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 2019/07/17

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.

42 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 2019/07/16

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.

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 2019/07/16

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.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019.

J Integr Bioinform. 2019 Jul 13;:

Authors: Schreiber F, Sommer B, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D

Abstract
This special issue of the Journal of Integrative Bioinformatics presents an overview of COMBINE standards and their latest specifications. The standards cover representation formats for computational modeling in synthetic and systems biology and include BioPAX, CellML, NeuroML, SBML, SBGN, SBOL and SED-ML. The articles in this issue contain updated specifications of SBGN Process Description Level 1 Version 2, SBML Level 3 Core Version 2 Release 2, SBOL Version 2.3.0, and SBOL Visual Version 2.1.

PMID: 31301675 [PubMed - as supplied by publisher]

Smart and dual-targeted BSA nanomedicine with controllable release by high autolysosome levels.

Colloids Surf B Biointerfaces. 2019 Jul 02;182:110325

Authors: Zhang Z, Dong C, Yu G, Cheng W, Liang Y, Pan Y, Li H, Ji H

Abstract
Targeting modifications and smart responsiveness of nanomedicines can enable anticancer drugs to be selectively delivered to and controllably released in tumour cells or tissues, which can reduce the treatment's toxicity and side effects. Good biocompatibility is crucial for the clinical application of any nanomedicine. In this study, a double-targeting molecule, an RGD peptide- and 4-(2-aminoethyl) morpholine-modified, doxorubicin (DOX)-loaded bovine serum albumin (BSA) nanomedicine, that can be controllably released by the high levels of autophagic lysosomes in tumour cells was developed. The size of the spherical BSA nanoparticles is approximately 60 nm. In vitro experiments indicated that the RGD peptide- and 4-(2-aminoethyl) morpholine-modified, DOX-loaded BSA nanomedicine has a better therapeutic effect than free DOX. In vivo experiments suggested that the BSA nanomedicine can successfully suppress the progression of PC9 xenograft tumours. This phenomenon may be attributable to the endocytosis of a relatively large amount of nanomedicine and the effective release of the loaded chemotherapeutic agent, as induced by high levels of autolysosomes. Collectively, the results of this study provide a smart approach for increasing therapeutic efficacy using a double-targeting molecule-modified BSA nanomedicine.

PMID: 31301582 [PubMed - as supplied by publisher]

Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities.

Water Res. 2019 Jul 04;162:437-445

Authors: Bengtsson-Palme J, Milakovic M, Švecová H, Ganjto M, Jonsson V, Grabic R, Udikovic-Kolic N

Abstract
Antibiotic resistance is an emerging global health crisis, driven largely by overuse and misuse of antibiotics. However, there are examples in which the production of these antimicrobial agents has polluted the environment with active antibiotic residues, selecting for antibiotic resistant bacteria and the genes they carry. In this work, we have used shotgun metagenomics to investigate the taxonomic structure and resistance gene composition of sludge communities in a treatment plant in Croatia receiving wastewater from production of the macrolide antibiotic azithromycin. We found that the total abundance of antibiotic resistance genes was three times higher in sludge from the treatment plant receiving wastewater from pharmaceutical production than in municipal sludge from a sewage treatment plant in Zagreb. Surprisingly, macrolide resistance genes did not have higher abundances in the industrial sludge, but genes associated with mobile genetic elements such as integrons had. We conclude that at high concentrations of antibiotics, selection may favor taxonomic shifts towards intrinsically resistant species or strains harboring chromosomal resistance mutations rather than acquisition of mobile resistance determinants. Our results underscore the need for regulatory action also within Europe to avoid release of antibiotics into the environment.

PMID: 31301473 [PubMed - as supplied by publisher]

Engineering Corynebacterium glutamicum for high-titer biosynthesis of hyaluronic acid.

Metab Eng. 2019 Jul 10;:

Authors: Cheng F, Yu H, Stephanopoulos G

Abstract
Hyaluronic acid (HA) is a member of the glycosaminoglycan family and has been widely used in clinical, medical, cosmetic and food industries. In this study, we constructed a superior cell factory in Corynebacterium glutamicum for high-titer HA biosynthesis through systematic design and metabolic engineering based on a genome-scale metabolic model iCW773. The OptForceMUST algorithm was used in iCW773 to determine genetic interventions by using flux balance analysis. Enhancement of HA biosynthesis pathway, attenuation of the glycolysis pathway, the pentose phosphate pathway and the dehydrogenation of pyruvate were predicted as targets for genetic modulations. Various genetic strategies were thereby employed, including additional promoter PdapB driving hasB expression, asRNA-mediated attenuation of fba, zwf deletion and lactate/acetate pathway knockout. The integrated genetic changes in recombinant C. glutamicum produced 24.5 g/L HA in a fed-batch culture. Finally, pyruvate dehydrogenase activity was further reduced by asRNA and initial codon mutation to divert carbon flux from byproducts to HA. The corresponding modified strain, CgHA25, achieved a titer of 28.7 g/L, which is the highest ever reported. Byproduct concentration was reduced by half, and the major Mw component was 0.21 MDa. This work reports a significant improvement to the HA titer in a safe and efficient host by systematic metabolic engineering.

PMID: 31301358 [PubMed - as supplied by publisher]

Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities.

Environ Sci Pollut Res Int. 2019 Jul 12;:

Authors: Sonthiphand P, Ruangroengkulrith S, Mhuantong W, Charoensawan V, Chotpantarat S, Boonkaewwan S

Abstract
Microbial communities in groundwater are diverse and each may respond differently to environmental change. The goal of this study was to investigate the diversity, abundance, and dynamics of microbial communities in impacted groundwater and correlate them to the corresponding land use and groundwater geochemistry, using an Illumina MiSeq platform targeting the V3 and V4 regions of the 16S rRNA gene. The resulting MiSeq sequencing revealed the co-occurrence patterns of both abundant and rare microbial taxa within an impacted groundwater basin. Proteobacteria were the most common groundwater-associated bacterial phylum, mainly composed of the classes Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The phyla detected at less abundances were the Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, OD1, and Nitrospirae. The members of detected groundwater microorganisms involved in natural biogeochemical processes such as nitrification, anammox, methane oxidation, sulfate reduction, and arsenic transformation. Some of the detected microorganisms were able to perform anaerobic degradation of organic pollutants. The resulting PCA indicates that major land usage within the sampling area seemed to be significantly linked to the groundwater microbial distributions. The distinct microbial pattern was observed in the groundwater collected from a landfill area. This study suggests that the combinations of anthropogenic and natural effects possibly led to a unique pattern of microbial diversity across different locations at the impacted groundwater basin.

PMID: 31300992 [PubMed - as supplied by publisher]

Oxidative stress as candidate therapeutic target to overcome microenvironmental protection of CLL.

Leukemia. 2019 Jul 12;:

Authors: Yosifov DY, Idler I, Bhattacharya N, Reichenzeller M, Close V, Ezerina D, Scheffold A, Jebaraj BMC, Kugler S, Bloehdorn J, Bahlo J, Robrecht S, Eichhorst B, Fischer K, Weigel A, Busch H, Lichter P, Döhner H, Dick TP, Stilgenbauer S, Mertens D

Abstract
Chronic lymphocytic leukemia (CLL) cells depend on microenvironmental non-malignant cells for survival. We compared the transcriptomes of primary CLL cells cocultured or not with protective bone marrow stromal cells (BMSCs) and found that oxidative phosphorylation, mitochondrial function, and hypoxic signaling undergo most significant dysregulation in non-protected CLL cells, with the changes peaking at 6-8 h, directly before induction of apoptosis. A subset of CLL patients displayed a gene expression signature resembling that of cocultured CLL cells and had significantly worse progression-free and overall survival. To identify drugs blocking BMSC-mediated support, we compared the relevant transcriptomic changes to the Connectivity Map database. Correlation was found with the transcriptomic signatures of the cardiac glycoside ouabain and of the ipecac alkaloids emetine and cephaeline. These compounds were highly active against protected primary CLL cells (relative IC50's 287, 190, and 35 nM, respectively) and acted by repressing HIF-1α and disturbing intracellular redox homeostasis. We tested emetine in a murine model of CLL and observed decreased CLL cells in peripheral blood, spleen, and bone marrow, recovery of hematological parameters and doubling of median survival (31.5 vs. 15 days, P = 0.0001). Pathways regulating redox homeostasis are thus therapeutically targetable mediators of microenvironmental support in CLL cells.

PMID: 31300746 [PubMed - as supplied by publisher]

Plant Networks as Traits and Hypotheses: Moving Beyond Description.

Trends Plant Sci. 2019 Jul 09;:

Authors: Marshall-Colón A, Kliebenstein DJ

Abstract
Biology relies on the central thesis that the genes in an organism encode molecular mechanisms that combine with stimuli and raw materials from the environment to create a final phenotypic expression representative of the genomic programming. While conceptually simple, the genotype-to-phenotype linkage in a eukaryotic organism relies on the interactions of thousands of genes and an environment with a potentially unknowable level of complexity. Modern biology has moved to the use of networks in systems biology to try to simplify this complexity to decode how an organism's genome works. Previously, biological networks were basic ways to organize, simplify, and analyze data. However, recent advances are allowing networks to move beyond description and become phenotypes or hypotheses in their own right. This review discusses these efforts, like mapping responses across biological scales, including relationships among cellular entities, and the direct use of networks as traits or hypotheses.

PMID: 31300195 [PubMed - as supplied by publisher]

Corrigendum to "Proteomic identification of predictive biomarkers for malignant transformation in complete hydatidiform moles" [Placenta 77 (2019) 58-64].

Placenta. 2019 Jul 09;:

Authors: Vanichtantikul A, Hodge KG, Somparn P, Saethang T, Triratanachat S, Pisitkun T, Lertkhachonsuk R

PMID: 31300166 [PubMed - as supplied by publisher]

Expression patterns of small numbers of transcripts from functionally-related pathways predict survival in multiple cancers.

BMC Cancer. 2019 Jul 12;19(1):686

Authors: Mandel J, Wang H, Normolle DP, Chen W, Yan Q, Lucas PC, Benos PV, Prochownik EV

Abstract
BACKGROUND: Genetic profiling of cancers for variations in copy number, structure or expression of certain genes has improved diagnosis, risk-stratification and therapeutic decision-making. However the tumor-restricted nature of these changes limits their application to certain cancer types or sub-types. Tests with broader prognostic capabilities are lacking.
METHODS: Using RNAseq data from 10,227 tumors in The Cancer Genome Atlas (TCGA), we evaluated 212 protein-coding transcripts from 12 cancer-related pathways. We employed t-distributed stochastic neighbor embedding (t-SNE) to identify expression pattern difference among each pathway's transcripts. We have previously used t-SNE to show that survival in some cancers correlates with expression patterns of transcripts encoding ribosomal proteins and enzymes for cholesterol biosynthesis and fatty acid oxidation.
RESULTS: Using the above 212 transcripts, t-SNE-assisted transcript pattern profiling identified patient cohorts with significant survival differences in 30 of 34 different cancer types comprising 9350 tumors (91.4% of all TCGA cases). Small subsets of each pathway's transcripts, comprising no more than 50-60 from the original group, played particularly prominent roles in determining overall t-SNE patterns. In several cases, further refinements in long-term survival could be achieved by sequential t-SNE profiling with two pathways' transcripts, by a combination of t-SNE plus whole transcriptome profiling or by employing t-SNE on immuno-histochemically defined breast cancer subtypes. In two cancer types, individuals with Stage IV disease at presentation could be readily subdivided into groups with highly significant survival differences based on t-SNE-based tumor sub-classification.
CONCLUSIONS: t-SNE-assisted profiling of a small number of transcripts allows the prediction of long-term survival across multiple cancer types.

PMID: 31299925 [PubMed - in process]

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 2019/07/13

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.

20 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 2019/07/12

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.

45 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 2019/07/11

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.

91 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 2019/07/10

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.

Stress-Induced Changes in Bone Marrow Stromal Cell Populations Revealed through Single-Cell Protein Expression Mapping.

Cell Stem Cell. 2019 Jun 26;:

Authors: Severe N, Karabacak NM, Gustafsson K, Baryawno N, Courties G, Kfoury Y, Kokkaliaris KD, Rhee C, Lee D, Scadden EW, Garcia-Robledo JE, Brouse T, Nahrendorf M, Toner M, Scadden DT

Abstract
Stromal cell populations that maintain hematopoietic stem and progenitor cells (HSPCs) are generally characterized in steady-state conditions. Here, we report a comprehensive atlas of bone marrow stromal cell subpopulations under homeostatic and stress conditions using mass cytometry (CyTOF)-based single-cell protein analysis. We identified 28 subsets of non-hematopoietic cells during homeostasis, 14 of which expressed hematopoietic regulatory factors. Irradiation-based conditioning for HSPC transplantation led to the loss of most of these populations, including the LeptinR+ and Nestin+ subsets. In contrast, a subset expressing Ecto-5'-nucleotidase (CD73) was retained and a specific CD73+NGFRhigh population expresses high levels of cytokines during homeostasis and stress. Genetic ablation of CD73 compromised HSPC transplantation in an acute setting without long-term changes in bone marrow HSPCs. Thus, this protein-based expression mapping reveals distinct sets of stromal cells in the bone marrow and how they change in clinically relevant stress settings to contribute to early stages of hematopoietic regeneration.

PMID: 31279774 [PubMed - as supplied by publisher]

Structure of the MORN4/Myo3a Tail Complex Reveals MORN Repeats as Protein Binding Modules.

Structure. 2019 Jun 28;:

Authors: Li J, Liu H, Raval MH, Wan J, Yengo CM, Liu W, Zhang M

Abstract
Tandem repeats are basic building blocks for constructing proteins with diverse structures and functions. Compared with extensively studied α-helix-based tandem repeats such as ankyrin, tetratricopeptide, armadillo, and HEAT repeat proteins, relatively little is known about tandem repeat proteins formed by β hairpins. In this study, we discovered that the MORN repeats from MORN4 function as a protein binding module specifically recognizing a tail cargo binding region from Myo3a. The structure of the MORN4/Myo3a complex shows that MORN4 forms an extended single-layered β-sheet structure and uses a U-shaped groove to bind to the Myo3a tail with high affinity and specificity. Sequence and structural analyses further elucidated the unique sequence features for folding and target binding of MORN repeats. Our work establishes that the β-hairpin-based MORN repeats are protein-protein interaction modules.

PMID: 31279628 [PubMed - as supplied by publisher]

Hard Limits and Performance Tradeoffs in a Class of Antithetic Integral Feedback Networks.

Cell Syst. 2019 Jun 28;:

Authors: Olsman N, Baetica AA, Xiao F, Leong YP, Murray RM, Doyle JC

Abstract
Feedback regulation is pervasive in biology at both the organismal and cellular level. In this article, we explore the properties of a particular biomolecular feedback mechanism called antithetic integral feedback, which can be implemented using the binding of two molecules. Our work develops an analytic framework for understanding the hard limits, performance tradeoffs, and architectural properties of this simple model of biological feedback control. Using tools from control theory, we show that there are simple parametric relationships that determine both the stability and the performance of these systems in terms of speed, robustness, steady-state error, and leakiness. These findings yield a holistic understanding of the behavior of antithetic integral feedback and contribute to a more general theory of biological control systems.

PMID: 31279505 [PubMed - as supplied by publisher]

18 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 2019/07/07

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.