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Biological complex systems

Svetlana E Soboleva, Evgeniya E Burkova, Pavel S Dmitrenok, Dmitrii V Bulgakov, Natalia I Menzorova, Valentina N Buneva, Georgy A Nevinsky
It was proposed that most biological processes are performed by different protein complexes. In contrast to individual proteins and enzymes, their complexes usually have other biological functions, and their formation may be important system process for the expansion of diversity and biological functions of different molecules. Identification and characterization of embryonic components including proteins and their multiprotein complexes seem to be very important for an understanding of embryo function. We have isolated and analyzed for the first time a very stable multiprotein complex (SPC; approximately 1100 kDa) from the soluble fraction of extracts of the sea urchin embryos...
August 14, 2018: Journal of Molecular Recognition: JMR
Shabir H Wani, Prateek Tripathi, Abbu Zaid, Ghana S Challa, Anuj Kumar, Vinay Kumar, Jyoti Upadhyay, Rohit Joshi, Manoj Bhatt
The current review provides an updated, new insights into the regulation of transcription mediated underlying mechanisms of wheat plants to osmotic stress perturbations. Osmotic stress tolerance mechanisms being complex are governed by multiple factors at physiological, biochemical and at the molecular level, hence approaches like "OMICS" that can underpin mechanisms behind osmotic tolerance in wheat is of paramount importance. The transcription factors (TFs) are a class of molecular proteins, which are involved in regulation, modulation and orchestrating the responses of plants to a variety of environmental stresses...
August 14, 2018: Plant Molecular Biology
Xuena Huang, Shiguo Li, Yangchun Gao, Aibin Zhan
Biological response to rapid changing environments is an outstanding research question in ecology and evolution. Biological invasions provide excellent "natural" experiments to study such a complex response process, as invaders often encounter rapidly changing environments during biological invasions. The regulation of heat shock proteins (Hsp) is a common pathway responsible for various environmental stresses; however, the comprehensive study on Hsp system across the whole genome and potential roles in determining invasion success are still largely unexplored...
2018: Frontiers in Physiology
Benjamin Titze, Christel Genoud, Rainer W Friedrich
We present SBEMimage , an open-source Python-based application to operate serial block-face electron microscopy (SBEM) systems. SBEMimage is designed for complex, challenging acquisition tasks, such as large-scale volume imaging of neuronal tissue or other biological ultrastructure. Advanced monitoring, process control, and error handling capabilities improve reliability, speed, and quality of acquisitions. Debris detection, autofocus, real-time image inspection, and various other quality control features minimize the risk of data loss during long-term acquisitions...
2018: Frontiers in Neural Circuits
Huayao Li, Lijuan Liu, Cun Liu, Jing Zhuang, Chao Zhou, Jing Yang, Chundi Gao, Gongxi Liu, Qingliang Lv, Changgang Sun
Qingdai, a traditional Chinese medicine (TCM) used for the treatment of chronic myeloid leukemia (CML) with good efficacy, has been used in China for decades. However, due to the complexity of traditional Chinese medicinal compounds, the pharmacological mechanism of Qingdai needs further research. In this study, we investigated the pharmacological mechanisms of Qingdai in the treatment of CML using network pharmacology approaches. First, components in Qingdai that were selected by pharmacokinetic profiles and biological activity predicted putative targets based on a combination of 2D and 3D similarity measures with known ligands...
August 15, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Arwen W Gao, Mark G Sterken, Jelmi Uit de Bos, Jelle van Creij, Rashmi Kamble, Basten L Snoek, Jan E Kammenga, Riekelt H Houtkooper
Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium, leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitative genetic analysis using a population of 199 recombinant inbred lines (RILs) in the nematode Caenorhabditis elegans We focused on the genomic regions that control metabolite levels by measuring fatty acid (FA) and amino acid (AA) composition in the RILs using targeted metabolomics...
August 14, 2018: Genome Research
Nora M Bello, Vera C Ferreira, Daniel Gianola, Guilherme J M Rosa
Understanding causal mechanisms among variables is critical to efficient management of complex biological systems such as animal agriculture production. The increasing availability of data from commercial livestock operations offers unique opportunities for attaining causal insight, despite the inherently observational nature of these data. Causal claims based on observational data are substantiated by recent theoretical and methodological developments in the rapidly evolving field of causal inference. Thus, the objectives of this review are as follows: 1) to introduce a unifying conceptual framework for investigating causal effects from observational data in livestock, 2) to illustrate its implementation in the context of the animal sciences, and 3) to discuss opportunities and challenges associated with this framework...
August 9, 2018: Journal of Animal Science
Huiying Zhao, Ghazaleh Taherzadeh, Yaoqi Zhou, Yuedong Yang
Protein-carbohydrate interaction is essential for biological systems, and carbohydrate-binding proteins (CBPs) are important targets when designing antiviral and anticancer drugs. Due to the high cost and difficulty associated with experimental approaches, many computational methods have been developed as complementary approaches to predict CBPs or carbohydrate-binding sites. However, most of these computational methods are not publicly available. Here, we provide a comprehensive review of related studies and demonstrate our two recently developed bioinformatics methods...
August 14, 2018: Current Protocols in Protein Science
Kenneth H Mayer
Since the turn of the current century, syphilis incidence and prevalence have been increasing more rapidly among men who have sex with men (MSM) than any other US subpopulation, exceeding their previously high rates in the 1970s and 1980s, before the AIDS epidemic. The reasons for these trends are multifactorial and complex, involving individual behavioral, sociocultural, structural, and biological factors, which will be reviewed in this article. Men who have sex with men tend to have more sexual partners than heterosexuals, and engage in practices (e...
September 2018: Sexually Transmitted Diseases
Anne E Otwell, Adrián López García de Lomana, Sean M Gibbons, Mónica V Orellana, Nitin S Baliga
Through complex interspecies interactions, microbial processes drive nutrient cycling and biogeochemistry. However, we still struggle to predict specifically which organisms, communities, and biotic and abiotic processes are determining ecosystem function and how environmental changes will alter their roles and stability. While the tools to create such a predictive microbial ecology capability exist, cross-disciplinary integration of high-resolution field measurements, detailed laboratory studies, and computation is essential...
August 14, 2018: Environmental Microbiology
Mahesh Kandasamy, Ludwig Aigner
The brain is a dynamic organ of the biological renaissance due to the existence of neuroplasticity. Adult neurogenesis abides by every aspect of neuroplasticity in the intact brain and contributes to neural regeneration in response to brain diseases and injury. The occurrence of adult neurogenesis has unequivocally been witnessed in human subjects, experimental and wildlife research including rodents, bats and cetaceans. Adult neurogenesis is a complex cellular process, in which generation of neuroblasts namely, neuroblastosis appears to be an integral process that occur in the limbic system and basal ganglia in addition to the canonical neurogenic niches...
August 2018: Neural Regeneration Research
Henry J Benns, Edward W Tate, Matthew A Child
Parasites exist within most ecological niches, often transitioning through biologically and chemically complex host environments over the course of their parasitic life cycles. While the development of technologies for genetic engineering has revolutionised the field of functional genomics, parasites have historically been less amenable to such modification. In light of this, parasitologists have often been at the forefront of adopting new small-molecule technologies, repurposing drugs into biological tools and probes...
August 14, 2018: Current Topics in Microbiology and Immunology
Juliana de A S Gomes, Fernanda F de Araújo, Daniele M Vitelli-Avelar, Renato Sathler-Avelar, Paula S Lage, Ana P B Wendling, Isabela N P C do Vale, João C P Dias, Silvana M Elói-Santos, Andréa Teixeira-Carvalho, Olindo A Martins-Filho
The systems biology approach has become an innovative tool when it comes to shedding light on the complex immune response underlying the development/maintenance of distinct clinical forms of Chagas disease. The goal of this study was to describe an integrative overview of Fc-γR expression, cytokine microenvironment and anti- Trypanosoma cruzi IgG interface in indeterminate-(IND) and cardiac-(CARD) patients. Data demonstrated that IND displayed an overall higher Fcγ-R expression (CD16; CD32; CD64) on neutrophils-(NEU), along with (CD16; CD64) on monocytes-(MON) as compared to CARD...
2018: Frontiers in Microbiology
Astrid Avellan, Marie Simonin, Eric McGivney, Nathan Bossa, Eleanor Spielman-Sun, Jennifer D Rocca, Emily S Bernhardt, Nicholas K Geitner, Jason M Unrine, Mark R Wiesner, Gregory V Lowry
Predicting nanoparticle fate in aquatic environments requires mimicking of ecosystem complexity to observe the geochemical processes affecting their behaviour. Here, 12 nm Au nanoparticles were added weekly to large-scale freshwater wetland mesocosms. After six months, ~70% of Au was associated with the macrophyte Egeria densa, where, despite the thermodynamic stability of Au0 in water, the pristine Au0 nanoparticles were fully oxidized and complexed to cyanide, hydroxyls or thiol ligands. Extracted biofilms growing on E...
August 13, 2018: Nature Nanotechnology
Chiharu Ishii, Takeyuki Akita, Masashi Mita, Tomomi Ide, Kenji Hamase
An automated two-dimensional HPLC-MS/MS system was designed and developed for the highly selective determination of trace levels of d-amino acids. As the targets, frequently observed ones in mammalian physiological fluids, Ala, Asp, Glu, Leu, Pro and Ser, were selected because these d-amino acids are the potential biomarkers for the early and sensitive diagnoses of various diseases. The target analytes were derivatized with 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F), then isolated by a reversed-phase column in the first dimension...
July 29, 2018: Journal of Chromatography. A
Aicha Hennia, Maria Graça Miguel, Said Nemmiche
Myrtus communis L. (myrtle) and Myrtus nivellei Batt. & Trab. (Saharan myrtle) have been used in folk medicine for alleviating some ailments. M. communis is largely distributed in the Mediterranean Basin, whereas M. nivellei is confined in specific zones of the central Saharan mountains. The chemical composition and antioxidant activity of berry and leaf extracts isolated from myrtle are deeply documented, whereas those isolated from Saharan myrtle extracts are less studied. In both species, the major groups of constituents include gallic acid derivatives, flavonols, flavonol derivatives, and hydroxybenzoic acids...
August 11, 2018: Medicines (Basel, Switzerland)
Maksim Kouza, Anirban Banerji, Andrzej Kolinski, Irina Buhimschi, Andrzej Kloczkowski
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered molecular dynamics (SMD) to assess the strength of protein-peptide interactions. The idea behind using SMD simulations is that the mechanical stability can be used as a promising and an efficient alternative to computationally highly demanding estimation of binding affinity...
August 10, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Jialu Zhao, Xu Liu, Chunyue Huo, Tian Zhao, Haihong Ye
MK-801, a non-competitive NMDA receptor antagonist, disturbs NMDA receptor function in rodents and induces psychological and behavioral changes similar to schizophrenia (SCZ). However, the effects of MK-801 treatment on gene expression are largely unknown. Here we performed RNA-sequencing on the prefrontal cortex of MK-801-exposed male mice in order to analyze gene expression and co-expression patterns related to SCZ and to identify mechanisms that underlie the molecular etiology of this disorder. Transcriptome analysis revealed that the differentially expressed genes were more often associated with biological processes that included postsynaptic transmission, immune system process, response to external stimulus and hemostasis...
August 10, 2018: Neuroscience
Ramsia Sreij, Sylvain François Prévost, Rajeev Dattani, Carina Dargel, Yvonne Hertle, Oliver Wrede, Thomas Hellweg
The understanding of the interaction of drugs with biologically active compounds in biological membranes is of fundamental importance for the evaluation of physiological effects and the development and improvement of medicinal formulations. In the present study we investigate the interaction of the saponin aescin, a biosurfactant which is derived from the horse chestnut tree aesculus hippocastanum, with the non-steroidal anti-inflammatory drug (NSAID) ibuprofen in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) model membranes...
August 13, 2018: Molecular Pharmaceutics
Shila Ghazanfar, Dario Strbenac, John T Ormerod, Jean Y H Yang, Ellis Patrick
Motivation: Genes act as a system and not in isolation. Thus, it is important to consider coordinated changes of gene expression rather than single genes when investigating biological phenomena such as the aetiology of cancer. We have developed an approach for quantifying how changes in the association between pairs of genes may inform the outcome of interest called Differential Correlation across Ranked Samples (DCARS). Modelling gene correlation across a continuous sample ranking does not require the dichotomisation of samples into two distinct classes and can identify differences in gene correlation across early, mid or late stages of the outcome of interest...
August 9, 2018: Bioinformatics
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