support specifically designed for phylogenomic data, as the previous phylogenies were based on 100% bootstrap support. Our findings consistently provide strong evidence favoring lungfish as the closest living relative of tetrapods. This conclusion is based on high internode certainty, relative gene support, and high gene concordance factor. The evidence stems from five previous datasets derived from lungfish transcriptomes. These results yield fresh insights into the three hypotheses regarding the phylogenies of tetrapods, lungfishes, and coelacanths. Importantly, these hypotheses are not mere conjectures but are substantiated by a significant number of genes. Analyzing real biological data further demonstrates that the inclusion of additional taxa leads to more diverse tree topologies. Consequently, gene trees and species trees may not be identical even when whole-genome sequencing data is utilized. However, it is worth noting that many gene trees can accurately reflect the species tree if an appropriate number of taxa, typically ranging from six to ten, are sampled. Therefore, it is crucial to carefully select the number of taxa and an appropriate outgroup, such as slow-evolving species, while excluding fast-evolving taxa as outgroups to mitigate the adverse effects of long-branch attraction and achieve an accurate reconstruction of the species tree. This is particularly important as more whole-genome sequencing data becomes available.

Keywords: novel measures of phylogenetic support for phylogenomic data, gene concordance factor confidence, relative gene support, internode certainty, origin of tetrapods

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Authors: Özlem Ateş Sönmezoğlu, Begüm Terzi, Ahmet Yıldırım, Leyla Gündüz

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Durum wheat quality is defined as its suitability for pasta processing, that is pasta making quality. Another factor that determines the quality of durum wheat is the nutritional value of wheat or its final products. Wheat is a basic source of calories, proteins and minerals for humans in many countries of the world. For this reason, improvement of wheat nutritional value is of great importance. In recent years, deficiencies in protein and micronutrients, particularly in iron and zinc, have seriously increased. Therefore, basic foods such as wheat must be improved for micronutrient content. The effects of some major genes for grain quality established. Gpc-B1 locus is one of the genes increased protein and micronutrients content, and used in improvement studies of durum wheat nutritional value. The aim of this study was to increase the protein content and the micronutrient (Fe, Zn ve Mn) contents of an advanced durum wheat line (TMB 1) that was previously improved for its protein quality. For this purpose, TMB1 advanced durum wheat line were used as the recurrent parent and also, UC1113-Gpc-B1 line containing the Gpc-B1 gene was used as the gene source. In all of the generations, backcrossed plants carrying the targeted gene region were selected by marker assisted selection (MAS). BC4F1 plants MAS method was employed in combination with embryo culture and rapid plant growth in a controlled greenhouse conditions in order to shorten the duration of the transition between generations in backcross breeding. The Gpc-B1 gene was selected specific molecular markers. Since Yr-36 gene associated with Gpc-B1 allele, it was also transferred to the Gpc-B1 transferred lines. Thus, the backcrossed plants selected by MAS are resistance to yellow rust disease. This research has been financially supported by TÜBİTAK (112T910).

Keywords: Durum wheat, Gpc-B1, MAS, Triticum durum, Yr-36

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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: Samia Dahmani

Abstract:

The research investigated the process and outcomes of an ongoing project “Den Grønne Rute”: a network of recreational rooms to be implemented throughout a former vulnerable neighborhood: Trekanten in the city of Holstebro in Denmark. The aim of the project is to better integrate Trekanten in the city and which initiated reflections upon the (dis)connection and the integration in relation to urban planning and city management, as well as the extent to which the project considers diversity since Holstebro is a growing multicultural city. With this research, it was first verified if Trekanten is splintered from Holstebro city, and secondly if planning for diversity, by engaging people in the process via place-making approaches, can help redress the disconnection between the neighborhood and the rest of the city. More specifically, the paper aims at exploring the role of place-making “Den Grønne Rute” in Trekanten in promoting planning for diversity and reassembling the splintering in the city. The theoretical and conceptual framework served to analyze the relationship between the splintering urbanism concept and the community involvement’s role in an inclusive process. The field study examines the detachment between Trekanten and Holstebro and the extent to which the project can overcome the disconnection. Methodologically a mix-methods approach was adopted where two semi-structured interviews, a focus group, and an online survey were conducted. Contrary to prior assumptions, the results showed that not only is Trekanten splintered from the city, but also the city is greatly disconnected from Trekanten, and hence Holstebro is a splintered city. The surprise was that Trekanten is moreover inner-splintered. The splintering urbanism accordingly has different dimensions. Even though the project’s design seemed to incorporate diverse ages and groups of people, its process lacks an understanding of the diversity’s relevance in promoting inclusiveness. In fact, the analysis revealed socio-cultural and psychological splintering. Since place-making, as a collaborative approach in planning, is itself an expression of diversity (since it brings differences into play), reconsidering diversity within the process by engaging people at the early stages of planning was recommended. Another suggestion was not to limit the project to a destination but more as an experience to remember and a story to tell. Only by bringing people together in re-imagining the place can Trekanten reassemble with Holstebro and vice versa. The aim of the research was to add a new perspective to the splintering urbanism and planning for diversity so to advance place-making as an approach in promoting the latter and redressing the former.

Keywords: the splintering urbanism, place-making, planning for diversity, Den Grønne Rute, Trekanten, Holstebro

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Authors: Peter. M. Kusen, Georg Wandrey, Christopher Probst, Dietrich Kohlheyer, Jochen Buchs, Jorg Pietruszkau

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Light as a stimulus provides the capability to develop regulation techniques for customizable gene expression. A great advantage is the extremely flexible and accurate dosing that can be performed in a non invasive and sterile manner even for high throughput technologies. Therefore, light regulation in a multiwell microbioreactor system was realized providing the opportunity to control gene expression with outstanding complexity. A light-regulated gene expression system in Saccharomyces cerevisiae was designed applying the strategy of caged compounds. These compounds are photo-labile protected and therefore biologically inactive regulator molecules which can be reactivated by irradiation with certain light conditions. The “caging” of a repressor molecule which is consumed after deprotection was essential to create a flexible expression system. Thereby, gene expression could be temporally repressed by irradiation and subsequent release of the active repressor molecule. Afterwards, the repressor molecule is consumed by the yeast cells leading to reactivation of gene expression. A yeast strain harboring a construct with the corresponding repressible promoter in combination with a fluorescent marker protein was applied in a Photo-BioLector platform which allows individual irradiation as well as online fluorescence and growth detection. This device was used to precisely control the repression duration by adjusting the amount of released repressor via different irradiation times. With the presented screening platform the regulation of complex expression procedures was achieved by combination of several repression/derepression intervals. In particular, a stepwise increase of temporally-constant expression levels was demonstrated which could be used to study concentration dependent effects on cell functions. Also linear expression rates with variable slopes could be shown representing a possible solution for challenging protein productions, whereby excessive production rates lead to misfolding or intoxication. Finally, the very flexible regulation enabled accurate control over the expression induction, although we used a repressible promoter. Summing up, the continuous online regulation of gene expression has the potential to synchronize gene expression levels to optimize metabolic flux, artificial enzyme cascades, growth rates for co cultivations and many other applications addicted to complex expression regulation. The developed light-regulated expression platform represents an innovative screening approach to find optimization potential for production processes.

Keywords: caged-compounds, gene expression regulation, optogenetics, photo-labile protecting group

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Authors: Samia Dahmani

Abstract:

The research investigated the process and outcomes of an ongoing project, “Den Grønne Rute”: a network of recreational rooms to be implemented throughout a former vulnerable neighborhood: Trekanten, in the city of Holstebro in Denmark. The aim of the project is to better integrate Trekanten in the city and which initiated reflections upon the (dis)connection and the integration in relation to urban planning and city management, as well as the extent to which the project considers diversity since Holstebro is a growing multicultural city. With this research, it was first verified if Trekanten is splintered from Holstebro city, and secondly if planning for diversity, by engaging people in the process via place-making approaches, can help redress the disconnection between the neighborhood and the rest of the city. More specifically, the paper aims at exploring the role of place-making “Den Grønne Rute” in Trekanten in promoting planning for diversity and reassembling the splintering in the city. The theoretical and conceptual framework served to analyze the relationship between the splintering urbanism concept and the community involvement’s role for an inclusive process. The field study examines the detachment between Trekanten and Holstebro and the extent to which the project can overcome the disconnection. Methodologically a mix-methods approach was adopted where two semi-structured interviews, a focus group, and an online survey were conducted. Contrary to prior assumptions, the results showed that not only is Trekanten splintered from the city, but also the city is greatly disconnected from Trekanten, and hence Holstebro is a splintered city. The surprise was that Trekanten is moreover inner-splintered. The splintering urbanism accordingly has different dimensions. Even though the project’s design seemed to incorporate diverse ages and groups of people, its process lacks an understanding of the diversity’s relevance in promoting inclusiveness. In fact, the analysis revealed socio-cultural and psychological splintering. Since place-making, as a collaborative approach in planning, is itself an expression of diversity (since it brings differences into play), reconsidering diversity within the process by engaging people at the early sages of planning was recommended. Another suggestion was not to limit the project to a destination but more as an experience to remember and a story to tell. Only by bringing people together in re-imagining the place, can Trekanten reassemble with Holstebro and vice versa. The aim with the research was to add a new perspective to the splintering urbanism and planning for diversity so to advance place-making as an approach in promoting the latter and redressing the former.

Keywords: the splintering urbanism, placemaking, planning for diversity, den grønne rute, trekanten, holstebro

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Authors: Dedy Pratama, Akhmadu Muradi, Hilman Ibrahim, Raden Suhartono, Alexander Jayadi Utama, Patrianef Darwis, S. Dwi Anita, Luluk Yunaini, Kemas Dahlan

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Introduction: Vascular endothelial growth factor (VEGF) gene shows association with various angiogenesis conditions including Diabetic Foot Ulcer (DFU) disease. In this study, we performed this study to examine VEGF gene polymorphism associated with DFU. Methods: Case-control study of polymorphism of VEGF gene +405 C>G and -460 T>C, of diabetes mellitus (DM) type 2 with Diabetic Foot Ulcer (DFU) in Cipto Mangunkusumo National Hospital (RSCM) Jakarta from June to December 2016. Results: There were 203 patients, 102 patients with DFU and 101 patients without DFU. Forty-nine point 8 percent of total samples is male and 50,2% female with mean age 56,06 years. Distribution of the wild-type genotype VEGF +405 C>G wild type CC was found in 6,9% of respondents, the number of mutant heterozygote CG was 69,5% and mutant homozygote GG was 19,7%. Cumulatively, there were 6,9% wild-type and 85,2% mutant and 3,9% of total blood samples could not be detected on PCR-RFLP. Distribution of VEGF allele +405 C>G C alleles were 43% and G alleles were 57%. Distribution of genotype from VEGF gene -460 T>C is wild type TT 42,9%, mutant heterozygote TC 37,9% and mutant homozygote CC 13,3%. Cumulatively, there were 42,9% wild-type and 51% mutant type. Distribution of VEGF -460 T>C were 62% T allele and 38% C allele. Conclusion: In this study we found the distribution of alleles from VEGF +405 C>G is C 43% and G 57% and from VEGF -460 T>C; T 62% and C 38%. We propose that G allele in VEGF +405 C>G can act as a protective allele and on the other hands T allele in VEGF -460 T>C could be acted as a risk factor for DFU in diabetic patients.

Keywords: diabetic foot ulcer, diabetes mellitus, polymorphism, VEGF

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Authors: Natasha Petrovska, Mirjana Pavlovic, Maria M. Larrondo-Petrie

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Neural stem cells (NSCs) are multi-potent, self-renewing cells that generate new neurons. Three subtypes of NSCs can be separated regarding the stages of NSC lineage: quiescent neural stem cells (qNSCs), activated neural stem cells (aNSCs) and neural progenitor cells (NPCs), but their gene expression signatures are not utterly understood yet. Single-cell examinations have started to elucidate the complex structure of NSC populations. Nevertheless, there is a lack of thorough molecular interpretation of the NSC lineage heterogeneity and an increasing need for tools to analyze and improve the efficiency and correctness of single-cell sequencing data. Feature selection and ordering can identify and classify the gene expression signatures of these subtypes and can discover novel subpopulations during the NSCs activation and differentiation processes. The aim here is to review the implementation of the feature selection technique on NSC subtypes and the classification techniques that have been used for the identification of gene expression signatures.

Keywords: feature selection, feature similarity, neural stem cells, genes, feature selection methods

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Authors: Aleksandr Nagay, Gulnoz Khamidullayeva

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It is known that an unbalanced intake of salt (NaCI), lifestyle and genetic predisposition to pathology is a key component of the risk and the development of essential hypertension (EH). Purpose: To study the relationship between salt-sensitivity and blood pressure (BP) on systolic (SBP) and diastolic (DBP) blood pressure, depending on the C825T polymorphism of GNB3 in individuals of Uzbek nationality with EH. Method: studied 148 healthy and 148 patients with EH with I-II degree (WHO/ISH, 2003) with disease duration 6,5±1,3 years. Investigation of the gene GNB3 was produced by PCR-RFLP method. Determination of salt-sensitivity was performed by the method of R. Henkin. Results: For a comparative analysis of BP, the groups with carriage of CТ and TT genotypes were combined. The analysis showed that carriers of CC genotype and low salt-sensitivity were determined by higher levels of SBP compared with carriers of CT and TT genotypes, and low salt-sensitivity of SBP: 166,2±4,3 against 158,2±9,1 mm Hg (p=0,000). A similar analysis on the values of DBP also showed significantly higher values of blood pressure in carriers of CC genotype DBP: 105,8±10,6 vs. 100,5±7,2 mm Hg, respectively (p=0,001). The average values of SBP and DBP in groups with carriers of CC genotype at medium or high salt-sensitivity in comparison with carriers of CT or TT genotype did not differ statistically SBP: 165,0±0,1 vs. 160,0±8,6 mm Hg (p=0,275) and DBP: 100,1±0,1 vs. 101,6±7,6 mm Hg (p=0,687), respectively. Conclusion: It is revealed that in patients with EH CC genotype of the gene GNB3 given salt-sensitivity has a negative effect on blood pressure profile. Since patients with EH with the CC genotype of GNB3 gene with low-salt taste sensitivity is determined by a higher level of blood pressure, both on SBP and DBP.

Keywords: salt sensitivity, essential hypertension EH, blood pressure BP, genetic predisposition

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Authors: Bintou Jobe

Abstract:

Background: The research is focused on the concept of equality, diversity, and inclusion (EDI) and the need to achieve equity by treating individuals according to their circumstances and needs. The research is rooted in the UK Equality Act 2010, which emphasizes the importance of equal opportunities for all individuals regardless of their background and social life. However, inequality persists in society, particularly for those from minority backgrounds who face discrimination. Research Aim: The aim of this research is to promote equality, diversity, and inclusion by encouraging the regeneration of minds and the eradication of stereotypes. The focus is on promoting good Equality, Diversity and Inclusion practices in various settings, including schools, colleges, universities, and workplaces, to create environments where every individual feels a sense of belonging. Methodology: The research utilises a literature review approach to gather information on promoting inclusivity, diversity, and inclusion. Findings: The research highlights the significance of promoting equality, diversity, and inclusion practices to ensure that individuals receive the respect and dignity they deserve. It emphasises the importance of treating individuals based on their unique circumstances and needs rather than relying on stereotypes. The research also emphasises the benefits of diversity and inclusion in enhancing innovation, creativity, and productivity. The theoretical importance of this research is to raise awareness about the importance of regenerating minds, challenging stereotypes, and promoting equality, diversity, and inclusion. The emphasis is on treating individuals based on their circumstances and needs rather than relying on generalizations. Diversity and inclusion are beneficial in different settings, as highlighted by the research. By raising awareness about the importance of mind regeneration, eradicating stereotypes, and promoting equality, diversity, and inclusion, this research makes a significant contribution to the subject area. It emphasizes the necessity of treating individuals based on their unique circumstances instead of relying on generalizations. However, the methodology could be strengthened by incorporating primary research to complement the literature review approach. Data Collection and Analysis Procedures: The research utilised a literature review approach to gather relevant information on promoting inclusivity, diversity, and inclusion. NVivo software application was used to analysed and synthesize the findings to identify themes and support the research aim and objectives. Question Addressed: This research addresses the question of how to promote inclusivity, diversity, and inclusion and reduce the prevalence of stereotypes and prejudice. It explores the need to treat individuals based on their unique circumstances and needs rather than relying on generic assumptions. Encourage individuals to adopt a more inclusive approach. Provide managers with responsibility and training that helps them understand the importance of their roles in shaping the workplace culture. Have an equality, diversity, and inclusion manager from a majority background at the senior level who can speak up for underrepresented groups and flag any issues that need addressing. Conclusion: The research emphasizes the importance of promoting equality, diversity, and inclusion practices to create a fairer society. It highlights the need to challenge stereotypes, treat individuals according to their circumstances and needs, and promote a culture of respect and dignity.

Keywords: equality, fairer society, inclusion, diversity

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Authors: Bououden Soraya

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This paper aims to study the existence of the change of coordinates which permits to transform a class of nonlinear dynamical systems into the so-called nonlinear observer canonical form (NOCF). Moreover, an algorithm to construct such a change of coordinates is given. Based on this form, we can design an observer with a linear error dynamic. This enables us to estimate the state of a nonlinear dynamical system. A concrete example (biological model) is provided to illustrate the feasibility of the proposed results.

Keywords: nonlinear observer canonical form, observer, design, gene regulation, gene expression

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Authors: Manjula Weerasekera, Chris Sissons, Lisa Wong, Sally Anderson, Ann Holmes, Richard Cannon

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The aim of this study was to characterize bacterial population and yeasts in saliva by Polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR-DGGE) and measure yeast levels by culture. PCR-DGGE was performed to identify oral bacteria and yeasts in 24 saliva samples. DNA was extracted and used to generate DNA amplicons of the V2–V3 hypervariable region of the bacterial 16S rDNA gene using PCR. Further universal primers targeting the large subunit rDNA gene (25S-28S) of fungi were used to amplify yeasts present in human saliva. Resulting PCR products were subjected to denaturing gradient gel electrophoresis using Universal mutation detection system. DGGE bands were extracted and sequenced using Sanger method. A potential relationship was evaluated between groups of bacteria identified by cluster analysis of DGGE fingerprints with the yeast levels and with their diversity. Significant interpersonal variation of salivary microbiome was observed. Cluster and principal component analysis of the bacterial DGGE patterns yielded three significant major clusters, and outliers. Seventeen of the 24 (71%) saliva samples were yeast positive going up to 10³ cfu/mL. Predominately, C. albicans, and six other species of yeast were detected. The presence, amount and species of yeast showed no clear relationship to the bacterial clusters. Microbial community in saliva showed a significant variation between individuals. A lack of association between yeasts and the bacterial fingerprints in saliva suggests the significant ecological person-specific independence in highly complex oral biofilm systems under normal oral conditions.

Keywords: bacteria, denaturing gradient gel electrophoresis, oral biofilm, yeasts

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Authors: Argyro Maria Skourmalla

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Internationalization and management of linguistic diversity in Higher Education (HE) have gained much attention in research in the last few years. Internationalization policies in HE aims at promoting the dual role of Higher Education Institutions (HEIs), civilization and competitiveness. In the context of the European Union, the European Education Area initiative aims at “inclusive national education and training systems” through networking and exchange between HEIs. However, the use of English as a ‘lingua academica’ in the place of the official, national, and regional/minority languages raises questions regarding linguistic diversity, linguistic rights and concerns that have to do with the scientific weakening of these languages. In fact, the European Civil Society Platform for Multilingualism, in the Declaration for Multilingualism in Higher Education, draws attention to the use of English at the expense of other regional/national languages and the impact of English-only language policy on an epistemological level. The above issues were brought up during semi-structured interviews with lecturing staff coming from three multilingual Universities in Europe. Lecturers shared their experiences and the practices they use to manage linguistic diversity in these three Universities. Findings show that even though different languages are used in teaching across disciplines, English -or ‘Globish’ as mentioned during an interview- is widely used in research. Despite English being accepted as the “lingua academica,” issues regarding loss of identity come up

Keywords: higher education, internationalization, linguistic diversity, teaching, research, English

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Authors: Soyhan Egitim

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This case study aims to investigate leadership practices in diversity management in the liberal arts department of a Japanese university. In 2013, the Japanese Ministry of Education, Sports, Science, and Technology (MEXT) revealed their English education reform plan in response to rapid globalization. Based on the new reform plan, Japanese universities would expand their international faculty in order to promote globalization through an increased number of intercultural communication and content-based language classes in English. The study employed a two-phased qualitative approach to gain a deeper understanding of the management strategies employed in diversity management, and the leadership practices influenced those management strategies. In the first phase, a closed-ended qualitative survey was conducted with ten adjunct faculty members from the liberal arts department. The results indicate that syllabus design, grading scheme, textbook choices, and class management policies are strictly regulated by the tenured Japanese faculty. In the second phase, semi-structured interviews were held with international faculty members to understand their personal experiences. Their responses revealed that top-down management approaches are counter-effective in the department’s efforts to promote diversity and thus, a new organizational culture needs to be nurtured to emphasize inclusion alongside diversity. In this regard, the study proposes collaborative leadership as an inclusive leadership practice to minimize power differences in the hierarchy and increase opportunities for inclusion in the rapidly diversifying workforce.

Keywords: collaborative leadership, diversity, inclusion, international faculty, top-down

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Authors: Chao Sima, Shanaz Ghandhi, Sally A. Amundson, Michael L. Bittner, David J. Brenner

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In a large-scale radiologic emergency, potentially affected population need to be triaged efficiently using various biomarkers where personal dosimeters are not likely worn by the individuals. It has long been established that radiation injury can be estimated effectively using panels of genetic biomarkers. Furthermore, the rate of radiation, in addition to dose of radiation, plays a major role in determining biological responses. Therefore, a better and more accurate triage involves estimating both the dose level of the exposure and the length of time of that exposure. To that end, a large in vivo study was carried out on mice with internal emitter caesium-137 (¹³⁷Cs). Four different injection doses of ¹³⁷Cs were used: 157.5 μCi, 191 μCi, 214.5μCi, and 259 μCi. Cohorts of 6~7 mice from the control arm and each of the dose levels were sacrificed, and blood was collected 2, 3, 5, 7 and 14 days after injection for microarray RNA gene expression analysis. Using a generalized linear model with penalized maximum likelihood, a panel of 244 genes was established and both the doses of injection and the number of days after injection were accurately predicted for all 155 subjects using this panel. This has proven that microarray gene expression can be used effectively in radiation biodosimetry in predicting both the dose levels and the length of exposure time, which provides a more holistic view on radiation exposure and helps improving radiation damage assessment and treatment.

Keywords: caesium-137, gene expression microarray, multivariate responses prediction, radiation biodosimetry

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Authors: Jake Gonzalez, Tommy Dang

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This paper proposes a temporal graph approach to visualize and analyze the evolution of gene relationships and nomenclature over time. An interactive web-based tool implements this temporal graph, enabling researchers to traverse a timeline and observe coupled dynamics in network topology and naming conventions. Analysis of a real human genomic dataset reveals the emergence of densely interconnected functional modules over time, representing groups of genes involved in key biological processes. For example, the antimicrobial peptide DEFA1A3 shows increased connections to related alpha-defensins involved in infection response. Tracking degree and betweenness centrality shifts over timeline iterations also quantitatively highlight the reprioritization of certain genes’ topological importance as knowledge advances. Examination of the CNR1 gene encoding the cannabinoid receptor CB1 demonstrates changing synonymous relationships and consolidating naming patterns over time, reflecting its unique functional role discovery. The integrated framework interconnecting these topological and nomenclature dynamics provides richer contextual insights compared to isolated analysis methods. Overall, this temporal graph approach enables a more holistic study of knowledge evolution to elucidate complex biology.

Keywords: temporal graph, gene relationships, nomenclature evolution, interactive visualization, biological insights

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Authors: Minhas Alam, Muhammad Hidayat Rasool, Mohsin Khurshid, Bilal Aslam

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The genus Acinetobacter has emerged as a significant concern in hospital-acquired infections, particularly due to the versatility of Acinetobacter baumannii in causing nosocomial infections. The organism's remarkable metabolic adaptability allows it to thrive in various environments, including the environment, animals, and humans. However, the extent of antimicrobial resistance in Acinetobacter species from veterinary settings, especially in developing countries like Pakistan, remains unclear. This study aimed to isolate and characterize Acinetobacter spp. from veterinary settings in Punjab, Pakistan. A total of 2,230 specimens were collected, including 1,960 samples from veterinary settings (nasal and rectal swabs from dairy and beef cattle), 200 from the environment, and 70 from human clinical settings. Isolates were identified using routine microbiological procedures and confirmed by polymerase chain reaction (PCR). Antimicrobial susceptibility was determined by the disc diffusion method, and minimum inhibitory concentration (MIC) was measured by the micro broth dilution method. Molecular techniques, such as PCR and DNA sequencing, were used to screen for antimicrobial-resistant determinants. Genetic diversity was assessed using standard techniques. The results showed that the overall prevalence of A. baumannii in cattle was 6.63% (65/980). However, among cattle, a higher prevalence of A. baumannii was observed in dairy cattle, 7.38% (54/731), followed by beef cattle, 4.41% (11/249). Out of 65 A. baumannii isolates, the carbapenem resistance was found in 18 strains, i.e. 27.7%. The prevalence of A. baumannii in nasopharyngeal swabs was higher, i.e., 87.7% (57/65), as compared to rectal swabs, 12.3% (8/65). Class D β-lactamases genes blaOXA-23 and blaOXA-51 were present in all the CRAB from cattle. Among carbapenem-resistant isolates, 94.4% (17/18) were positive for class B β-lactamases gene blaIMP, whereas the blaNDM-1 gene was detected in only one isolate of A. baumannii. Among 70 clinical isolates of A. baumannii, 58/70 (82.9%) were positive for the blaOXA-23-like gene, and 87.1% (61/70) were CRAB isolates. Among all clinical isolates of A. baumannii, blaOXA-51-like gene was present. Hence, the co-existence of blaOXA-23 and blaOXA-51 was found in 82.85% of clinical isolates. From the environmental settings, a total of 18 A. baumannii isolates were recovered; among these, 38.88% (7/18) strains showed carbapenem resistance. All environmental isolates of A. baumannii harbored class D β-lactamases genes, i.e., blaOXA-51 and blaOXA-23 were detected in 38.9% (7/18) isolates. Hence, the co-existence of blaOXA-23 and blaOXA-51 was found in 38.88% of isolates. From environmental settings, 18 A. baumannii isolates were recovered, with 38.88% showing carbapenem resistance. All environmental isolates harbored blaOXA-51 and blaOXA-23 genes, with co-existence in 38.88% of isolates. MLST results showed ten different sequence types (ST) in clinical isolates, with ST 589 being the most common in carbapenem-resistant isolates. In veterinary isolates, ST2 was most common in CRAB isolates from cattle. Immediate control measures are needed to prevent the transmission of CRAB isolates among animals, the environment, and humans. Further studies are warranted to understand the mechanisms of antibiotic resistance spread and implement effective disease control programs.

Keywords: Acinetobacter baumannii, carbapenemases, drug resistance, MSLT

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Authors: Catherine Felce, Lior Pachter

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Current methods for building phylogenetic trees from gene expression data consider mean expression levels. With single-cell technologies, we can leverage more information about cell dynamics by considering the entire distribution of gene expression across cells. Using biophysical modeling, we propose a method for constructing phylogenetic trees from scRNA-seq data, building on Felsenstein's method of continuous characters. This method can highlight genes whose level of expression may be unchanged between species, but whose rates of transcription/decay may have evolved over time.

Keywords: phylogenetics, single-cell, biophysical modeling, transcription

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Authors: Kumaran Narayanan, Andrew N. Osahor

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E. coli has been engineered by our group and by others as a vector to deliver DNA into cultured human and animal cells. However, so far conditions to improve gene delivery using this vector have not been investigated, resulting in a major gap in our understanding of the requirements for this vector to function optimally. Our group recently published novel data showing that simple addition of the DNA transfection reagent Lipofectamine increased the efficiency of the E. coli vector by almost 3-fold, providing the first strong evidence that further optimization of bactofection is possible. This presentation will discuss advances that demonstrate the effects of several intracellular strategies that improve the efficiency of this vector. Conditions that promote endosomal escape of internalized bacteria to evade lysosomal destruction after entry in the cell, a known obstacle limiting this vector, are elucidated. Further, treatments that increase bacterial lysis so that the vector can release its transgene into the mammalian environment for expression will be discussed. These experiments will provide valuable new insight to advance this E. coli system as an important class of vector technology for genetic correction of human disease models in cells and whole animals.

Keywords: DNA, E. coli, gene expression, vector

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Authors: Fuad M. Alkoot

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Different experimental technologies such as microarray sequencing have been proposed to generate high-resolution genetic data, in order to understand the complex dynamic interactions between complex diseases and the biological system components of genes and gene products. However, the generated samples have a very large dimension reaching thousands. Therefore, hindering all attempts to design a classifier system that can identify diseases based on such data. Additionally, the high overlap in the class distributions makes the task more difficult. The data we experiment with is generated for the identification of autism. It includes 142 samples, which is small compared to the large dimension of the data. The classifier systems trained on this data yield very low classification rates that are almost equivalent to a guess. We aim at reducing the data dimension and improve it for classification. Here, we experiment with applying a multistage PCA on the genetic data to reduce its dimensionality. Results show a significant improvement in the classification rates which increases the possibility of building an automated system for autism detection.

Keywords: PCA, gene expression, dimensionality reduction, classification, autism

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Authors: K. Petrosyan, R. Piwowarczyk, K. Ruraż, S. Thijs, J. Vangronsveld, W. Kaca

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Holoparasitic plants are flowering heterotrophic angiosperms which with the help of an absorbing organ - haustorium, attach to another plant, the so-called the host. Due to the different hosts, unusual lifestyle, lack of roots, chlorophylls and photosynthesis, these plants are interesting and unique study objects for global biodiversity. The seeds germination of the parasitic plants also is unique: they germinate only in response to germination stimulants, namely strigolactones produced by the root of an appropriate host. Resistance of the seeds on different environmental conditions allow them to stay viable in the soil for more than 20 years. Among the wide range of plant protection mechanisms the endophytic communities have a specific role. In this way, they have the potential to mitigate the impacts of adverse conditions such as soil salinization. The major objective of our study was to compare the bacterial endo-microbiomes from seeds of two holoparasitic plants from Orobanchaceae family, Cistanche – C. armena (Armenia) and C. phelypaea (Portugal) – from saline habitats different in soil water status. The research aimed to perform how environmental conditions influence on the diversity of the bacterial communities of C. armena and C. phelypaea seeds. This was achieved by comparison of the endophytic microbiomes of two species and isolation of culturable bacteria. A combination of culture-dependent and molecular techniques was employed for the identification of the seed endomicrobiome (culturable and unculturable). Using the V3-V4 hypervariable region of the 16S rRNA gene, four main taxa were identified: Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, but the relative proportion of the taxa was different in each type of seed. Generally, sixteen phyla, 323 genera and 710 bacterial species were identified, mainly Gram negative, halotolerant bacteria with an environmental origin. However, also some unclassified and unexplored taxonomic groups were found in the seeds of both plants. 16S rRNA gene sequencing analysis from both species identified the gram positive, endospore forming, halotolerant and alkaliphile Bacillus spp. which suggests that the endophytic bacteria of examined seeds possess traits that are correlated with the natural habitat of their hosts. The cultivable seed endophytes from C. armena and C. phelypaea were rather similar, notwithstanding the big distances between their growth habitats - Armenia and Portugal. Although the seed endophytic microbiomes of C. armena and C. phelypaea contain a high number of common bacterial taxa, also remarkable differences exist. We demonstrated that the environmental conditions or abiotic stresses influence on diversity of the bacterial communities of holoparasiotic seeds. To the best of our knowledge the research is the first report of endophytes from seeds of holoparasitic Cistanche armena and C. phelypaea plants.

Keywords: microbiome, parasitic plant, salinity, seeds

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Authors: Harunori Kawabe, Hideyuki Aoshima, Koji Murakami, Minoru Kawakami, Yuka Nakano, David D. Ordinario, C. W. Crawford, Iri Sato-Baran

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With the recent advances in gene editing technologies allowing the rewriting of genetic sequences, additional market growth in the global floriculture market beyond previous trends is anticipated through increasingly sophisticated plant breeding techniques. As a prerequisite for gene editing, the gene sequence of the target plant must first be identified. This necessitates the genetic analysis of plants with unknown gene sequences, the extraction of RNA, and comprehensive expression analysis. Consequently, a technology capable of consistently and effectively extracting high-purity DNA and RNA from plants is of paramount importance. Although model plants, such as Arabidopsis and tobacco, have established methods for DNA and RNA extraction, floricultural species such as roses present unique challenges. Different techniques to extract DNA and RNA from various floricultural species were investigated. Upon sampling and grinding the petals of several floricultural species, it was observed that nucleic acid extraction from the ground petal solutions of low viscosity was straightforward; solutions of high viscosity presented a significant challenge. It is postulated that the presence of substantial quantities of polysaccharides and polyphenols in the plant tissue was responsible for the inhibition of nucleic acid extraction. Consequently, attempts were made to extract high-purity DNA and RNA by improving the CTAB method and combining it with commercially available nucleic acid extraction kits. The quality of the total extracted DNA and RNA was evaluated using standard methods. Finally, the effectiveness of the extraction method was assessed by determining whether it was possible to create a library that could be applied as a suitable template for a next-generation sequencer. In conclusion, a method was developed for consistent and accurate nucleic acid extraction from high-viscosity floricultural samples. These results demonstrate improved techniques for DNA and RNA extraction from flowers, help facilitate gene editing of floricultural species and expand the boundaries of research and commercial opportunities.

Keywords: floriculture, gene editing, next-generation sequencing, nucleic acid extraction

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Authors: Caterina Calicchio, Talia Sbardella

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The ability to move through geographical and symbolic spaces is key for building new nodes and social relationships. Especially in the framework of language learning, accepting and valuing diversity can help to create a constructive atmosphere of cooperation, innovation, and creativity. Thus, it is important to outline the stages of forming a learning community, focusing on the characteristics that can favor its development. It is known that elements like curiosity and motivation are significant for individual language learning; hence, the study attempts to investigate how factors like openness to diversity and cultural immersion could improve Italian learning and teaching. This paper aims to indicate the factors that could be significant for the development of a Learning Community by presenting a case study on a course on Italian as a second language for beginners: first, the theoretical matrices underlying social learning will be outlined. Secondly, a quantitative study will be described based on an adaptation of the openness to diversity and some insights psychometric scale questionnaire developed at the Umbra Institute. The questionnaire was delivered to 52 American college students with open-ended and closed-ended questions. Students were asked to specify their level of agreement to a set of statements on a six-point Likert scale ranging from (1) Strongly disagree to (6) Strongly agree. The data has been analyzed with a quantitative and qualitative method and has been represented in a pie chart and in a histogram. Moreover, mean and frequency have been calculated. The research findings demonstrate that openness to diversity and challenge enhances cross-cutting skills such as intercultural and communicative competence: through cultural immersion and the facility of speaking with locals, the participants have been able to develop their own Italian L2 language community. The goal is to share with the scientific community some insights to trace possible future lines of research.

Keywords: Italian as second language, language learning, learning community, openness to diversity

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Authors: Mehdi Nasr-Esfahani, Leila Mohammad Bagheri, Ava Nasr-Esfahani

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Root and collar rot disease caused by Phytophthora capsici (Leonian) is one of the most serious diseases in pepper, Capsicum annuum L. In this study, a diverse collection of 37 commercial edible and ornamental pepper genotypes infected with P. capsici were investigated for biomass parameters and enzymatic activity of peroxidase or peroxide reductases (EC), superoxide dismutase (SOD), polyphenol oxidase (PPOs), catalase (CAT) and phenylalanine ammonia-lyase (PAL). Seven candidate DEG genes were also evaluated on resistant and susceptible pepper cultivars, through measuring product formation, using spectrophotometry and real-time polymerase chain reaction. All the five enzymes and seven defense-gene candidates were up-regulated in all inoculated pepper accessions to P. capsici. But, the enzymes and DEG genes were highly expressed in resistant cv. 19OrnP-PBI, 37ChillP-Paleo, and “23CherryP-Orsh". The expression level of enzymes were 1.5 to 5.6-fold higher in the resistant peppers, than the control non-inoculated genotypes. Also, the transcriptional levels of related candidate DEG genes were 3.16 to 5.90-fold higher in the resistant genotypes. There was a direct and high correlation coefficient between resistance, bio-mass parameters, enzymatic activity, and resistance gene expression. The related enzymes and candidate genes expressed herein will provide a basis for further gene cloning and functional verification studies, and also will aid in an understanding of the regulatory mechanism of pepper resistance to P. capsici.

Keywords: AP2/ERF, cDNA, enzymes, MIP gene, q-RTPCR, XLOC

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Authors: Priya Arora, Ashutosh Mishra

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Gene identification, towards the pursuit of mutated genes, leading to Parkinson’s disease, puts forward a challenge towards proactive cure of the disorder itself. Computational analysis is an effective technique for exploring genes in the form of protein sequences, as the theoretical and manual analysis is infeasible. The limitations and effectiveness of a particular computational method are entirely dependent on the previous data that is available for disease identification. The article presents a sequence-based classification method for the identification of genes responsible for Parkinson’s disease. During the initiation phase, the physicochemical properties of amino acids transform protein sequences into a feature vector. The second phase of the method employs Jaccard distances to select negative genes from the candidate population. The third phase involves artificial neural networks for making final predictions. The proposed approach is compared with the state of art methods on the basis of F-measure. The results confirm and estimate the efficiency of the method.

Keywords: disease gene identification, Parkinson’s disease, physicochemical properties of amino acid, protein sequences

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Authors: Swati Gautam, Amita Jain, Shyampyari Jaiswar

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Objective: To elucidate the role of (ApaI&TaqI) VDR gene polymorphism in the pathogenesis of female genital tuberculosis (FGTB) cases. Background: Female genital TB represents about 15-20% of total extra-pulmonary TB (EPTB). Female subjects with vitamin D deficiency have been shown to be at higher risk of pulmonary TB as well as FGTB. In same context few functional polymorphism in vitamin D receptor (VDR) gene has been considered as an important genetic risk factor that modulate the development of FGTB. Therefore we aimed, to elucidate the role of (ApaI&TaqI) VDR gene polymorphism in the pathogenesis of FGTB. Study design: Case-Control study. Sample size: Cases (60) and Controls (60). Study site: Department of Obstetrics & Gynecology & Department of Microbiology, K.G.M.U. Lucknow, (UP). Inclusion criteria: Cases: Women with age group 20-35 years, premenstrual endometrial aspiration collected and included in the study, those were positive with acid-fast bacilli (AFB)/ TB-PCR/ LJ culture/ liquid culture. Controls: Women with age group 20-35 years having no history of ATT and all test negative for TB recruited as control. Exclusion criteria: -Women with endometriosis, polycystic ovaries (PCOD), positive on Chlamydia & gonorrhea, already on anti-tubercular therapy (ATT) excluded. Materials and Methods: Blood samples were collected in EDTA tubes from cases and controls stored at -20ºC. Genomic DNA extraction was carried out by salting-out method. Genotyping of VDR gene (ApaI&TaqI) polymorphism was performed by using single amplification refractory mutation system (ARMS) PCR technique. PCR products were analyzed by electrophoresis on 2% agarose gel. Statistical analysis was done by SPSS16.3 software & computing odds ratio (OR) with 95% CI. Results: Increased risk of female genital tuberculosis was observed in AA genotype (OR =1.1419-6.212 95% CI, P*<0.036) and A allele (OR =1.255-3.518, 95% CI, P* < 0.006) in FGTB as compared to controls. Moreover A allele was found more frequent in FGTB patients. No significant difference was observed in TaqI gene polymorphism of VDR gene. Conclusion: The ApaI polymorphism is significantly associated with etiology of FGTB and plays an important role as a genetic risk factor in FGTB women.

Keywords: ARMS, ATT, EPTB, FGTB, VDR

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Authors: Abdullah Alaklabi, Ibrahim A. Arif, Sameera O. Bafeel, Ahmad H. Alfarhan, Anis Ahamed, Jacob Thomas, Mohammad A. Bakir

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Diospyros mespiliformis (Hochst. ex A.DC.; Ebenaceae) is a large deciduous medicinal plant. This plant species is currently listed as endangered in Saudi Arabia. Molecular identification of this plant species based on short sequence regions (571 and 664 bp) of plastid rbcL (ribulose-1, 5-biphosphate carboxylase) gene was investigated in this study. The endangered plant specimens were collected from Al-Baha, Saudi Arabia (GPS coordinate: 19.8543987, 41.3059349). Phylogenetic tree inferred from the rbcL gene sequences showed that this species is very closely related with D. brandisiana. The close relationship was also observed among D. bejaudii, D. Philippinensis and D. releyi (≥99.7% sequence homology). The partial rbcL gene sequence region (571 bp) that was amplified by rbcL primer-pair rbcLaF-rbcLaR failed to discriminate D. mespiliformis from the closely related plant species, D. brandisiana. In contrast, primer-pair rbcL1F-rbcL724R yielded longer amplicon, discriminated the species from D. brandisiana and demonstrated nucleotide variations in 3 different sites (645G>T; 663A>C; 710C>G). Although D. mespiliformis (EU980712) and D. brandisiana (EU980656) are very closely related species (99.4%); however, studied specimen showed 100% sequence homology with D. mespiliformis and 99.6% with D. brandisiana. The present findings showed that rbcL short sequence region (664 bp) of plastid rbcL gene, amplified by primer-pair rbcL1F-rbcL724R, can be used for authenticating samples of D. mespiliforformis and may provide help in authentic identification and management process of this medicinally valuable endangered plant species.

Keywords: Diospyros mespiliformis, endangered plant, identification partial rbcL

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Authors: Raghav Lakhotia, Sameer Ganu, Anshul Goel, Abhishek Kumar

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In the age and times where women’s empowerment is a significant topic of discussion, we aim to analyze the potential gender diversity influence on box office revenues. The following research is carried out by collecting data from 400 Hollywood movies between the years 2014-2017 and performing regression analysis to find a correlation between the presence of female characters in movies and their return on investment (ROI). The paper finds that there is a positive relationship between the performance of the movies (its ROI) and the gender diversity i.e. the more the number of female characters, the higher the revenue generated. Another factor such as Number of Votes also has a direct impact on the revenue of the movie. The research not only takes into consideration the mere presence of women on screen but also the exchange of at least one dialogue among themselves, which is presented by the Bechdel Score of the movie.

Keywords: Bechdel, diversity, Hollywood, return on investment

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Authors: Data Collete Bob-Manuel

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In light of global financial crisis in 2007-2008 various factors including board diversity, succession planning and board evaluation have been identified as essential ingredients in ensuring board effectiveness. The composition and structure of the board is of outmost importance in assessing a board’s ability and success in achieving its objectives. Following the corporate frauds and accounting scandals such as Enron, WorldCom, Parmalat, Oceanic Bank Nigeria and AfriBank Nigeria, there has been a notable amount of research about the effectiveness of the board of directors in the corporate governance of firms. The need to have an effective board cannot be over emphasized as it results in a more stable and thriving company. There has been an overarching need in the business world for a more diverse workforce and board of directors. Big corporations like Texaco, Ford Motors and DuPont have stated how diversity at every level of the workforce including the board of directors has been cited as a vital element for a company to succeed. Developed countries are also seeking for companies to have a more diverse board. For instance Norway has implemented a 60:40 board ratio to all companies. In West Africa, particularly Nigeria, the topic of diversity has received little attention as most studies conducted have focused on the gender aspect of diversity, which results found to have a negative impact on firm performance. This paper seeks to examine four variables of diversity; age, ethnicity, gender and skills to weigh the positive or negative impact the variables have on firm performance, based on evidence from the Nigerian Financial sector. Information used for this study will be gathered from financial statements and annual reports so as to enable the researcher to reflect on past years to know what is being done differently today. The findings of this study will help the researcher to develop a working definition for ethnicity with regards to the West African context where the issue of “tribe” is a sensitive topic.

Keywords: Board of Directors, Board Diversity, Firm Performance, Nigeria

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