Fluctuation relations between hierarchical kinetically equivalent networks with Arrhenius-type transitions and their roles in systems and structural biology.

Phys Rev E. 2017 Jun;95(6-1):062401

Authors: Deng DM, Lu YT, Chang CH

Abstract
The legality of using simple kinetic schemes to determine the stochastic properties of a complex system depends on whether the fluctuations generated from hierarchical equivalent schemes are consistent with one another. To analyze this consistency, we perform lumping processes on the stochastic differential equations and the generalized fluctuation-dissipation theorem and apply them to networks with the frequently encountered Arrhenius-type transition rates. The explicit Langevin force derived from those networks enables us to calculate the state fluctuations caused by the intrinsic and extrinsic noises on the free energy surface and deduce their relations between kinetically equivalent networks. In addition to its applicability to wide classes of network related systems, such as those in structural and systems biology, the result sheds light on the fluctuation relations for general physical variables in Keizer's canonical theory.

PMID: 28709185 [PubMed - in process]

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"systems biology"

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"systems biology"

These pubmed results were generated on 2017/07/14

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Greenhouse gas emissions from dung pats vary with dung beetle species and with assemblage composition.

PLoS One. 2017;12(7):e0178077

Authors: Piccini I, Arnieri F, Caprio E, Nervo B, Pelissetti S, Palestrini C, Roslin T, Rolando A

Abstract
Cattle farming is a major source of greenhouse gases (GHGs). Recent research suggests that GHG fluxes from dung pats could be affected by biotic interactions involving dung beetles. Whether and how these effects vary among beetle species and with assemblage composition is yet to be established. To examine the link between GHGs and different dung beetle species assemblages, we used a closed chamber system to measure fluxes of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) from cattle dung pats. Targeting a total of four dung beetle species (a pat-dwelling species, a roller of dung balls, a large and a small tunnelling species), we ran six experimental treatments (four monospecific and two mixed) and two controls (one with dung but without beetles, and one with neither dung nor beetles). In this setting, the overall presence of beetles significantly affected the gas fluxes, but different species contributed unequally to GHG emissions. When compared to the control with dung, we detected an overall reduction in the total cumulative CO2 flux from all treatments with beetles and a reduction in N2O flux from the treatments with the three most abundant dung beetle species. These reductions can be seen as beneficial ecosystem services. Nonetheless, we also observed a disservice provided by the large tunneler, Copris lunaris, which significantly increased the CH4 flux-an effect potentially traceable to the species' nesting strategy involving the construction of large brood balls. When fluxes were summed into CO2-equivalents across individual GHG compounds, dung with beetles proved to emit less GHGs than did beetle-free dung, with the mix of the three most abundant species providing the highest reduction (-32%). As the mix of multiple species proved the most effective in reducing CO2-equivalents, the conservation of diverse assemblages of dung beetles emerges as a priority in agro-pastoral ecosystems.

PMID: 28700590 [PubMed - in process]

TFH-derived dopamine accelerates productive synapses in germinal centres.

Nature. 2017 Jul 12;:

Authors: Papa I, Saliba D, Ponzoni M, Bustamante S, Canete PF, Gonzalez-Figueroa P, McNamara HA, Valvo S, Grimbaldeston M, Sweet RA, Vohra H, Cockburn IA, Meyer-Hermann M, Dustin ML, Doglioni C, Vinuesa CG

Abstract
Protective high-affinity antibody responses depend on competitive selection of B cells carrying somatically mutated B-cell receptors by follicular helper T (TFH) cells in germinal centres. The rapid T-B-cell interactions that occur during this process are reminiscent of neural synaptic transmission pathways. Here we show that a proportion of human TFH cells contain dense-core granules marked by chromogranin B, which are normally found in neuronal presynaptic terminals storing catecholamines such as dopamine. TFH cells produce high amounts of dopamine and release it upon cognate interaction with B cells. Dopamine causes rapid translocation of intracellular ICOSL (inducible T-cell co-stimulator ligand, also known as ICOSLG) to the B-cell surface, which enhances accumulation of CD40L and chromogranin B granules at the human TFH cell synapse and increases the synapse area. Mathematical modelling suggests that faster dopamine-induced T-B-cell interactions increase total germinal centre output and accelerate it by days. Delivery of neurotransmitters across the T-B-cell synapse may be advantageous in the face of infection.

PMID: 28700579 [PubMed - as supplied by publisher]

Nano-palladium is a cellular catalyst for in vivo chemistry.

Nat Commun. 2017 Jul 12;8:15906

Authors: Miller MA, Askevold B, Mikula H, Kohler RH, Pirovich D, Weissleder R

Abstract
Palladium catalysts have been widely adopted for organic synthesis and diverse industrial applications given their efficacy and safety, yet their biological in vivo use has been limited to date. Here we show that nanoencapsulated palladium is an effective means to target and treat disease through in vivo catalysis. Palladium nanoparticles (Pd-NPs) were created by screening different Pd compounds and then encapsulating bis[tri(2-furyl)phosphine]palladium(II) dichloride in a biocompatible poly(lactic-co-glycolic acid)-b-polyethyleneglycol platform. Using mouse models of cancer, the NPs efficiently accumulated in tumours, where the Pd-NP activated different model prodrugs. Longitudinal studies confirmed that prodrug activation by Pd-NP inhibits tumour growth, extends survival in tumour-bearing mice and mitigates toxicity compared to standard doxorubicin formulations. Thus, here we demonstrate safe and efficacious in vivo catalytic activity of a Pd compound in mammals.

PMID: 28699627 [PubMed - in process]

Identification of antineoplastic targets with systems approaches, using resveratrol as an in-depth case study.

Curr Pharm Des. 2017 Jul 10;:

Authors: Singh N, Freiesleben S, Gupta SK, Shukla Y, Wolkenhauer O

Abstract
The identification and validation of novel drug-target combinations are key steps in the drug discovery processes. Cancer is a complex disease that involves several genetic and environmental factors. High-throughput omics technologies are now widely available, however the integration of multi-omics data to identify viable anticancer drug-target combinations that allow for a better clinical outcome when considering the efficacy-toxicity spectrum, is challenging. In this review, we provide an overview of systems approaches that can help integrate a broad spectrum of technologies and data. We focus on network approaches and investigate the anticancer mechanism and biological targets of resveratrol using reverse pharmacophore mapping as an in-depth case study. The results of this case study demonstrate the use of systems approaches for a better understanding of the behavior of small molecule inhibitors in receptor binding sites. The presented network analysis approach helps in formulating hypotheses and provides mechanistic insights of resveratrol in neoplastic transformations.

PMID: 28699531 [PubMed - as supplied by publisher]

P-Rex1 Expression in Invasive Breast Cancer in relation to Receptor Status and Distant Metastatic Site.

Int J Breast Cancer. 2017;2017:4537532

Authors: Marotti JD, Muller KE, Tafe LJ, Demidenko E, Miller TW

Abstract
BACKGROUND: Phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1 (P-Rex1) has been implicated in cancer growth, metastasis, and response to phosphatidylinositol 3-kinase (PI3K) inhibitor therapy. The aim of this study was to determine whether P-Rex1 expression differs between primary and metastatic human breast tumors and between breast cancer subtypes.
DESIGN: P-Rex1 expression was measured in 133 specimens by immunohistochemistry: 40 and 42 primary breast tumors from patients who did versus did not develop metastasis, respectively, and 51 breast-derived tumors from metastatic sites (36 of which had matching primary tumors available for analysis).
RESULTS: Primary breast tumors showed significant differences in P-Rex1 expression based on receptor subtype. ER+ and HER2+ primary tumors showed higher P-Rex1 expression than primary triple-negative tumors. HER2+ metastases from all sites showed significantly higher P-Rex1 expression compared to other metastatic receptor subtypes. Solid organ (i.e., brain, lung, and liver) metastases showed higher P-Rex1 expression compared to bone metastases.
CONCLUSIONS: P-Rex1 expression is increased in ER+ and HER2+ breast cancers compared to triple-negative tumors. P-Rex1 may be differentially expressed in metastatic tumors based on site and receptor status. The role of P-Rex1 in the development of breast cancer metastases and as a predictive biomarker of therapeutic response warrants further investigation.

PMID: 28698809 [PubMed - in process]

Reading-induced shifts of perceptual speech representations in auditory cortex.

Sci Rep. 2017 Jul 11;7(1):5143

Authors: Bonte M, Correia JM, Keetels M, Vroomen J, Formisano E

Abstract
Learning to read requires the formation of efficient neural associations between written and spoken language. Whether these associations influence the auditory cortical representation of speech remains unknown. Here we address this question by combining multivariate functional MRI analysis and a newly-developed 'text-based recalibration' paradigm. In this paradigm, the pairing of visual text and ambiguous speech sounds shifts (i.e. recalibrates) the perceptual interpretation of the ambiguous sounds in subsequent auditory-only trials. We show that it is possible to retrieve the text-induced perceptual interpretation from fMRI activity patterns in the posterior superior temporal cortex. Furthermore, this auditory cortical region showed significant functional connectivity with the inferior parietal lobe (IPL) during the pairing of text with ambiguous speech. Our findings indicate that reading-related audiovisual mappings can adjust the auditory cortical representation of speech in typically reading adults. Additionally, they suggest the involvement of the IPL in audiovisual and/or higher-order perceptual processes leading to this adjustment. When applied in typical and dyslexic readers of different ages, our text-based recalibration paradigm may reveal relevant aspects of perceptual learning and plasticity during successful and failing reading development.

PMID: 28698606 [PubMed - in process]

Proteomics and metabolomics in ageing research: from biomarkers to systems biology.

Essays Biochem. 2017 Jul 15;61(3):379-388

Authors: Hoffman JM, Lyu Y, Pletcher SD, Promislow DEL

Abstract
Age is the single greatest risk factor for a wide range of diseases, and as the mean age of human populations grows steadily older, the impact of this risk factor grows as well. Laboratory studies on the basic biology of ageing have shed light on numerous genetic pathways that have strong effects on lifespan. However, we still do not know the degree to which the pathways that affect ageing in the lab also influence variation in rates of ageing and age-related disease in human populations. Similarly, despite considerable effort, we have yet to identify reliable and reproducible 'biomarkers', which are predictors of one's biological as opposed to chronological age. One challenge lies in the enormous mechanistic distance between genotype and downstream ageing phenotypes. Here, we consider the power of studying 'endophenotypes' in the context of ageing. Endophenotypes are the various molecular domains that exist at intermediate levels of organization between the genotype and phenotype. We focus our attention specifically on proteins and metabolites. Proteomic and metabolomic profiling has the potential to help identify the underlying causal mechanisms that link genotype to phenotype. We present a brief review of proteomics and metabolomics in ageing research with a focus on the potential of a systems biology and network-centric perspective in geroscience. While network analyses to study ageing utilizing proteomics and metabolomics are in their infancy, they may be the powerful model needed to discover underlying biological processes that influence natural variation in ageing, age-related disease, and longevity.

PMID: 28698311 [PubMed - in process]

Systems modelling ageing: from single senescent cells to simple multi-cellular models.

Essays Biochem. 2017 Jul 15;61(3):369-377

Authors: Martinez Guimera A, Welsh C, Dalle Pezze P, Fullard N, Nelson G, Roger MF, Przyborski SA, Shanley DP

Abstract
Systems modelling has been successfully used to investigate several key molecular mechanisms of ageing. Modelling frameworks to allow integration of models and methods to enhance confidence in models are now well established. In this article, we discuss these issues and work through the process of building an integrated model for cellular senescence as a single cell and in a simple tissue context.

PMID: 28698310 [PubMed - in process]

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires.

MBio. 2017 Jul 11;8(4):

Authors: Silas S, Makarova KS, Shmakov S, Páez-Espino D, Mohr G, Liu Y, Davison M, Roux S, Krishnamurthy SR, Fu BXH, Hansen LL, Wang D, Sullivan MB, Millard A, Clokie MR, Bhaya D, Lambowitz AM, Kyrpides NC, Koonin EV, Fire AZ

Abstract
Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains. Nearly all such RTs are present within type III CRISPR-Cas loci, but their phylogeny does not parallel the CRISPR-Cas type classification, indicating that RT-Cas1 is an autonomous functional module that is disseminated by horizontal gene transfer and can function with diverse type III systems. To compare the sequence pools sampled by RT-Cas1-associated and RT-lacking CRISPR-Cas systems, we obtained samples of a commercially grown cyanobacterium-Arthrospira platensis Sequencing of the CRISPR arrays uncovered a highly diverse population of spacers. Spacer diversity was particularly striking for the RT-Cas1-containing type III-B system, where no saturation was evident even with millions of sequences analyzed. In contrast, analysis of the RT-lacking type III-D system yielded a highly diverse pool but reached a point where fewer novel spacers were recovered as sequencing depth was increased. Matches could be identified for a small fraction of the non-RT-Cas1-associated spacers, and for only a single RT-Cas1-associated spacer. Thus, the principal source(s) of the spacers, particularly the hypervariable spacer repertoire of the RT-associated arrays, remains unknown.IMPORTANCE While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures of Arthrospira platensis, a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic.

PMID: 28698278 [PubMed - in process]

Bioinformatics in the Plant Genomic and Phenomic Domain: The German Contribution to Resources, Services and Perspectives.

J Biotechnol. 2017 Jul 08;:

Authors: Schmutzer T, Bolger ME, Rudd S, Chen J, Gundlach H, Arend D, Oppermann M, Weise S, Lange M, Spannagl M, Usadel B, Mayer KFX, Scholz U

Abstract
Plant genetic resources are a substantial opportunity for plant breeding, preservation and maintenance of biological diversity. As part of the German Network for Bioinformatics Infrastructure (de.NBI) the German Crop BioGreenformatics Network (GCBN) focuses mainly on crop plants and provides both data and software infrastructure which are tailored to the needs of the plant research community. Our mission and key objectives include: (1) provision of transparent access to germplasm seeds, (2) the delivery of improved workflows for plant gene annotation, and (3) implementation of bioinformatics services that link genotypes and phenotypes. This review introduces the GCBN's spectrum of web-services and integrated data resources that address common research problems in the plant genomics community.

PMID: 28698099 [PubMed - as supplied by publisher]

From grass to gas: microbiome dynamics of grass biomass acidification under mesophilic and thermophilic temperatures.

Biotechnol Biofuels. 2017;10:171

Authors: Abendroth C, Simeonov C, Peretó J, Antúnez O, Gavidia R, Luschnig O, Porcar M

Abstract
BACKGROUND: Separating acidification and methanogenic steps in anaerobic digestion processes can help to optimize the process and contribute to producing valuable sub-products such as methane, hydrogen and organic acids. However, the full potential of this technology has not been fully explored yet. To assess the underlying fermentation process in more detail, a combination of high-throughput sequencing and proteomics on the acidification step of plant material (grass) at both mesophilic and thermophilic temperatures (37 and 55 °C, respectively) was applied for the first time.
RESULTS: High-strength liquor from acidified grass biomass exhibited a low biodiversity, which differed greatly depending on temperature. It was dominated by Bacteroidetes and Firmicutes at 37 °C, and by Firmicutes and Proteobacteria at 55 °C. At the methane stage, Methanosaeta, Methanomicrobium and Methanosarcina proved to be highly sensitive to environmental changes as their abundance in the seed sludges dropped dramatically after transferring the seed sludges from the respective reactors into the experimental setup. Further, an increase in Actinobacteria coincided with reduced biogas production at the end of the experiment. Over 1700 proteins were quantified from the first cycle of acidification samples using label-free quantitative proteome analysis and searching protein databases. The most abundant proteins included an almost complete set of glycolytic enzymes indicating that the microbial population is basically engaged in the degradation and catabolism of sugars. Differences in protein abundances clearly separated samples into two clusters corresponding to culture temperature. More differentially expressed proteins were found under mesophilic (120) than thermophilic (5) conditions.
CONCLUSION: Our results are the first multi-omics characterisation of a two-stage biogas production system with separated acidification and suggest that screening approaches targeting specific taxa such as Methanosaeta, Methanomicrobium and Methanosarcina could be useful diagnostic tools as indicators of environmental changes such as temperature or oxidative stress or, as in the case of Actinobacteria, they could be used as a proxy of the gas production potential of anaerobic digesters. Metaproteome analyses only detected significant expression differences in mesophilic samples, whereas thermophilic samples showed more stable protein composition with an abundance of chaperones suggesting a role in protein stability under thermal stress.

PMID: 28690680 [PubMed]

33 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2017/07/12

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

16 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2017/07/11

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Apoptotic and genotoxic effects of low-intensity ultrasound on healthy and leukemic human peripheral mononuclear blood cells.

J Med Ultrason (2001). 2017 Jul 08;:

Authors: Saliev T, Begimbetova D, Baiskhanova D, Abetov D, Kairov U, Gilman CP, Matkarimov B, Tachibana K

Abstract
PURPOSE: To scrutinize the apoptotic and genotoxic effects of low-intensity ultrasound and an ultrasound contrast agent (SonoVue; Bracco Diagnostics Inc., EU) on human peripheral mononuclear blood cells (PMBCs).
METHODS: PMBCs were subjected to a low-intensity ultrasound field (1-MHz frequency; spatial peak temporal average intensity 0.18 W/cm2) followed by analysis for apoptosis and DNA damage (single-strand breaks + double-strand breaks). The comet assay was then repeated after 2 h to examine the ability of cells to repair DNA breaks.
RESULTS: The results demonstrated that low-intensity ultrasound was capable of selectively inducing apoptosis in leukemic PMBCs, but not in healthy cells. The introduction of ultrasound contrast agent SonoVue resulted in an increase in apoptosis in both groups. DNA analysis after ultrasound exposure indicated that ultrasound triggered DNA damage in leukemic PMBCs (66.05 ± 13.36%), while the damage was minimal (7.01 ± 0.89%) in control PMBCs. However, both cell lines demonstrated an ability to repair DNA single- and double-strand breaks 2 h after sonication.
CONCLUSIONS: The study demonstrated that low-intensity ultrasound selectively induced apoptosis in cancer PMBCs. Ultrasound-induced DNA damage was observed primarily in leukemic PMBCs. Nevertheless, both cell lines were able to repair ultrasound-mediated DNA strand breaks.

PMID: 28689300 [PubMed - as supplied by publisher]

Evaluating Amber force fields using computed NMR chemical shifts.

Proteins. 2017 Jul 08;:

Authors: Koes DR, Vries JK

Abstract
NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations. Imperfections in force fields generate flawed atomic coordinates. Chemical shifts obtained from flawed coordinates have errors that can be traced back to these imperfections. We use this approach to evaluate a series of AMBER force fields that have been refined over the course of two decades (ff94, ff96, ff99SB, ff14SB, ff14ipq and ff15ipq). For each force field a series of MD simulations are carried out for eight model proteins. The calculated chemical shifts for the (1) H, (15) N and (13) C(a) atoms are compared with experimental values. Initial evaluations are based on root mean squared (RMS) errors at the protein level. These results are further refined based on secondary structure and the types of atoms involved in non-bonded interactions. The best chemical shift for identifying force field differences is the shift associated with peptide protons. Examination of the model proteins on a residue by residue basis reveals that force field performance is highly dependent on residue position. Examination of the time course of non-bonded interactions at these sites provides explanations for chemical shift differences at the atomic coordinate level. Results show that the newer ff14ipq and ff15ipq force fields developed with the implicitly polarized charge method perform better than the older force fields. This article is protected by copyright. All rights reserved.

PMID: 28688107 [PubMed - as supplied by publisher]

CCM111, the water extract of Antrodia cinnamomea, regulates immune-related activity through STAT3 and NF-κB pathways.

Sci Rep. 2017 Jul 07;7(1):4862

Authors: Lin IY, Pan MH, Lai CS, Lin TT, Chen CT, Chung TS, Chen CL, Lin CH, Chuang WC, Lee MC, Lin CC, Ma N

Abstract
Antrodia cinnamomea (AC) exhibits many bioactivities, including anti-inflammatory, anti-cancer, and hepatoprotection activities. Many researchers have studied the functions of the components or fractions of AC, but the functions of the original extractions of AC have not been studied. In addition, the detailed relationship between AC and immune-related signaling pathways is unclear. In this study, we screened the effects of CCM111, which is the extract of AC, on seven immune-related signaling pathways and further investigated whether CCM111 can influence inflammation. Interestingly, our results showed that CCM111 significantly inhibited the IL-6-stimulated STAT3 pathway and the LPS-stimulated NF-κB pathway in macrophages. CCM111 also decreased the phosphorylation of STAT3, Tyk2 and the nuclear translocation of p65. Moreover, CCM111 and F4, a fraction of CCM111, down-regulated nitric oxide (NO) production, the protein levels of iNOS and COX-2, and inflammatory cytokines in macrophage cells. Therefore, our study suggested that CCM111 has the potential to be developed as an effective anti-inflammatory agent.

PMID: 28687744 [PubMed - in process]

Zn(II) mediates vancomycin polymerization and potentiates its antibiotic activity against resistant bacteria.

Sci Rep. 2017 Jul 07;7(1):4893

Authors: Zarkan A, Macklyne HR, Chirgadze DY, Bond AD, Hesketh AR, Hong HJ

Abstract
Vancomycin is known to bind to Zn(II) and can induce a zinc starvation response in bacteria. Here we identify a novel polymerization of vancomycin dimers by structural analysis of vancomycin-Zn(II) crystals and fibre X-ray diffraction. Bioassays indicate that this structure is associated with an increased antibiotic activity against bacterial strains possessing high level vancomycin resistance mediated by the reprogramming of peptidoglycan biosynthesis to use precursors terminating in D-Ala-D-Lac in place of D-Ala-D-Ala. Polymerization occurs via interaction of Zn(II) with the N-terminal methylleucine group of vancomycin, and we show that the activity of other glycopeptide antibiotics with this feature can also be similarly augmented by Zn(II). Construction and analysis of a model strain predominantly using D-Ala-D-Lac precursors for peptidoglycan biosynthesis during normal growth supports the hypothesis that Zn(II) mediated vancomycin polymerization enhances the binding affinity towards these precursors.

PMID: 28687742 [PubMed - in process]