55 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 2018/11/28

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.

53 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 2018/11/28

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.

43 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 2018/11/27

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.

43 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 2018/11/27

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.

Hierarchical parameter estimation of GRN based on topological analysis.

IET Syst Biol. 2018 Dec;12(6):294-303

Authors: Zhang W, Zhang F, Zhang J, Wang N

Abstract
Reverse engineering of gene regulatory network (GRN) is an important and challenging task in systems biology. Existing parameter estimation approaches that compute model parameters with the same importance are usually computationally expensive or infeasible, especially in dealing with complex biological networks.In order to improve the efficiency of computational modeling, the paper applies a hierarchical estimation methodology in computational modeling of GRN based on topological analysis. This paper divides nodes in a network into various priority levels using the graph-based measure and genetic algorithm. The nodes in the first level, that correspond to root strongly connected components(SCC) in the digraph of GRN, are given top priority in parameter estimation. The estimated parameters of vertices in the previous priority level ARE used to infer the parameters for nodes in the next priority level. The proposed hierarchical estimation methodology obtains lower error indexes while consuming less computational resources compared with single estimation methodology. Experimental outcomes with insilico networks and a realistic network show that gene networks are decomposed into no more than four levels, which is consistent with the properties of inherent modularity for GRN. In addition, the proposed hierarchical parameter estimation achieves a balance between computational efficiency and accuracy.

PMID: 30472694 [PubMed - in process]

Cancers classification based on deep neural networks and emotional learning approach.

IET Syst Biol. 2018 Dec;12(6):258-263

Authors: Jafarpisheh N, Teshnehlab M

Abstract
In the present era, enormous factors contribute to causing cancer. So cancer classification cannot rely only on doctor's thoughts. As a result, intelligent algorithms concerning doctor's help are inevitable. Therefore, the authors are motivated to suggest a novel algorithm to classify three cancer datasets; colon, ALL-AML, and leukaemia cancers. Their proposed algorithm is based on the deep neural network and emotional learning process. First of all, by applying the principal component analysis, they had a feature reduction. Then, they used deep neural as a feature extraction. Then, they implemented different classifiers; multi-layer perceptron, support vector machine (SVM), decision tree, and Gaussian mixture model. In the end, because in the real world, especially when working on systems biology, unpredictable events, and uncertainties are undeniable, the robustness of their model against uncertainties is important. So they added Gaussian noise to the input features of the first encoder in each dataset, then, they applied the stacked denoising method. Experimental results disclosed that, generally, using emotional learning increased the accuracy. In addition, the highest accuracy was gained by SVM, 91.66, 92.27, and 96.56% for colon, ALL-AML, and leukaemia, respectively. However, GMM led to the lowest accuracy. The best accuracy gained by GMM was 60%.

PMID: 30472689 [PubMed - in process]

Immunological and clinical effects of low-dose interleukin-2 across 11 autoimmune diseases in a single, open clinical trial.

Ann Rheum Dis. 2018 Nov 24;:

Authors: Rosenzwajg M, Lorenzon R, Cacoub P, Pham HP, Pitoiset F, El Soufi K, RIbet C, Bernard C, Aractingi S, Banneville B, Beaugerie L, Berenbaum F, Champey J, Chazouilleres O, Corpechot C, Fautrel B, Mekinian A, Regnier E, Saadoun D, Salem JE, Sellam J, Seksik P, Daguenel-Nguyen A, Doppler V, Mariau J, Vicaut E, Klatzmann D

Abstract
OBJECTIVE: Regulatory T cells (Tregs) prevent autoimmunity and control inflammation. Consequently, any autoimmune or inflammatory disease reveals a Treg insufficiency. As low-dose interleukin-2 (ld-IL2) expands and activates Tregs, it has a broad therapeutic potential.
AIM: We aimed to assess this potential and select diseases for further clinical development by cross-investigating the effects of ld-IL2 in a single clinical trial treating patients with 1 of 11 autoimmune diseases.
METHODS: We performed a prospective, open-label, phase I-IIa study in 46 patients with a mild to moderate form of either rheumatoid arthritis, ankylosing spondylitis, systemic lupus erythematosus, psoriasis, Behcet's disease, granulomatosis with polyangiitis, Takayasu's disease, Crohn's disease, ulcerative colitis, autoimmune hepatitis and sclerosing cholangitis. They all received ld-IL2 (1 million IU/day) for 5 days, followed by fortnightly injections for 6 months. Patients were evaluated by deep immunomonitoring and clinical evaluation.
RESULTS: ld-IL2 was well tolerated whatever the disease and the concomitant treatments. Thorough supervised and unsupervised immunomonitoring demonstrated specific Treg expansion and activation in all patients, without effector T cell activation. Indication of potential clinical efficacy was observed.
CONCLUSION: The dose of IL-2 and treatment scheme used selectively activate and expand Tregs and are safe across different diseases and concomitant treatments. This and preliminary indications of clinical efficacy should licence the launch of phase II efficacy trial of ld-IL2 in various autoimmune and inflammatory diseases.
TRIAL REGISTRATION NUMBER: NCT01988506.

PMID: 30472651 [PubMed - as supplied by publisher]

Mitochondria are a Substrate of Cellular Memory.

Free Radic Biol Med. 2018 Nov 22;:

Authors: Cheikhi A, Wallace C, Croix CS, Cohen C, Tang WY, Wipf P, Benos PV, Ambrosio F, Barchowsky A

Abstract
Cellular memory underlies cellular identity, and thus constitutes a unifying mechanism of genetic disposition, environmental influences, and cellular adaptation. Here, we demonstrate that enduring physicochemical changes of mitochondrial networks invoked by transient stress, a phenomenon we term 'mitoengrams', underlie the transgenerational persistence of epigenetically scripted cellular behavior. Using C2C12 myogenic stem-like cells, we show that stress memory elicited by transient, low-level arsenite exposure is stored within a self-renewing subpopulation of progeny cells in a mitochondrial-dependent fashion. Importantly, we demonstrate that erasure of mitoengrams by administration of mitochondria-targeted electron scavenger was sufficient to reset key epigenetic marks of cellular memory and redirect the identity of the mitoengram-harboring progeny cells to a non-stress-like state. Together, our findings indicate that mnemonic information emanating from mitochondria support the balance between the persistence and transience of cellular memory.

PMID: 30472365 [PubMed - as supplied by publisher]

Kinetic understanding of nitrogen supply condition on biosynthesis of polyhydroxyalkanoate from benzoate by Pseudomonas putida KT2440.

Bioresour Technol. 2018 Nov 12;273:538-544

Authors: Xu Z, Li X, Hao N, Pan C, de la Torre L, Ahamed A, Miller JH, Ragauskas AJ, Yuan J, Yang B

Abstract
Nitrogen supply is critical to the synthesis of intracellular PHA in various bacteria. However, the specific role of the nitrogen in synthesizing PHA from benzoate, a lignin model compound use for the study of bacteria catabolism of aromatics, is still not clear. In this study, two culture conditions were maintained for Pseudomonas putida KT2440 to produce PHA using benzoate as a carbon source. Under nitrogen-limited and surplus conditions, the accumulation of PHA was to 37.3% and 0.25% of cell dry weight, respectively. A model fit to the kinetics of biomass growth and PHA accumulation showed good agreement with data. GC-MS and NMR showed that PHA contained six hydroxyl fatty acid monomers under nitrogen-limited conditions, while two monomers were identified under nitrogen surplus conditions. The average molecular weight of PHA increased after the nitrogen source was exhausted. These results provide a promising strategy for optimization of lignin to PHA yields.

PMID: 30472353 [PubMed - as supplied by publisher]

Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity.

Cell Host Microbe. 2018 Nov 09;:

Authors: Li P, Wei Y, Mei M, Tang L, Sun L, Huang W, Zhou J, Zou C, Zhang S, Qin CF, Jiang T, Dai J, Tan X, Zhang QC

Abstract
Zika virus (ZIKV) strains can be classified into the ancestral African and contemporary Asian lineages, with the latter responsible for recent epidemics associated with neurological conditions. To understand how Asian strains lead to exacerbated disease, a crucial step is identifying genomic variations that affect infectivity and pathogenicity. Here we use two high-throughput sequencing approaches to assess RNA secondary structures and intramolecular RNA-RNA interactions in vivo for the RNA genomes of Asian and African ZIKV lineages. Our analysis identified functional RNA structural elements and a functional long-range intramolecular interaction specific for the Asian epidemic strains. Mutants that disrupt this extended RNA interaction between the 5' UTR and the E protein coding region reduce virus infectivity, which is partially rescued with compensatory mutants, restoring this RNA-RNA interaction. These findings illuminate the structural basis of ZIKV regulation and provide a resource for the discovery of RNA structural elements important for ZIKV infection.

PMID: 30472207 [PubMed - as supplied by publisher]

Quantitative Clonal Analysis and Single-Cell Transcriptomics Reveal Division Kinetics, Hierarchy, and Fate of Oral Epithelial Progenitor Cells.

Cell Stem Cell. 2018 Nov 07;:

Authors: Jones KB, Furukawa S, Marangoni P, Ma H, Pinkard H, D'Urso R, Zilionis R, Klein AM, Klein OD

Abstract
The oral mucosa is one of the most rapidly dividing tissues in the body and serves as a barrier to physical and chemical insults from mastication, food, and microorganisms. Breakdown of this barrier can lead to significant morbidity and potentially life-threatening infections for patients. Determining the identity and organization of oral epithelial progenitor cells (OEPCs) is therefore paramount to understanding their roles in homeostasis and disease. Using lineage tracing and label retention experiments, we show that rapidly dividing OEPCs are located broadly within the basal layer of the mucosa throughout the oral cavity. Quantitative clonal analysis demonstrated that OEPCs undergo population-asymmetrical divisions following neutral drift dynamics and that they respond to chemotherapy-induced damage by altering daughter cell fates. Finally, using single-cell RNA-seq, we establish the basal layer population structure and propose a model that defines the organization of cells within the basal layer.

PMID: 30472156 [PubMed - as supplied by publisher]

Editorial commentary: Ecology of cardio-metabolic diseases: Low-income countries also matter.

Trends Cardiovasc Med. 2018 Nov 16;:

Authors: Eze IC, Probst-Hensch N

PMID: 30471986 [PubMed - as supplied by publisher]

Growth-inhibitory effects of TGFαL3-SEB chimeric protein on colon cancer cell line.

Biomed Pharmacother. 2018 Nov 21;110:190-196

Authors: Maleki F, Sadeghifard N, Hosseini HM, Bakhtiyari S, Goleij Z, Behzadi E, Sedighian H, Imani Fooladi AA

Abstract
BACKGROUND: TGFαL3-SEB chimeric protein is a synthetic protein, which is produced by combining the third loop (L3) of transforming growth factor-α (TGF-α) with staphylococcal enterotoxin type B. To the best of our knowledge, anti-cancer activity of this chimeric protein against colon cancer that overexpresses epidermal growth factor receptor (EGFR) has not yet been studied. Thus, in the present study, the anti-tumor effects of TGFαL3-SEB chimeric protein on HT-29 colon cancer cells were evaluated.
MATERIALS AND METHODS: The TGFαL3-SEB chimeric protein was previously designed and cloned in Escherichia coli (E. coli) [1,2]. The level of expression and the purity of this novel protein were examined for further analysis. For this purpose, the cells were treated with different concentrations (25, 50 and 75 μg/ml) of TGFαL3-SEB and then the proliferation was detected using the MTT assay. The apoptosis-inducing potential of TGFαL3-SEB in HT-29 and HEK-293 cells was evaluated by flow cytometry using Annexin V/PI double staining method; in addition, bax/bcl2 mRNA ratio, caspase-3 and caspase-9 activity were also assessed.
RESULTS: In the present study, TGFαL3-SEB chimeric protein was produced in E. coli. After effective purification, its growth inhibitory effect was evaluated. Our results indicated that the incubation of HT-29 colon cancer cell with 25, 50 and 75 μg/ml of TGFαL3-SEB for 24 h leads to significant reduction of proliferation in a dose-dependent manner (P < 0.05). Further analysis indicated that exposure of EGFR expressing HT-29 cells to TGFαL3-SEB leads to significant increase of the caspase-3 and caspase-9 activity in a concentration-dependent manner (P < 0.05). Bax/bcl-2 ratio also confirmed that TGFαL3-SEB has the pro-apoptotic effect. Flow cytometry analysis of TGFαL3-SEB treated cells showed that in addition to apoptotic cells, necrotic cells were also increased significantly at the concentration of 25, 50 and 75 μg/ml (P < 0.05).
CONCLUSION: In conclusion, our results demonstrated that TGFαL3-SEB chimeric protein induced cell death through both mechanisms of apoptosis and necrosis in HT-29 colon cancer cells. This paper has highlighted that TGFαL3-SEB has the potential to target EGFR expressing cancer cell.

PMID: 30471512 [PubMed - as supplied by publisher]

Yeast chemogenomic screen identifies distinct metabolic pathways required to tolerate exposure to phenolic fermentation inhibitors ferulic acid, 4-hydroxybenzoic acid and coniferyl aldehyde.

Metab Eng. 2018 Nov 21;:

Authors: Fletcher E, Gao K, Mercurio K, Ali M, Baetz K

Abstract
The conversion of plant material into biofuels and high value products is a two-step process of hydrolysing plant lignocellulose and next fermenting the sugars produced. However, lignocellulosic hydrolysis not only frees sugars for fermentation it simultaneously generates toxic chemicals, including phenolic compounds which severely inhibit yeast fermentation. To understand the molecular basis of phenolic compound toxicity, we performed genome-wide chemogenomic screens in Saccharomyces cerevisiae to identify deletion mutants that were either hypersensitive or resistant to three common phenolic compounds found in hydrolysates: coniferyl aldehyde, ferulic acid and 4-hydroxybenzoic acid. Despite being similar in structure, our screen revealed that the cell utilizes distinct pathways to tolerate phenolic compound exposure. Furthermore, although each phenolic compound induced reactive oxygen species (ROS), ferulic acid and 4-hydroxybenzoic acid-induced a general cytoplasmic ROS distribution while coniferyl aldehyde-induced ROS partially localized to the mitochondria and to a lesser extent, the endoplasmic reticulum. We found that the glucose-6-phosphate dehydrogenase pentose enzyme Zwf1, which is the first rate limiting step of pentose phosphate pathway, is required for reducing the production of coniferyl aldehyde-induced ROS, potentially through the sequestering of Zwf1 to sites ROS accumulation. Our novel insights into biological impact of three common phenolic inhibitors will inform the engineering of yeast strains with improve the efficiency of biofuel and biochemical production in the presence hydrolysate-derived phenolic compounds.

PMID: 30471359 [PubMed - as supplied by publisher]

Entropy production rate is maximized in non-contractile actomyosin.

Nat Commun. 2018 Nov 23;9(1):4948

Authors: Seara DS, Yadav V, Linsmeier I, Tabatabai AP, Oakes PW, Tabei SMA, Banerjee S, Murrell MP

Abstract
The actin cytoskeleton is an active semi-flexible polymer network whose non-equilibrium properties coordinate both stable and contractile behaviors to maintain or change cell shape. While myosin motors drive the actin cytoskeleton out-of-equilibrium, the role of myosin-driven active stresses in the accumulation and dissipation of mechanical energy is unclear. To investigate this, we synthesize an actomyosin material in vitro whose active stress content can tune the network from stable to contractile. Each increment in activity determines a characteristic spectrum of actin filament fluctuations which is used to calculate the total mechanical work and the production of entropy in the material. We find that the balance of work and entropy does not increase monotonically and the entropy production rate is maximized in the non-contractile, stable state of actomyosin. Our study provides evidence that the origins of entropy production and activity-dependent dissipation relate to disorder in the molecular interactions between actin and myosin.

PMID: 30470750 [PubMed - in process]

Assessing the generation, recycling and disposal practices of electronic/electrical-waste (E-Waste) from major cities in Pakistan.

Waste Manag. 2018 Nov 21;:

Authors: Sajid M, Syed JH, Iqbal M, Abbas Z, Hussain I, Baig MA

Abstract
Rapid increase in the quantity of electronic/electrical-waste (e-waste) has become an emerging issue throughout the world. To avoid higher expenditures on safe disposal and recycling, large quantities of e-waste are being exported from developed to developing countries like Pakistan. Emerging issue of e-waste in Pakistan demands its effective management strategy for the country. However, it cannot be achieved until assessment of e-waste quantification and disposal is carried out. The main objective of this study was to quantify the e-waste inventory and it's processing from major cities of Pakistan to evaluate its generation (domestic/import) and recycling practices. This study comprises the information of only those e-waste items (desktop computers, laptops/notebooks, computer monitors and liquid-crystal display units) which form the major portion of e-waste imported to Pakistan. Survey based data collected from three major cities/areas have been extrapolated to develop an e-waste generation inventory for the country. The study reveals that approximately 50 kt of e-waste is being imported as scrap in addition to its local generation of about 38 kt per year. During field visits and data collection surveys, it has been observed that the processing of e-waste in the country is being carried out in crude manner without safety gears. Findings of our study strongly recommend dire need for urgent and effective monitoring as well as control of informal e-waste management in Pakistan.

PMID: 30470632 [PubMed - as supplied by publisher]

Early life immunity in the era of systems biology: understanding development and disease.

Genome Med. 2018 Nov 23;10(1):88

Authors: Schaffert S, Khatri P

Abstract
Systems immunology has the potential to offer invaluable insights into the development of the immune system. Two recent studies offer an in-depth view of both the dynamics of immune system development and the heritability of the levels of key immune modulators at birth.

PMID: 30470248 [PubMed - in process]

Transcriptomic analysis of short-term 17α-ethynylestradiol exposure in two Californian sentinel fish species sardine (Sardinops sagax) and mackerel (Scomber japonicus).

Environ Pollut. 2019 Jan;244:926-937

Authors: Renaud L, Agarwal N, Richards DJ, Falcinelli S, Hazard ES, Carnevali O, Hyde J, Hardiman G

Abstract
Endocrine disrupting chemicals (EDCs) are substances which disrupt normal functioning of the endocrine system by interfering with hormone regulated physiological pathways. Aquatic environments provide the ultimate reservoir for many EDCs as they enter rivers and the ocean via effluent discharges and accumulate in sediments. One EDC widely dispersed in municipal wastewater effluent discharges is 17α-ethynylestradiol (EE2), which is one of the most widely prescribed medicines. EE2 is a bio-active estrogen employed in the majority of oral contraceptive pill formulations. As evidence of the health risks posed by EDCs mount, there is an urgent need to improve diagnostic tools for monitoring the effects of pollutants. As the cost of high throughput sequencing (HTS) diminishes, transcriptional profiling of an organism in response to EDC perturbation presents a cost-effective way of screening a wide range of endocrine responses. Coastal pelagic filter feeding fish species analyzed using HTS provide an excellent tool for EDC risk assessment in the marine environment. Unfortunately, there are limited genome sequence data and annotation for many of these species including Pacific sardine (Sardinops sagax) and chub mackerel (Scomber japonicus), which limits the utility of molecular tools such as HTS to interrogate the effects of endocrine disruption. In this study, we carried out RNA sequencing (RNAseq) of liver RNA harvested from wild sardine and mackerel exposed for 5 h under laboratory conditions to a concentration of 12.5 pM EE2 in the tank water. We developed an analytical framework for transcriptomic analyses of species with limited genomic information. EE2 exposure altered expression patterns of key genes involved in important metabolic and physiological processes. The systems approach presented here provides a powerful tool for obtaining a comprehensive picture of endocrine disruption in aquatic organisms.

PMID: 30469287 [PubMed - in process]

15 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 2018/11/24

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 2018/11/24

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.