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 2020/07/22

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.

31 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 2020/07/22

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.

38 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 2020/07/21

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.

Analysis of Transformed Upstream Bioprocess Data Provides Insights into Biological System Variation.

Biotechnol J. 2020 Jul 19;:e2000113

Authors: Richelle A, Lee BW, Portela RMC, Raley J, von Stosch M

Abstract
In recent years, multivariate data analysis (MVDA) and modeling approaches have found increasing applications for upstream bioprocess studies (e.g., monitoring, development, optimization, scale-up, etc.). Many of these studies look at variations in the concentrations of metabolites and cell-based measurements. However, these measures are subject to system inherent variations (e.g., changes in metabolic activity) but also intentional operational changes. We propose to perform MVDA and modeling on data representative of the underlying biological system operation, i.e., the specific rates, which are per se independent of the scale, operational strategy (e.g., batch, fed-batch) and biomass content. Two industrial case studies are highlighted to showcase the approach: one HEK medium performance comparison study and one CHO scale-up/-down study. It is shown that analyzing processes in this way reveals insights into behavior of the underlying biological system, which cannot to the same degree be deducted from the analysis of concentrations. This article is protected by copyright. All rights reserved.

PMID: 32683769 [PubMed - as supplied by publisher]

Triphenyl phosphate is a selective PPARγ modulator that does not induce brite adipogenesis in vitro and in vivo.

Arch Toxicol. 2020 Jul 18;:

Authors: Kim S, Rabhi N, Blum BC, Hekman R, Wynne K, Emili A, Farmer S, Schlezinger JJ

Abstract
Triphenyl phosphate (TPhP) is an environmental PPARγ ligand, and growing evidence suggests that it is a metabolic disruptor. We have shown previously that the structurally similar ligand, tributyltin, does not induce brite adipocyte gene expression. Here, using in vivo and in vitro models, we tested the hypothesis that TPhP is a selective PPARγ ligand, which fails to induce brite adipogenesis. C57BL/6 J male mice were fed either a low or very high-fat diet for 13 weeks. From weeks 7-13, mice were injected intraperitoneally, daily, with vehicle, rosiglitazone (Rosi), or TPhP (10 mg/kg). Compared to Rosi, TPhP did not induce expression of browning-related genes (e.g. Elovl3, Cidea, Acaa2, CoxIV) in mature adipocytes isolated from inguinal adipose. To determine if this resulted from an effect directly on the adipocytes, 3T3-L1 cells and primary human preadipocytes were differentiated into adipocytes in the presence of Rosi or TPhP. Rosi, but not TPhP, induced expression of brite adipocyte genes, mitochondrial biogenesis and cellular respiration. Further, Rosi and TPhP-induced distinct proteomes and phosphoproteomes; Rosi enriched more regulatory pathways related to fatty acid oxidation and mitochondrial proteins. We assessed the role of phosphorylation of PPARγ in these differences in 3T3-L1 cells. Only Rosi protected PPARγ from phosphorylation at Ser273. TPhP gained the ability to stimulate brite adipocyte gene expression in the presence of the CDK5 inhibitor and in 3T3-L1 cells expressing alanine at position 273. We conclude that TPhP is a selective PPARγ modulator that fails to protect PPARγ from phosphorylation at ser273.

PMID: 32683515 [PubMed - as supplied by publisher]

Effects of long-term exposure to microfibers on ecosystem services provided by coastal mussels.

Environ Pollut. 2020 Jul 10;266(Pt 3):115184

Authors: Christoforou E, Dominoni DM, Lindström J, Stilo G, Spatharis S

Abstract
The biofiltration capacity of bivalve populations is known to alleviate the effects of coastal eutrophication. However, this important ecosystem service could potentially be impaired by the increasing microplastic abundance in near shore environments. It is known that relatively large microplastics (∼500 μm) impair the filtration capacity of bivalves. However, the effect of smaller microplastics, and specifically microfibers, is not known even though they are more common in many natural systems and similar in size to phytoplankton, the main food source of mussels. Here, we investigated the effects of long-term exposure to microfibers (MFs), which are smaller than 100 μm, on the biofiltration capacity of the blue mussel, Mytilus edulis. Our findings show that long-term exposure (here 39 days) to microfibers significantly reduced (21%) the clearance of phytoplankton (Tetraselmis sp). While previous studies have shown that larger microplastics can decrease the filtration capacity of mussels after short-term exposure, our findings suggest that, for smaller MFs, mussel's clearance capacity is significantly affected after long-term exposure (39 days in this study). This may be due to the accumulation of MFs in the digestive system. In addition, the most efficient phytoplankton consumers were more susceptible to MF accumulation in the digestive system. This suggests that prolonged exposure to MF of coastal mussels could negatively impact the biofiltration of more potent individuals, thus decreasing the ecosystem service potential of the population as a whole.

PMID: 32683089 [PubMed - as supplied by publisher]

Integrated transcriptomic and metabolomic analyses of glutamine metabolism genes unveil key players in Oryza sativa (L.) to ameliorate the unique and combined abiotic stress tolerance.

Int J Biol Macromol. 2020 Jul 16;:

Authors: Muthuramalingam P, Jeyasri R, Selvaraj A, Pandian SK, Ramesh M

Abstract
Plants can be considered to biosynthesize the specialized metabolites to adapt to various environmental stressors mainly on abiotic stresses (AbS). Among specialized metabolites, glutamine (Gln) is an essential plant metabolite to achieve sustainable plant growth, yield and food security. In this pilot study, swe employed computational metabolomics genome wide association survey (cmGWAS) of Gln metabolite profiling in Oryza sativa, targeting at the identification of abiotic stress responsible (AbSR) - Gln metabolite producing genes (GlnMPG). Identified 5 AbSR-GlnMPG alter the metabolite levels and play a predominant role in delineating the physiological significance of rice. These genes were systematically analysed for their biological features via OryzaCyc. Spatio-temporal and plant hormonal expression pattern of AbSR-GlnMPG was analysed and their differential expression profiling were noted in 48 different tissues and hormones, respectively. Furthermore, comparative ideogram of these genes revealed the chromosomal synteny with C4 grass genomes. Molecular crosstalks of these proteins, unravelled the various metabolic interaction. The systems expression profiling of AbSR-GlnMPG will lead to unravel the metabolite signaling and putative responses in multiple AbS. On the whole, this holistic study provides deeper insights on biomolecular features of AbSR-GlnMPG, which could be analysed further to decipher their functional metabolisms in AbS dynamism.

PMID: 32682969 [PubMed - as supplied by publisher]

Convergence and Divergence in the Genetics of Psychiatric Disorders From Pathways to Developmental Stages.

Biol Psychiatry. 2020 May 28;:

Authors: Shohat S, Amelan A, Shifman S

Abstract
In the past decade, the identification of susceptibility genes for psychiatric disorders has become routine, but understanding the biology underlying these discoveries has proven extremely difficult. The large number of potential risk genes and the genetic overlap between disorders are major obstacles for studying the etiology of these conditions. Systems biology approaches relying on gene ontologies, gene coexpression, and protein-protein interactions are used to identify convergence of the genes in relation to biological processes, cell types, brain areas, and developmental stages. Across psychiatric disorders, there is a clear enrichment for genes expressed in the brain and especially in the cortex, but a higher resolution is vastly dependent on sample size and statistical power. There is indication that susceptibility genes tend to be expressed in the brain during periods preceding the typical onset of the disorders. Thus, the role of genes in prenatal brain development is more pronounced for childhood-onset disorders, such as autism spectrum disorder and attention-deficit/hyperactivity disorder, but is much less so for bipolar disorder and depression. One of the most consistent findings across multiple disorders and classes of genetic variants is the role of genes intolerant to mutations in psychiatric disorders, yet this association is more pronounced for disorders with a clear neurodevelopmental component. Notwithstanding, a detailed understanding of the neurobiology of psychiatric disorders is still lacking. It is possible that it will only be revealed by studying the risk genes at the level of the development and function of neuronal networks and circuits.

PMID: 32682568 [PubMed - as supplied by publisher]

Functional relationship of particulate matter (PM) emissions, animal species, and moisture content during manure application.

Environ Int. 2020 Jul 14;143:105577

Authors: Kabelitz T, Ammon C, Funk R, Münch S, Biniasch O, Nübel U, Thiel N, Rösler U, Siller P, Amon B, Aarnink AJA, Amon T

Abstract
Livestock manure is recycled to agricultural land as organic fertilizer. Due to the extensive usage of antibiotics in conventional animal farming, antibiotic-resistant bacteria are highly prevalent in feces and manure. The spread of wind-driven particulate matter (PM) with potentially associated harmful bacteria through manure application may pose a threat to environmental and human health. We studied whether PM was aerosolized during the application of solid and dried livestock manure and the functional relationship between PM release, manure dry matter content (DM), treatment and animal species. In parallel, manure and resulting PM were investigated for the survival of pathogenic and antibiotic-resistant bacterial species. The results showed that from manure with a higher DM smaller particles were generated and more PM was emitted. A positive correlation between manure DM and PM aerosolization rate was observed. There was a species-dependent critical dryness level (poultry: 60% DM, pig: 80% DM) where manure began to release PM into the environment. The maximum PM emission potentials were 1 and 3 kg t-1 of applied poultry and pig manure, respectively. Dried manure and resulting PM contained strongly reduced amounts of investigated pathogenic and antibiotic-resistant microorganisms compared to fresh samples. An optimal manure DM regarding low PM emissions and reduced pathogen viability was defined from our results, which was 55-70% DM for poultry manure and 75-85% DM for pig manure. The novel findings of this study increase our detailed understanding and basic knowledge on manure PM emissions and enable optimization of manure management, aiming a manure DM that reduces PM emissions and pathogenic release into the environment.

PMID: 32682052 [PubMed - as supplied by publisher]

Development, spread and persistence of antibiotic resistance genes (ARGs) in the soil microbiomes through co-selection.

Rev Environ Health. 2020 Jul 20;:

Authors: Maurya AP, Rajkumari J, Bhattacharjee A, Pandey P

Abstract
Bacterial pathogens resistant to multiple antibiotics are emergent threat to the public health which may evolve in the environment due to the co-selection of antibiotic resistance, driven by poly aromatic hydrocarbons (PAHs) and/or heavy metal contaminations. The co-selection of antibiotic resistance (AMR) evolves through the co-resistance or cross-resistance, or co-regulatory mechanisms, present in bacteria. The persistent toxic contaminants impose widespread pressure in both clinical and environmental setting, and may potentially cause the maintenance and spread of antibiotic resistance genes (ARGs). In the past few years, due to exponential increase of AMR, numerous drugs are now no longer effective to treat infectious diseases, especially in cases of bacterial infections. In this mini-review, we have described the role of co-resistance and cross-resistance as main sources for co-selection of ARGs; while other co-regulatory mechanisms are also involved with cross-resistance that regulates multiple ARGs. However, co-factors also support selections, which results in development and evolution of ARGs in absence of antibiotic pressure. Efflux pumps present on the same mobile genetic elements, possibly due to the function of Class 1 integrons (Int1), may increase the presence of ARGs into the environment, which further is promptly changed as per environmental conditions. This review also signifies that mutation plays important role in the expansion of ARGs due to presence of diverse types of anthropogenic pollutants, which results in overexpression of efflux pump with higher bacterial fitness cost; and these situations result in acquisition of resistant genes. The future aspects of co-selection with involvement of systems biology, synthetic biology and gene network approaches have also been discussed.

PMID: 32681784 [PubMed - as supplied by publisher]

Mapping Transcriptome-Wide and Genome-Wide RNA-DNA Contacts with Chromatin-Associated RNA Sequencing (ChAR-seq).

Methods Mol Biol. 2020;2161:115-142

Authors: Limouse C, Jukam D, Smith OK, Fryer KA, Straight AF

Abstract
RNAs play key roles in the cell as molecular intermediates for protein synthesis and as regulators of nuclear processes such as splicing, posttranscriptional regulation, or chromatin remodeling. Various classes of non-coding RNAs, including long non-coding RNAs (lncRNAs), can bind chromatin either directly or via interaction with chromatin binding proteins. It has been proposed that lncRNAs regulate cell-state-specific genes by coordinating the locus-dependent activity of chromatin-modifying complexes. Yet, the vast majority of lncRNAs have unknown functions, and we know little about the specific loci they regulate. A key step toward understanding chromatin regulation by RNAs is to map the genomic loci with which every nuclear RNA interacts and, reciprocally, to identify all RNAs that target a given locus. Our ability to generate such data has been limited, until recently, by the lack of methods to probe the genomic localization of more than a few RNAs at a time. Here, we describe a protocol for ChAR-seq, an RNA-DNA proximity ligation method that maps the binding loci for thousands of RNAs at once and without the need for specific RNA or DNA probe sequences. The ChAR-seq approach generates chimeric RNA-DNA molecules in situ and then converts those chimeras to DNA for next-generation sequencing. Using ChAR-seq we detect many types of chromatin-associated RNA, both coding and non-coding. Understanding the RNA-DNA interactome and its changes during differentiation or disease with ChAR-seq will likely provide key insights into chromatin and RNA biology.

PMID: 32681510 [PubMed - as supplied by publisher]

Author Correction: The Apostasia genome and the evolution of orchids.

Nature. 2020 Jul 17;:

Authors: Zhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, Wang JY, Lin YC, Xu Q, Chen LJ, Yoshida K, Fujiwara S, Wang ZW, Zhang YQ, Mitsuda N, Wang M, Liu GH, Pecoraro L, Huang HX, Xiao XJ, Lin M, Wu XY, Wu WL, Chen YY, Chang SB, Sakamoto S, Ohme-Takagi M, Yagi M, Zeng SJ, Shen CY, Yeh CM, Luo YB, Tsai WC, Van de Peer Y, Liu ZJ

Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.

PMID: 32681116 [PubMed - as supplied by publisher]

Slc6a3-dependent expression of a CAPS-associated Nlrp3 allele results in progressive behavioral abnormalities and neuroinflammation in aging mice.

J Neuroinflammation. 2020 Jul 17;17(1):213

Authors: von Herrmann KM, Anderson FL, Martinez EM, Young AL, Havrda MC

Abstract
BACKGROUND: An association between neuroinflammation and age-related neurologic disorders has been established but the molecular mechanisms and cell types involved have not been thoroughly characterized. Activity of the proinflammatory NLRP3 inflammasome is implicated in Alzheimer's and Parkinson's disease and our recent studies in patients suggest that dopaminergic neurons within the degenerating mesencephalon express NLRP3 throughout the progression of PD. Here, we directly test the impact of enhanced inflammasome activity in mesencephalic neurons by characterizing motor function, tissue integrity, and neuroinflammation in aging mice harboring hyperactivating mutations within the endogenous murine Nlrp3 locus, enabled only in cells expressing the dopaminergic neuron-specific Slc6a3 promoter.
METHODS: We compared mice harboring inducible alleles encoding the cryopyrin-associated periodic syndrome activating mutations Nlrp3A350V and Nlrp3L351P inserted into the endogenous mouse Nlrp3 locus. Tissue specific expression was driven by breeding these animals with mice expressing Cre recombinase under the control of the dopaminergic neuron-specific Slc6a3 promoter. The experimental mice, designed to express hyperactive NLRP3 only when the endogenous mouse Nlrp3 promotor is active in dopaminergic neurons, were analyzed throughout 18 months of aging using longitudinal motor function assessments. Biochemical and histologic analyses of mesencephalic tissues were conducted in 1- and 18-month-old animals.
RESULTS: We observed progressive and significant deficits in motor function in animals expressing Nlrp3L351P, compared with animals expressing Nlrp3WT and Nlrp3A350V. Age-dependent neuroinflammatory changes in the mesencephalon were noted in all animals. Analysis of GFAP-immunoreactive astrocytes in the substantia nigra revealed a significant increase in astrocyte number in animals expressing Nlrp3L351P compared with Nlrp3WT and Nlrp3A350V. Further analysis of Nlrp3L351P striatal tissues indicated genotype specific gliosis, elevated Il1b expression, and both morphologic and gene expression indicators of proinflammatory A1 astrocytes.
CONCLUSIONS: Dopaminergic neurons have the potential to accumulate NLRP3 inflammasome activators with age, including reactive oxygen species, dopamine metabolites, and misfolded proteins. Results indicate the Nlrp3 locus is active in dopaminergic neurons in aging mice, and that the hyperactive Nlrp3L351P allele can drive neuroinflammatory changes in association with progressive behavioral deficits. Findings suggest neuronal NLRP3 inflammasome activity may contribute to neuroinflammation observed during normal aging and the progression of neurologic disorders.

PMID: 32680528 [PubMed - as supplied by publisher]

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 2020/07/18

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.

31 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 2020/07/18

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 2020/07/17

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.

31 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 2020/07/17

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.

44 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 2020/07/16

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 2020/07/15

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.

44 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 2020/07/14

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.