scholarly journals Research on Plants for the Understanding of Diseases of Nuclear and Mitochondrial Origin

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Claudia P. Spampinato ◽  
Diego F. Gomez-Casati
Keyword(s):  
Current Knowledge ◽  
Model System ◽  
Human Diseases ◽  
Model Organisms ◽  
Human Cell Lines ◽  
Molecular Defects ◽  
Human Genes ◽  
Clinical Disorders ◽  
Mitochondrial Origin ◽  
Experimental Findings

Different model organisms, such asEscherichia coli,Saccharomyces cerevisiae,Caenorhabditis elegans,Drosophila melanogaster, mouse, cultured human cell lines, among others, were used to study the mechanisms of several human diseases. Since human genes and proteins have been structurally and functionally conserved in plant organisms, the use of plants, especiallyArabidopsis thaliana, as a model system to relate molecular defects to clinical disorders has recently increased. Here, we briefly review our current knowledge of human diseases of nuclear and mitochondrial origin and summarize the experimental findings of plant homologs implicated in each process.

scholarly journals Studying Lipid-Related Pathophysiology Using the Yeast Model

2021 ◽  
Vol 12 ◽  
Author(s):  
Tyler Ralph-Epps ◽  
Chisom J. Onu ◽  
Linh Vo ◽  
Michael W. Schmidtke ◽  
Anh Le ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Disorder ◽  
Model System ◽  
Complete Loss ◽  
Barth Syndrome ◽  
Human Diseases ◽  
Model Organisms ◽  
Loss Of Function ◽  
Parkinson’S Diseases ◽  
Yeast Model

Saccharomyces cerevisiae, commonly known as baker’s yeast, is one of the most comprehensively studied model organisms in science. Yeast has been used to study a wide variety of human diseases, and the yeast model system has proved to be an especially amenable tool for the study of lipids and lipid-related pathophysiologies, a topic that has gained considerable attention in recent years. This review focuses on how yeast has contributed to our understanding of the mitochondrial phospholipid cardiolipin (CL) and its role in Barth syndrome (BTHS), a genetic disorder characterized by partial or complete loss of function of the CL remodeling enzyme tafazzin. Defective tafazzin causes perturbation of CL metabolism, resulting in many downstream cellular consequences and clinical pathologies that are discussed herein. The influence of yeast research in the lipid-related pathophysiologies of Alzheimer’s and Parkinson’s diseases is also summarized.

The glycomes of Caenorhabditis elegans and other model organisms

2002 ◽  
Vol 69 ◽  
pp. 117-134 ◽  
Author(s):  
Stuart M. Haslam ◽  
David Gems ◽  
Howard R. Morris ◽  
Anne Dell
Keyword(s):  
Caenorhabditis Elegans ◽  
Current Knowledge ◽  
Structural Data ◽  
Model Organisms ◽  
Entire Genome ◽  
C Elegans ◽  
The Face ◽  
Area Of Concern ◽  
Nematode Worm

There is no doubt that the immense amount of information that is being generated by the initial sequencing and secondary interrogation of various genomes will change the face of glycobiological research. However, a major area of concern is that detailed structural knowledge of the ultimate products of genes that are identified as being involved in glycoconjugate biosynthesis is still limited. This is illustrated clearly by the nematode worm Caenorhabditis elegans, which was the first multicellular organism to have its entire genome sequenced. To date, only limited structural data on the glycosylated molecules of this organism have been reported. Our laboratory is addressing this problem by performing detailed MS structural characterization of the N-linked glycans of C. elegans; high-mannose structures dominate, with only minor amounts of complex-type structures. Novel, highly fucosylated truncated structures are also present which are difucosylated on the proximal N-acetylglucosamine of the chitobiose core as well as containing unusual Fucα1–2Gal1–2Man as peripheral structures. The implications of these results in terms of the identification of ligands for genomically predicted lectins and potential glycosyltransferases are discussed in this chapter. Current knowledge on the glycomes of other model organisms such as Dictyostelium discoideum, Saccharomyces cerevisiae and Drosophila melanogaster is also discussed briefly.

scholarly journals Remedying the Mitochondria to Cure Human Diseases by Natural Products

2020 ◽  
Vol 2020 ◽  
pp. 1-18
Author(s):  
Jian-Kang Mu ◽  
Yan-Qin Li ◽  
Ting-Ting Shi ◽  
Li-Ping Yu ◽  
Ya-Qin Yang ◽  
...  
Keyword(s):  
Natural Products ◽  
Mitochondrial Dysfunction ◽  
Mechanism Of Action ◽  
Current Knowledge ◽  
Human Diseases ◽  
Mitochondrial Regulation ◽  
The Relationship

Mitochondria are the ‘engine’ of cells. Mitochondrial dysfunction is an important mechanism in many human diseases. Many natural products could remedy the mitochondria to alleviate mitochondria-involved diseases. In this review, we summarized the current knowledge of the relationship between the mitochondria and human diseases and the regulation of natural products to the mitochondria. We proposed that the development of mitochondrial regulators/nutrients from natural products to remedy mitochondrial dysfunction represents an attractive strategy for a mitochondria-involved disorder therapy. Moreover, investigating the mitochondrial regulation of natural products can potentiate the in-depth comprehension of the mechanism of action of natural products.

scholarly journals Conserved long-range base pairings are associated with pre-mRNA processing of human genes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Svetlana Kalmykova ◽  
Marina Kalinina ◽  
Stepan Denisov ◽  
Alexey Mironov ◽  
Dmitry Skvortsov ◽  
...  
Keyword(s):  
Long Range ◽  
Rna Folding ◽  
Current Knowledge ◽  
Rna Structures ◽  
Base Pairs ◽  
Protein Coding ◽  
Proximity Ligation ◽  
Transcriptional Suppression ◽  
Human Genes ◽  
Cleavage And Polyadenylation

AbstractThe ability of nucleic acids to form double-stranded structures is essential for all living systems on Earth. Current knowledge on functional RNA structures is focused on locally-occurring base pairs. However, crosslinking and proximity ligation experiments demonstrated that long-range RNA structures are highly abundant. Here, we present the most complete to-date catalog of conserved complementary regions (PCCRs) in human protein-coding genes. PCCRs tend to occur within introns, suppress intervening exons, and obstruct cryptic and inactive splice sites. Double-stranded structure of PCCRs is supported by decreased icSHAPE nucleotide accessibility, high abundance of RNA editing sites, and frequent occurrence of forked eCLIP peaks. Introns with PCCRs show a distinct splicing pattern in response to RNAPII slowdown suggesting that splicing is widely affected by co-transcriptional RNA folding. The enrichment of 3’-ends within PCCRs raises the intriguing hypothesis that coupling between RNA folding and splicing could mediate co-transcriptional suppression of premature pre-mRNA cleavage and polyadenylation.

scholarly journals Suprabasin—A Review

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 108
Author(s):  
Miroslav Pribyl ◽  
Zdenek Hodny ◽  
Iva Kubikova
Keyword(s):  
Glioblastoma Multiforme ◽  
Poor Prognosis ◽  
Current Knowledge ◽  
Original Description ◽  
Oesophageal Carcinoma ◽  
Secreted Proteins ◽  
Cornified Envelope ◽  
Physiological Conditions ◽  
Signalling Molecules ◽  
Human Genes

Among the ~22,000 human genes, very few remain that have unknown functions. One such example is suprabasin (SBSN). Originally described as a component of the cornified envelope, the function of stratified epithelia-expressed SBSN is unknown. Both the lack of knowledge about the gene role under physiological conditions and the emerging link of SBSN to various human diseases, including cancer, attract research interest. The association of SBSN expression with poor prognosis of patients suffering from oesophageal carcinoma, glioblastoma multiforme, and myelodysplastic syndromes suggests that SBSN may play a role in human tumourigenesis. Three SBSN isoforms code for the secreted proteins with putative function as signalling molecules, yet with poorly described effects. In this first review about SBSN, we summarised the current knowledge accumulated since its original description, and we discuss the potential mechanisms and roles of SBSN in both physiology and pathology.

scholarly journals Autophagy Modulation in Cancer: Current Knowledge on Action and Therapy

2018 ◽  
Vol 2018 ◽  
pp. 1-18 ◽  
Author(s):  
Mija Marinković ◽  
Matilda Šprung ◽  
Maja Buljubašić ◽  
Ivana Novak
Keyword(s):  
Therapeutic Strategy ◽  
Current Knowledge ◽  
Therapeutic Agents ◽  
Therapeutic Strategies ◽  
Human Diseases ◽  
The Core ◽  
Future Drug ◽  
Autophagic Activity ◽  
Tumor Types ◽  
Catabolic Process

In the last two decades, accumulating evidence pointed to the importance of autophagy in various human diseases. As an essential evolutionary catabolic process of cytoplasmatic component digestion, it is generally believed that modulating autophagic activity, through targeting specific regulatory actors in the core autophagy machinery, may impact disease processes. Both autophagy upregulation and downregulation have been found in cancers, suggesting its dual oncogenic and tumor suppressor properties during malignant transformation. Identification of the key autophagy targets is essential for the development of new therapeutic agents. Despite this great potential, no therapies are currently available that specifically focus on autophagy modulation. Although drugs like rapamycin, chloroquine, hydroxychloroquine, and others act as autophagy modulators, they were not originally developed for this purpose. Thus, autophagy may represent a new and promising pharmacologic target for future drug development and therapeutic applications in human diseases. Here, we summarize our current knowledge in regard to the interplay between autophagy and malignancy in the most significant tumor types: pancreatic, breast, hepatocellular, colorectal, and lung cancer, which have been studied in respect to autophagy manipulation as a promising therapeutic strategy. Finally, we present an overview of the most recent advances in therapeutic strategies involving autophagy modulators in cancer.

scholarly journals Calcium Signaling in Vertebrate Development and Its Role in Disease

2018 ◽  
Vol 19 (11) ◽  
pp. 3390 ◽  
Author(s):  
Sudip Paudel ◽  
Regan Sindelar ◽  
Margaret Saha
Keyword(s):  
Calcium Signaling ◽  
Critical Role ◽  
Molecular Techniques ◽  
Model Organisms ◽  
Vertebrate Development ◽  
Developmental Defects ◽  
Calcium Activity ◽  
Human Genes ◽  
Underlying Mechanisms

Accumulating evidence over the past three decades suggests that altered calcium signaling during development may be a major driving force for adult pathophysiological events. Well over a hundred human genes encode proteins that are specifically dedicated to calcium homeostasis and calcium signaling, and the majority of these are expressed during embryonic development. Recent advances in molecular techniques have identified impaired calcium signaling during development due to either mutations or dysregulation of these proteins. This impaired signaling has been implicated in various human diseases ranging from cardiac malformations to epilepsy. Although the molecular basis of these and other diseases have been well studied in adult systems, the potential developmental origins of such diseases are less well characterized. In this review, we will discuss the recent evidence that examines different patterns of calcium activity during early development, as well as potential medical conditions associated with its dysregulation. Studies performed using various model organisms, including zebrafish, Xenopus, and mouse, have underscored the critical role of calcium activity in infertility, abortive pregnancy, developmental defects, and a range of diseases which manifest later in life. Understanding the underlying mechanisms by which calcium regulates these diverse developmental processes remains a challenge; however, this knowledge will potentially enable calcium signaling to be used as a therapeutic target in regenerative and personalized medicine.

Automatic extraction, prioritization and analysis of gut microbial metabolites from biomedical literature

2019 ◽  
Author(s):  
Quangqiu Wang ◽  
Rong Xu
Keyword(s):  
Human Genetics ◽  
Microbial Metabolism ◽  
Integrated Approach ◽  
Biomedical Literature ◽  
Human Diseases ◽  
Data Driven ◽  
Microbial Metabolites ◽  
Microbial Metabolite ◽  
Relationship Extraction ◽  
Human Genes

Abstract Background: Many diseases are driven by gene-environment interactions. One important environmental factor is the metabolic output of human gut microbiota. A comprehensive catalog of human metabolites originated in microbes is critical for data-driven approaches to understand how microbial metabolism contributes to human health and diseases. Here we present a novel integrated approach to automatically extract and analyze microbial metabolites from 28 million published biomedical records. Results: First, we classified 28,851,232 MEDLINE records into microbial metabolism-related or not. Second, candidate microbial metabolites were extracted from the classified texts. Third, we developed signal prioritization algorithms to further differentiate microbial metabolites from metabolites originated from other resources. Finally, we systematically analyzed the interactions between extracted microbial metabolites and human genes. A total of 11,846 metabolites were extracted from 28 million MEDLINE articles. The combined text classification and signal prioritization significantly enriched true positives among top: manual curation of top 100 metabolites showed a true precision of 0.55, representing a significant 38.3-fold enrichment as compared to the precision of 0.014 for baseline extraction. More importantly, 29% extracted microbial metabolites have not been captured by existing databases. Our data-driven analysis of the interactions between the extracted microbial metabolite and human genetics provides mechanistic insights into how microbiota may contribute to human diseases. Conclusions: This study represents the first effort towards building a comprehensive knowledge base of microbial metabolites, which can set the foundation for future tasks of microbial metabolite relationship extraction from literature and facilitate data-driven studies of how microbial metabolism contributes to human diseases.

scholarly journals Local Secretory Trafficking Pathways in Neurons and the Role of Dendritic Golgi Outposts in Different Cell Models

2020 ◽  
Vol 13 ◽  
Author(s):  
Jingqi Wang ◽  
Lou Fourriere ◽  
Paul A. Gleeson
Keyword(s):  
Cell Body ◽  
Membrane Trafficking ◽  
Current Knowledge ◽  
Neurological Diseases ◽  
Model Organisms ◽  
Neuronal Structure ◽  
Anterograde Transport ◽  
Transport Pathways ◽  
Human Neurons

A fundamental characteristic of neurons is the relationship between the architecture of the polarized neuron and synaptic transmission between neurons. Intracellular membrane trafficking is paramount to establish and maintain neuronal structure; perturbation in trafficking results in defects in neurodevelopment and neurological disorders. Given the physical distance from the cell body to the distal sites of the axon and dendrites, transport of newly synthesized membrane proteins from the central cell body to their functional destination at remote, distal sites represents a conundrum. With the identification of secretory organelles in dendrites, including endoplasmic reticulum (ER) and Golgi outposts (GOs), recent studies have proposed local protein synthesis and trafficking distinct from the conventional anterograde transport pathways of the cell body. A variety of different model organisms, including Drosophila, zebrafish, and rodents, have been used to probe the organization and function of the local neuronal secretory network. Here, we review the evidence for local secretory trafficking pathways in dendrites in a variety of cell-based neuronal systems and discuss both the similarities and differences in the organization and role of the local secretory organelles, especially the GOs. In addition, we identify the gaps in the current knowledge and the potential advances using human induced pluripotent stem cells (iPSCs) in defining local membrane protein trafficking in human neurons and in understanding the molecular basis of neurological diseases.

Lessons from Worm Dendritic Patterning

2019 ◽  
Vol 42 (1) ◽  
pp. 365-383 ◽  
Author(s):  
Sharon Inberg ◽  
Anna Meledin ◽  
Veronika Kravtsov ◽  
Yael Iosilevskii ◽  
Meital Oren-Suissa ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Animal Model ◽  
Light And Electron Microscopy ◽  
Dendritic Tree ◽  
Model System ◽  
Model Organisms ◽  
Structural Units ◽  
The Past ◽  
Structural And Functional Properties ◽  
Made In

The structural and functional properties of neurons have intrigued scientists since the pioneering work of Santiago Ramón y Cajal. Since then, emerging cutting-edge technologies, including light and electron microscopy, electrophysiology, biochemistry, optogenetics, and molecular biology, have dramatically increased our understanding of dendritic properties. This advancement was also facilitated by the establishment of different animal model organisms, from flies to mammals. Here we describe the emerging model system of a Caenorhabditis elegans polymodal neuron named PVD, whose dendritic tree follows a stereotypical structure characterized by repeating candelabra-like structural units. In the past decade, progress has been made in understanding PVD's functions, morphogenesis, regeneration, and aging, yet many questions still remain.

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