SciCombinator

Discover the most talked about and latest scientific content & concepts.

Journal: Journal of biosciences

155

The role of protein-lipid interactions is increasingly recognized to be of importance in numerous biological processes. Bioinformatics is being increasingly used as a helpful tool in studying protein-lipid interactions. Especially recently developed approaches recognizing lipid binding regions in proteins can be implemented. In this study one of those bioinformatics approaches specialized in identifying lipid binding helical regions in proteins is expanded. The approach is explored further by features which can be easily obtained manually. Some interesting examples of members of the amphitropic protein family have been investigated in order to demonstrate the additional features of this bioinformatics approach. The results in this study seem to indicate interesting characteristics of amphitropic proteins and provide insight into the mechanistic functioning and overall understanding of this intriguing class of proteins. Additionally, the results demonstrate that the presented bioinformatics approach might be either an interesting starting point in protein-lipid interactions studies or a good tool for selecting new focus points for more detailed experimental research of proteins with known overall protein-lipid binding abilities.

Concepts: DNA, Proteins, Protein, Bioinformatics, Molecular biology, Metabolism, Proteome, Cdx protein family

7

This article reviews the production of different phenotypes from the same genotype in the same environment by stochastic cellular events, nonlinear mechanisms during patterning and morphogenesis, and probabilistic self-reinforcing circuitries in the adult life. These aspects of phenotypic variation are summarized under the term ‘stochastic developmental variation’ (SDV) in the following. In the past, SDV has been viewed primarily as a nuisance, impairing laboratory experiments, pharmaceutical testing, and true-to-type breeding. This article also emphasizes the positive biological effects of SDV and discusses implications for genotype-to-phenotype mapping, biological individuation, ecology, evolution, and applied biology. There is strong evidence from experiments with genetically identical organisms performed in narrowly standardized laboratory set-ups that SDV is a source of phenotypic variation in its own right aside from genetic variation and environmental variation. It is obviouslymediated bymolecular and higher-order epigeneticmechanisms. Comparison of SDV in animals, plants, fungi, protists, bacteria, archaeans, and viruses suggests that it is a ubiquitous and phylogenetically old phenomenon. In animals, it is usually smallest for morphometric traits and highest for life history traits and behaviour. SDV is thought to contribute to phenotypic diversity in all populations but is particularly relevant for asexually reproducing and genetically impoverished populations, where it generates individuality despite genetic uniformity. In each generation, SDV produces a range of phenotypes around a well-adapted target phenotype, which is interpreted as a bet-hedging strategy to cope with the unpredictability of dynamic environments. At least some manifestations of SDV are heritable, adaptable, selectable, and evolvable, and therefore, SDV may be seen as a hitherto overlooked evolution factor. SDV is also relevant for husbandry, agriculture, and medicine because most pathogens are asexuals that exploit this third source of phenotypic variation tomodify infectivity and resistance to antibiotics. Since SDV affects all types of organisms and almost all aspects of life, it urgently requires more intense research and a better integration into biological thinking.

Concepts: Gene, Genetics, Natural selection, Genotype, Evolution, Biology, Organism, Life

0

The vertebrate inner nuclear membrane protein, lamin B receptor, has an N-terminal ~200 residue nucleoplasmic domain (NTD), and a ~420 residue C-terminal domain (CTD) that anchors the NTD to the INM. Chen et al (2016) showed the NTD interacts with Xist long noncoding RNA to effect X chromosome inactivation in female mammals. Tsai et al (2016) showed the CTD has sterol reductase activity that is essential for viability. And Nikolakaki et al (2017) proposed a model to interconnect these disparate functions of this chimeric protein. It amuses me now to think back to 24 years ago, when I was concerned that these domains might have come together in a cloning artifact.

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Mitochondrial mechanisms and pathways have recently emerged as critical determinants of organismal aging. While nuclear sirtuins have been shown to regulate aging, whether mitochondrial sirtuins do so is still unclear. Here, we report that mitochondrial dSirt4 mediates organismal aging. We establish that absence of dSirt4 leads to reduced lifespan independent of dietary inputs. Further by assaying locomotion, a key correlate of aging, we demonstrate that dSirt4 null flies are severely physically impaired with a significant reduction in locomotion. In summary, we report that mitochondrial dSirt4 is a key determinant of longevity and its loss leads to early aging.

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Cervical cancer is fourth most common fatal cancer in women worldwide. Lupeol is a dietary triterpenoid and has shown its anticancer efficacy against various cancer types with selectivity in targeting cancer cells. In the present study, anticancer efficacy and mechanism of action of a phytochemical, lupeol, in human cervical carcinoma (HeLa) cells has been examined. The anticancer efficacy of lupeol was assessed by trypan blue cell counting, annexin Vassay, cell cycle analysis, expression of apoptotic proteins by RT-PCR and Western blotting and assessment of mitochondrial ROS generation by mitosox and mitotracker assays. Our results demonstrated that lupeol decreased cell proliferation and viability of HeLa cells significantly (p less than 0.001). Lupeol induced S-phase cell cycle arrest and also decreased the expression of S-phase Cyclins and CDKs and increased the expression of cyclin-dependent kinase inhibitors, p21 at transcriptional and translational level. Further, lupeol induced apoptosis and increased the expression of apoptosis markers such as cleaved PARP and Bax:Bcl-2 ratio. Furthermore, mitosox and mitotracker dye incubation followed by FACS analysis showed an increase in mitochondrial superoxide generation and reduction in healthy mitochondrial mass. These results suggest that lupeol could be an effective chemotherapeutic agent against cervical carcinoma due to its growth inhibitory activity through induction of S-phase cell cycle arrest and apoptosis.

0

Electromagnetic radiation (EMR) can induce or modulate several neurobehavioral disorders. Duration and frequency of exposure of EMR is critical to develop cognitive disorders. Even though EMR-2450 is widely used, its effects on cognition in relation to mitochondrial function and apoptosis would provide better understanding of its pathophysiological effects. Therefore, a comparative study of different frequencies of EMR exposure would give valuable information on effects of discrete frequencies of EMR on cognition. Male rats were exposed to EMR (900, 1800 and 2450 MHz) every day for 1 h for 28 consecutive days. The cognitive behavior in terms of novel arm entries in Y-maze paradigm was evaluated every week after 1 h to last EMR exposure. Animals exposed to EMR-2450 MHz exhibited significant cognitive deficits. EMR- 2450 MHz caused loss of mitochondrial function and integrity, an increase in amyloid beta expression. There was release of cytochrome-c and activation of apoptotic factors such as caspase-9 and -3 in the hippocampus. Further, there was decrease in levels of acetylcholine, and increase in activity of acetyl cholinesterase, indicating impairment of cholinergic system. Therefore, exposure of EMR-2450 in rats caused cognitive deficit with related pathophysiological changes in mitochondrial and cholinergic function, and amyloidogenesis.

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Secretory phospholipase A2-IIA (sPLA2-IIA) is one of the key enzymes causing lipoprotein modification and vascular inflammation. Maslinic acid is a pentacyclic triterpene which has potential cardioprotective and anti-inflammatory properties. Recent research showed that maslinic acid interacts with sPLA2-IIA and inhibits sPLA2-IIA-mediated monocyte differentiation and migration. This study elucidates the potential of maslinic acid in modulating sPLA2-IIA-mediated inflammatory effects in THP-1 macrophages. We showed that maslinic acid inhibits sPLA2-IIA-mediated LDL modification and suppressed foam cell formation. Further analysis revealed that sPLA2-IIA only induced modest LDL oxidation and that inhibitory effect of maslinic acid on sPLA2-IIA-mediated foam cells formation occurred independently of its anti-oxidative properties. Interestingly, maslinic acid was also found to significantly reduce lipid accumulation observed in macrophages treated with sPLA2-IIA only. Flow cytometry analysis demonstrated that the effect observed in maslinic acid might be contributed in part by suppressing sPLA2-IIA-induced endocytic activity, thereby inhibiting LDL uptake. The study further showed that maslinic acid suppresses sPLA2-IIA-induced up-regulation of PGE2 levels while having no effects on COX-2 activity. Other pro-inflammatory mediators TNF-a and IL-6 were not induced in sPLA2-IIA-treated THP-1 macrophages. The findings of this study showed that maslinic acid inhibit inflammatory effects induced by sPLA2-IIA, including foam cells formation and PGE2 production.

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Non-alcoholic fatty liver disease (NAFLD) is one of the leading causes of chronic liver diseases around the world and commonly associated with insulin resistance and hyperlipidemia. Chlorogenic acid (CG) was reported to have insulinsensitizing activity and exert hypocholesterolemic and hypoglycemic effect. However, the involvement of CG in NAFLD remains far from being addressed. In this study, a high-fat diet-induced NAFLD rat model was used to investigate the biological roles and underlying mechanism of CG in NAFLD. The results showed that high-fat diet-fed rats exhibited an increase in body weight, glucose tolerance, liver injury, insulin resistance, as well as autophagy and C-Jun N-terminal kinase (JNK) pathway. Nevertheless, all these effects were alleviated by CG treatment. Moreover, angiotensin treatment in CG group activated the JNK pathway, and promoted autophagy, insulin resistance, and liver injury. In conclusion, our findings demonstrated that CG ameliorated liver injury and insulin resistance by suppressing autophagy via inactivation of JNK pathway in a rat model of NAFLD. Therefore, CG might be a potential application for the treatment of NAFLD.

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The ErbB signalling pathway has been studied extensively owing to its role in normal physiology and its dysregulation in cancer. Reverse engineering by mathematical models use the reductionist approach to characterize the network components. For an emergent, system-level view of the network, we propose a data analytics pipeline that can learn from the data generated by reverse engineering and use it to re-engineer the system with an agent-based approach. Data from a kinetic model that estimates the parameters by fitting to experiments on cell lines, were encoded into rules, for the interactions of the molecular species (agents) involved in biochemical reactions. The agent model, a digital representation of the cell line system, tracks the activation of ErbB1-3 receptors on binding with ligands, resulting in their dimerization, phosphorylation, trafficking and stimulation of downstream signalling through P13-Akt and Erk pathways. The analytics pipeline has been used to mechanistically link HER expression profile to receptor dimerization and activation of downstream signalling pathways. When applied to drug studies, the efficacy of a drug can be investigated in silico. The anti-tumour activity of Pertuzumab, a monoclonal antibody that inhibits HER2 dimerization, was simulated by blocking 80% of the cellular HER2 available, to observe the effect on signal activation.

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According to recent research, smart polymers can affect different kind of mammalian cells such as endothelial cells. It is known that conductive polymers have great features, e.g. electrical conductivity, and can help increase electrical cell communication. To clarify the effect of one of these smart materials on endothelial cells, which are not inherently electrically dependent, poly(3, 4-ethylene dioxythiophene) polystyrene sulfonate (PEDOT:PSS) was chosen. Scaffolds were composed of gelatin, alginate, and PEDOT:PSS and made through solvent casting. Human umbilical vein endothelial cells (HUVECs) were cultured on the scaffold with different PEDOT:PSS concentrations. SEM, MTT assay, cell attachment, nitric oxide measurement, real-time PCR and immunohistochemistry analysis were employed to assess endothelial cell responses. Although there was no significant difference in swelling ratio, mass loss, and cell attachment when PEDOT:PSS concentration increased in scaffold construction, cell proliferation noticeably increased after seven days. The cells showed a significant increase in proliferation and NO release to the scaffold with 1% PEDOT:PSS concentration. The results indicated increases in the amount of expression of platelet endothelial cell adhesion molecule-1 (PECAM-1, CD31), kinase insert domain receptor (KDR), vascular-endothelial Cadherin (VE. Cadherin), and von Will brand factor (vWf) in the group which contained a conductive polymer in comparison with the non-conductive scaffold. Therefore, as a conductive polymer, PEDOT:PSS can affect the endothelial cell behaviours.