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Archives of Proteomics and Bioinformatics
ISSN: 2767-391X
Volume 1, Issue 1, p1-46
Articles published in this issue are Open Access and licensed under Creative Commons Attribution License (CC BY NC) where the readers can reuse, download, distribute the article in whole or part by mentioning proper credits to the authors.
A Bioinformatics Protocol for Rational Design of Peptide Vaccines and the COVID-19 Rampage
The currently ongoing coronavirus pandemic, the SARSCOV- 2, interchangeably referred to as the COVID-19 infection, has in a short span of time altered the ways and means of almost all of mankind. So strong has been its effect that all human activity ceased in one way or another for a considerable time, led to significant loss of life and economic drain of.
Arch Proteom and Bioinform, 2020, Volume 1, Issue 1, p1-8 | DOI: 10.33696/Proteomics.1.001Comment on “Systematic Identification and Analysis of Light-responsive Circular RNA and Coexpression Networks in Lettuce (Lactuca sativa)”
Light is one of the most important environmental factors that affect plant growth and development, and it is also the main energy source for plants and other living things. Plants use light to assimilate inorganic matter into organic matter through photosynthesis and store them in the form of chemical energy. As an environmental signal, light mediates the
Arch Proteom and Bioinform, 2020, Volume 1, Issue 1, p9-12 | DOI: 10.33696/Proteomics.1.002Identification of the Molecular Basis of Anti-fibrotic Effects of Soluble Guanylate Cyclase Activator Using the Human Lung Fibroblast
Idiopathic pulmonary fibrosis (IPF) is an irreversible fibrotic lung disease with unknown etiology [1-3]. Although two approved medications, pirfenidone and nintedanib, are able to slow down lung function decline in IPF patients, many other chronic pathologic conditions such as dyspnea and pulmonary hypertension (PH) and overall disease progression,
Arch Proteom and Bioinform, 2020, Volume 1, Issue 1, p13-30 | DOI: 10.33696/Proteomics.1.003RANDOMIZE: A Web Server for Data Randomization
Deoxyribonucleic acid (DNA) methylation is a critical type of epigenetic modification that typically occurs in a specialized region of DNA, CpG-rich regions in the mammalian genome and is associated with regulating gene expression. Previous studies have revealed a strong association of change in DNA methylation with various diseases such as cancer, obesity and posttraumatic stress disorder (PTSD).
Arch Proteom and Bioinform, 2020, Volume 1, Issue 1, p31-37 | DOI: 10.33696/Proteomics.1.004Ramifications of the Diverse mRNA Patterns in Acanthamoeba royreba
Acanthamoeba was first described by Castellani and represents single-cell eukaryotes existing as either cellular trophozoites (25–40 ?m) or under adverse conditions (desiccation, lack of food, and extreme pH or temperature fluctuations), as dormant cysts (13–20 ?m). The cysts are known to be resistant to antibiotics, the effects of chlorine, and very low temperatures, and have been shown to maintain viability for over 20 years.
Arch Proteom and Bioinform, 2020, Volume 1, Issue 1, p38-46 | DOI: 10.33696/Proteomics.1.005A Bioinformatics Protocol for Rational Design of Peptide Vaccines and the COVID-19 Rampage
The currently ongoing coronavirus pandemic, the SARSCOV- 2, interchangeably referred to as the COVID-19 infection, has in a short span of time altered the ways and means of almost all of mankind. So strong has been its effect that all human activity ceased in one way or another for a considerable time, led to significant loss of life and economic drain of.
DNA Nanotechnology Engineered Vesicle for Mimicking Biomolecular Signaling
Bio-inspired strategy is kind of interesting to fabricate devices and perform dynamic operations [1]. Various devices have been made, such as airplane, radar and submarine. In life science, as the fundamental entity, million years’ evolution enables cell becomes the most successful functionality.
Identification of the Molecular Basis of Anti-fibrotic Effects of Soluble Guanylate Cyclase Activator Using the Human Lung Fibroblast
Idiopathic pulmonary fibrosis (IPF) is an irreversible fibrotic lung disease with unknown etiology [1-3]. Although two approved medications, pirfenidone and nintedanib, are able to slow down lung function decline in IPF patients, many other chronic pathologic conditions such as dyspnea and pulmonary hypertension (PH) and overall disease progression,
Commentary on “Integrative Transcriptomics, Proteomics, and Metabolomics Data Analysis Exploring the Injury Mechanism of Ricin on Human Lung Epithelial Cells”
Ricin toxin (RT) is classified as a potential bio-threat agent in assassinations and terrorism due to its extreme toxicity. Due to aerosol RT exposure is the most lethal route, it is urgent to study its injury mechanism.
The Link of Nutrient Fluxes to Hepatic Insulin Resistance at Gene Expression
Insulin resistance has been studied extensively at systemic, organ, tissue and cellular and molecular levels. Overnutrition plays an essential role in the development of chronic metabolic diseases such as obesity and type 2 diabetes. For subjects without genetic defects, the development of insulin resistance and type 2 diabetes is a graduate process. How the transition from an insulinsensitive state to an insulin-resistant state occurs, and what the roles of nutrients are in the process have not been fully understood. Here, we try to summarize the current understanding of insulin-regulate gene expression in the liver, and describe a phenomenon of hepatic insulin resistance at gene expression (HIRAGE), which may be linked to overnutrition.
Dexamethasone: The First Drug to be Shown to Decrease Mortality in Critically Ill Patients with COVID-19
The precise role of corticosteroids for treatment of coronavirus disease 2019 (COVID-19) is unclear due to lack of randomized trials.
How to Prevent Rehospitalization in Patients with COVID-19
Since December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused by 2019 Novel Coronavirus (2019-nCoV) has resulted in 89,000 cases of Corona Virus Disease 2019 (COVID-19), formerly known as Novel Coronavirus Pneumonia (NCP) in China, including 2,450 deaths.
Evaluation and Management of chronic Hypertension in Pregnancy
Chronic hypertension is present in 1-2% of pregnant women. Women with chronic hypertension are at an increased risk of maternal and perinatal complications when compared with normotensive women.
Preparing for a More Public Health-Aware Practice of Medicine in Response to COVID-19
After one year in a pandemic, we mourn the loss of over half a million lives in the United States, and over four million worldwide, and remain concerned over the challenges facing the families of 35 million people in the United States, and 200 million worldwide, who have suffered from cases of COVID-19.
The Use of Hydroxychloroquine and Interferons for the Prophylaxis of COVID-19
At the beginning of Covid-19 pandemic, we proposed to use hydroxychloroquine (HCQ) and intranasal interferon (IFN) a-2b spray to prevent SARS-CoV-2.
PRMT1-catalyzed SMAD7 Arginine Methylation Bridges EMT and Stemness
Epithelial-mesenchymal transition (EMT), a lineage transition from epithelium to mesenchyme, is induced by a convergence of signaling pathways and often driven by TGFß/SMAD signaling. Except for its critical roles on cell shape and motility during cancer invasion and metastasis, TGFß/SMAD activation-induced EMT has also been reported to be involved in cancer stem cell (CSC) generation.
Methylation Status of Tumor Suppressor Genes in Circulating DNA of PDAC Patients: Facts and Hopes
Pancreatic cancer is one of the most lethal solid tumor malignancies and it is projected to become a leading cause of cancer related deaths in coming years. It is often diagnosed at an advanced stage owing to the lack of specific symptoms and rapid invasion.
Commentary on: Echocardiography in Pulmonary Arterial Hypertension: Is It Time to Reconsider Its Prognostic Utility?
Pulmonary Arterial Hypertension (PAH) represents a rare but devastating disease due to small pulmonary arterial vessels remodelling and increased pulmonary vascular resistance leading to right ventricular dysfunction, right heart failure and death.
Hyperglycemia and diabetes in hospitalized patients with COVID-19
The prevalence of diabetes in COVID-19 patients ranges from 5.3% to 58% representing the second comorbidity after hypertension. However, when adjusted for age, diabetes prevalence among COVID-19 patients is similar to its prevalence in the general population.
Succinate Accumulation Links Mitochondrial MnSOD Depletion to Aberrant Nuclear DNA Methylation and Altered Cell Fate
Epigenetic processes provide a mechanism for integrating metabolic inputs and translating them into various phenotypic outputs [1,2]. Indeed, epigenetic modifiers often require or are inhibited by key citric acid cycle (CAC) metabolites (e.g. succinate,
Management of Diagnostic and Treatment Centers in the Second Wave of COVID-19
COVID-19 has challenged global health and affected many countries. The disease had infected more than 16 million people and killed over 650,000 ones by the end of July 2020. According to Sahu et al., COVID-19 epidemic is the third most common coronavirus in the 21st century, resulting in numerous deaths all over the world. It has caused severe psychological stress and increased hospital visits along with increased tiredness and burnout of medical staff. The disease has also raised many problems for the management of hospitals and diagnostic-treatment centers, so that many of them have no capacity to receive patients.
News About the Extracellular Vesicles from Mesenchymal Stem Cells: Functions, Therapy and Protection from COVID-19
The present Commentary is a critical follow-up of a previous review about “Extracellular vesicles, news about their role in immune cells: physiology, pathology and diseases”, appeared in Clinical and Experimental Immunology last June 2019 [1].
Possible Therapeutic Use of Natural Compounds Against COVID-19
The outbreak of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has led to coronavirus disease-19 (COVID-19); a pandemic disease that has resulted in devastating social, economic, morbidity and mortality burdens. SARS-CoV-2 infects cells following receptor-mediated endocytosis and priming by cellular proteases.
Ectodomain Shedding May Play a Pivotal Role in Disease Severity in COVID-19
Ectodomain shedding mediated by a disintegrin and metalloprotease 10/17 (ADAM10/17) modulates the function of immune effector cells and may be involved in the novel coronavirus disease COVID-19. Toll-like receptor 7/8 (TLR7/8) recognizes single-strand RNA from viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, the virus that causes COVID-19) during the innate immune response
Adapting the Escape Room to Engage Learners Two Ways During COVID-19
When creating the project, “An Escape Room Simulation Focused on Renal-Impairment for Prelicensure Nursing Students” [1] the author’s goal was to increase positive health outcomes for patients with acute kidney injury (AKI). AKI is complicated, but nurses who can help identify those at risk for the disorder and help initiate early treatment can improve patients’ results.
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