28 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 2019/09/13

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.

34 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 2019/09/12

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.

30 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 2019/09/12

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.

48 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 2019/09/11

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.

37 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 2019/09/10

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.

High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification.

Mol Oncol. 2019 Sep 08;:

Authors: Zhu Y, Weiss T, Zhang Q, Sun R, Wang B, Yi X, Wu Z, Gao H, Cai X, Ruan G, Zhu T, Xu C, Lou S, Yu X, Gillet L, Blattmann P, Saba K, Fankhauser CD, Schmid MB, Rutishauser D, Ljubicic J, Christiansen A, Fritz C, Rupp NJ, Poyet C, Rushing E, Weller M, Roth P, Haralambieva E, Hofer S, Chen C, Jochum W, Gao X, Teng X, Chen L, Zhong Q, Wild PJ, Aebersold R, Guo T

Abstract
Formalin-fixed, paraffin-embedded (FFPE), biobanked tissue samples offer an invaluable resource for clinical and biomarker research. Here we developed a pressure cycling technology (PCT)-SWATH mass spectrometry workflow to analyze FFPE tissue proteomes and applied it to the stratification of prostate cancer (PCa) and diffuse large B-cell lymphoma (DLBCL) samples. We show that the proteome patterns of FFPE PCa tissue samples and their analogous fresh frozen (FF) counterparts have a high degree of similarity and we confirmed multiple proteins consistently regulated in PCa tissues in an independent sample cohort. We further demonstrate temporal stability of proteome patterns from FFPE samples that were stored between one to 15 years in a biobank and show a high degree of the proteome pattern similarity between two types of histological regions in small FFPE samples, i.e. punched tissue biopsies and thin tissue sections of micrometer thickness, despite the existence of a certain degree of biological variations. Applying the method to two independent DLBCL cohorts we identified myeloperoxidase (MPO), a peroxidase enzyme, as a novel prognostic marker. In summary, this study presents a robust proteomic method to analyze bulk and biopsy FFPE tissues and reports the first systematic comparison of proteome maps generated from FFPE and FF samples. Our data demonstrate the practicality and superiority of FFPE over FF samples for proteome in biomarker discovery. Promising biomarker candidates for PCa and DLBCL have been discovered. This article is protected by copyright. All rights reserved.

PMID: 31495056 [PubMed - as supplied by publisher]

The Sponge-Associated Fungus Eurotium chevalieri MUT 2316 and its Bioactive Molecules: Potential Applications in the Field of Antifouling.

Mar Biotechnol (NY). 2019 Sep 07;:

Authors: Bovio E, Fauchon M, Toueix Y, Mehiri M, Varese GC, Hellio C

Abstract
The need for new environmentally friendly antifouling and the observation that many marine organisms have developed strategies to keep their surface free of epibionts has stimulated the search for marine natural compounds with antifouling activities. Sponges and in particular fungi associated with them represent one of the most appropriate sources of defence molecules and could represent a promising biomass for the supply of new antifouling compounds. The objective of this work was therefore to evaluate the antifouling potency of 7 compounds isolated from the sponge derived fungus Eurotium chevalieri MUT 2316. The assessment of their activity targeted the inhibition of the adhesion and/or growth of selected marine bacteria (5) and microalgae (5), as well as the inhibition of the mussel's byssus thread formation (tyrosinase activity). The 7 compounds showed bioactivity, with various levels of selectivity for species. Cyclo-L-Trp-L-Ala was the most promising active compound, and led to the inhibition, at very low concentrations (0.001 μg ml-1 in 61.5% of cases), of adhesion and growth of all the microalgae, of selected bacteria, and towards the inhibition of tyrosinase. Promising results were also obtained for echinulin, neoechinulin A, dihydroauroglaucin and flavoglaucin, respectively, leading to inhibition of adhesion and/or growth of 9, 7, 8 and 8 microfouling species at various concentrations.

PMID: 31494811 [PubMed - as supplied by publisher]

Gene networks and microRNAs: Promises and challenges for treating epilepsies and their comorbidities.

Epilepsy Behav. 2019 Sep 04;:106488

Authors: Lovisari F, Simonato M

Abstract
Neurobiology research has used an essentially reductionist approach for many years, dissecting out the brain in more simple elements. Recent technical advances, like systems biology, have made now possible to embrace a more holistic vision and try to tackle the complexity of the system. In this short review, we describe how these approaches, in particular analyses or gene networks and of microRNAs, may be useful for epilepsy research. We will describe and discuss recent studies that illustrate how these research approaches can lead to the identification of therapeutic targets and pharmacological strategies to prevent or treat some forms of epilepsy. We aim to show that studying epilepsy and its comorbidities within a complex system framework is a promising integration to the traditional reductionist approaches, and that it will become more and more important in the future for developing new therapies. This article is part of the Special Issue "NEWroscience 2018."

PMID: 31494060 [PubMed - as supplied by publisher]

The relationship between environmental factors and different Parkinson's disease subtypes in Greece: Data analysis of the Hellenic Biobank of Parkinson's disease.

Parkinsonism Relat Disord. 2019 Aug 26;:

Authors: Angelopoulou E, Bozi M, Simitsi AM, Koros C, Antonelou R, Papagiannakis N, Maniati M, Poula D, Stamelou M, Vassilatis DK, Michalopoulos I, Geronikolou S, Scarmeas N, Stefanis L

Abstract
INTRODUCTION: The aim of this study is to investigate the association between environmental factors (smoking, coffee, pesticide exposure) and Parkinson's disease (PD) subtypes (early-onset, mid-and-late onset, familial and sporadic) in the Greek population.
METHODS: The Hellenic Biobank of PD recorded information of PD cases and controls from two centers in Greece during 2006-2017. Patients with the A53T mutation in SNCA or GBA mutations were excluded. Associations of environmental factors with PD overall (and PD subtypes) versus controls were explored with logistic regression models adjusting for age, gender and each environmental factor.
RESULTS: 686 patients and 356 controls were included. Smoking was associated with a reduced risk of PD overall (OR 0.48, 95% CI 0.35-0.67), mid-and-late onset (0.46, 0.32-0.66), familial (0.53, 0.34-0.83) and sporadic (0.46, 0.32-0.65), but not early-onset PD. There was an inverse linear association with pack-years of smoking, except for early-onset PD. Early-onset PD was the only PD subtype inversely associated with coffee consumption when dichotomously treated. Compared to never-coffee drinkers, only those at the upper tertile had lower odds for PD overall (0.52, 0.29-0.91), early-onset (0.16, 0.05-0.53) and familial PD (0.36, 0.17-0.75). No associations were found between pesticides and PD.
CONCLUSIONS: Our study shows that the well-known negative association of smoking with PD occurs across all PD subtypes in the Greek population, apart from early-onset PD. Early-onset PD was also most strongly inversely associated with coffee consumption, highlighting a potential distinct underlying physiopathology in this PD subset that may involve specific gene-environment interactions.

PMID: 31494049 [PubMed - as supplied by publisher]

11 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 2019/09/08

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.

36 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 2019/09/07

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.

35 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 2019/09/07

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.

17 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 2019/09/06

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.

40 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 2019/09/05

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.

41 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 2019/09/04

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.

13 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 2019/09/03

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.

Peroxide-driven catalysis of the heme domain of A. radioresistens cytochrome P450 116B5 for sustainable aromatic rings oxidation and drug metabolites production.

N Biotechnol. 2019 Aug 29;:

Authors: Ciaramella A, Catucci G, Di Nardo G, Sadeghi SJ, Gilardi G

Abstract
The heme domain of cytochrome P450 116B5 from Acinetobacter radioresistens (P450 116B5hd), a self-sufficient class VII P450, was functionally expressed in Escherichia coli, purified and characterised in active form. Its unusually high reduction potential (-144 ± 42 mV) and stability in the presence of hydrogen peroxide make this enzyme a good candidate for driving catalysis with the so-called peroxide shunt, avoiding the need for a reductase and the expensive cofactor NAD(P)H. The enzyme is able to carry out the peroxide-driven hydroxylation of aromatic compounds such as p-nitrophenol (KM = 128.85 ± 29.51 μM and kcat = 2.65 ± 0.14 min-1), 10-acetyl-3,7-dihydroxyphenoxazine (KM = 6.01 ± 0.32 μM and kcat = 0.33 ± 0.03 min-1), and 3,5,3',5'tetramethylbenzidine (TMB). Moreover, it catalyses different reactions on well-known drugs such as hydroxylation of diclofenac (KM = 49.60 ± 6.30 μM and kcat = 0.06 ± 0.01 min-1) and N-desmethylation of tamoxifen (KM = 57.20 ± 7.90 μM and kcat = 0.79 ± 0.04 min-1). The data demonstrate that P450 116B5hd is an efficient biocatalyst for sustainable applications in bioremediation and human drug metabolite production.

PMID: 31473254 [PubMed - as supplied by publisher]

MicroRNA-17 Acts as a Tumor Chemosensitizer by Targeting JAB1/CSN5 in Triple-Negative Breast Cancer.

Cancer Lett. 2019 Aug 29;:

Authors: Wang S, Oh DY, Leventaki V, Drakos E, Zhang R, Sahin AA, Resetkova E, Edgerton ME, Wu W, Claret FX

Abstract
Triple-negative breast cancer (TNBC) is the breast cancer subtype with the poorest prognosis. Evidence indicates that aberrant JAB1/CSN5 expression is associated with advanced tumor stage and poor prognosis in breast cancer. In this study, we evaluated expression of JAB1 in TNBC and potential mechanisms regulating this expression. We found that miR-17 expression was lower in TNBC than in normal breast tissue, and miR-17 expression in patients with TNBC was associated with a good prognosis. Furthermore, JAB1 expression was regulated by miR-17 in TNBC cells, and mice with miR-17-overexpressing tumors had less tumor growth and lower tumor JAB1 expression than control mice. We also demonstrated that miR-17 suppressed JAB1's oncogenic function, leading to tumor growth inhibition and sensitizing TNBC cells to chemotherapy treatment. JAB1 knockdown in TNBC cells mimicked the effect of miR-17 overexpression and led to significant decreases in cell proliferation, colony formation, and migration, increased p27 expression, and enhanced cisplatin sensitivity. Our findings suggest that miR-17 acts as a tumor suppressor by directly targeting JAB1 in TNBC; this may lead to novel therapeutic targets and strategies for treating TNBC patients.

PMID: 31473252 [PubMed - as supplied by publisher]

сWnt signaling modulation results in a change of the colony architecture in a hydrozoan.

Dev Biol. 2019 Aug 29;:

Authors: Bagaeva TS, Kupaeva DM, Vetrova AA, Kosevich IA, Kraus YA, Kremnyov SV

Abstract
At the polyp stage, most hydrozoan cnidarians form highly elaborate colonies with a variety of branching patterns, which makes them excellent models for studying the evolutionary mechanisms of body plan diversification. At the same time, molecular mechanisms underlying the robust patterning of the architecturally complex hydrozoan colonies remain unexplored. Using non-model hydrozoan Dynamena pumila we showed that the key components of the Wnt/β-catenin (cWnt) pathway (β-catenin, TCF) and the cWnt-responsive gene, brachyury 2, are involved in specification and patterning of the developing colony shoots. Strikingly, pharmacological modulation of the cWnt pathway leads to radical modification of the monopodially branching colony of Dynamena which acquire branching patterns typical for colonies of other hydrozoan species. Our results suggest that modulation of the cWnt signaling to be the driving force promoting the evolution of the vast variety of the body plans in hydrozoan colonies and offer an intriguing possibility that the involvement of the cWnt pathway in the regulation of branching morphogenesis might represent an ancestral feature predating the cnidarian-bilaterian split.

PMID: 31473187 [PubMed - as supplied by publisher]

Rapid and high-precision sizing of single particles using parallel suspended microchannel resonator arrays and deconvolution.

Rev Sci Instrum. 2019 Aug;90(8):085004

Authors: Stockslager MA, Olcum S, Knudsen SM, Kimmerling RJ, Cermak N, Payer KR, Agache V, Manalis SR

Abstract
Measuring the size of micron-scale particles plays a central role in the biological sciences and in a wide range of industrial processes. A variety of size parameters, such as particle diameter, volume, and mass, can be measured using electrical and optical techniques. Suspended microchannel resonators (SMRs) are microfluidic devices that directly measure particle mass by detecting a shift in resonance frequency as particles flow through a resonating microcantilever beam. While these devices offer high precision for sizing particles by mass, throughput is fundamentally limited by the small dimensions of the resonator and the limited bandwidth with which changes in resonance frequency can be tracked. Here, we introduce two complementary technical advancements that vastly increase the throughput of SMRs. First, we describe a deconvolution-based approach for extracting mass measurements from resonance frequency data, which allows an SMR to accurately measure a particle's mass approximately 16-fold faster than previously possible, increasing throughput from 120 particles/min to 2000 particles/min for our devices. Second, we describe the design and operation of new devices containing up to 16 SMRs connected fluidically in parallel and operated simultaneously on the same chip, increasing throughput to approximately 6800 particles/min without significantly degrading precision. Finally, we estimate that future systems designed to combine both of these techniques could increase throughput by nearly 200-fold compared to previously described SMR devices, with throughput potentially as high as 24 000 particles/min. We envision that increasing the throughput of SMRs will broaden the range of applications for which mass-based particle sizing can be employed.

PMID: 31472632 [PubMed - in process]