Search results for: integrative bioinformatics

Authors: Keaghan Brown

Abstract:

The prioritization of drug resistance mutations impacting protein folding or protein-drug and protein-DNA interactions within macromolecular systems is critical to the success of treatment regimens. With a continual increase in computational tools to assess these impacts, the need for scalability and reproducibility became an essential component of computational analysis and experimental research. Here it introduce a bioinformatics pipeline that combines several structural analysis tools in a simplified workflow, by optimizing the present computational hardware and software to automatically ease the flow of data transformations. Utilizing preestablished software tools, it was possible to develop a pipeline with a set of pre-defined functions that will automate mutation introduction into the HIV-1 Integrase protein structure, calculate the gain and loss of polar interactions and calculate the change in energy of protein fold. Additionally, an automated molecular dynamics analysis was implemented which reduces the constant need for user input and output management. The resulting pipeline, Automated Mutation Introduction and Analysis (AMIA) is an open source set of scripts designed to introduce and analyse the effects of mutations on the static protein structure as well as the results of the multi-conformational states from molecular dynamic simulations. The workflow allows the user to visualize all outputs in a user friendly manner thereby successfully enabling the prioritization of variant systems for experimental validation.

Keywords: automated workflow, variant prioritization, drug resistance, HIV Integrase

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Authors: Oluwafunmibi Omotayo Fasanya, Augustine Kena Adjei

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Diabetic nephropathy (DN) is a major complication of diabetes, with fibrosis and propionate metabolism playing critical roles in its progression. Identifying biomarkers linked to these pathways may provide novel insights into DN diagnosis and treatment. This study aims to identify biomarkers associated with fibrosis and propionate metabolism in DN. Analyze the biological pathways and regulatory mechanisms of these biomarkers. Develop a machine learning model to predict DN-related biomarkers and validate their functional roles. Publicly available transcriptome datasets related to DN (GSE96804 and GSE104948) were obtained from the GEO database (https://www.ncbi.nlm.nih.gov/gds), and 924 propionate metabolism-related genes (PMRGs) and 656 fibrosis-related genes (FRGs) were identified. The analysis began with the extraction of DN-differentially expressed genes (DN-DEGs) and propionate metabolism-related DEGs (PM-DEGs), followed by the intersection of these with fibrosis-related genes to identify key intersected genes. Instead of relying on traditional models, we employed a combination of deep neural networks (DNNs) and ensemble methods such as Gradient Boosting Machines (GBM) and XGBoost to enhance feature selection and biomarker discovery. Recursive feature elimination (RFE) was coupled with these advanced algorithms to refine the selection of the most critical biomarkers. Functional validation was conducted using convolutional neural networks (CNN) for gene set enrichment and immunoinfiltration analysis, revealing seven significant biomarkers—SLC37A4, ACOX2, GPD1, ACE2, SLC9A3, AGT, and PLG. These biomarkers are involved in critical biological processes such as fatty acid metabolism and glomerular development, providing a mechanistic link to DN progression. Furthermore, a TF–miRNA–mRNA regulatory network was constructed using natural language processing models to identify 8 transcription factors and 60 miRNAs that regulate these biomarkers, while a drug–gene interaction network revealed potential therapeutic targets such as UROKINASE–PLG and ATENOLOL–AGT. This integrative approach, leveraging deep learning and ensemble models, not only enhances the accuracy of biomarker discovery but also offers new perspectives on DN diagnosis and treatment, specifically targeting fibrosis and propionate metabolism pathways.

Keywords: diabetic nephropathy, deep neural networks, gradient boosting machines (GBM), XGBoost

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Authors: M. L. W. P. De Silva, R. A. C. Rabel, N. Smith, L. McIntyre, T. J Parkinson, K. A. N. Wijayawardhane

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Curricular integration is an important concept in medical education for developing students’ ability to create connections between different medical disciplines. Problem-Based Learning (PBL) is one of the vehicles through which such integration can be achieved. During the recent review of the veterinary curriculum at the University of Peradeniya, a series of courses in Integrative Veterinary Science (IVS) were introduced, in which PBL was the primary teaching methodology. The objectives of this study were to evaluate students’ opinions on PBL as a teaching method: it should be noted that, within the context of secondary and tertiary education in Sri Lanka, this would be an entirely novel learning experience for the students. Opinions were sought at the conclusion of IVS sessions where students of semesters 2, 4, 6, and 7 (of an 8-semester program) were exposed to a two, 2-hour PBL-based case scenario. The PBL-based case scenario in semesters 2, 4, and 7 were delivered using material previously developed by an experienced PBL practitioner, whilst material for semester 6 was prepared de novo by a less experienced practitioner. Each student (semesters 2: n=38, 4: n=37, 6: n=55, and 7: n=40) completed a questionnaire which asked whether: (i) the course had improved their critical thinking skills; (ii) the learning environment was sufficiently comfortable to express/share student’s opinion; (iii) there was sufficient facilitator guidance; (iv) the online study environment enhanced learning; and (v) the students were overall satisfied with the PBL approach and IVS concept. Responses were given on a 5-point Likert-scale (strongly agree (SA), agree (A), neutral (N), disagree (D), and strongly disagree (SD)). SA and A responses were summed to provide an overall ‘satisfactory’ response. Results were subjected to frequency-distribution statistical analysis. A total of 88.5% of students gave SA+A scores to their overall satisfaction. The proportion of SA+A scores differed between different semesters, such that 95% of semester 2, 4, and 7 students gave SA+A scores, whereas only 69% of semester 6 students did so for their respective sessions. Overall, 96% of the students gave SA+A scores to the question relating to the improvement of critical thinking skills: semester 6 students’ scores were marginally, but not significantly, lower (91% SA+A) than those in other semesters. The difference of scores between semester 6 and the other semesters may be attributed to the different PBL-material used and/or the different experience levels of the practitioners that developed the study material. The use of PBL as a means of teaching IVS curriculum-integration courses was well-received by the students in terms of their overall satisfaction and their perceptions of improved critical thinking skills. Importantly, this was achieved in the face of a methodology that was entirely novel to the students. Finally, the delivery of the PBL medium was readily mastered by the practitioner to whom it was also a novel methodology.

Keywords: critical thinking skills, integration, problem based learning, veterinary education

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Authors: Ioana Simina Frincu

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As institutional initiatives often fail to provide good practices when it comes to heritage management or to adapt to the changing environment in which they function and to the audiences they address, private actions represent viable strategies for sustainable knowledge acquisition. Information dissemination to future generations is one of the key aspects in preserving cultural heritage and is successfully feasible even in the absence of original artifacts. Combined with the (re)discovery of natural landscape, open-air exploratory approaches (archeoparks) versus an enclosed monodisciplinary rigid framework (traditional museums) are more likely to 'speak the language' of a larger number of people, belonging to a variety of categories, ages, and professions. Interactive sites are efficient ways of stimulating heritage awareness and increasing the number of visitors of non-interactive/static cultural institutions owning original pieces of history, delivering specialized information, and making continuous efforts to preserve historical evidence (relics, manuscripts, etc.). It is high time entrepreneurs took over the role of promoting cultural heritage, bet it under a more commercial yet more attractive form (business). Inclusive, participatory type of activities conceived by experts from different domains/fields (history, anthropology, tourism, sociology, business management, integrative sustainability, etc.) have better chances to ensure long term cultural benefits for both adults and children, especially when and where the educational discourse fails. These unique self-experience leisure activities, which offer everyone the opportunity to recreate history by him-/her-self, to relive the ancestors’ way of living, surviving and exploring should be regarded not as pseudo-scientific approaches but as important pre-steps to museum experiences. In order to support this theory, focus will be laid on two different examples: one dynamic, in the outdoors (the Boario Terme Archeopark from Italy) and one experimental, held indoor (the reconstruction of the Neolithic sanctuary of Parta, Romania as part of a transdisciplinary academic course) and their impact on young generations. The conclusion of this study shows that the increasingly lower engagement of youth (students) in discovering and understanding history, archaeology, and heritage can be revived by entrepreneurial projects.

Keywords: archeopark, educational tourism, open air museum, Parta sanctuary, prehistory

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Authors: Vinod Nair, C. Sadasivan

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Beta-lactam antibiotics are the most frequently prescribed medications in modern medicine. The antibiotic resistance by the production of enzyme beta-lactamase is an important mechanism seen in microorganisms. Resistance to beta-lactams mediated by beta-lactamases can be overcome successfully with the use of beta-lactamase inhibitors. New generations of the antibiotics contain mostly synthetic compounds, and many side effects have been reported for them. Combinations of beta-lactam and beta-lactamase inhibitors have become one of the most successful antimicrobial strategies in the current scenario of bacterial infections. Plant-based drugs are very cheap and having lesser adverse effect than synthetic compounds. The synergistic effect of eugenol acetate with beta-lactams restores the activity of beta-lactams, allowing their continued clinical use. It is reported here the enhanced inhibitory effect of phytochemical, eugenol acetate, isolated from the plant Syzygium aromaticum with beta-lactams on beta-lactamase. The compound was found to have synergistic effect with the antibiotic amoxicillin against antibiotic-resistant strain of S.aureus. The enzyme was purified from the organism and incubated with the compound. The assay showed that the compound could inhibit the enzymatic activity of beta-lactamase. Modeling and molecular docking studies indicated that the compound can fit into the active site of beta-lactamase and can mask the important residue for hydrolysis of beta-lactams. The synergistic effects of eugenol acetate with beta-lactam antibiotics may justify, the use of these plant compounds for the preparation of β-lactamase inhibitors against β-lactam resistant S.aureus.

Keywords: betalactamase, eugenol acetate, synergistic effect, molecular modeling

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Authors: Junwen Chen, Celina Feleppa, Tingyue Sun, Satoko Sasagawa, Michael Smithson

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School refusal behaviours refer to behaviours to avoid school attendance, chronic lateness in arriving at school, or regular early dismissal. Poor attendance in schools is highly correlated with anxiety, depression, suicide attempts, delinquency, violence, and substance use and abuse. Poor attendance is also a strong indicator of lower achievement in school, as well as problematic social-emotional development. Long-term consequences of school refusal behaviours include fewer opportunities for higher education, employment, and social difficulties, and high risks of later psychiatric illness. Given its negative impacts on youth educational outcomes and well-being, a thorough understanding of factors that are involved in the development of this phenomenon is warranted for developing effective management approaches. This study investigated parental and adolescent factors that may contribute to school refusal behaviours by specifically focusing on the role of parental and adolescents’ anxiety and depression, emotion dysregulation, and parental rearing style. Findings are expected to inform the identification of both parental and adolescents’ factors that may contribute to school refusal behaviours. This knowledge will enable novel and effective approaches that incorporate these factors to managing school refusal behaviours in adolescents, which in turn improve their school and daily functioning. Results are important for an integrative understanding of school refusal behaviours. Furthermore, findings will also provide information for policymakers to weigh the benefits of interventions targeting school refusal behaviours in adolescents. One-hundred-and-six adolescents aged 12-18 years (mean age = 14.79 years old, SD = 1.78, males = 44) and their parents (mean age = 47.49 years old, SD = 5.61, males = 27) completed an online questionnaire measuring both parental and adolescents’ anxiety, depression, emotion dysregulation, parental rearing styles, and adolescents’ school refusal behaviours. Adolescents with school refusal behaviours reported greater anxiety and depression, with their parents showing greater emotion dysregulation. Parental emotion dysregulation and adolescents’ anxiety and depression predicted school refusal behaviours independently. To date, only limited studies have investigated the interplay between parental and youth factors in relation to youth school refusal behaviours. Although parental emotion dysregulation has been investigated in relation to youth emotion dysregulation, little is known about its role in the context of school refusal. This study is one of the very few that investigated both parental and adolescent factors in relation to school refusal behaviours in adolescents. The findings support the theoretical models that emphasise the role of youth and parental psychopathology in school refusal behaviours. Future management of school refusal behaviours should target adolescents’ anxiety and depression while incorporating training for parental emotion regulation skills.

Keywords: adolescents, school refusal behaviors, parental factors, anxiety and depression, emotion dysregulation

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Authors: Felix Schumann, Giorgia Carratta, Tobias Dauth, Liv Jaeckel

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In the last few decades, the rapid growth of the use and disposal of plastic items has led to their overaccumulation in the environment. As a result, plastic pollution has become a subject of global concern. Today plastics are used as raw materials in almost every industry. While the recognition of the ecological, social, and economic impact of plastics in academic research is on the rise, the potential role of the ‘plastic industry’ in dealing with such issues is still largely underestimated. Therefore, the literature on sustainable plastic management is still nascent and fragmented. Working towards sustainability requires a fundamental shift in the way companies employ plastics in their day-to-day business. For that reason, the applicability of the business model concept has recently gained momentum in environmental research. Business model innovation is increasingly recognized as an important driver to re-conceptualize the purpose of the firm and to readily integrate sustainability in their business. It can serve as a starting point to investigate whether and how sustainability can be realized under industry- and firm-specific circumstances. Yet, there is no comprehensive view in the plastic industry on how firms start refining their business models to embed sustainability in their operations. Our study addresses this gap, looking primarily at the industrial sectors responsible for the production of the largest amount of plastic waste today: plastic packaging, consumer goods, construction, textile, and transport. Relying on the archetypes of sustainable business models and applying them to the aforementioned sectors, we try to identify companies’ current strategies to make their business models more sustainable. Based on the thematic clustering, we can develop an integrative framework for the plastic industry. The findings are underpinned and illustrated by a variety of relevant plastic management solutions that the authors have identified through a systematic literature review and analysis of existing, empirically grounded research in this field. Using the archetypes, we can promote options for business model innovations for the most important sectors in which plastics are used. Moreover, by linking the proposed business model archetypes to the plastic industry, our research approach guides firms in exploring sustainable business opportunities. Likewise, researchers and policymakers can utilize our classification to identify best practices. The authors believe that the study advances the current knowledge on sustainable plastic management through its broad empirical industry analyses. Hence, the application of business model archetypes in the plastic industry will be useful for shaping companies’ transformation to create and deliver more sustainability and provides avenues for future research endeavors.

Keywords: business models, environmental economics, plastic management, plastic pollution, sustainability

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Authors: Emma Avoyan

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The safety standards for flood protection in the Netherlands have been revised recently. It is expected that all major flood-protection structures will have to be reinforced to meet the new standards. The Dutch Flood Protection Programme aims at accomplishing this task through innovative integrated projects such as construction of multi-functional flood defenses. In these projects, flood safety purposes will be combined with spatial planning, nature development, emergency management or other sectoral objectives. Therefore, implementation of dike reinforcement projects requires early involvement and collaboration between public and private sectors, different governmental actors and agencies. The development and implementation of such integrated projects has been an issue in Dutch flood risk management since long. Therefore, this article analyses how cross-sector collaboration within flood risk governance in the Netherlands has evolved over time, and how this development can be explained. The integrative framework for collaborative governance is applied as an analytical tool to map external factors framing possibilities as well as constraints for cross-sector collaboration in Dutch flood risk domain. Supported by an extensive document and literature analysis, the paper offers insights on how the system context and different drivers changing over time either promoted or hindered cross-sector collaboration between flood protection sector, urban development, nature conservation or any other sector involved in flood risk governance. The system context refers to the multi-layered and interrelated suite of conditions that influence the formation and performance of complex governance systems, such as collaborative governance regimes, whereas the drivers initiate and enable the overall process of collaboration. In addition, by applying a method of process tracing we identify a causal and chronological chain of events shaping cross-sectoral interaction in Dutch flood risk management. Our results indicate that in order to evaluate the performance of complex governance systems, it is important to firstly study the system context that shapes it. Clear understanding of the system conditions and drivers for collaboration gives insight into the possibilities of and constraints for effective performance of complex governance systems. The performance of the governance system is affected by the system conditions, while at the same time the governance system can also change the system conditions. Our results show that the sequence of changes within the system conditions and drivers over time affect how cross-sector interaction in Dutch flood risk governance system happens now. Moreover, we have traced the potential of this governance system to shape and change the system context.

Keywords: collaborative governance, cross-sector interaction, flood risk management, the Netherlands

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Authors: Shantanu Prakash, Suruchi Shukla, Amita Jain

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Introduction: The hepatitis C virus (HCV) is a major public health problem and a leading cause of chronic liver disease. Injection drug use and individuals receiving blood and blood products are the primary modes of HCV transmission. Our study aims to establish the prevalent genotypes/ subtypes of HCV circulating in Uttar Pradesh, North India, as reported from a tertiary care hospital. Methods: It is a retrospective observational analysis of consecutive 404 HCV RNA positive cases referred to our hospital during September 2014 to April 2017. The study was approved by an institutional ethics committee. Written informed consent was taken from each participant. Clinical and demographic details of these patients were recorded using predesigned questionnaires. All the laboratory testing was carried on stored serum sample of enrolled cases. Genotyping of all 404 strains was done by Sanger’s sequencing of the core region. The phylogenetic analysis of 179 HCV strains with high -quality sequencing data was performed. Results: The distribution of prevalent genotypes/ subtypes as noted in the present study was; Genotype (GT)1a [n-101(25%)], GT1b [n-12(2.9%)], GT1c [1(0.25%)], GT3a [275(68.07%)], GT3b [9(2.2%)], GT3g [2(0.49%)], GT3i [3(0.74%)], and GT4a [1(0.24%)]. HCV genotypes GT2, GT5 and GT6 were not detected from our region. Sequence analysis showed high genotypic variability in HCV GT3. Phylogenetic analysis showed that HCV GT3 and GT1 circulating in our region were related to Indian strains reported earlier. Conclusions: HCV genotypes 3a and 1a are commonest circulating genotypes in Uttar Pradesh (UP), India.

Keywords: Hepatitis C virus, genetic variation, bioinformatics, genotype, HCV

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Authors: Anna Bak-Klimek, Emily Spencer, Siew Lee, Karen Campbell, Wendy McInally

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Background & Significance: Over half of Teenagers and Young Adults (TYAs) say that they experience psychological distress after cancer diagnosis and TYAs with cancer are at higher risk of developing distress compared to other age groups. Despite this there are no age-appropriate interventions to help TYAs manage distress and there is a lack of conceptual understanding of what causes distress in this population group. This makes it difficult to design a targeted, developmentally appropriate intervention. This review aims to identify the key determinants of distress in TYAs affected by cancer and to propose an integrative model of cancer-related distress for TYAs. Method: A literature search was performed in Cochrane Database of Systematic Reviews, MEDLINE, PsycINFO, CINAHL, EMBASE and PsycArticles in May-June, 2022. Quantitative literature was systematically reviewed on the relationship between psychological distress experienced by TYAs affected by cancer and a wide range of factors i.e. individual (demographic, psychological, developmental, and clinical factors) and contextual (social/environmental) factors. Evidence was synthesized and correlates were categorized using the Biopsychosocial Model. The full protocol is available from PROSPERO (CRD42022322069) Results: Thirty eligible quantitative studies met criteria for the review. A total of twenty-six studies were cross-sectional, three were longitudinal and one study was a case control study. The evidence on the relationship between the socio-demographic, illness and treatment-related factors and psychological distress is inconsistent and unclear. There is however consistent evidence on the link between psychological factors and psychological distress. For instance, the use of cognitive and defence coping, negative meta-cognitive beliefs, less optimism, a lack of sense of meaning and lower resilience levels were significantly associated with higher psychological distress. Furthermore, developmental factors such as poor self-image, identity issues and perceived conflict were strongly associated with higher distress levels. Conclusions: The current review suggests that psychological and developmental factors such as ineffective coping strategies, poor self-image and identity issues may play a key role in the development of psychological distress in TYAs affected by cancer. The review proposes a Positive Developmental Psychology Model of Distress for Teenagers and Young Adults affected by cancer. The review highlights that implementation of psychological interventions that foster optimism, improve resilience and address self-image may result in reduced distress in TYA’s with cancer.

Keywords: cancer, determinant, psychological distress, teenager and young adult, theoretical model

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Authors: James Beauchemin

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Introduction: The incarceration of people with mental illness and substance use disorders is a major public health issue, with social, clinical, and economic implications. Yoga participation has been associated with numerous psychological benefits; however, there is a paucity of research examining impacts of yoga with incarcerated populations. The purpose of this study was to evaluate effectiveness of a six-week yoga intervention on several mental health-related variables, including emotion regulation, body awareness, and warnings of substance relapse among incarcerated females. Methods: This study utilized a pre-post, three-arm design, with participants assigned to intervention, therapeutic community, or general population groups. A between-groups analysis of covariance (ANCOVA) was conducted across groups to assess intervention effectiveness using the Difficulties in Emotion Regulation Scale (DERS), Scale of Body Connection (SBC), and Warnings of Relapse (AWARE) Questionnaire. Results: ANCOVA results for warnings of relapse (AWARE) revealed significant between-group differences F(2, 80) = 7.15, p = .001; np2 = .152), with significant pairwise comparisons between the intervention group and both the therapeutic community (p = .001) and the general population (p = .005) groups. Similarly, significant differences were found for emotional regulation (DERS) F(2, 83) = 10.521, p = .000; np2 = .278). Pairwise comparisons indicated a significant difference between the intervention and general population (p = .01). Finally, significant differences between the intervention and control groups were found for body awareness (SBC) F(2, 84) = 3.69, p = .029; np2 = .081). Between-group differences were clarified via pairwise comparisons, indicating significant differences between the intervention group and both the therapeutic community (p = .028) and general population groups (p = .020). Implications: Study results suggest that yoga may be an effective addition to integrative mental health and substance use treatment for incarcerated women, and contributes to increasing evidence that holistic interventions may be an important component for treatment with this population. Specifically, given the prevalence of mental health and substance use disorders, findings revealed that changes in body awareness and emotion regulation may be particularly beneficial for incarcerated populations with substance use challenges as a result of yoga participation. From a systemic perspective, this proactive approach may have long-term implications for both physical and psychological well-being for the incarcerated population as a whole, thereby decreasing the need for traditional treatment. By integrating a more holistic, salutogenic model that emphasizes prevention, interventions like yoga may work to improve the wellness of this population, while providing an alternative or complementary treatment option for those with current symptoms.

Keywords: yoga, mental health, incarceration, wellness

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Authors: Li-Te Lin, Chia-Jung Li, Kuan-Hao Tsui

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Cuproptosis, a newly identified cell death mechanism, has attracted attention for its association with various diseases. However, the genetic interplay between cuproptosis and ovarian aging remains largely unexplored. This study aims to address this gap by analyzing datasets related to ovarian aging and cuproptosis. Spatial transcriptome analyses were conducted in the ovaries of both young and aged female mice to elucidate the role of FDX1. Comprehensive bioinformatics analyses, facilitated by R software, identified FDX1 as a potential cuproptosis-related gene with implications for ovarian aging. Clinical infertility biopsies were examined to validate these findings, showing consistent results in elderly infertile patients. Furthermore, pharmacogenomic analyses of ovarian cell lines explored the intricate association between FDX1 expression levels and sensitivity to specific small molecule drugs. Spatial transcriptome analyses revealed a significant reduction in FDX1 expression in aging ovaries, supported by consistent findings in biopsies from elderly infertile patients. Pharmacogenomic investigations indicated that modulating FDX1 could influence drug responses in ovarian-related therapies. This study pioneers the identification of FDX1 as a cuproptosis-related gene linked to ovarian aging. These findings not only contribute to understanding the mechanisms of ovarian aging but also position FDX1 as a potential diagnostic biomarker and therapeutic target. Further research may establish FDX1's pivotal role in advancing precision medicine and therapies for ovarian-related conditions.

Keywords: cuproptosis, FDX1, ovarian aging, biomarker

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Authors: Madhat Abu Al-Naeem, Ismail Yusoff, Ng Tham Fatt, Yatimah Alias

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Groundwater in Gaza strip is increasingly being exposed to anthropic and natural factors that seriously impacted the groundwater quality. Physiochemical data of groundwater can offer important information on changes in groundwater quality that can be useful in improving water management tactics. An integrative hydrochemical and statistical techniques (Hierarchical cluster analysis (HCA) and factor analysis (FA)) have been applied on the existence ten physiochemical data of 84 samples collected in (2000/2001) using STATA, AquaChem, and Surfer softwares to: 1) Provide valuable insight into the salinization sources and the hydrochemical processes controlling the chemistry of groundwater. 2) Differentiate the influence of natural processes and man-made activities. The recorded large diversity in water facies with dominance Na-Cl type that reveals a highly saline aquifer impacted by multiple complex hydrochemical processes. Based on WHO standards, only (15.5%) of the wells were suitable for drinking. HCA yielded three clusters. Cluster 1 is the highest in salinity, mainly due to the impact of Eocene saline water invasion mixed with human inputs. Cluster 2 is the lowest in salinity also due to Eocene saline water invasion but mixed with recent rainfall recharge and limited carbonate dissolution and nitrate pollution. Cluster 3 is similar in salinity to Cluster 2, but with a high diversity of facies due to the impact of many sources of salinity as sea water invasion, carbonate dissolution and human inputs. Factor analysis yielded two factors accounting for 88% of the total variance. Factor 1 (59%) is a salinization factor demonstrating the mixing contribution of natural saline water with human inputs. Factor 2 measure the hardness and pollution which explained 29% of the total variance. The negative relationship between the NO3- and pH may reveal a denitrification process in a heavy polluted aquifer recharged by a limited oxygenated rainfall. Multivariate statistical analysis combined with hydrochemical analysis indicate that the main factors controlling groundwater chemistry were Eocene saline invasion, seawater invasion, sewage invasion and rainfall recharge and the main hydrochemical processes were base ion and reverse ion exchange processes with clay minerals (water rock interactions), nitrification, carbonate dissolution and a limited denitrification process.

Keywords: dendrogram and cluster analysis, water facies, Eocene saline invasion and sea water invasion, nitrification and denitrification

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Authors: Girija Madhavanprabhakaran, Frincy Franacis, Sheeba Elizabeth John

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Introduction: A wide range of prenatal genetic screening is introduced with increasing incidences of congenital anomalies even in low-risk pregnancies and is an emerging standard of care. Being frontline caretakers, the role and responsibilities of nurses and midwives are critical as they are working along with couples to provide evidence-based supportive educative care. The increasing genetic disorders and advances in prenatal genetic screening with limited genetic counselling facilities urge nurses and midwifery nurses with essential competencies to help couples to take informed decision. Objective: This integrative literature review aimed to explore nurse midwives’ knowledge and role in prenatal screening and genetic counselling competency and the challenges faced by them to cater to all pregnant women to empower their autonomy in decision making and ensuring psychological comfort. Method: An electronic search using keywords prenatal screening, genetic counselling, prenatal counselling, nurse midwife, nursing education, genetics, and genomics were done in the PUBMED, SCOPUS and Medline, Google Scholar. Finally, based on inclusion criteria, 8 relevant articles were included. Results: The main review results suggest that nurses and midwives lack essential support, knowledge, or confidence to be able to provide genetic counselling and help the couples ethically to ensure client autonomy and decision making. The majority of nurses and midwives reported inadequate levels of knowledge on genetic screening and their roles in obtaining family history, pedigrees, and providing genetic information for an affected client or high-risk families. The deficiency of well-recognized and influential clinical academic midwives in midwifery practice is also reported. Evidence recommended to update and provide sound educational training to improve nurse-midwife competence and confidence. Conclusion: Overcoming the challenges to achieving informed choices about fetal anomaly screening globally is a major concern. Lack of adequate knowledge and counselling competency, communication insufficiency, need for education and policy are major areas to address. Prenatal nurses' and midwives’ knowledge on prenatal genetic screening and essential counselling competencies can ensure services to the majority of pregnant women around the globe to be better-informed decision-makers and enhances their autonomy, and reduces ethical dilemmas.

Keywords: challenges, genetic counselling, prenatal screening, prenatal counselling

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Authors: Beatriz Garcia-Juan, Ana B. Escrig-Tena, Vicente Roca-Puig

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The aim of this article is to conduct a theoretical and empirical study in order to examine how the goal orientation (GO) of public employees affects the relationship between the structural and psychological empowerment that they experience at their workplaces. In doing so, we follow structural empowerment (SE) and psychological empowerment (PE) conceptualizations, and relate them to the public administration framework. Moreover, we review arguments from GO theories, and previous related contributions. Empowerment has emerged as an important issue in the public sector organization setting in the wake of mainstream New Public Management (NPM), the new orientation in the public sector that aims to provide a better service for citizens. It is closely linked to the drive to improve organizational effectiveness through the wise use of human resources. Nevertheless, it is necessary to combine structural (managerial) and psychological (individual) approaches in an integrative study of empowerment. SE refers to a set of initiatives that aim the transference of power from managerial positions to the rest of employees. PE is defined as psychological state of competence, self-determination, impact, and meaning that an employee feels at work. Linking these two perspectives will lead to arrive at a broader understanding of the empowerment process. Specifically in the public sector, empirical contributions on this relationship are therefore important, particularly as empowerment is a very useful tool with which to face the challenges of the new public context. There is also a need to examine the moderating variables involved in this relationship, as well as to extend research on work motivation in public management. It is proposed the study of the effect of individual orientations, such as GO. GO concept refers to the individual disposition toward developing or confirming one’s capacity in achievement situations. Employees’ GO may be a key factor at work and in workforce selection processes, since it explains the differences in personal work interests, and in receptiveness to and interpretations of professional development activities. SE practices could affect PE feelings in different ways, depending on employees’ GO, since they perceive and respond differently to such practices, which is likely to yield distinct PE results. The model is tested on a sample of 521 Spanish local authority employees. Hierarchical regression analysis was conducted to test the research hypotheses using SPSS 22 computer software. The results do not confirm the direct link between SE and PE, but show that learning goal orientation has considerable moderating power in this relationship, and its interaction with SE affects employees’ PE levels. Therefore, the combination of SE practices and employees’ high levels of LGO are important factors for creating psychologically empowered staff in public organizations.

Keywords: goal orientation, moderating effect, psychological empowerment, structural empowerment

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Authors: James D. Beauchemin

Abstract:

Introduction: The incarceration of people with mental illness and substance use disorders is a major public health issue with social, clinical, and economic implications. Yoga participation has been associated with numerous psychological benefits; however, there is a paucity of research examining impacts of yoga with incarcerated populations. The purpose of this study was to evaluate effectiveness of a six-week yoga intervention on several mental health-related variables, including emotion regulation, body awareness, and warnings of substance relapse among incarcerated females. Methods: This study utilized a pre-post, three-arm design, with participants assigned to intervention, therapeutic community, or general population groups. A between-group analysis of covariance (ANCOVA) was conducted across groups to assess intervention effectiveness using the Difficulties in Emotion Regulation Scale (DERS), Scale of Body Connection (SBC), and Warnings of Relapse (AWARE) Questionnaire. Results: ANCOVA results for warnings of relapse (AWARE) revealed significant between-group differences F(2, 80) = 7.15, p = .001; np2 = .152), with significant pairwise comparisons between the intervention group and both the therapeutic community (p = .001) and the general population (p = .005) groups. Similarly, significant differences were found for emotional regulation (DERS) F(2, 83) = 10.521, p = .000; np2 = .278). Pairwise comparisons indicated a significant difference between the intervention and general population (p = .01). Finally, significant differences between the intervention and control groups were found for body awareness (SBC) F(2, 84) = 3.69, p = .029; np2 = .081). Between-group differences were clarified via pairwise comparisons, indicating significant differences between the intervention group and both the therapeutic community (p = .028) and general population groups (p = .020). Implications: Study results suggest that yoga may be an effective addition to integrative mental health and substance use treatment for incarcerated women and contributes to increasing evidence that holistic interventions may be an important component for treatment with this population. Specifically, given the prevalence of mental health and substance use disorders, findings revealed that changes in body awareness and emotion regulation might be particularly beneficial for incarcerated populations with substance use challenges as a result of yoga participation. From a systemic perspective, this proactive approach may have long-term implications for both physical and psychological well-being for the incarcerated population as a whole, thereby decreasing the need for traditional treatment. By integrating a more holistic, salutogenic model that emphasizes prevention, interventions like yoga may work to improve the wellness of this population while providing an alternative or complementary treatment option for those with current symptoms.

Keywords: wellness, solution-focused coaching, college students, prevention

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Authors: Christina Killian, Katie Wall, Séamus Fanning, Guerrino Macori

Abstract:

Deep-level metagenomics offers a useful technical approach to explore the three dynamic One Health axes: healthcare, domiciliary and veterinary. There is currently limited understanding of the composition of complex biofilms, natural abundance of AMR genes and gene transfer occurrence in these ecological niches. By using a newly established small-scale complex biofilm model, COMBAT has the potential to provide new information on microbial diversity, antimicrobial resistance (AMR)-encoding gene abundance, and their transfer in complex biofilms of importance to these three One Health axes. Shotgun metagenomics has been used to sample the genomes of all microbes comprising the complex communities found in each biofilm source. A comparative analysis between untreated and biocide-treated biofilms is described. The basic steps include the purification of genomic DNA, followed by library preparation, sequencing, and finally, data analysis. The use of long-read sequencing facilitates the completion of metagenome-assembled genomes (MAG). Samples were sequenced using a PromethION platform, and following quality checks, binning methods, and bespoke bioinformatics pipelines, we describe the recovery of individual MAGs to identify mobile gene elements (MGE) and the corresponding AMR genotypes that map to these structures. High-throughput sequencing strategies have been deployed to characterize these communities. Accurately defining the profiles of these niches is an essential step towards elucidating the impact of the microbiota on each niche biofilm environment and their evolution.

Keywords: COMBAT, biofilm, metagenomics, high-throughput sequencing

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Authors: Narjes Ebrahimi, Soheila Alyasin, Navid Nezafat, Hossein Esmailzadeh, Younes Ghasemi, Seyed Hesamodin Nabavizadeh

Abstract:

Immunotherapy with allergy vaccines is of great importance in allergen-specific immunotherapy. In recent years, B-cell epitope-based vaccines have attracted considerable attention and the prediction of epitopes is crucial to design these types of allergy vaccines. B-cell epitopes might be linear or conformational. The prerequisite for the identification of conformational epitopes is the information about allergens' tertiary structures. Bioinformatics approaches have paved the way towards the design of epitope-based allergy vaccines through the prediction of tertiary structures and epitopes. Mite allergens are one of the major allergy contributors. Several mite allergens can elicit allergic reactions; however, their structures and epitopes are not well established. So, B-cell epitopes of various groups of mite allergens (24 allergens in 6 allergen groups) were predicted in the present work. Tertiary structures of 17 allergens with unknown structure were predicted and refined with RaptorX and GalaxyRefine servers, respectively. The predicted structures were further evaluated by Rampage, ProSA-web, ERRAT and Verify 3D servers. Linear and conformational B-cell epitopes were identified with Ellipro, Bcepred, and DiscoTope 2 servers. To improve the accuracy level, consensus epitopes were selected. Fifty-four conformational and 133 linear consensus epitopes were predicted. Furthermore, overlapping epitopes in each allergen group were defined, following the sequence alignment of the allergens in each group. The predicted epitopes were also compared with the experimentally identified epitopes. The presented results provide valuable information for further studies about allergy vaccine design.

Keywords: B-cell epitope, Immunotherapy, In silico prediction, Mite allergens, Tertiary structure

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Authors: J. F. Pollo Gaspary, F. Peron Gaspary, E. M. Simão, R. Concatto Beltrame, G. Orengo de Oliveira, M. S. Ristow Ferreira, J.C. Mairesse Siluk, I. F. Minello, F. dos Santos de Oliveira

Abstract:

Background: Although palliative care policies and services have been developed, research in this area continues to lag. An integrated model of palliative care is suggested, which includes complementary and alternative services aimed at improving the well-being of patients and their families. The palliative aquatics care multi-device (AuBento) uses several electromagnetic techniques to decrease pain and promote well-being through relaxation and interaction among patients, specialists, and family members. Aim: The scope of this paper is to present a preliminary design study of a device capable of exploring the various existing theories on the biomedical application of magnetic fields. This will be achieved by standardizing clinical data collection with sensory integration, and adding new therapeutic options to develop an advanced palliative aquatics care, innovating in symptom and pain management. Methods: The research methodology was based on the Work Package Methodology for the development of projects, separating the activities into seven different Work Packages. The theoretical basis was carried out through an integrative literature review according to the specific objectives of each Work Package and provided a broad analysis, which, together with the multiplicity of proposals and the interdisciplinarity of the research team involved, generated consistent and understandable complex concepts in the biomedical application of magnetic fields for palliative care. Results: Aubento ambience was idealized with restricted electromagnetic exposure (avoiding data collection bias) and sensory integration (allowing relaxation associated with hydrotherapy, music therapy, and chromotherapy or like floating tank). This device has a multipurpose configuration enabling classic or exploratory options on the use of the biomedical application of magnetic fields at the researcher's discretion. Conclusions: Several patients in diverse therapeutic contexts may benefit from the use of magnetic fields or fluids, thus validating the stimuli to clinical research in this area. A device in controlled and multipurpose environments may contribute to standardizing research and exploring new theories. Future research may demonstrate the possible benefits of the aquatics care multi-device AuBento to improve the well-being and symptom control in palliative care patients and their families.

Keywords: advanced palliative aquatics care, magnetic field therapy, medical device, research design

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Authors: P. Senthilraja, C. Rukumani Khandhan, M. Palaniappan, S. L. Rama, P. Sai Sushimitha, R. Madhan, J. Vinumathi, N. Vijayarangan

Abstract:

Nowadays, the logistics achieve a vast improvement in efficient delivery of goods. The technology improvement also helps to improve its development, but still the owners of transport vehicles face problems, i.e., fuel theft in vehicles by the drivers or by an unknown person. There is no proper solution to overcome the problems. This scheme is to determine the amount of fuel that has been stolen and also to determine the position of the vehicle at a particular time using the technologies like GPS, GSM, ultrasonic fuel level sensor and numeric lock system. The ultrasonic sensor uses the ultrasonic waves to calculate the height of the tank up to which the fuel is available. Based on height it is possible to calculate the amount of fuel. The Global Positioning System (GPS) is a satellite-based navigation system. The scientific community uses GPS for its precision timing capability and position information. The GSM provides the periodic information about the fuel level. A numeric lock system has been provided for fuel tank opening lever. A password is provided to access the fuel tank lever and this is authenticated only by the driver and the owner. Once the fuel tank is opened an alert is sent to owner through a SMS including the timing details. Third party monitoring software is a user interface that updates the information automatically into the database which helps to retrieve the data as and when required. Third party monitoring software provides vehicle’s information to the owner and also shows the status of the vehicle. The techniques that are to be proposed will provide an efficient output. This project helps to overcome the theft and hence to put forth fuel economy.

Keywords: fuel theft, third party monitoring software, bioinformatics, biomedicine

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Authors: Krishna Pal Singh, Shailendra Kumar Gupta, Olaf Wolkenhauer

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Background: Our study aimed to identify common genes and potential targets across the four diseases, which include rheumatoid arthritis, melanoma metastasis, ulcerative colitis, and Crohn’s disease. We used a network and systems biology approach to identify the hub gene, which can act as a potential target for all four disease conditions. The regulatory network was extracted from the PPI using the MCODE module present in Cytoscape. Our objective was to investigate the significance of hub genes in these diseases using gene ontology and KEGG pathway enrichment analysis. Methods: Our methodology involved collecting disease gene-related information from DisGeNET databases and performing protein-protein interaction (PPI) network and core genes screening. We then conducted gene ontology and KEGG pathway enrichment analysis. Results: We found that IL6 plays a critical role in all disease conditions and in different pathways that can be associated with the development of all four diseases. Conclusions: The theoretical importance of our research is that we employed various systems and structural biology techniques to identify a crucial protein that could serve as a promising target for treating multiple diseases. Our data collection and analysis procedures involved rigorous scrutiny, ensuring high-quality results. Our conclusion is that IL6 plays a significant role in all four diseases, and it can act as a potential target for treating them. Our findings may have important implications for the development of novel therapeutic interventions for these diseases.

Keywords: melanoma metastasis, rheumatoid arthritis, inflammatory bowel diseases, integrated bioinformatics analysis

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Authors: Shu-Pin Huang, Pai-Chi Teng, Hao-Han Chang, Chia-Hsin Liu, Yung-Lun Lin, Shu-Chi Wang, Hsin-Chih Yeh, Chih-Pin Chuu, Jiun-Hung Geng, Li-Hsin Chang, Wei-Chung Cheng, Chia-Yang Li

Abstract:

The emergence of immune checkpoint inhibitors (ICIs) targeting proteins like PD-1 and PD-L1 has changed the treatment paradigm of bladder cancer. However, not all patients benefit from ICIs, with some experiencing early death. There's a significant need for biomarkers associated with the PD-1 pathway in bladder cancer. Current biomarkers focus on tumor PD-L1 expression, but a more comprehensive understanding of PD-1-related biology is needed. Our study has developed a seven-gene risk score panel, employing a comprehensive bioinformatics strategy, which could serve as a potential prognostic and predictive biomarker for bladder cancer. This panel incorporates the FYN, GRAP2, TRIB3, MAP3K8, AKT3, CD274, and CD80 genes. Additionally, we examined the relationship between this panel and immune cell function, utilizing validated tools such as ESTIMATE, TIDE, and CIBERSORT. Our seven-genes panel has been found to be significantly associated with bladder cancer survival in two independent cohorts. The panel was also significantly correlated with tumor infiltration lymphocytes, immune scores, and tumor purity. These factors have been previously reported to have clinical implications on ICIs. The findings suggest the potential of a PD-1 pathway-based transcriptomic panel as a prognostic and predictive biomarker in bladder cancer, which could help optimize treatment strategies and improve patient outcomes.

Keywords: bladder cancer, programmed cell death protein 1, prognostic biomarker, immune checkpoint inhibitors, predictive biomarker

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Authors: Chi-Ching Lee, Po-Jung Huang, Kuo-Yang Huang, Petrus Tang

Abstract:

Background: Recent advances in high-throughput research technologies such as new-generation sequencing and multi-dimensional liquid chromatography makes it possible to dissect the complete transcriptome and proteome in a single run for the first time. However, it is almost impossible for many laboratories to handle and analysis these “BIG” data without the support from a bioinformatics team. We aimed to provide a web-based analysis platform for users with only limited knowledge on bio-computing to study the functional genomics and proteomics. Method: We use NCI-60 as an example dataset to demonstrate the power of the web-based analysis platform and data delivering system: C-eXpress takes a simple text file that contain the standard NCBI gene or protein ID and expression levels (rpkm or fold) as input file to generate a distribution map of gene/protein expression levels in a heatmap diagram organized by color gradients. The diagram is hyper-linked to a dynamic html table that allows the users to filter the datasets based on various gene features. A dynamic summary chart is generated automatically after each filtering process. Results: We implemented an integrated database that contain pre-defined annotations such as gene/protein properties (ID, name, length, MW, pI); pathways based on KEGG and GO biological process; subcellular localization based on GO cellular component; functional classification based on GO molecular function, kinase, peptidase and transporter. Multiple ways of sorting of column and rows is also provided for comparative analysis and visualization of multiple samples.

Keywords: cancer, visualization, database, functional annotation

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Authors: Mohammed Ahmed Ahmed Odah

Abstract:

DNA barcoding is a crucial method for assessing and monitoring species diversity amidst escalating threats to global biodiversity. The author explores DNA barcoding's potential as a robust and reliable tool for biodiversity assessment. It begins with a comprehensive review of existing literature, delving into the theoretical foundations, methodologies and applications of DNA barcoding. The suitability of various DNA regions, like the COI gene, as universal barcodes is extensively investigated. Additionally, the advantages and limitations of different DNA sequencing technologies and bioinformatics tools are evaluated within the context of DNA barcoding. To evaluate the efficacy of DNA barcoding, diverse ecosystems, including terrestrial, freshwater and marine habitats, are sampled. Extracted DNA from collected specimens undergoes amplification and sequencing of the target barcode region. Comparison of the obtained DNA sequences with reference databases allows for the identification and classification of the sampled organisms. Findings demonstrate that DNA barcoding accurately identifies species, even in cases where morphological identification proves challenging. Moreover, it sheds light on cryptic and endangered species, aiding conservation efforts. The author also investigates patterns of genetic diversity and evolutionary relationships among different taxa through the analysis of genetic data. This research contributes to the growing knowledge of DNA barcoding and its applicability for biodiversity assessment. The advantages of this approach, such as speed, accuracy and cost-effectiveness, are highlighted, along with areas for improvement. By unlocking the genetic code, DNA barcoding enhances our understanding of biodiversity, supports conservation initiatives and informs evidence-based decision-making for the sustainable management of ecosystems.

Keywords: DNA barcoding, biodiversity assessment, genetic code, species identification, taxonomic resolution, next-generation sequencing

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Authors: Mouna Baassi, Mohamed Moussaoui, Hatim Soufi, Sanchaita RajkhowaI, Ashwani Sharma, Subrata Sinha, Said Belaaouad

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Human Immunodeficiency Virus type 1 protease (HIV-1 PR) is one of the most challenging targets of antiretroviral therapy used in the treatment of AIDS-infected people. The performance of protease inhibitors (PIs) is limited by the development of protease mutations that can promote resistance to the treatment. The current study was carried out using statistics and bioinformatics tools. A series of thirty-three compounds with known enzymatic inhibitory activities against HIV-1 protease was used in this paper to build a mathematical model relating the structure to the biological activity. These compounds were designed by software; their descriptors were computed using various tools, such as Gaussian, Chem3D, ChemSketch and MarvinSketch. Computational methods generated the best model based on its statistical parameters. The model’s applicability domain (AD) was elaborated. Furthermore, one compound has been proposed as efficient against HIV-1 protease with comparable biological activity to the existing ones; this drug candidate was evaluated using ADMET properties and Lipinski’s rule. Molecular Docking performed on Wild Type and Mutant Type HIV-1 proteases allowed the investigation of the interaction types displayed between the proteases and the ligands, Darunavir (DRV) and the new drug (ND). Molecular dynamics simulation was also used in order to investigate the complexes’ stability, allowing a comparative study of the performance of both ligands (DRV & ND). Our study suggested that the new molecule showed comparable results to that of Darunavir and may be used for further experimental studies. Our study may also be used as a pipeline to search and design new potential inhibitors of HIV-1 proteases.

Keywords: QSAR, ADMET properties, molecular docking, molecular dynamics simulation.

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Authors: Ronald Villamar-Torres, Michael Staudt, Christopher Viot

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Cotton Gossypium hirsutum L. is one of the most important industrial crops, producing the world leading natural textile fiber, but is very prone to arthropod attacks that reduce crop yield and quality. Cotton cultivation, therefore, makes an outstanding use of chemical pesticides. In reaction to herbivorous arthropods, cotton plants nevertheless show natural defense reactions, in particular through volatile organic compounds (VOCs) emissions. These natural defense mechanisms are nowadays underutilized but have a very high potential for cotton cultivation, and elucidating their genetic bases will help to improve their use. Simulating herbivory attacks by mechanical wounding of cotton plants in greenhouse, we studied by qPCR the changes in gene expression for genes of the terpenoids biosynthesis pathway. Differentially expressed genes corresponded to higher levels of the terpenoids biosynthesis pathway and not to enzymes synthesizing particular terpenoids. The genes were mapped on the G. hirsutum L. reference genome; their global relationships inside the general metabolic pathways and the biosynthesis of secondary metabolites were visualized with iPath2. The chromatographic profiles of VOCs emissions indicated first monoterpenes and sesquiterpenes emissions, dominantly four molecules known to be involved in plant reactions to arthropod attacks. As a result, the study permitted to identify potential key genes for the emission of volatile terpenoids by cotton plants in reaction to an arthropod attack, opening possibilities for molecular-assisted cotton breeding in benefit of smallholder cotton growers.

Keywords: biosynthesis pathways, cotton, mechanisms of plant defense, terpenoids, volatile organic compounds

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Authors: Matthew J. B. Wilson

Abstract:

Disaster Risk Reduction relies heavily on the effective cooperation of both humanitarian and development actors, particularly in the wake of a disaster, implementing lasting recovery measures that better protect communities from disasters to come. This can be seen to fit within a broader discussion around integrating humanitarian and development work stretching back to the 1980s. Over time, a number of key concepts have been put forward, including Linking Relief, Rehabilitation, and Development (LRRD), Early Recovery (ER), ‘Build Back Better’ (BBB), and the most recent ‘Humanitarian-Development-Peace Nexus’ or ‘Triple Nexus’ (HDPN) to define these goals and relationship. While this discussion has evolved greatly over time, from a continuum to a more integrative synergistic relationship, there remains a lack of consensus around how to describe it, and as such, the reality of effectively closing this gap has yet to be seen. The objective of this research was twofold. First, to map these four identified concepts (LRRD, ER, BBB & HDPN) used in the literature since 1995 to understand the overall trends in how this relationship is discussed. Second, map articles reference a combination of these concepts to understand their interrelationship. A scoping review was conducted for each concept identified. Results were gathered from Google Scholar by firstly inputting specific boolean search phrases for each concept as they related specifically to disasters each year since 1995 to identify the total number of articles discussing each concept over time. A second search was then done by pairing concepts together within a boolean search phrase and inputting the results into a matrix to understand how many articles contained references to more than one of the concepts. This latter search was limited to articles published after 2017 to account for the more recent emergence of HDPN. It was found that ER and particularly BBB are referred to much more widely than LRRD and HDPN. ER increased particularly in the mid-2000’s coinciding with the formation of the ER cluster, and BBB, whilst emerging gradually in the mid-2000s due to its usage in the wake of the Boxing Day Tsunami, increased significantly from about 2015 after its prominent inclusion in Sendai Framework. HDPN has only just started to increase in the last 4-5 years. In regards to the relationship between concepts, it was found the vast majority of all concepts identified were referred to in isolation from each other. The strongest relationship was between LRRD and HDPN (8% of articles referring to both), whilst ER-BBB and ER-HDPN both were about 3%, LRRD-ER 2%, and BBB-HDPN 1% and BBB-LRRD 1%. This research identified a fundamental issue around the lack of consensus and even awareness of different approaches referred to within academic literature relating to integrating humanitarian and development work. More research into synthesizing and learning from a range of approaches could work towards better closing this gap.

Keywords: build back better, disaster risk reduction, early recovery, linking relief rehabilitation and development, humanitarian development integration, humanitarian-development (peace) nexus, recovery, triple nexus

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

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

Keywords: totiviridae, killer virus, proteomics, transcriptomics

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Authors: Peng Hou

Abstract:

Natural products produced from marine bacteria serve as an immense reservoir for anti-infective drugs and therapeutic agents. Nowadays, heterologous expression of gene clusters of interests has been widely adopted as an effective strategy for natural product discovery. Briefly, the heterologous expression flowchart would be: biosynthetic gene cluster identification, pathway construction and expression, and product detection. However, gene cluster capture using traditional Transformation-associated recombination (TAR) protocol is low-efficient (0.5% positive colony rate). To make things worse, most of these putative new natural products are only predicted by bioinformatics analysis such as antiSMASH, and their corresponding natural products biosynthetic pathways are either not expressed or expressed at very low levels under laboratory conditions. Those setbacks have inspired us to focus on seeking new technologies to efficiently edit and refractor of biosynthetic gene clusters. Recently, two cutting-edge techniques have attracted our attention - the CRISPR-Cas9 and Gibson Assembly. By now, we have tried to pretreat Brevibacillus laterosporus strain genomic DNA with CRISPR-Cas9 nucleases that specifically generated breaks near the gene cluster of interest. This trial resulted in an increase in the efficiency of gene cluster capture (9%). Moreover, using Gibson Assembly by adding/deleting certain operon and tailoring enzymes regardless of end compatibility, the silent construct (~80kb) has been successfully refactored into an active one, yielded a series of analogs expected. With the appearances of the novel molecular tools, we are confident to believe that development of a high throughput mature pipeline for DNA assembly, transformation, product isolation and identification would no longer be a daydream for marine natural product discovery.

Keywords: biosynthesis, CRISPR-Cas9, DNA assembly, refactor, TAR cloning

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Authors: Umairah Natasya Binti Mohd Omeershffudin, Suresh Kumar

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Klebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. Particular concern is the global emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae. Characterization of antibiotic resistance determinants at the genomic level plays a critical role in understanding, and potentially controlling, the spread of multidrug-resistant (MDR) pathogens. In this study, drug-resistant Klebsiella pneumoniae strain 825795-1 was investigated with extensive computational approaches aimed at identifying novel drug targets among hypothetical proteins. We have analyzed 1099 hypothetical proteins available in genome. We have used in-silico genome subtraction methodology to design potential and pathogen-specific drug targets against Klebsiella pneumoniae. We employed bioinformatics tools to subtract the strain-specific paralogous and host-specific homologous sequences from the bacterial proteome. The sorted 645 proteins were further refined to identify the essential genes in the pathogenic bacterium using the database of essential genes (DEG). We found 135 unique essential proteins in the target proteome that could be utilized as novel targets to design newer drugs. Further, we identified 49 cytoplasmic protein as potential drug targets through sub-cellular localization prediction. Further, we investigated these proteins in the DrugBank databases, and 11 of the unique essential proteins showed druggability according to the FDA approved drug bank databases with diverse broad-spectrum property. The results of this study will facilitate discovery of new drugs against Klebsiella pneumoniae.

Keywords: pneumonia, drug target, hypothetical protein, subtractive genomics

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