Changes In Molecular Functions Research Articles

Analyzing Biomedical Datasets with Symbolic Tree Adaptive Resonance Theory

Biomedical datasets distill many mechanisms of human diseases, linking diseases to genes and phenotypes (signs and symptoms of disease), genetic mutations to altered protein structures, and altered proteins to changes in molecular functions and biological processes. It is desirable to gain new insights from these data, especially with regard to the uncovering of hierarchical structures relating disease variants. However, analysis to this end has proven difficult due to the complexity of the connections between multi-categorical symbolic data. This article proposes symbolic tree adaptive resonance theory (START), with additional supervised, dual-vigilance (DV-START), and distributed dual-vigilance (DDV-START) formulations, for the clustering of multi-categorical symbolic data from biomedical datasets by demonstrating its utility in clustering variants of Charcot–Marie–Tooth disease using genomic, phenotypic, and proteomic data.

MicroRNA expression profiles of stress susceptibility and resilience in the prelimbic and infralimbic cortex of rats after single prolonged stress.

The experience of traumatic stress can engender lasting memories associated with the trauma, often resulting in post-traumatic stress disorder (PTSD). However, only a minority of individuals develop PTSD symptoms upon exposure. The neurobiological mechanisms underlying the pathology of PTSD are poorly understood. Utilizing a rat model of PTSD, the Single Prolonged Stress (SPS) paradigm, we were able to differentiate between resilient and susceptible individuals. Fourteen days after the SPS exposure, we conducted the behavioral analyses using Elevated Plus Maze (EPM) and Open Field (OF) tests to identify male rats as trauma resilient or susceptible. We focused on the microRNA (miRNA) profiles of the infralimbic (IL) and prelimbic (PL) cortical regions, known to be crucial in regulating the stress response. Our investigation of stressed rats exposed to the SPS procedure yielded divergent response, and differential expression microRNAs (DEmiRs) analysis indicated significant differences in the IL and PL transcriptional response. In the IL cortex, the GO analysis revealed enriched GO terms in the resilient versus control comparison, specifically related to mitogen-activated protein kinase and MAP kinase signaling pathways for their molecular functions as well as cytosol and nucleoplasm for the biological process. In the susceptible versus resilient comparison, the changes in molecular functions were only manifested in the functions of regulation of transcription involved in the G1/S transition of the mitotic cell cycle and skeletal muscle satellite cell activation. However, no enriched GO terms were found in the susceptible versus control comparison. In the PL cortex, results indicated that the DEmiRs were enriched exclusively in the cellular component level of the endoplasmic reticulum lumen in the comparison between resilient and control rats. Overall, our study utilized an animal model of PTSD to investigate the potential correlation between stress-induced behavioral dysfunction and variations in miRNA expression. The aforementioned discoveries have the potential to pave the way for novel therapeutic approaches for PTSD, which could involve the targeted regulation of transcriptome expression.

Analysis of the Differentially Expressed Proteins and Metabolic Pathways of Honeybush (Cyclopia subternata) in Response to Water Deficit Stress.

Honeybush (Cyclopia spp.) is a rich source of antioxidant properties and phenolic compounds. Water availability plays a crucial role in plant metabolic processes, and it contributes to overall quality. Thus, this study aimed to investigate changes in molecular functions, cellular components, and biological processes of Cyclopia subternata exposed to different water stress conditions, which include well-watered (as Control, T1), semi-water stressed (T2), and water-deprived (T3) potted plants. Samples were also collected from a well-watered commercial farm first cultivated in 2013 (T13) and then cultivated in 2017 (T17) and 2019 (T19). Differentially expressed proteins extracted from C. subternata leaves were identified using LC-MS/MS spectrometry. A total of 11 differentially expressed proteins (DEPs) were identified using Fisher's exact test (p < 0.00100). Only α-glucan phosphorylase was found to be statistically common between T17 and T19 (p < 0.00100). Notably, α-glucan phosphorylase was upregulated in the older vegetation (T17) and downregulated in T19 by 1.41-fold. This result suggests that α-glucan phosphorylase was needed in T17 to support the metabolic pathway. In T19, five DEPs were upregulated, while the other six were downregulated. Based on gene ontology, the DEPs in the stressed plant were associated with cellular and metabolic processes, response to stimulus, binding, catalytic activity, and cellular anatomical entity. Differentially expressed proteins were clustered based on the Kyoto Encyclopedia of Genes and Genomes (KEGG), and sequences were linked to metabolic pathways via enzyme code and KEGG ortholog. Most proteins were involved in photosynthesis, phenylpropanoid biosynthesis, thiamine, and purine metabolism. This study revealed the presence of trans-cinnamate 4-monooxygenase, an intermediate for the biosynthesis of a large number of substances, such as phenylpropanoids and flavonoids.

Potato tuber degradation is regulated by carbohydrate metabolism: Results of transcriptomic analysis.

Tuber number is an essential factor determining yield and commodity in potato production. The initiation number has long been considered the sole determinant of the final total tuber number. In this study, we observed that tuber numbers at harvest were lower than at the tuber bulking stage; some formed tubers that were smaller than 3 cm degraded during development. Carbohydrate metabolism plays a crucial role in tuber degradation by coordinating the source–sink relationship. The contents of starch and sucrose, and the C:N ratio, are dramatically reduced in degradating tubers. Transcriptomic study showed that “carbohydrate metabolic processes” are Gene Ontology (GO) terms associated with tuber degradation. A polysaccharide degradation‐related gene, LOC102601831, and a sugar transport gene, LOC102587850 (SWEET6a), are dramatically up‐regulated in degradating tubers according to transcriptomic analysis, as validated by qRT‐PCT. The terms “peptidase inhibitor activity” and “hydrolase activity” refer to the changes in molecular functions that degradating tubers exhibit. Nitrogen supplementation during potato development alleviates tuber degradation to a certain degree. This study provides novel insight into potato tuber development and possible management strategies for improving potato cultivation.

Relevance of the Isoflavone Absorption and Testicular Function: A Systematic Review of Preclinical Evidence.

Isoflavone is a phytoestrogen found in different types of food that can act as endocrine disrupters leading to testicular dysfunction. Currently, fragmented data on the action of this compound in the testicles make it difficult to assess its effects to define a safe dose. Thus, we systematically reviewed the preclinical evidence of the impact of isoflavone on testicular function. We also determined which form (aglycones or glycosylated) was the most used, which allowed us to understand the main biological processes involved in testicular function after isoflavone exposure. This systematic review was carried out according to the PRISMA guidelines using a structured search on the biomedical databases MEDLINE (PubMed), Scopus, and Web of Science, recovering and analyzing 22 original studies. The bias analysis and the quality of the studies were assessed by the criteria described in the risk of bias tool developed by SYRCLE (Systematic Review Centre for Laboratory Animal Experimentation). The aglycones and glycosylated isoflavones proved to be harmful to the reproductive health, and the glycosylates at doses of 50, 100, 146, 200, 300, 500, and 600 mg/kg, in addition to 190 and 1000 mg/L, appear to be even more harmful. The main testicular pathologies resulting from the use of isoflavones are associated with Leydig cells resulting from changes in molecular functions and cellular components. The most used isoflavone to evaluate testicular changes was the genistein/daidzein conjugate. The consumption of high doses of isoflavones promotes changes in the functioning of Leydig cells, inducing testicular changes and leading to infertility in murine models.

Syndecan-1 Overexpressing Mesothelioma Cells Inhibit Proliferation, Wound Healing, and Tube Formation of Endothelial Cells.

Simple SummaryThe transmembrane proteoglycan syndecan-1 (SDC-1) is an important mediator of cell-matrix interactions. The heparan sulfate side-chains of SDC-1 can bind to a multitude of growth factors, cytokines, and chemokines, thereby regulating a plethora of physiological and pathological processes, including angiogenesis. The extracellular region of SDC-1 can be released from the cell surface by the action of sheddases including matrix metalloproteinase-7 and 9, resulting in a soluble protein that is still active and can act as a competitive activator or inhibitor of the cell surface receptor. Accelerated shedding and loss of cell surface SDC-1 is associated with epithelial to mesenchymal transition (EMT) and achievement of a more invasive phenotype in malignant mesothelioma (MM). Transfection with SDC-1 reverts the morphology in epithelioid direction and inhibits the proliferation and migration of MM cells. This study aimed to investigate the role of SDC-1 in angiogenesis. We demonstrate that overexpression and silencing of SDC-1 alters the secretion of angiogenic proteins in MM cells. Upon SDC-1 overexpression, several factors collectively inhibit the proliferation, wound closure, and tube formation of endothelial cells, whereas SDC-1 silencing only affects wound healing.Malignant mesothelioma (MM) is an aggressive tumor of the serosal cavities. Angiogenesis is important for mesothelioma progression, but so far, anti-angiogenic agents have not improved patient survival. Our hypothesis is that better understanding of the regulation of angiogenesis in this tumor would largely improve the success of such a therapy. Syndecan-1 (SDC-1) is a transmembrane heparan sulfate proteoglycan that acts as a co-receptor in various cellular processes including angiogenesis. In MM, the expression of SDC-1 is generally low but when present, SDC-1 associates to epithelioid differentiation, inhibition of tumor cell migration and favorable prognosis, meanwhile SDC-1 decrease deteriorates the prognosis. In the present study, we studied the effect of SDC-1 overexpression and silencing on MM cells ability to secrete angiogenic factors and monitored the downstream effect of SDC-1 modulation on endothelial cells proliferation, wound healing, and tube formation. This was done by adding conditioned medium from SDC-1 transfected and SDC-1 silenced mesothelioma cells to endothelial cells. Moreover, we investigated the interplay and molecular functional changes in angiogenesis in a co-culture system and characterized the soluble angiogenesis-related factors secreted to the conditioned media. We demonstrated that SDC-1 over-expression inhibited the proliferation, wound healing, and tube formation of endothelial cells. This effect was mediated by a multitude of angiogenic factors comprising angiopoietin-1 (Fold change ± SD: 0.65 ± 0.07), FGF-4 (1.45 ± 0.04), HGF (1.33 ± 0.07), NRG1-β1 (1.35 ± 0.08), TSP-1 (0.8 ± 0.02), TIMP-1 (0.89 ± 0.01) and TGF-β1 (1.35 ± 0.01). SDC-1 silencing increased IL8 (1.33 ± 0.06), promoted wound closure, but did not influence the tube formation of endothelial cells. Pleural effusions from mesothelioma patients showed that Vascular Endothelial Growth Factor (VEGF) levels correlate to soluble SDC-1 levels and have prognostic value. In conclusion, SDC-1 over-expression affects the angiogenic factor secretion of mesothelioma cells and thereby inhibits endothelial cells proliferation, tube formation, and wound healing. VEGF could be used in prognostic evaluation of mesothelioma patients together with SDC-1.

Identification of differentially expressed genes and biological pathways in sanguinarine-treated ovarian cancer by integrated bioinformatics analysis

Aim: This study was intended to identify potentially target genes and underlying biological pathway of sanguinarine in ovarian cancer. Methods: We obtained the expression changes of downstream target genes and underlying biological pathways regulated by control and sanguinarine groups via Affymetrix gene expression profile chip in ovarian cancer cells. An Affymetrix Genechip Agilent mRNA Array was used to recognize differentially expressed genes (DEGs). Afterward, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed for the DEGs using the DAVID database. Results: A total of 1185 DEGs between sanguinarine and control groups were identified, including 835 upregulated and 350 downregulated DEGs. The result of GO analysis recommended that the DEGs were mostly enriched in biological processes, including negative regulation of gene expression, nitrogen compound metabolic process, and transcription from RNA polymerase II promoter. Alterations in cellular components (CC) were suggestively enriched in the cytoskeleton and endoplasmic reticulum. The changes in molecular function were suggestively enriched in nucleic acid-binding transcription factor activity, protein dimerization activity, and enzyme binding. The results of the KEGG pathway analysis indicated that the DEGs were mostly concentrated in “Systemic lupus erythematosus,” “MAPK signalling pathway,” “Pathways in cancer,” and “Metabolic pathways.” Conclusion: The present study provided insights into the mechanism underlying sanguinarine target genes in ovarian cancer cells, which might be used as effective targets for OC diagnosis and treatment.

Abstract 904: Disrupted Mechanobiology Links the Molecular and Cellular Phenotypes in Familial Dilated Cardiomyopathy

Familial dilated cardiomyopathy (DCM) is a leading cause of sudden cardiac death and a major indicator for heart transplant. The disease is frequently caused by mutations of sarcomeric proteins; however, one of the outstanding challenges in the field has been connecting mutation-induced changes in molecular function with the phenotype seen in cardiomyocytes. Many of the DCM mutation-induced changes in contractility at the molecular scale are subtle, begging the question of what other factors could link molecular-scale changes in contractile proteins with the cellular phenotype. We hypothesized that disease-causing mutations of sarcomeric proteins would likely affect not only contraction, but also how cardiomyocytes sense and respond to changes in their mechanical environment associated with aging and disease. To test this hypothesis, we studied the molecular and cellular consequences of a DCM mutation in troponin-T, deltaK210. We determined the molecular mechanism of deltaK210 using biochemical and biophysical tools, and then we used computational modeling to predict that the mutation should reduce the force per sarcomere in cells. In mutant human stem cell derived cardiomyocytes, we found that deltaK210 not only reduces contractility, but also causes cellular hypertrophy and impairs cardiomyocytes’ ability to adapt to changes in substrate stiffness (e.g., heart tissue fibrosis that occurs with aging and disease). These results link the molecular and cellular phenotypes and implicate impaired mechanosensing as an under-appreciated mechanism in the pathogenesis and progression of dilated cardiomyopathies. These results also have important implications for our understanding of multiple heart diseases and the design of precision therapeutics.

Convergence of Domain Architecture, Structure, and Ligand Affinity in Animal and Plant RNA-Binding Proteins.

Reconstruction of ancestral protein sequences using phylogenetic methods is a powerful technique for directly examining the evolution of molecular function. Although ancestral sequence reconstruction (ASR) is itself very efficient, downstream functional, and structural studies necessary to characterize when and how changes in molecular function occurred are often costly and time-consuming, currently limiting ASR studies to examining a relatively small number of discrete functional shifts. As a result, we have very little direct information about how molecular function evolves across large protein families. Here we develop an approach combining ASR with structure and function prediction to efficiently examine the evolution of ligand affinity across a large family of double-stranded RNA binding proteins (DRBs) spanning animals and plants. We find that the characteristic domain architecture of DRBs—consisting of 2–3 tandem double-stranded RNA binding motifs (dsrms)—arose independently in early animal and plant lineages. The affinity with which individual dsrms bind double-stranded RNA appears to have increased and decreased often across both animal and plant phylogenies, primarily through convergent structural mechanisms involving RNA-contact residues within the β1–β2 loop and a small region of α2. These studies provide some of the first direct information about how protein function evolves across large gene families and suggest that changes in molecular function may occur often and unassociated with major phylogenetic events, such as gene or domain duplications.

Metabolic gene expression profiling of Zebrafish embryos exposed to silver nanocolloids and nanotubes

Nanosilver is produced in various shapes, size and coatings to increase its nanomaterial effects. However, the nanotoxicity related with the physiochemical properties of nanomaterials. When nanomaterials attach, reacted or be though the cell membrane, the first barriers they face are cell proteins (e.g., receptors, enzymes, and carriers). Nanomaterials could affect metabolic mechanisms through their reaction with cell proteins. Therefore, this study analyzed changes in metabolic processes to identify corresponding changes in molecular functions and biological processes. We compared the gene expression profiling results of zebrafish embryos exposed to silver nanocolloids (Ag NCs, 10 μg/L) and silver nanotubes (Ag NTs, 1 μg/L); the results revealed that 198 genes were upregulated and 99 downregulated by Ag NCs and Ag NTs. The major genes of molecular function were associated with binding and catalytic activity, and the related genes of biological processes were involved in nucleobase-containing compound and protein metabolic processes. This study suggests that the two types of nanosilver caused similar patterns of metabolic process change regardless of nanosilver shape.

Aortic and Carotid Arterial Stiffness and Epigenetic Regulator Gene Expression Changes Precede Blood Pressure Rise in Stroke-Prone Dahl Salt-Sensitive Hypertensive Rats

Multiple clinical studies show that arterial stiffness, measured as pulse wave velocity (PWV), precedes hypertension and is an independent predictor of hypertension end organ diseases including stroke, cardiovascular disease and chronic kidney disease. Risk factor studies for arterial stiffness implicate age, hypertension and sodium. However, causal mechanisms linking risk factor to arterial stiffness remain to be elucidated. Here, we studied the causal relationship of arterial stiffness and hypertension in the Na-induced, stroke-prone Dahl salt-sensitive (S) hypertensive rat model, and analyzed putative molecular mechanisms. Stroke-prone and non-stroke-prone male and female rats were studied at 3- and 6-weeks of age for arterial stiffness (PWV, strain), blood pressure, vessel wall histology, and gene expression changes. Studies showed that increased left carotid and aortic arterial stiffness preceded hypertension, pulse pressure widening, and structural wall changes at the 6-week time-point. Instead, differential gene induction was detected implicating molecular-functional changes in extracellular matrix (ECM) structural constituents, modifiers, cell adhesion, and matricellular proteins, as well as in endothelial function, apoptosis balance, and epigenetic regulators. Immunostaining testing histone modifiers Ep300, HDAC3, and PRMT5 levels confirmed carotid artery-upregulation in all three layers: endothelial, smooth muscle and adventitial cells. Our study recapitulates observations in humans that given salt-sensitivity, increased Na-intake induced arterial stiffness before hypertension, increased pulse pressure, and structural vessel wall changes. Differential gene expression changes associated with arterial stiffness suggest a molecular mechanism linking sodium to full-vessel wall response affecting gene-networks involved in vascular ECM structure-function, apoptosis balance, and epigenetic regulation.

Alterations in molecular networks of metastatic colorectal carcinoma reveal organ-specific signatures: Implications for targeted therapy of metastatic disease

3532 Background: Proteomic analysis of aberrant protein kinase activity is poised to provide crucial knowledge that could drive molecular-targeted therapeutics and personalized medicine. Many cancers are detected at late stages when metastasis has already occurred. Knowledge about the molecular derangements in the metastatic lesion is crucial for the rational selection of therapeutics. Very little is known about the signaling networks in the metastatic microenvironment. We employed reverse phase protein microarrays coupled to laser capture microdissection for a multiplexed phosphoproteomic fingerprint of colorectal metastatic disease to begin to understand the molecular functional changes that occur upon metastasis. Methods: 68 frozen cases of patient-matched colorectal cancer and hepatic metastasis, 15 cases of pulmonary metastasis, and 27 cases of hepatic metastasis of other primary cancers including breast, melanoma, pancreatic, ovarian, and stomach cancers (all taken at the same time at surgery), were subjected to laser capture microdissection. Procured tumor epithelia (20,000 cells per sample), were lysed and subjected to reverse phase protein microarray analysis. Using this technique, we measured the phosphorylation state of 75 kinase substrates. Molecular network analysis was performed using commercially available software. Results: Our results indicate that, unlike analysis of gene microarray data, we observe a significant difference between the molecular networks of activated kinase substrates within the metastatic lesion compared to the patient-matched primary tumor. In fact, despite overall patient-specific heterogeneity of the portraits, organ specific signatures that were independent of the primary origin of the tumor were identified. Conculsions: Effective treatment in the new era of personalized targeted therapeutics will require the ability to understand the functional activation of cellular signaling pathways since these are the drug targets themselves. Our results indicate that treatment of metastatic disease, and patient stratification for matching with the appropriate therapy may be organ-specific and not predicated upon the primary site of the disease. No significant financial relationships to disclose.

Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference.

Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and evolutionary processes over the course of evolution and are used to infer adaptation and convergence. Maximum likelihood (ML) is generally thought to provide relatively accurate reconstructed sequences compared to parsimony, but both methods lead to the inference of multiple directional changes in nucleotide frequencies in primate mitochondrial DNA (mtDNA). To better understand this surprising result, as well as to better understand how parsimony and ML differ, we constructed a series of computationally simple "conditional pathway" methods that differed in the number of substitutions allowed per site along each branch, and we also evaluated the entire Bayesian posterior frequency distribution of reconstructed ancestral states. We analyzed primate mitochondrial cytochrome b (Cyt-b) and cytochrome oxidase subunit I (COI) genes and found that ML reconstructs ancestral frequencies that are often more different from tip sequences than are parsimony reconstructions. In contrast, frequency reconstructions based on the posterior ensemble more closely resemble extant nucleotide frequencies. Simulations indicate that these differences in ancestral sequence inference are probably due to deterministic bias caused by high uncertainty in the optimization-based ancestral reconstruction methods (parsimony, ML, Bayesian maximum a posteriori). In contrast, ancestral nucleotide frequencies based on an average of the Bayesian set of credible ancestral sequences are much less biased. The methods involving simpler conditional pathway calculations have slightly reduced likelihood values compared to full likelihood calculations, but they can provide fairly unbiased nucleotide reconstructions and may be useful in more complex phylogenetic analyses than considered here due to their speed and flexibility. To determine whether biased reconstructions using optimization methods might affect inferences of functional properties, ancestral primate mitochondrial tRNA sequences were inferred and helix-forming propensities for conserved pairs were evaluated in silico. For ambiguously reconstructed nucleotides at sites with high base composition variability, ancestral tRNA sequences from Bayesian analyses were more compatible with canonical base pairing than were those inferred by other methods. Thus, nucleotide bias in reconstructed sequences apparently can lead to serious bias and inaccuracies in functional predictions.

Piecing Together the Clock in Plants

The circadian clocks translate cyclic changes in molecular function into daily cycles that anticipate and coordinate with environmental cues. Alabadí et al. now delve into the molecular rhythms of the plant circadian clock and define the molecular partners. A pair of transcriptions factors, LHY and CCA1, begin the morning and, throughout the day, gradually turn over the reins to the evening gene, TOC1. The reciprocating balance between these various genes establishes the basis of the circadian cycle in Arabidopsis.D. Alabadí, T. Oyama, M. J. Yanovsky, F. G. Harmon, P. Más, S. A. Kay, Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293, 880-883 (2001). [Abstract] [Full Text]

Piecing Together the Clock in Plants

The circadian clocks translate cyclic changes in molecular function into daily cycles that anticipate and coordinate with environmental cues. Alabadí et al. now delve into the molecular rhythms of the plant circadian clock and define the molecular partners. A pair of transcriptions factors, LHY and CCA1, begin the morning and, throughout the day, gradually turn over the reins to the evening gene, TOC1 . The reciprocating balance between these various genes establishes the basis of the circadian cycle in Arabidopsis . D. Alabadí, T. Oyama, M. J. Yanovsky, F. G. Harmon, P. Más, S. A. Kay, Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293 , 880-883 (2001). [Abstract] [Full Text]