scholarly journals Application of Metabolomics in the Study of Starvation-Induced Autophagy in Saccharomyces cerevisiae: A Scoping Review

2021 ◽  
Vol 7 (11) ◽  
pp. 987
Author(s):  
Muhammad Luqman Nasaruddin ◽  
Khaizurin Tajul Arifin
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Scoping Review ◽  
Energy Levels ◽  
Nutritional Stress ◽  
Rna Degradation ◽  
Pentose Phosphate ◽  
Glucose Starvation ◽  
Research Papers ◽  
Exclusion Criteria ◽  
Underlying Mechanisms

This scoping review is aimed at the application of the metabolomics platform to dissect key metabolites and their intermediates to observe the regulatory mechanisms of starvation-induced autophagy in Saccharomyces cerevisiae. Four research papers were shortlisted in this review following the inclusion and exclusion criteria. We observed a commonly shared pathway undertaken by S. cerevisiae under nutritional stress. Targeted and untargeted metabolomics was applied in either of these studies using varying platforms resulting in the annotation of several different observable metabolites. We saw a commonly shared pathway undertaken by S. cerevisiae under nutritional stress. Following nitrogen starvation, the concentration of cellular nucleosides was altered as a result of autophagic RNA degradation. Additionally, it is also found that autophagy replenishes amino acid pools to sustain macromolecule synthesis. Furthermore, in glucose starvation, nucleosides were broken down into carbonaceous metabolites that are being funneled into the non-oxidative pentose phosphate pathway. The ribose salvage allows for the survival of starved yeast. Moreover, acute glucose starvation showed autophagy to be involved in maintaining ATP/energy levels. We highlighted the practicality of metabolomics as a tool to better understand the underlying mechanisms involved to maintain homeostasis by recycling degradative products to ensure the survival of S. cerevisiae under starvation. The application of metabolomics has extended the scope of autophagy and provided newer intervention targets against cancer as well as neurodegenerative diseases in which autophagy is implicated.

Wearable Sensors and Their Metrics for Measuring Comprehensive Occupational Fatigue: A Scoping Review

2017 ◽  
Vol 61 (1) ◽  
pp. 1041-1045 ◽  
Author(s):  
Yibo Zhu ◽  
Rasik R Jankay ◽  
Laura C Pieratt ◽  
Ranjana K. Mehta
Keyword(s):  
Heart Rate ◽  
Scoping Review ◽  
Wearable Sensors ◽  
Health And Safety ◽  
Exclusion Criteria ◽  
Multidimensional Construct ◽  
Ovid Medline ◽  
Rate Sensor ◽  
Sleep Length ◽  
Occupational Fatigue

Extensive research has been conducted to study the effects of physical and sleep related fatigue on occupational health and safety. However, fatigue is a complex multidimensional construct, that is task- and occupation-dependent, and our knowledge on how to measure this complex construct is limited. A scoping review was conducted to: 1) review sensors and their metrics currently employed in occupational fatigue studies, 2) identify overlap between sensors and associated metrics that can be leveraged to assess comprehensive fatigue, 3) investigating the effectiveness of the sensors/metrics, and 4) recommended potential sensor/metric combinations to evaluate comprehensive fatigue. 512 unique abstracts were identified through Ovid-MEDLINE, MEDLINE, Embase and Cinal databases and application of the inclusion/exclusion criteria resulted in 27 articles that were included for the review. Heart rate sensors and actigraphs were identified to be the most suitable devices to study comprehensive fatigue. Heart rate trend within the heart rate sensor, and sleep length and sleep efficiency within actigraphs were found to be the most popular and reliable metrics for measuring occupational fatigue.

scholarly journals Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Kanhaiya Kumar ◽  
Vishwesh Venkatraman ◽  
Per Bruheim
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Growth Rate ◽  
Amino Acid ◽  
Growth Rates ◽  
Pentose Phosphate Pathway ◽  
Pentose Phosphate ◽  
Relative Reduction ◽  
Central Metabolism ◽  
Cultivation Conditions ◽  
Biological Studies

Abstract Background Saccharomyces cerevisiae is a well-known popular model system for basic biological studies and serves as a host organism for the heterologous production of commercially interesting small molecules and proteins. The central metabolism is at the core to provide building blocks and energy to support growth and survival in normal situations as well as during exogenous stresses and forced heterologous protein production. Here, we present a comprehensive study of intracellular central metabolite pool profiling when growing S. cerevisiae on different carbon sources in batch cultivations and at different growth rates in nutrient-limited glucose chemostats. The latest versions of absolute quantitative mass spectrometry-based metabolite profiling methodology were applied to cover glycolytic and pentose phosphate pathway metabolites, tricarboxylic acid cycle (TCA), complete amino acid, and deoxy-/nucleoside phosphate pools. Results Glutamate, glutamine, alanine, and citrate were the four most abundant metabolites for most conditions tested. The amino acid is the dominant metabolite class even though a marked relative reduction compared to the other metabolite classes was observed for nitrogen and phosphate limited chemostats. Interestingly, glycolytic and pentose phosphate pathway (PPP) metabolites display the largest variation among the cultivation conditions while the nucleoside phosphate pools are more stable and vary within a closer concentration window. The overall trends for glucose and nitrogen-limited chemostats were increased metabolite pools with the increasing growth rate. Next, comparing the chosen chemostat reference growth rate (0.12 h−1, approximate one-fourth of maximal unlimited growth rate) illuminates an interesting pattern: almost all pools are lower in nitrogen and phosphate limited conditions compared to glucose limitation, except for the TCA metabolites citrate, isocitrate and α-ketoglutarate. Conclusions This study provides new knowledge-how the central metabolism is adapting to various cultivations conditions and growth rates which is essential for expanding our understanding of cellular metabolism and the development of improved phenotypes in metabolic engineering.

The Current State of Relationship Science: A Cross-Disciplines Review of Key Themes, Theories, Researchers and Journals

2021 ◽  
pp. 026540752110476
Author(s):  
Jennifer A Sharkey ◽  
Jacqueline S Feather ◽  
Sonja Goedeke
Keyword(s):  
Scoping Review ◽  
Scientific Knowledge ◽  
Interdisciplinary Research ◽  
Romantic Relationship ◽  
Descriptive Analysis ◽  
Theory Development ◽  
Current State ◽  
Relationship Processes ◽  
State Of Research ◽  
Underlying Mechanisms

This article provides a circumscribed descriptive analysis of the current state of research worldwide related to adult romantic relationship processes and their underlying mechanisms. A scoping review was used to gather data. This yielded 15,418 eligible articles from 1,687 different academic journals. From these, we outline key themes and theories arising in the last seven decades and note the most prolific journals and authors. The study of relational wellbeing has focused on overt behaviors such as communication and commitment, on underlying attitudes and motives such as empathy and contempt, and on substrates and circumstances such as neurobiological functioning and life stressors. The results reveal the strong interdisciplinary research underpinnings of the field of relationship science and show up key influences over its expansion. Results are intended to give an overview of key peer reviewed research that has contributed to the development of current scientific knowledge and theory development in this field.

Priorities for reorienting traditional institutions of higher education toward online teaching and learning: Thinking beyond the COVID-19 experience

2021 ◽  
pp. 204275302110388
Author(s):  
Talha A Sharadgah ◽  
Rami A Sa’di
Keyword(s):  
Higher Education ◽  
Distance Learning ◽  
Online Teaching ◽  
Teaching And Learning ◽  
Institutions Of Higher Education ◽  
Review Of The Literature ◽  
Research Papers ◽  
Exclusion Criteria ◽  
Online Teaching And Learning ◽  
Traditional Institutions

The purpose of this study is to suggest priorities for reorienting traditional institutions of higher education (IHE) toward online teaching and learning beyond the COVID-19 experience. This research applied the qualitative research method. Data collection sources included both a systematic literature review relating to how COVID-19 informed online distance learning across the globe and an analysis of circulars germane to the pandemic that were issued by the Ministry of Education (MOE) in Saudi Arabia and by Prince Sattam bin Abdulaziz University (PSAU). Guided by those two types of data, that is, review of the literature in general and the MOE and PSAU circulars in particular, and also illuminated by their own experiences of online teaching during the lockdown, the researchers were able to put forward those priorities. For the systematic review of the literature, five steps were performed: (1) identifying search terms and developing and applying a search strategy; (2) screening the obtained research papers, removing duplicates and papers outside the focal point, and establishing inclusion/exclusion criteria; (3) assessing the research papers against the inclusion/exclusion criteria; (4) data extraction; and (5) data synthesis. Although this article does not suggest traditional IHE should go entirely digital, it highlights the need for IHE to ensure access to online learning content, develop more partnerships with community, develop online self-study skills, get students to shift from passive to active learning, and a need to reconsider current e-assessment. Additionally, the study emphasizes the need to provide additional support for faculty members, how university buildings should be gradually reopened, controlling factors influencing online learning outcomes, and addressing the issue of dropouts in IHE. Finally, the study underlines the need to add further emphasis to the importance of integrating blended learning in the university curriculum and navigating toward developing global distance learning programs.

Mobility Assistants to Support Multi-Modal Routes in Smart Cities: A Scoping Review

2021 ◽  
Vol 3 (1) ◽  
pp. 26-40
Author(s):  
Nelson Pacheco Rocha ◽  
Gonçalo Santinha ◽  
Mário Rodrigues ◽  
Carlos Rodrigues ◽  
Alexandra Queirós ◽  
...  
Keyword(s):  
Scoping Review ◽  
Early Stage ◽  
Smart Cities ◽  
Research Trends ◽  
Exclusion Criteria ◽  
Major Barrier ◽  
Stage Of Development ◽  
Electronic Search ◽  
Inclusion Results

Objectives - This study aimed to identify: (i) the current research trends related to mobility assistants to support multi-modal routes in smart cities; (ii) the types of smart cities’ data being used; (iii) the methods applied to assess the proposed solutions; and iv) the major barriers for their dissemination. Methods - An electronic search was conducted in several databases, combining relevant keywords. Then titles and abstracts were screened against inclusion and exclusion criteria. Finally, the full texts of the eligible articles were retrieved and screened for inclusion. Results - A total of 19 articles were included. These articles either propose algorithms to optimize routes planning or presenting specific applications that make use of a broad range of smart cities’ data. Conclusion - The number of included articles is very reduced when compared with the total number of articles related to smart cities, which means that the mobility assistants to support multi-modal routes are still not significant within the smart cities’ research. Moreover, most of the included articles report applications in an early stage of development, which is a major barrier for the respective dissemination.

Real-time video telemedicine applications in the emergency department: a scoping review of literature

CJEM ◽  
2017 ◽  
Vol 20 (6) ◽  
pp. 920-928 ◽  
Author(s):  
Danielle K. Kelton ◽  
Adam Szulewski ◽  
Daniel Howes
Keyword(s):  
Emergency Department ◽  
Real Time ◽  
Scoping Review ◽  
Exclusion Criteria ◽  
Current State ◽  
Study Selection ◽  
Cochrane Database ◽  
The World ◽  
Data Source ◽  
Widespread Interest

AbstractObjectivesTo collect and synthesize the literature describing the use of real-time video-based technologies to provide support in the care of patients presenting to emergency departments.Data SourceSix electronic databases were searched, including Medline, CINAHL, Embase, the Cochrane Database, DARE, and PubMed for all publications since the earliest date available in each database to February 2016.Study SelectionSelected articles were full text articles addressing the use of telemedicine to support patient care in pre-hospital or emergency department settings. The search yielded 2976 articles for review with 11 studies eligible for inclusion after application of the inclusion and exclusion criteria. A scoping review of the selected articles was performed to better understand the different systems in place around the world and the current state of evidence supporting telemedicine use in the emergency department.ConclusionsTelemedicine support for emergency department physicians is an application with significant potential but is still lacking evidence supporting improved patient outcomes. Advances in technology, combined with more attractive price-points have resulted in widespread interest and implementation around the world. Applications of this technology that are currently being studied include support for minor treatment centres, patient transfer decision-making, management of acutely ill patients and scheduled teleconsultations.

scholarly journals Ccr4 is a novel shuttle factor required for ubiquitin-dependent proteolysis by the 26S proteasome

2020 ◽  
Author(s):  
Ganapathi Kandasamy ◽  
Ashis Kumar Pradhan ◽  
R Palanimurugan
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Degradation ◽  
Ubiquitin Proteasome System ◽  
Proteasomal Degradation ◽  
Rna Degradation ◽  
26S Proteasome ◽  
Cellular Proteins ◽  
Cellular Homeostasis ◽  
Substrate Degradation ◽  
Ubiquitin Proteasome

AbstractDegradation of short-lived and abnormal proteins are essential for normal cellular homeostasis. In eukaryotes, such unstable cellular proteins are selectively degraded by the ubiquitin proteasome system (UPS). Furthermore, abnormalities in protein degradation by the UPS have been linked to several human diseases. Ccr4 protein is a known component of the Ccr4-Not complex, which has established roles in transcription, mRNA de-adenylation and RNA degradation etc. Excitingly in this study, we show that Ccr4 protein has a novel function as a shuttle factor that promotes ubiquitin-dependent degradation of short-lived proteins by the 26S proteasome. Using a substrate of the well-studied ubiquitin fusion degradation (UFD) pathway, we found that its UPS-mediated degradation was severely impaired upon deletion of CCR4 in Saccharomyces cerevisiae. Additionally, we show that Ccr4 binds to cellular ubiquitin conjugates and the proteasome. In contrast to Ccr4, most other subunits of the Ccr4-Not complex proteins are dispensable for UFD substrate degradation. From our findings we conclude that Ccr4 functions in the UPS as a shuttle factor targeting ubiquitylated substrates for proteasomal degradation.

scholarly journals Transcriptomic Changes Induced by Deletion of Transcriptional Regulator GCR2 on Pentose Sugar Metabolism in Saccharomyces cerevisiae

2021 ◽  
Vol 9 ◽  
Author(s):  
Minhye Shin ◽  
Heeyoung Park ◽  
Sooah Kim ◽  
Eun Joong Oh ◽  
Deokyeol Jeong ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Xylose Fermentation ◽  
Sugar Metabolism ◽  
Pentose Phosphate ◽  
Biofuel Production ◽  
Rna Seq ◽  
Loss Of Function ◽  
Lignocellulosic Biofuel ◽  
Pentose Sugar ◽  
Transcriptomic Changes

Being a microbial host for lignocellulosic biofuel production, Saccharomyces cerevisiae needs to be engineered to express a heterologous xylose pathway; however, it has been challenging to optimize the engineered strain for efficient and rapid fermentation of xylose. Deletion of PHO13 (Δpho13) has been reported to be a crucial genetic perturbation in improving xylose fermentation. A confirmed mechanism of the Δpho13 effect on xylose fermentation is that the Δpho13 transcriptionally activates the genes in the non-oxidative pentose phosphate pathway (PPP). In the current study, we found a couple of engineered strains, of which phenotypes were not affected by Δpho13 (Δpho13-negative), among many others we examined. Genome resequencing of the Δpho13-negative strains revealed that a loss-of-function mutation in GCR2 was responsible for the phenotype. Gcr2 is a global transcriptional factor involved in glucose metabolism. The results of RNA-seq confirmed that the deletion of GCR2 (Δgcr2) led to the upregulation of PPP genes as well as downregulation of glycolytic genes, and changes were more significant under xylose conditions than those under glucose conditions. Although there was no synergistic effect between Δpho13 and Δgcr2 in improving xylose fermentation, these results suggested that GCR2 is a novel knockout target in improving lignocellulosic ethanol production.

scholarly journals Pentose Phosphate Pathway Regulates Tolerogenic Apoptotic Cell Clearance and Immune Tolerance

2022 ◽  
Vol 12 ◽  
Author(s):  
Dan He ◽  
Qiangdongzi Mao ◽  
Jialin Jia ◽  
Zhiyu Wang ◽  
Yu Liu ◽  
...  
Keyword(s):  
Inflammatory Response ◽  
Immune Tolerance ◽  
Lupus Erythematosus ◽  
Pentose Phosphate Pathway ◽  
Apoptotic Cell ◽  
Pentose Phosphate ◽  
Metabolic Reprogramming ◽  
Macrophage Phagocytosis ◽  
Cell Clearance ◽  
Underlying Mechanisms

The efficient removal of apoptotic cells (ACs), a process termed as efferocytosis, is essential for immune homeostasis. While recent work has established an important interplay between efferocytosis and cellular metabolic changing, underlying mechanisms remain poorly known. Here, we discovered that pentose phosphate pathway (PPP) regulates tolerogenic ACs clearance and immune tolerance. ACs decreased levels of PPP-related genes and metabolites in macrophages. AG1, the agonist of PPP, increased the activity of PPP but greatly reduced macrophage phagocytosis of ACs and enhanced the inflammatory response during efferocytosis. miR-323-5p regulated the expression of PPP-related genes and its levels increased during efferocytosis. miR-323-5p inhibitor greatly promoted levels of PPP-related genes, reduced the macrophage phagocytosis of ACs, and increased inflammatory response during efferocytosis, suggesting that miR-323-5p was essential in regulating PPP activity and ACs clearance in macrophages. Correspondingly, the PPP agonist AG1 exacerbated the lupus-like symptoms in the AC-induced systemic lupus erythematosus (SLE) model. Our study reveals that regulating PPP-dependent metabolic reprogramming is critical for tolerogenic ACs phagocytosis and immune tolerance.

Repurposing Ruxolitinib in Combating COVID-19: a mini review

2021 ◽  
Vol 02 ◽  
Author(s):  
Inshia Begum ◽  
Fathima Murthuza ◽  
Juwairiya Syed Iqbaluddin ◽  
Hafsah Fatima Arsal
Keyword(s):  
Clinical Trials ◽  
Severity Of Illness ◽  
Current Evidence ◽  
Public Healthcare ◽  
Inclusion Criteria ◽  
Research Papers ◽  
Exclusion Criteria ◽  
Mixed Treatment ◽  
Marked Selectivity ◽  
Insight Into

Background: The pandemic caused by Coronavirus Disease 2019 (COVID-19), also known as Severe Acute Respiratory Syndrome-Related Coronavirus (SARS-CoV-2), is believed to be one of the greatest threats to global health in the 21st century. Recent collective evidence has warranted Ruxolitinib as a potential agent in recovery. Ruxolitinib is a potent and selective inhibitor of Jack kinase (JAK) 1 and 2 with modest to marked selectivity against tyrosine kinase two and JAK3. Objective: The review aims to outline the current evidence regarding the repurposed treatment for COVID- 19 and give insight into the clinical trials. There has been considerable interest in introducing existing therapeutic agents against COVID-19 to reduce the severity of illness and ease the burden on public healthcare systems. Method: A literature search was conducted using keywords like ‘Ruxolitinib trial’ and ‘COVID-19 Ruxolitinib’ on PubMed, Google Scholar, Science Direct, and Cochrane databases to select research papers and articles on the topic published from January to October 2020. Inclusion criteria were restricted to articles on Ruxolitinib and COVID. In contrast, the exclusion criteria stipulated that any study done on COVID-19 involving a mixed treatment regimen with Ruxolitinib and other drug/s or any studies not pertinent to the purpose of the study would be omitted. Conclusion: Based on the successful outcomes of various researches conducted and clinical trials performed, the use of Ruxolitinib has shown significant improvement and faster clinical recovery among COVID-19 patients of varying severity of infection, advanced age, and multiple comorbidities. This review provides an overview of various such studies with their promising outcomes.

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