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 2020/10/22

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 2020/10/22

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.

132 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 2020/10/21

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.

152 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 2020/10/21

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.

161 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 2020/10/19

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.

39 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 2020/10/14

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.

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 2020/10/13

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.

Inflammation as a Mechanism of Bipolar Disorder Neuroprogression.

Curr Top Behav Neurosci. 2020 Oct 11;:

Authors: Barichello T, V Giridharan V, Bhatti G, Sayana P, Doifode T, Macedo D, Quevedo J

Abstract
Bipolar disorder (BD) is a severe, debilitating psychiatric condition with onset in adolescence or young adulthood and often follows a relapsing and remitting course throughout life. The concept of neuroprogression in BD refers to the progressive path with an identifiable trajectory that takes place with recurrent mood episodes, which eventually leads to cognitive, functional, and clinical deterioration in the course of BD. Understanding the biological basis of neuroprogression helps to explain the subset of BD patients who experience worsening of their disorder over time. Additionally, the study of the neurobiological mechanisms underpinning neuroprogression will help BD staging based on systems biology. Replicated epidemiological studies have suggested inflammatory mechanisms as primary contributors to the neuroprogression of mood disorders. It is known that dysregulated inflammatory/immune pathways are often associated with BD pathophysiology. Hence, in this chapter, we focus on the evidence for the involvement of inflammation and immune regulated pathways in the neurobiological consequences of BD neuroprogression. Herein we put forth the evidence of immune markers from autoimmune disorders, chronic infections, and gut-brain axis that lead to BD neuroprogression. Further, we highlighted the peripheral and central inflammatory components measured along with BD progression.

PMID: 33040314 [PubMed - as supplied by publisher]

Systematically gap-filling the genome-scale metabolic model of CHO cells.

Biotechnol Lett. 2020 Oct 10;:

Authors: Fouladiha H, Marashi SA, Li S, Li Z, Masson HO, Vaziri B, Lewis NE

Abstract
OBJECTIVE: Chinese hamster ovary (CHO) cells are the leading cell factories for producing recombinant proteins in the biopharmaceutical industry. In this regard, constraint-based metabolic models are useful platforms to perform computational analysis of cell metabolism. These models need to be regularly updated in order to include the latest biochemical data of the cells, and to increase their predictive power. Here, we provide an update to iCHO1766, the metabolic model of CHO cells.
RESULTS: We expanded the existing model of Chinese hamster metabolism with the help of four gap-filling approaches, leading to the addition of 773 new reactions and 335 new genes. We incorporated these into an updated genome-scale metabolic network model of CHO cells, named iCHO2101. In this updated model, the number of reactions and pathways capable of carrying flux is substantially increased.
CONCLUSIONS: The present CHO model is an important step towards more complete metabolic models of CHO cells.

PMID: 33040240 [PubMed - as supplied by publisher]

Efficient dynamic variation graphs.

Bioinformatics. 2020 Jul 16;:

Authors: Eizenga JM, Novak AM, Kobayashi E, Villani F, Cisar C, Heumos S, Hickey G, Colonna V, Paten B, Garrison E

Abstract
MOTIVATION: Pangenomics is a growing field within computational genomics. Many pangenomic analyses use bidirected sequence graphs as their core data model. However, implementing and correctly using this data model can be difficult, and the scale of pangenomic datasets can be challenging to work at. These challenges have impeded progress in this field.
RESULTS: Here, we present a stack of two C++ libraries, libbdsg and libhandlegraph, which use a simple, field-proven interface, designed to expose elementary features of these graphs while preventing common graph manipulation mistakes. The libraries also provide a Python binding. Using a diverse collection of pangenome graphs, we demonstrate that these tools allow for efficient construction and manipulation of large genome graphs with dense variation. For instance, the speed and memory usage are up to an order of magnitude better than the prior graph implementation in the VG toolkit, which has now transitioned to using libbdsg's implementations.
AVAILABILITY AND IMPLEMENTATION: libhandlegraph and libbdsg are available under an MIT License from https://github.com/vgteam/libhandlegraph and https://github.com/vgteam/libbdsg.

PMID: 33040146 [PubMed - as supplied by publisher]

Cohort profile: molecular signature in pregnancy (MSP): longitudinal high-frequency sampling to characterise cross-omic trajectories in pregnancy in a resource-constrained setting.

BMJ Open. 2020 Oct 10;10(10):e041631

Authors: Brummaier T, Syed Ahamed Kabeer B, Wilaisrisak P, Pimanpanarak M, Win AK, Pukrittayakamee S, Marr AK, Kino T, Al Khodor S, Terranegra A, Carrara VI, Nosten F, Utzinger J, Chaussabel D, Paris DH, McGready R

Abstract
PURPOSE: A successful pregnancy relies on the interplay of various biological systems. Deviations from the norm within a system or intersystemic interactions may result in pregnancy-associated complications and adverse pregnancy outcomes. Systems biology approaches provide an avenue of unbiased, in-depth phenotyping in health and disease. The molecular signature in pregnancy (MSP) cohort was established to characterise longitudinal, cross-omic trajectories in pregnant women from a resource constrained setting. Downstream analysis will focus on characterising physiological perturbations in uneventful pregnancies, pregnancy-associated complications and adverse outcomes.
PARTICIPANTS: First trimester pregnant women of Karen or Burman ethnicity were followed prospectively throughout pregnancy, at delivery and until 3 months post partum. Serial high-frequency sampling to assess whole blood transcriptomics and microbiome composition of the gut, vagina and oral cavity, in conjunction with assessment of gene expression and microbial colonisation of gestational tissue, was done for all cohort participants.
FINDINGS TO DATE: 381 women with live born singletons averaged 16 (IQR 15-18) antenatal visits (13 094 biological samples were collected). At 5% (19/381) the preterm birth rate was low. Other adverse events such as maternal febrile illness 7.1% (27/381), gestational diabetes 13.1% (50/381), maternal anaemia 16.3% (62/381), maternal underweight 19.2% (73/381) and a neonate born small for gestational age 20.2% (77/381) were more often observed than preterm birth.
FUTURE PLANS: Results from the MSP cohort will enable in-depth characterisation of cross-omic molecular trajectories in pregnancies from a population in a resource-constrained setting. Moreover, pregnancy-associated complications and unfavourable pregnancy outcomes will be investigated at the same granular level, with a particular focus on population relevant needs such as effect of tropical infections on pregnancy. More detailed knowledge on multiomic perturbations will ideally result in the development of diagnostic tools and ultimately lead to targeted interventions that may disproportionally benefit pregnant women from this resource-limited population.
TRIAL REGISTRATION NUMBER: NCT02797327.

PMID: 33040018 [PubMed - as supplied by publisher]

Genomic, proteomic, and systems biology approaches in biomarker discovery for multiple sclerosis.

Cell Immunol. 2020 Sep 20;358:104219

Authors: Chase Huizar C, Raphael I, Forsthuber TG

Abstract
Multiple sclerosis (MS) is a neuroinflammatory disorder characterized by autoimmune-mediated inflammatory lesions in CNS leading to myelin damage and axonal loss. MS is a heterogenous disease with variable and unpredictable disease course. Due to its complex nature, MS is difficult to diagnose and responses to specific treatments may vary between individuals. Therefore, there is an indisputable need for biomarkers for early diagnosis, prediction of disease exacerbations, monitoring the progression of disease, and for measuring responses to therapy. Genomic and proteomic studies have sought to understand the molecular basis of MS and find biomarker candidates. Advances in next-generation sequencing and mass-spectrometry techniques have yielded an unprecedented amount of genomic and proteomic data; yet, translation of the results into the clinic has been underwhelming. This has prompted the development of novel data science techniques for exploring these large datasets to identify biologically relevant relationships and ultimately point towards useful biomarkers. Herein we discuss optimization of omics study designs, advances in the generation of omics data, and systems biology approaches aimed at improving biomarker discovery and translation to the clinic for MS.

PMID: 33039896 [PubMed - as supplied by publisher]

Palmitic acid negatively regulates tumor suppressor PTEN through T366 phosphorylation and protein degradation.

Cancer Lett. 2020 Oct 08;:

Authors: Bai D, Wu Y, Deol P, Nobumori Y, Zhou Q, Sladek FM, Liu X

Abstract
Chronic elevated free fatty (FFA) levels are linked to metabolic disorders and tumorigenesis. However, the molecular mechanism by which FFAs induce cancer remains poorly understood. Here, we show that the tumor suppressor PTEN protein levels were decreased in high fat diet (HFD) fed mice. As palmitic acid (PA, C16:0) showed a significant increase in the HFD fed mice, we further investigated its role in PTEN down regulation. Our studies revealed that exposure of cells to high doses of PA induced mTOR/S6K-mediated phosphorylation of PTEN at T366. The phosphorylation subsequently enhanced the interaction of PTEN with the E3 ubiquitin ligase WW domain-containing protein 2 (WWP2), which promoted polyubiquitination of PTEN and protein degradation. Consistent with PTEN degradation, exposure of cells to increased concentrations of PA also promoted PTEN-mediated AKT activation and cell proliferation. Significantly, a higher level of S6K activation, PTEN T366 phosphorylation, and AKT activation were also observed in the livers of the HFD fed mice. These results provide a molecular mechanism by which a HFD and elevated PA regulates cell proliferation through inactivation of tumor suppressor PTEN.

PMID: 33039560 [PubMed - as supplied by publisher]

Noisy stimulation effect in calcium dynamics on cardiac cells.

Exp Cell Res. 2020 Oct 08;:112319

Authors: Ramírez Hurtado AL, Martínez FV, Diaz Galindo CA, Cuellar KG, Villareal Reyna SZ, Sánchez Herrera DP, Rodríguez González J

Abstract
Noise is present in nature, and it affects the nervous and cardiovascular system. Noise added to stimuli may change the performance of excitable cells. In this paper, we study the effect of noise on the two main heart cell types: pacemaker and myocardial cells. This study investigates whether noise can induce changes in calcium dynamics on the two main heart cell types: pacemaker and myocardial cells, when stimuli with periodic electrical signals are disturbed by Gaussian white noise. Calcium dynamic parameters were obtained using imaging signals. Our results show that low intensities of noise favor amplitude and raise rate calcium dynamics, although our results show that the pacemaker cells are not affected by a noisy stimulus. Altogether, these findings suggest that noise plays a key role in calcium dynamics.

PMID: 33039368 [PubMed - as supplied by publisher]

Serum miRNA125a-5p, miR-125b-5p, and miR-433-5p as biomarkers to differentiate between posterior circulation stroke and peripheral vertigo.

BMC Neurol. 2020 Oct 10;20(1):372

Authors: Kijpaisalratana N, Nimsamer P, Khamwut A, Payungporn S, Pisitkun T, Chutinet A, Utoomprurkporn N, Kerr SJ, Vongvasinkul P, Suwanwela NC

Abstract
BACKGROUND: Acute vertigo is a common presentation of inner ear disease. However, it can also be caused by more serious conditions, especially posterior circulation stroke. Differentiating between these two conditions by clinical presentations and imaging studies during the acute phase can be challenging. This study aimed to identify serum microRNA (miRNA) candidates that could differentiate between posterior circulation stroke and peripheral vertigo, among patients presenting with acute vertigo.
METHODS: Serum levels of six miRNAs including miR-125a-5p, miR-125b-5p, miR-143-3p, miR-342-3p, miR-376a-3p, and miR-433-5p were evaluated. Using quantitative reverse-transcription polymerase chain reaction (RT-qPCR), the serum miRNAs were assessed in the acute phase and at a 90 day follow-up visit.
RESULTS: A total of 58 patients with posterior circulation stroke (n = 23) and peripheral vertigo (n = 35) were included in the study. Serum miR-125a-5p (P = 0.001), miR-125b-5p (P <  0.001), miR-143-3p (P = 0.014) and miR-433-5p (P = 0.0056) were present at significantly higher levels in the acute phase, in the patients with posterior circulation infarction. Based on the area under the receiver operating characteristic curve (AUROC) only miR-125a-5p (0.75), miR-125b-5p(0.77), and miR-433-5p (0.71) had an acceptable discriminative ability to differentiate between the central and peripheral vertigo. A combination of miRNAs revealed no significant improvement of AUROC when compared to single miRNAs.
CONCLUSION: This study demonstrated the potential of serum miR-125a-5p, miR-125b-5p, and miR-433-5p as biomarkers to assist in the diagnosis of posterior circulation infarction among patients presenting with acute vertigo.

PMID: 33038923 [PubMed - as supplied by publisher]

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 2020/10/11

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.

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 2020/10/11

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.

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 2020/10/10

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.

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 2020/10/10

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.

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 2020/10/09

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.