Search results for: genomic diversity

Authors: Mateen A Khan, Taj Mohammad, Md. Imtaiyaz Hassan

Abstract:

Alzheimer’s disease is characterized by the accumulation of the processing products of the amyloid beta peptide cleaved by amyloid precursor protein (APP). Iron increases the synthesis of amyloid beta peptides, which is why iron is present in Alzheimer's disease patients' amyloid plaques. Iron misregulation in the brain is linked to the overexpression of APP protein, which is directly related to amyloid-β aggregation in Alzheimer’s disease. The APP 5'-UTR region encodes a functional iron-responsive element (IRE) stem-loop that represents a potential target for modulating amyloid production. Targeted regulation of APP gene expression through the modulation of 5’-UTR sequence function represents a novel approach for the potential treatment of AD because altering APP translation can be used to improve both the protective brain iron balance and provide anti-amyloid efficacy. The molecular docking analysis of APP IRE RNA with eukaryotic translation initiation factors yields several models exhibiting substantial binding affinity. The finding revealed that the interaction involved a set of functionally active residues within the binding sites of eIF4F. Notably, APP IRE RNA and eIF4F interaction were stabilized by multiple hydrogen bonds with residues of APP IRE RNA and eIF4F. It was evident that APP IRE RNA exhibited a structural complementarity that tightly fit within binding pockets of eIF4F. The simulation studies further revealed the stability of the complexes formed between RNA and eIF4F, which is crucial for assessing the strength of these interactions and subsequent roles in the pathophysiology of Alzheimer’s disease. In addition, MD simulations would capture conformational changes in the IRE RNA and protein molecules during their interactions, illustrating the mechanism of interaction, conformational change, and unbinding events and how it may affect aggregation propensity and subsequent therapeutic implications. Our binding studies correlated well with the translation efficiency of APP mRNA. Overall, the outcome of this study suggests that the genomic modification and/or inhibiting the expression of amyloid protein by targeting APP IRE RNA can be a viable strategy to identify potential therapeutic targets for AD and subsequently be exploited for developing novel therapeutic approaches.

Keywords: Alzheimer's disease, Protein-RNA interaction analysis, molecular docking simulations, conformational dynamics, binding stability, binding kinetics, protein synthesis.

Procedia PDF Downloads 64

Authors: Astrid Rivera, Diego Villatoro

Abstract:

The world population increases at an accelerated pace, and it is essential to find solutions to feed the population. Nevertheless, crop diversity has significantly decreased in the last years, and the increase in food production is not the optimal solution. It is essential to consider the origin of the food, the nutriment contributions, among other dimensions. In this regard, biodiversity plays an indispensable role when designing an effective strategy to face the actual food security problems. Consequently, the purpose of this work is to analyze biodiversity in the Mexican national food production and suggest a proper crop selection based on companion plants, for which empirical and experimental knowledge shows a better scenery than current efforts. As a result, we get a set of crop recommendations to increase production in sustainable and nutritive planning. It is essential to explore more feasible options to advance sustainable development goals beyond an economic aspect.

Keywords: biodiversity, food security, companion plats, nutrition

Procedia PDF Downloads 198

Authors: Chougrani Fadela, Cheriguene Abderrahim

Abstract:

Fifty three strains of thermophilic and mesophilic lactic acid bacteria were isolated from the ewe’s milk. Identification reveals the presence of nineteen strains (36%) of Lactobacillus sp., seventeen strains (32%) of Lactococcus sp., nine strains (17%) of Streptococcus thermophilus and eight strains (15%) of Leuconostoc sp. The strains were characterized for their technological properties. A high diversity of properties among the studied strains was demonstrated. On the basis of technological characteristics, two strains (Lactobacillus bulgaricus and Streptococcus thermophilus) were screened with respect to their acid and flavour production for the preparation of a natural yogurt and compared to a commercial starter cultures. Sensorial analyses revealed that the product manufactured on the basis of the isolated strains have a cohesiveness and adhesiveness corresponding to standard products. The pH and the acidity recorded are also within accepted levels during all the period of conservation.

Keywords: Lactobacillus bulgaricus, Streptococcus thermophilus, yoghurt, cohesiveness, adhesiveness, Algerian ewe’s milk

Procedia PDF Downloads 344

Authors: Muhammad Usman Ghani

Abstract:

Religious tolerance is essential for the establishment of peace in the world. In the system created by Almighty Allah where a lot of diversity is found, still, this world holds unity itself. In today's world, human beings have been divided into clashes of civilizations or divided on the basis of religions or lingual differences. A religious scholar of Indo- Pak subcontinent describes four ethics, on the basis of which all religions of the world can unite. He says in his philosophy of religion that, there is a number of elements common in all religions but four are very common and they are: cleanliness, nobel deeds, relation to Almighty (existence of Almighty) and justice. He says that this universe also holds its integrity in itself. All humans are different in their attributes but to be a human being is common in them. Similarly, all species of the universe are different in their nature, but to be the creature of God is commonly shared by all of them.

Keywords: inter-religious relation, peace and harmony, unity, four common ethics/virtues

Procedia PDF Downloads 343

Authors: Amr A. EL Hanafy, Yasir Anwar, Saleh A. Mohamed, Saleh Mohamed Saleh Al-Garni, Jamal S. M. Sabir , Osama A. H. Abu Zinadah, Mohamed Morsi Ahmed

Abstract:

In the vicinity of the red sea about 15 fungi species were isolated from oil contaminated sites. On the basis of aptitude to degrade the crude oil and DCPIP assay, two fungal isolates were selected amongst 15 oil degrading strains. Analysis of ITS-1, ITS-2 and amplicon pyrosequencing studies of fungal diversity revealed that these strains belong to Penicillium and Aspergillus species. Two strains that proved to be the most efficient in degrading crude oil was Aspergillus niger (54 %) and Penicillium commune (48 %) Subsequent to two weeks of cultivation in BHS medium the degradation rate were recorded by using spectrophotometer and GC-MS. Hence, it is cleared that these fungal strains has the capability of degradation and can be utilized for cleaning the Saudi Arabian environment.

Keywords: fungal strains, hydrocarbon contaminants, molecular identification, biodegradation, GC-MS

Procedia PDF Downloads 522

Authors: Paul Shize Li, Frank Alber

Abstract:

A fundamental task of clinical genomics is to unravel the functions of genes and their associations with disorders. Although experimental biology has made efforts to discover and elucidate the molecular mechanisms of individual genes in the past decades, still about 40% of human genes have unknown functions, not to mention the diseases they may be related to. For those biologists who are interested in a particular gene with unknown functions, a powerful computational method tailored for inferring the functions and disease relevance of uncharacterized genes is strongly needed. Studies have shown that genes strongly linked to each other in multiple biological networks are more likely to have similar functions. This indicates that the densely connected subgraphs in multiple biological networks are useful in the functional and phenotypic annotation of uncharacterized genes. Therefore, in this work, we have developed an integrative network approach to identify the frequent local clusters, which are defined as those densely connected subgraphs that frequently occur in multiple biological networks and consist of the query gene that has few or no disease or function annotations. This is a local clustering algorithm that models multiple biological networks sharing the same gene set as a three-dimensional matrix, the so-called tensor, and employs the tensor-based optimization method to efficiently find the frequent local clusters. Specifically, massive public gene expression data sets that comprehensively cover dynamic, physiological, and environmental conditions are used to generate hundreds of gene co-expression networks. By integrating these gene co-expression networks, for a given uncharacterized gene that is of biologist’s interest, the proposed method can be applied to identify the frequent local clusters that consist of this uncharacterized gene. Finally, those frequent local clusters are used for function and disease annotation of this uncharacterized gene. This local tensor clustering algorithm outperformed the competing tensor-based algorithm in both module discovery and running time. We also demonstrated the use of the proposed method on real data of hundreds of gene co-expression data and showed that it can comprehensively characterize the query gene. Therefore, this study provides a new tool for annotating the uncharacterized genes and has great potential to assist clinical genomic diagnostics.

Keywords: local tensor clustering, query gene, gene co-expression network, gene annotation

Procedia PDF Downloads 168

Authors: Anshu Siwach, Qianlai Zhuang, Ratul Baishya

Abstract:

Context: This study focuses on the influence of moss cover and seasonality on soil microbial biomass and enzymatic activity in different Central Himalayan temperate forest types. Soil microbial biomass and enzymes are key indicators of microbial communities in soil and provide information on soil properties, microbial status, and organic matter dynamics. The activity of microorganisms in the soil varies depending on the vegetation type and environmental conditions. Therefore, this study aims to assess the effects of moss cover, seasons, and different forest types on soil microbial biomass carbon (SMBC), soil microbial biomass nitrogen (SMBN), and soil enzymatic activity in the Central Himalayas, Uttarakhand, India. Research Aim: The aim of this study is to evaluate the levels of SMBC, SMBN, and soil enzymatic activity in different temperate forest types under the influence of two ground covers (soil with and without moss cover) during the rainy and winter seasons. Question Addressed: This study addresses the following questions: 1. How does the presence of moss cover and seasonality affect soil microbial biomass and enzymatic activity? 2. What is the influence of different forest types on SMBC, SMBN, and enzymatic activity? Methodology: Soil samples were collected from different forest types during the rainy and winter seasons. The study utilizes the chloroform-fumigation extraction method to determine SMBC and SMBN. Standard methodologies are followed to measure enzymatic activities, including dehydrogenase, acid phosphatase, aryl sulfatase, β-glucosidase, phenol oxidase, and urease. Findings: The study reveals significant variations in SMBC, SMBN, and enzymatic activity under different ground covers, within the rainy and winter seasons, and among the forest types. Moss cover positively influences SMBC and enzymatic activity during the rainy season, while soil without moss cover shows higher values during the winter season. Quercus-dominated forests, as well as Cupressus torulosa forests, exhibit higher levels of SMBC and enzymatic activity, while Pinus roxburghii forests show lower levels. Theoretical Importance: The findings highlight the importance of considering mosses in forest management plans to improve soil microbial diversity, enzymatic activity, soil quality, and health. Additionally, this research contributes to understanding the role of lower plants, such as mosses, in influencing ecosystem dynamics. Conclusion: The study concludes that moss cover during the rainy season significantly influences soil microbial biomass and enzymatic activity. Quercus and Cupressus torulosa dominated forests demonstrate higher levels of SMBC and enzymatic activity, indicating the importance of these forest types in sustaining soil microbial diversity and soil health. Including mosses in forest management plans can improve soil quality and overall ecosystem dynamics.

Keywords: moss cover, seasons, soil enzymes, soil microbial biomass, temperate forest types

Procedia PDF Downloads 67

Authors: Terence Soule, Tami Al Ghamdi

Abstract:

To study how to transfer knowledge from multiple source problems to the target problem, we modeled the Transfer Learning (TL) process using Genetic Algorithms as the model solver. TL is the process that aims to transfer learned data from one problem to another problem. The TL process aims to help Machine Learning (ML) algorithms find a solution to the problems. The Genetic Algorithms (GA) give researchers access to information that we have about how the old problem is solved. In this paper, we have five different source problems, and we transfer the knowledge to the target problem. We studied different scenarios of the target problem. The results showed combined knowledge from multiple source problems improves the GA performance. Also, the process of combining knowledge from several problems results in promoting diversity of the transferred population.

Keywords: transfer learning, genetic algorithm, evolutionary computation, source and target

Procedia PDF Downloads 140

Authors: Goran Begović

Abstract:

In recent years, many researchers are focusing on non-intrusive measuring methods when it comes to human biosignals. These methods provide solutions for everyday use, whether it’s health monitoring or finessing the workout routine. One of the biggest issues with these solutions is that the sensors’ accuracy is highly variable due to many factors, such as ambiental light, skin color diversity, etc. That is why we wanted to explore different outcomes under those kinds of circumstances in order to find the most optimal algorithm(s) for extracting heart rate (HR) information. The optimization of such algorithms can benefit the wider, cheaper, and safer application of home health monitoring, without having to visit medical professionals as often when it comes to observing heart irregularities. In this study, we explored the accuracy of infrared (IR), red, and green LED sensorics in a controlled environment and compared the results with a medically accurate ECG monitoring device.

Keywords: data science, ECG, heart rate, holter monitor, LED sensors

Procedia PDF Downloads 127

Authors: Adeyemi, Samuel Olusegun

Abstract:

The paper reports on the result of experimental gill net assessment of the fishery of Gbedikere Lake in Kogi State between October 2006 and September 2008. Three stations A-C were sampled. Twelve species from ten families were represented in the experimental gill-net catches. These composed of families Protopteridae, Mormyridae, Clariidae, Mochokidae, Cichlidae, Cyprinidae, Malapteruridae, Osteoglossidae, Gymnarchidae, and Citharinidae. The Cichlids dominated the catches. This is made up of Oreochromis niloticus (17.90%), and Tilapia zilli (13.01%). These combined to make up 30.91% of the total number of fish caught. Also, the Cichlids formed 30.91% of the total catch by weight followed Heterotis niloticus (15.56%), Clarias gariepinus (13.16%), Gmynarchus niloticus (8.78%), Heterobranchus bidorsalis (7.14%), Synodontis nigrita (6.69%), Mormyrus rume (5.68%), Citharinus citharus (3.91%), Labeo senegalensis (2.93%), and Protopterus annectens (2.74%), respectively.

Keywords: experimental gill net, species diversity, abundance, distribution, Oxbow Lake and yield

Procedia PDF Downloads 502

Authors: Abdulmajeed Bashir Mlitan, Ethan Hack

Abstract:

Soil samples were collected from and around Alkomos cement factory, Alkomos town, Libya. Soil physiochemical properties were determined. In addition, olive leaves were scanned for their fungal content. This work can conclude that the results obtained for the examined physiochemical characteristics of soil in the area studied prove that cement dust from the Alkomos cement factory in Libya has had a significant impact on the soil. The affected soil properties are pH and total calcium content. These characteristics were found to be higher than those in similar soils from the same area. The increment of soil pH in the same area may be a result of precipitation of cement dust over the years. Different responses were found in each season and each site. For instance, the dominance of fungi of soil and leaves was lowest at 100 m from the factory and the evenness and diversity increased at this site compared to the control area and 250 m from the factory.

Keywords: pollution, soil microbial, alkomos, Libya

Procedia PDF Downloads 614

Authors: Mohamad Reza Asariha

Abstract:

Crises are an integral part of social life, and their diversity is increasing day by day. Every aspect of life for humans involves a crisis, and these crises are becoming more varied over time. In times of crisis, the media has a special responsibility to inform the public and raise awareness of the situation. The public can be calmed by the media and inspired to take positive action or vice versa; the media can terrorize the public and cause mayhem. Media are regarded as one of the most significant forms of communication in the information age. Media plays an important role in different stages of crises. Before a crisis occurs, they can prevent the spread of the crisis and reduce its losses by warning about the consequences. At the time of the crisis, they can minimize the crisis by creating a scientific and rational atmosphere, or as mediators between the crisis agents and the interest groups, they can minimize the political clashes and be effective in attracting and participating the audience in crisis management. There is widespread access to the media, so it has a significant role in moderating and changing public opinion.

Keywords: media, crisis, crisis communication, crisis management, emergency situations

Procedia PDF Downloads 85

Authors: Zakhile Somlata

Abstract:

In the context of international linguistic and cultural diversity, all languages can be used for all purposes. Africa in general and South Africa, in particular, is not an exception to multilingual and multicultural society. The multilingual and multicultural nature of South African society has a direct bearing to the heterogeneity of South African Universities in general. Universities as the centers of research, innovation, and transformation of the entire society should be at the forefront in leading multilingualism. The universities in South Africa had been using English and to a certain extent Afrikaans as the only academic languages during colonialism and apartheid regime. The democratic breakthrough of 1994 brought linguistic relief in South Africa. The Constitution of the Republic of South Africa recognizes 11 official languages that should enjoy parity of esteem for the realization of multilingualism. The elevation of the nine previously marginalized indigenous African languages as academic languages in higher education is central to multilingualism. It is high time that Afrocentric model instead of Eurocentric model should be the one which underpins education system in South Africa at all levels. Almost all South African universities have their language policies that seek to promote access and success of students through multilingualism, but the main dilemma is the implementation of language policies. This study is significant to respond to two objectives: (i) To evaluate how selected institutions use language policies for accessibility and success of students. (ii) To study how selected universities integrate African languages for both academic and administrative purposes. This paper reflects the language policy practices in one selected University of Technology (UoT) in South Africa. The UoT has its own language policy which depicts linguistic diversity of the institution and its commitment to promote multilingualism. Translanguaging pedagogy which accommodates minority languages' usage in the teaching and learning process plays a pivotal role in promoting multilingualism. This research paper employs mixed methods (quantitative and qualitative research) approach. Qualitative data has been collected from the key informants (insiders and experts), while quantitative data has been collected from a cohort of third-year students. A mixed methods approach with its convergent parallel design allows the data to be collected separately, analysed separately but with the comparison of the results. Language development initiatives have been discussed within the framework of language policy and policy implementation strategies. Theoretically, this paper is rooted in language as a problem, language as a right and language as a resource. The findings demonstrate that despite being a multilingual institution, there is a perpetuation of marginalization of African languages to be used as academic languages. Findings further display the hegemony of English. The promotion of status quo compromises the promotion of multilingualism, Africanization of Higher Education and intellectualization of indigenous African languages in South Africa under a democratic dispensation.

Keywords: afro-centric model, hegemony of English, language as a resource, translanguaging pedagogy

Procedia PDF Downloads 192

Authors: Geoffrey Gilfillan, Peter Barham, Lisa Smallwood, David Harper

Abstract:

The ‘Welland for People and Wildlife’ project aimed to improve the River Welland’s ecology and water quality, and to make it more accessible to the community of Market Harborough. A joint monitoring project by the Welland Rivers Trust & University of Leicester was incorporated into the design. The techniques that have been used to measure its success are hydrological, geomorphological, and water quality monitoring, species and habitat surveys, and community engagement. Early results show improvements to flow and habitat diversity, water quality and biodiversity of the river environment. Barrier removal has increased stickleback mating activity, and decreased parasitically infected fish in sample catches. The habitats provided by the berms now boast over 25 native plant species, and the river is clearer, cleaner and with better-oxygenated water.

Keywords: community engagement, ecological monitoring, river restoration, water quality

Procedia PDF Downloads 232

Authors: Aikaterini Tavoulari, Mike Richardson

Abstract:

Objective: This abstract presents a multisensory participatory design project, inspired by a deafblind PhD student's ambition to climb Mount Everest. The project aims to explore accessible routes for filmmaking and video content creation, catering to the needs of individuals with hearing and sight loss. By engaging participants from the Southwest area of England, recruited through multiple networks, the project seeks to gather qualitative data and insights to inform the development of inclusive media practices. Design: It will be a community-based participatory research design. The workshop will feature various stations that stimulate different senses, such as scent, touch, sight, hearing as well as movement. Participants will have the opportunity to engage with these multisensory experiences, providing valuable feedback on their effectiveness and potential for enhancing accessibility in filmmaking and video content. Methods: Brief semi-structured interviews will be conducted to collect qualitative data, allowing participants to share their perspectives, challenges, and suggestions for improvement. The participatory design approach emphasizes the importance of involving the target audience in the creative process. By actively engaging individuals with hearing and sight loss, the project aims to ensure that their needs and preferences are central to the development of accessible filmmaking techniques and video content. This collaborative effort seeks to bridge the gap between content creators and diverse audiences, fostering a more inclusive media landscape. Results: The findings from this study will contribute to the growing body of research on accessible filmmaking and video content creation. Via inductive thematic analysis of the qualitative data collected through interviews and observations, the researchers aim to identify key themes, challenges, and opportunities for creating engaging and inclusive media experiences for deafblind audiences. The insights will inform the development of best practices and guidelines for accessible filmmaking, empowering content creators to produce more inclusive and immersive video content. Conclusion: The abstract targets the hybrid International Conference for Disability and Diversity in Canada (January 2025), as this platform provides an excellent opportunity to share the outcomes of the project with a global audience of researchers, practitioners, and advocates working towards inclusivity and accessibility in various disability domains. By presenting this research at the conference in person, the authors aim to contribute to the ongoing discourse on disability and diversity, highlighting the importance of multisensory experiences and participatory design in creating accessible media content for the deafblind community and the community with sensory impairments more broadly.

Keywords: vision impairment, hearing impairment, deafblindness, accessibility, filmmaking

Procedia PDF Downloads 43

Authors: Ramesh Joshi, Nisha Khatik

Abstract:

Murraya koenigii (L.) Spreng locally known as “Curry patta” or “Meetha neem” belonging to the family Rutaceae that grows wildly in Southern Asia. Its aromatic leaves are commonly used as the raw material for traditional medicinal formulations in India. The leaves contain essential oil and also used as a condiment. Several monomeric and binary carbazol alkaloids present in the various plant parts. These alkaloids have been reported to possess anti-microbial, mosquitocidal, topo-isomerase inhibition and antioxidant properties. Some of the alkaloids reported in this plant have showed anti carcinogenic and anti-diabetic properties. The conventional method of propagation of this tree is limited to seeds only, which retain their viability for only a short period. Hence, a biotechnological approach might have an advantage edging over traditional breeding as well as the genetic improvement of M. koenigii within a short period. The development of a reproducible regeneration protocol is the prerequisite for ex situ conservation and micropropagation. An efficient protocol for high frequency regeneration of in vitro plants of Murraya koenigii via different explants such as- nodal segments, intermodal segments, leaf, root segments, hypocotyle, cotyledons and cotyledonary node explants is described. In the present investigation, assessment of clonal fidelity in the micropropagated plantlets of Murraya koenigii was attempted using RAPD and ISSR markers at different pathways of plant tissue culture technique. About 20 ISSR and 40 RAPD primers were used for all the samples. Genomic DNA was extracted by CTAB method. ISSR primer were found to be more suitable as compared to RAPD for the analysis of clonal fidelity of M. koenigii. The amplifications however, were finally performed using RAPD, ISSR markers owing to their better performance in terms of generation of amplification products. In RAPD primer maximum 75% polymorphism was recorded in OPU-2 series which exhibited out of 04 scorable bands, three bands were polymorphic with a band range of size 600-1500 bp. In ISSR primers the UBC 857 showed 50% polymorphism with 02 band were polymorphic of band range size between 400-1000 bp.

Keywords: genetic fidelity, Murraya koenigii, aromatic plants, ISSR primers

Procedia PDF Downloads 501

Authors: Saidatul A'isyah Ahmad Shukri, Haslina Arshad

Abstract:

This study was conducted to develop an application that provides Augmented Reality experience in identifying halal food products and beverages based on Malaysian Islamic Development Department (JAKIM) database for Muslim consumers in Malaysia. The applications is operating on the mobile device using the Android platform. This application aims to provide a new experience to the user how to use the Android application implements Augmentation Reality technology The methodology used is object-oriented analysis and design (OOAD). The programming language used is JAVA programming using the Android Software Development Kit (SDK) and XML. Android operating system is selected, and it is an open source operating system. Results from the study are implemented to further enhance diversity in presentation of information contained in this application and so can bring users using these applications from different angles.

Keywords: android, augmented reality, food, halal, Malaysia, products, XML

Procedia PDF Downloads 455

Authors: Mahpara Pirzada, Mansoor Ali Shah, Saima Pthan, Kamal Khan, Faiza

Abstract:

Present study based on biodiversity of aphid in different crops of Hyderabad district and its, surrounding area to observe the biodiversity of aphids, host plant range of the aphids in Hyderabad and their population also infestation and yield loss aphid on different crops. We have surveyed different fields of Hyderabad, Jamshoro, and collected the aphids from various parts of plants, grasses, and herb with the help of camel brush. They have been brought to the laboratory into plastic jars and preserved in Glycerin (Glycerol). As a result, 383 individuals belonging to 3 species were identified. These identified species were Aphis fabae, Myzus persicae, and Brevicoryne brassicae. Out of the 3 habitats the maximum richness, evenness, and diversity were recorded in agriculture crops followed by flowering vegetables and minimum in fodder crops. The most abundant specie is Myzus persicae.

Keywords: aphid species, biodiversity, Homoptera:Aphididae, Pakistan

Procedia PDF Downloads 328

Authors: Chen Wang, Jared Evans, Yan Asmann

Abstract:

With the quick evolvement of next-generation sequencing techniques, whole-exome or exome-panel data have become a cost-effective way for detection of small exonic mutations, but there has been a growing desire to accurately detect copy number variations (CNVs) as well. In order to address this research and clinical needs, we developed a sequencing coverage pattern-based method not only for copy number detections, data integrity checks, CNV calling, and visualization reports. The developed methodologies include complete automation to increase usability, genome content-coverage bias correction, CNV segmentation, data quality reports, and publication quality images. Automatic identification and removal of poor quality outlier samples were made automatically. Multiple experimental batches were routinely detected and further reduced for a clean subset of samples before analysis. Algorithm improvements were also made to improve somatic CNV detection as well as germline CNV detection in trio family. Additionally, a set of utilities was included to facilitate users for producing CNV plots in focused genes of interest. We demonstrate the somatic CNV enhancements by accurately detecting CNVs in whole exome-wide data from the cancer genome atlas cancer samples and a lymphoma case study with paired tumor and normal samples. We also showed our efficient reuses of existing exome sequencing data, for improved germline CNV calling in a family of the trio from the phase-III study of 1000 Genome to detect CNVs with various modes of inheritance. The performance of the developed method is evaluated by comparing CNV calling results with results from other orthogonal copy number platforms. Through our case studies, reuses of exome sequencing data for calling CNVs have several noticeable functionalities, including a better quality control for exome sequencing data, improved joint analysis with single nucleotide variant calls, and novel genomic discovery of under-utilized existing whole exome and custom exome panel data.

Keywords: bioinformatics, computational genetics, copy number variations, data reuse, exome sequencing, next generation sequencing

Procedia PDF Downloads 257

Authors: Yasser M. Saad, Heba El-Sebaie Abd El-Sadek

Abstract:

Some Metapenaeus monoceros cox1 gene fragments were isolated, purified, sequenced, and comparatively analyzed with some other Crustacean Cox1 gene sequences (obtained from National Center for Biotechnology Information). This work was designed for testing the efficiency of this system in reconstruction of phylogenetic relations among some Crustacean species belonging to four genera (Metapenaeus, Artemia, Daphnia and Calanus). The single nucleotide polymorphism and haplotype diversity were calculated for all estimated mt-DNA fragments. The genetic distance values were 0.292, 0.015, 0.151, and 0.09 within Metapenaeus species, Calanus species, Artemia species, and Daphnia species, respectively. The reconstructed phylogenetic tree is clustered into some unique clades. Cytochrome oxidase subunit 1 gene (cox1) was a powerful system in reconstruction of phylogenetic relations among evaluated crustacean species.

Keywords: crustaceans, genetics, Cox1, phylogeny

Procedia PDF Downloads 362

Authors: Swati Gautam, Amita Jain, Shyampyari Jaiswar

Abstract:

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

Procedia PDF Downloads 286

Authors: Khethiwe Mtshali, Zamantungwa T. H. Khumalo, Stanford Kwenda, Ismail Arshad, Oriel M. M. Thekisoe

Abstract:

Ecologically, the gut, mammary glands and bloodstream consist of distinct microbial communities of commensals, mutualists and pathogens, forming a complex ecosystem of niches. The by-products derived from these body sites i.e. faeces, milk and blood, respectively, have many uses in rural communities where they aid in the facilitation of day-to-day household activities and occasional rituals. Thus, although livestock rearing plays a vital role in the sustenance of the livelihoods of rural communities, it may serve as a potent reservoir of different pathogenic organisms that could have devastating health and economic implications. This study aimed to simultaneously explore the microbial profiles of corresponding faecal, milk and blood samples from lactating cows using 16S rRNA metagenomic sequencing. Bacterial communities were inferred through the Divisive Amplicon Denoising Algorithm 2 (DADA2) pipeline coupled with SILVA database v138. All downstream analyses were performed in R v3.6.1. Alpha-diversity metrics showed significant differences between faeces and blood, faeces and milk, but did not vary significantly between blood and milk (Kruskal-Wallis, P < 0.05). Beta-diversity metrics on Principal Coordinate Analysis (PCoA) and Non-Metric Dimensional Scaling (NMDS) clustered samples by type, suggesting that microbial communities of the studied niches are significantly different (PERMANOVA, P < 0.05). A number of taxa were significantly differentially abundant (DA) between groups based on the Wald test implemented in the DESeq2 package (Padj < 0.01). The majority of the DA taxa were significantly enriched in faeces than in milk and blood, except for the genus Anaplasma, which was significantly enriched in blood and was, in turn, the most abundant taxon overall. A total of 30 phyla, 74 classes, 156 orders, 243 families and 408 genera were obtained from the overall analysis. The most abundant phyla obtained between the three body sites were Firmicutes, Bacteroidota, and Proteobacteria. A total of 58 genus-level taxa were simultaneously detected between the sample groups, while bacterial signatures of at least 8 of these occurred concurrently in corresponding faeces, milk and blood samples from the same group of animals constituting a pool. The important taxa identified in this study could be categorized into four potentially pathogenic clusters: i) arthropod-borne; ii) food-borne and zoonotic; iii) mastitogenic and; iv) metritic and abortigenic. This study provides insight into the microbial composition of bovine faeces, milk, and blood and its extent of overlapping. It further highlights the potential risk of disease occurrence and transmission between the animals and the inhabitants of the sampled rural community, pertaining to their unsanitary practices associated with the use of cattle by-products.

Keywords: microbial profiling, 16S rRNA, NGS, feces, milk, blood, lactating cows, small-scale farmers

Procedia PDF Downloads 111

Authors: Charlotte Brenner

Abstract:

Teachers’ beleifs about inclusion are foundational to their implementation of inclusive teaching practices. Utilizing a longitudinal design and multiple case study methodology, this study investigates how teacher candidates’ instructional and practicum experiences shape their beliefs about inclusion in one teacher education program located in western Canada (N=20). Interview questions were developed through the lens of self-determinaiton theory and theory about teachers’ beleifs and inclusion. Preliminary thematic ananysis indicates that a 36-hour course focused on diversity and inclusion supports teacher candiates to deepen their understandings of: the need for inclusion in classrooms and strategies to promote inclusion. Furthermore, teacher candiates identified course components that fostered their developing understandings of inclusion. Future data will examine the stability of teacher candidates’ beliefs about inclusion and their implementation of inclusive teaching strategies throughout their practicum experiences.

Keywords: teacher candidates, inclusion, teacher education programs, beliefs

Procedia PDF Downloads 88

Authors: Hong-Nam Choi, Hyeong-Wook Song, Sungwan Hong, Hong-Kyu Kim

Abstract:

In Korea, elements that decide the quality of residential environment are not only diverse, but show deviation as well. However, people do not consider these elements and instead, they try to settle the uniformed style of residential environment, which focuses on the construction development of apartment housing and business based plans. Recently, block-unit redevelopment is becoming the standout alternative plan of standardize redevelopment projects, but constructions become inefficient because of indefinite planning criteria. In conclusion, the following research is about analyzing and categorizing the development method and legal ground of redevelopment project district, plan determinant and applicable standard. The purpose of this study is to become a basis in compatible analysis of planning standards that will happen in the future.

Keywords: shape restrictions, improvement of regulation, diversity of residential environment, classification of redevelopment project, planning criteria of redevelopment, special architectural district (SAD)

Procedia PDF Downloads 485

Authors: Nirmani Wijenayake, Louise Lutze-Mann, Lucy Jo, John Wilson, Vivian Yeung, Dean Lovett, Kim Snepvangers

Abstract:

Sessional academic staff at universities have the most influence and impact on student learning, engagement, and experience as they have the most direct contact with undergraduate students. A blended technology-enhanced program was created for the development and support of sessional staff to ensure adequate training is provided to deliver quality educational outcomes for the students. This program combines innovative mixed media educational modules, a peer-driven support forum, and face-to-face workshops to provide a comprehensive training and support package for staff. Additionally, the program encourages the development of learning communities and peer mentoring among the sessional staff to enhance their support system. In 2018, the program was piloted on 100 sessional staff in the School of Biotechnology and Biomolecular Sciences to evaluate the effectiveness of this model. As part of the program, rotoscope animations were developed to showcase ‘typical’ interactions between staff and students. These were designed around communication, confidence building, consistency in grading, feedback, diversity awareness, and mental health and wellbeing. When surveyed, 86% of sessional staff found these animations to be helpful in their teaching. An online platform (Moodle) was set up to disseminate educational resources and teaching tips, to host a discussion forum for peer-to-peer communication and to increase critical thinking and problem-solving skills through scenario-based lessons. The learning analytics from these lessons were essential in identifying difficulties faced by sessional staff to further develop supporting workshops to improve outcomes related to teaching. The face-to-face professional development workshops were run by expert guest speakers on topics such as cultural diversity, stress and anxiety, LGBTIQ and student engagement. All the attendees of the workshops found them to be useful and 88% said they felt these workshops increase interaction with their peers and built a sense of community. The final component of the program was to use an adaptive e-learning platform to gather feedback from the students on sessional staff teaching twice during the semester. The initial feedback provides sessional staff with enough time to reflect on their teaching and adjust their performance if necessary, to improve the student experience. The feedback from students and the sessional staff on this model has been extremely positive. The training equips the sessional staff with knowledge and insights which can provide students with an exceptional learning environment. This program is designed in a flexible and scalable manner so that other faculties or institutions could adapt components for their own training. It is anticipated that the training and support would help to build the next generation of educators who will directly impact the educational experience of students.

Keywords: designing effective instruction, enhancing student learning, implementing effective strategies, professional development

Procedia PDF Downloads 128

Authors: Chua Bee Seok, Shamsul Amri Baharuddin, Ferlis Bahari, Jasmine Adela Mutang, Lailawati Madlan, Rosnah Ismail, Asong Joseph

Abstract:

Malaysia is a country famously known for its multiple unique cultural and ethnic diversities. Despite the diversity of culture, customs and beliefs, respectively, Malaysia still be able to stand as a harmonious country. However, if there is an attitude of stereotypes, prejudice and discrimination among ethnic, it may seriously affect the solidarity between people in Malaysia. Thus, this study focuses on constructing a scale measuring the Malaysian experience, strategy and effect of ethnic discrimination. To develop a quantitative measure on ethnic discrimination directed against Malaysian, a three-step process is proposed: Exploratory factor analysis, validity analysis, and internal consistency reliability analysis. Results, limitations, and implications of the study are discussed.

Keywords: test development, Malaysian multi-ethnic discrimination scale, exploratory factor analysis, validity, multi-ethnic, reliability, psychometrics

Procedia PDF Downloads 742

Authors: Sharon Diaz Ruiz

Abstract:

The population of Latinx adult English language learners (ELLs) in the United States will increase in the next few years and become even more racially and linguistically diverse. Our classrooms reflect these demographic changes; therefore, there will always be the need to identify language teaching practices that would allow educators to meet this linguistic diversity. This qualitative study explores Latinx adult English language learners' perceptions of culturally responsive teaching strategies. Participants in this study will be enrolled in an English developmental course for the Fall of 2022. The data collection process will consist of overt observation during five presentations/activities, including culturally inclusive readings and student reflections. The teaching materials selected will align with the course module's goals and objectives. The result of this investigation will shed light on the gap in the literature documenting the application of culturally responsive pedagogy to Latino adult language learners.

Keywords: emergent bilinguals, adult learners, Latinx learners, ELL

Procedia PDF Downloads 101

Authors: Mingxi Xiao

Abstract:

Children’s experiences in the early years build and shape the brain. The early years learning environment plays a significantly important role in children’s development. A well-constructed environment will facilitate children’s physical and mental well-being. This case study used an early learning centre in Australia called SDN Hurstville as an example, describing the learning environment in the centre, as well as analyzing the functions of the affordances. In addition, this report talks about the sustainability of learning in the centre, and how the environment supports cultural diversity and indigenous learning. The early years for children are significant. Different elements in the early childhood centre should work together to help children develop better. This case study found that the natural environment and the artificial environment are both critical to children; only when they work together can children have better development in physical and mental well-being and have a sense of belonging when playing and learning in the centre.

Keywords: early childhood center, early childhood education, learning environment, Australia

Procedia PDF Downloads 242

Authors: Vakhtang Nozadze, Luiza Arutinova, Khatuna Martskvishvili

Abstract:

The social empowerment of most needed individuals is a challenging issue, especially for developing countries. The current study explores the effects of visual impairment on individuals’ satisfaction with different aspects of life (i.e. education, job, income, family) and coping strategies. Furthermore, the difference between groups according to health status is revealed. Other demographic variables (education, employment, and marital status) is also considered. The cross-sectional design and self-reported questionnaires were adopted. Seventy-two visually impaired males and females (age range 13-66) and seventy healthy individuals participated in the study. The results reveal the importance of health status on the accessibility of social amenities, individuals’ satisfaction with life, and a diversity of coping strategies, irrespective of the age. The research has an important implication for social integration research and policy.

Keywords: coping strategies, life satisfaction, social integration, visual impairment

Procedia PDF Downloads 332

Authors: Mona Kamel Hassan

Abstract:

Teaching a class of diverse learners poses a great challenge not only for foreign and second language teachers, but also for teachers in different disciplines as well as for curriculum designers. Thus, to contribute to previous research tackling language diversity, the current paper shares the experience of teaching a reading, writing and vocabulary building course to diverse Arabic as a Foreign Language learners in their advanced language proficiency level. Diversity is represented in students’ motivation, their prior knowledge, their various needs and interests, their level of anxiety, and their different learning styles and skills. While teaching this course the researcher adopted the universal design for learning (UDL) framework, which is a means to meet the various needs of diverse learners. UDL stresses the importance of enabling the entire diverse students to gain skills, knowledge, and enthusiasm to learn through the employment of teaching methods that respond to students' individual differences. Accordingly, the educational curriculum developed for this course and the teaching methods employed is modified. First, the researcher made the language curriculum vivid and attractive to inspire students' learning and to keep them engaged in their learning process. The researcher encouraged the entire students, from the first day, to suggest topics of their interest; political, social, cultural, etc. The authentic Arabic texts chosen are those that best meet students’ needs, interests, lives, and sociolinguistic issues, together with the linguistic and cultural components. In class and under the researcher’s guidance, students dig into these topics to find solutions for the tackled issues while working with their peers. Second, to gain equal opportunities to demonstrate learning, role-playing was encouraged to give students the opportunity to perform different linguistic tasks, to reflect and share their diverse interests and cultural backgrounds with their peers. Third, to bring the UDL into the classroom, students were encouraged to work on interactive, collaborative activities through technology to improve their reading and writing skills and reinforce their mastery of the accumulated vocabulary, idiomatic expressions, and collocations. These interactive, collaborative activities help to facilitate student-student communication and student-teacher communication and to increase comfort in this class of diverse learners. Detailed samples of the educational curriculum and interactive, collaborative activities developed, accompanied by methods of teaching employed to teach these diverse learners, are presented for illustration. Results revealed that students are responsive to the educational materials which are developed for this course. Therefore, they engaged in the learning process and classroom activities and discussions effectively. They also appreciated their instructor’s willingness to differentiate the teaching methods to suit students of diverse background knowledge, learning styles, level of anxiety, etc. Finally, the researcher believes that sharing this experience in teaching diverse learners will help both language teachers and teachers in other disciplines to develop a better understanding to meet their students' diverse needs. Results will also pave the way for curriculum designers to develop educational material that meets the needs of diverse learners.

Keywords: teaching, language, diverse, learners

Procedia PDF Downloads 99