25 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 2018/09/07

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 2018/09/07

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.

47 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 2018/09/06

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.

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 2018/09/05

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.

23 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 2018/09/04

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.

Androgen receptor is a negative regulator of contextual fear memory in male mice.

Horm Behav. 2018 Aug 30;:

Authors: Ramzan F, Azam AB, Monks DA, Zovkic IB

Abstract
Although sex-hormones have a well-documented role in memory formation, most literature has focused on estrogens, whereas the role of androgens and their receptor (the androgen receptor; AR) in fear memory is relatively unexplored. To address this gap, we used a transgenic mouse model of AR overexpression (CMV-AR) to determine if AR regulates fear memory, and if this effect can be reversed either by the removal of circulating androgens via gonadectomy, or by antagonising AR activity with flutamide. We found that AR overexpression results in reduced freezing in response to foot shock, and that this difference is reversed with both gonadectomy and flutamide treatment. Differences between genotypes were reinstated by testosterone replacement in gonadectomized mice, suggesting that reduced fear memory in mutants results from AR activation by testosterone and is not secondary to group differences in circulating testosterone. Potential transcriptional mechanisms by which CMV-AR exerts its effects on fear memory were assessed by quantitating the expression of memory-related genes in area CA1 of the hippocampus. Several genes that are altered with AR inhibition and activation, including genes that encode for the histone variant H2A.Z, cholinergic receptors, glutamate receptors, and brain-derived neurotrophic factor. Overall, our findings suggest that AR is a negative regulator of fear memory and identify potential gene targets through which AR may mediate this effect.

PMID: 30172646 [PubMed - as supplied by publisher]

Integrated LAMP and immunoassay platform for diarrheal disease detection.

Biosens Bioelectron. 2018 Aug 10;120:93-101

Authors: Phaneuf CR, Mangadu B, Tran HM, Light YK, Sinha A, Charbonier FW, Eckles TP, Singh AK, Koh CY

Abstract
The challenges of diagnosing infectious disease, especially in the developing world, and the shortcomings of available instrumentation have exposed the need for portable, easy-to-use diagnostic tools capable of detecting the wide range of causative microbes while operating in low resource settings. We present a centrifugal microfluidic platform that combines ultrasensitive immunoassay and isothermal amplification-based screening for the orthogonal detection of both protein and nucleic acid targets at the point-of-care. A disposable disc with automatic aliquoting inlets is paired with a non-contact heating system and precise rotary control system to yield an easy-to-use, field-deployable platform with versatile screening capabilities. The detection of three enterotoxins (cholera toxin, Staphylococcal enterotoxin B, and Shiga-like toxin 1) and three enteric bacteria (C. jejuni, E. coli, and S. typhimurium) were performed independently and shown to be highly sensitive (limit of detection = 1.35-5.50 ng/mL for immunoassays and 1-30 cells for isothermal amplification), highly exclusive in the presence of non-specific targets, and capable of handling a complex sample matrix like stool. The full panel of toxins and bacteria were reliably detected simultaneously on a single disc at clinically relevant sample concentrations in less than an hour. The ability of our technology to detect multiple analyte types in parallel at the point-of-care can serve a variety of needs, from routine patient care to outbreak triage, in a variety of settings to reduce disease impact and expedite effective treatment.

PMID: 30172236 [PubMed - as supplied by publisher]

From systems biology to metabolically engineered cells-an omics perspective on the development of industrial microbes.

Curr Opin Microbiol. 2018 Aug 29;45:180-188

Authors: Becker J, Wittmann C

Abstract
Green routes are indispensable for a sustainable production of energy, chemicals and materials, and health and nutrition products from renewable resources. Naturally, microbes are capable to conduct many of the desired biochemical conversions involved, however, only at rather low efficiency. It is therefore essential to metabolically engineer them towards efficient cell factories, which enable a high product titer, yield and productivity, exhibit a good process robustness and a broad substrate spectrum, and are safe to be used, to name a few prominent points from the wish list for industrial bio-production. Such optimization of a microbial cell typically involves the implementation of several up to multiple traits into its genome, which then mediate the desired phenotype. While the genetic modification step itself is straightforward due to the much advanced genome editing methods, the selection of what exactly has to be optimized out of the manifold possibilities is still a challenge. Here we will discuss, how systems biology can offer guidance to orchestrate the hundreds to thousands of biochemical conversions of a microbe into a concert of desired performance. To this end, we will highlight recent success stories, where systems biology approaches have enabled next-level cell factories and bioprocesses.

PMID: 30172106 [PubMed - as supplied by publisher]

Pentose metabolism in Saccharomyces cerevisiae: The need to engineer global regulatory systems.

Biotechnol J. 2018 Sep 01;:e1800364

Authors: Gopinarayanan VE, Nair NU

Abstract
Extending the host substrate range of industrially relevant microbes, such as Saccharomyces cerevisiae, has been a highly-active area of research since the conception of metabolic engineering. Yet, rational strategies that enable non-native substrate utilization in this yeast without the need for combinatorial and/or evolutionary techniques are underdeveloped. In this review, we focus on pentose metabolism in S. cerevisiae as a case study to highlight the challenges in this field. In the last three decades, work has focused on expressing exogenous pentose metabolizing enzymes as well as other endogenous enzymes for effective pentose assimilation, growth, and biofuel production. We go over the engineering strategies that have been employed for pentose assimilation in this yeast and compare it with metabolism and regulation of native sugar, galactose. In the case of galactose metabolism, multiple signals regulate and aid growth in the presence of the sugar. However, for pentoses that are non-native, it is unclear if similar growth and regulatory signals are activated. Such a comparative analysis aids in identifying missing links in xylose and arabinose utilization. While research on pentose metabolism have mostly concentrated on pathway level optimization, recent transcriptomics analyses highlight the need to consider more global regulatory, structural, and signaling components.

PMID: 30171750 [PubMed - as supplied by publisher]

Barrier properties and transcriptome expression in human iPSC-derived models of the blood-brain barrier.

Stem Cells. 2018 Sep 01;:

Authors: Delsing L, Dönnes P, Sánchez J, Clausen M, Voulgaris D, Falk A, Herland A, Brolén G, Zetterberg H, Hicks R, Synnergren J

Abstract
Cell-based models of the blood-brain barrier (BBB) are important for increasing the knowledge of BBB formation, degradation and brain exposure of drug substances. Human models are preferred over animal models because of inter-species differences in BBB structure and function. However, access to human primary BBB tissue is limited and has shown degeneration of BBB functions in vitro. Human induced pluripotent stem cells (iPSCs) can be used to generate relevant cell types to model the BBB with human tissue. We generated a human iPSC-derived model of the BBB that includes endothelial cells in co-culture with pericytes, astrocytes and neurons. Evaluation of barrier properties showed that the endothelial cells in our co-culture model have high transendothelial electrical resistance, functional efflux and ability to discriminate between CNS permeable and non-permeable substances. Whole genome expression profiling revealed transcriptional changes that occur in co-culture, including upregulation of tight junction proteins such as claudins and neurotransmitter transporters. Pathway analysis implicated changes in the WNT, TNF and PI3K-Akt pathways upon co-culture. Our data suggests that co-culture of iPSC-derived endothelial cells promotes barrier formation on a functional and transcriptional level. The information about gene expression changes in co-culture can be used to further improve iPSC-derived BBB models through selective pathway manipulation. © AlphaMed Press 2018.

PMID: 30171748 [PubMed - as supplied by publisher]

Mathematical Techniques for Understanding Platelet Regulation and the Development of New Pharmacological Approaches.

Methods Mol Biol. 2018;1812:255-279

Authors: Dunster JL, Panteleev MA, Gibbins JM, Sveshnikova AN

Abstract
Mathematical and computational modeling is currently in the process of becoming an accepted tool in the arsenal of methods utilized for the investigation of complex biological systems. For some problems in the field, like cellular metabolic regulation, neural impulse propagation, or cell cycle, progress is already unthinkable without use of such methods. Mathematical models of platelet signaling, function, and metabolism during the last years have not only been steadily increasing in their number, but have also been providing more in-depth insights, generating hypotheses, and allowing predictions to be made leading to new experimental designs and data. Here we describe the basic approaches to platelet mathematical model development and validation, highlighting the challenges involved. We then review the current theoretical models in the literature and how these are being utilized to increase our understanding of these complex cells.

PMID: 30171583 [PubMed - in process]

Precise Quantification of Platelet Proteins and Their Phosphorylation States.

Methods Mol Biol. 2018;1812:113-125

Authors: Mazet F, Fry MJ

Abstract
Systems biology and modeling approaches require quantitative data-rich temporal experiments to better understand the dynamics and regulation of the components of the signaling pathways that governs cell biology and physiology. Here we present a modified Western blotting method to rapidly analyze and accurately quantify protein copy number, and their respective phosphorylation states at specific sites over detailed time courses.

PMID: 30171575 [PubMed - in process]

Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study.

Nat Methods. 2018 Sep;15(9):669-676

Authors: Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Rezaei Adariani S, Ambrose B, Aznauryan M, Barth A, Birkedal V, Bowen ME, Chen H, Cordes T, Eilert T, Fijen C, Gebhardt C, Götz M, Gouridis G, Gratton E, Ha T, Hao P, Hanke CA, Hartmann A, Hendrix J, Hildebrandt LL, Hirschfeld V, Hohlbein J, Hua B, Hübner CG, Kallis E, Kapanidis AN, Kim JY, Krainer G, Lamb DC, Lee NK, Lemke EA, Levesque B, Levitus M, McCann JJ, Naredi-Rainer N, Nettels D, Ngo T, Qiu R, Robb NC, Röcker C, Sanabria H, Schlierf M, Schröder T, Schuler B, Seidel H, Streit L, Thurn J, Tinnefeld P, Tyagi S, Vandenberk N, Vera AM, Weninger KR, Wünsch B, Yanez-Orozco IS, Michaelis J, Seidel CAM, Craggs TD, Hugel T

Abstract
Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.

PMID: 30171252 [PubMed - in process]

Author Correction: Estrogen-related receptor gamma functions as a tumor suppressor in gastric cancer.

Nat Commun. 2018 Aug 31;9(1):3599

Authors: Kang MH, Choi H, Oshima M, Cheong JH, Kim S, Lee JH, Park YS, Choi HS, Kweon MN, Pack CG, Lee JS, Mills GB, Myung SJ, Park YY

Abstract
The original version of this Article contained errors in Figs. 4, 5, and 6. In Fig. 4d, the x-axis label incorrectly read 'blank, +, blank, +', and in Fig. 5e, the bars of the second graph from the left were coloured blue-orange-blue-orange. Both of these errors have been fixed in the PDF and HTML versions of the Article. Furthermore, in Fig. 6a, the right-hand image of AGS cells treated with 5 µM DY131 was inadvertently replaced with a duplicate of the left-hand image. The correct version of this figure panel appears in the Author Correction associated with this Article. For transparency, the error has not been corrected in the PDF or HTML versions of the Article.

PMID: 30171186 [PubMed - in process]

A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis.

Mol Cancer Res. 2018 Aug 31;:

Authors: Zhao Y, Schaafsma E, Gorlov IP, Hernando E, Thomas NE, Shen R, Turk MJ, Berwick M, Amos CI, Cheng C

Abstract
Melanoma is the most aggressive type of skin cancer in the United States with an increasing incidence. Melanoma lesions often exhibit high immunogenicity, with infiltrating immune cells playing important roles in regression of tumors occurring spontaneously or caused by therapeutic treatment. Computational and experimental methods have been used to estimate the abundance of immune cells in tumors, but their applications are limited by the requirement of large gene sets or multiple antibodies. While the prognostic role of immune cells has been appreciated, a systematic investigation of their association with clinical factors, genomic features, prognosis and treatment response in melanoma is still lacking. This study, identifies a 25-gene signature based on RNA-seq data from The Cancer Genome Atlas - Skin Cutaneous Melanoma (TCGA-SKCM) dataset. This signature was used to calculate sample-specific Leukocyte Infiltration Scores (LISs) in six independent melanoma microarray datasets and scores were found to vary substantially between different melanoma lesion sites and molecular subtypes. For metastatic melanoma, LIS was prognostic in all datasets with high LIS being associated with good survival. The current approach provided additional prognostic information over established clinical factors including age, tumor stage and gender. Additionally, LIS was predictive of patient survival in stage III melanoma, and treatment efficacy of tumor-specific antigen vaccine.
IMPLICATIONS: This study identifies a 25-gene signature that effectively estimates the level of immune cell infiltration in melanoma, which provides a robust biomarker for predicting patient prognosis.

PMID: 30171176 [PubMed - as supplied by publisher]

26 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 2018/09/01

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.

25 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 2018/09/01

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 2018/08/31

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 2018/08/31

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 2018/08/30

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.