49 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 2019/10/17

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.

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 2019/10/17

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.

32 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 2019/10/16

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.

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 2019/10/16

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.

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 2019/10/15

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.

icSHAPE-pipe: A comprehensive toolkit for icSHAPE data analysis and evaluation.

Methods. 2019 Oct 10;:

Authors: Li P, Shi R, Cliff Zhang Q

Abstract
RNA molecules have the intrinsic ability to fold into complex structures that are important in regulating many biological processes, including transcription, translation, processing and degradation. However, our knowledge for RNA structures remains very limited. Previously, we developed icSHAPE, a high-throughput method to probe single-stranded RNA nucleotide in cells. To recover the structural profile of an RNA or a transcript by icSHAPE, it is essential to accurately calculate an icSHAPE reactivity as the RNA structure score for each base. Here, we present icSHAPE-pipe, a comprehensive toolkit for the analysis of RNA structure sequencing data obtained from icSHAPE experiments. Compared to the original icSHAPE data processing protocol, icSHAPE-pipe calculates RNA structural information with higher accuracy and achieves higher coverage of the transcriptome. In addition, icSHAPE-pipe can perform quality control, and generate reports on sequencing data and the statistics of results. In sum, icSHAPE-pipe provides a convenient workflow for researchers to analyze RNA structural data from icSHAPE sequencing experiments.

PMID: 31606387 [PubMed - as supplied by publisher]

Inference of the High-Level Interaction Topology between the Metabolic and Cell-Cycle Oscillators from Single-Cell Dynamics.

Cell Syst. 2019 Oct 04;:

Authors: Özsezen S, Papagiannakis A, Chen H, Niebel B, Milias-Argeitis A, Heinemann M

Abstract
Recent evidence suggests that the eukaryotic metabolism is an autonomous oscillator. Together with oscillating elements of the cyclin/CDK machinery, this oscillator might form a coupled oscillator system, from which cell-cycle control emerges. The topology of interactions between the metabolic oscillator and the elements of the cyclin/CDK machinery, however, remains unknown. Using single-cell metabolic and cell-cycle dynamics in yeast, and solving an inverse problem with a system of Kuramoto oscillators, we inferred how the metabolic oscillator interacts with the cyclin/CDK machinery. The identified and experimentally validated interaction topology shows that the early and late cell cycle are independently driven by metabolism. While in this topology, the S phase is coordinated by START. We obtained no support for a strong interaction between early and late cell cycle. The identified high-level interaction topology will guide future efforts to discover the molecular links between metabolism and the cell cycle.

PMID: 31606371 [PubMed - as supplied by publisher]

Expression of authentic post-translationally modified proteins in organisms with expanded genetic codes.

Methods Enzymol. 2019;626:539-559

Authors: Mohler K, Rinehart J

Abstract
Cellular signaling and regulatory cascades often rely on post-translational modification of proteins, particularly phosphorylation, to quickly and effectively relay signals from a variety of inputs. Numerous kinases, the effectors of phosphorylation, and kinase networks have been implicated in human diseases. Until recently, an inability to produce high yields of physiologically phosphorylated proteins has proven to be a substantial barrier toward our understanding of many enzymatic processes. Orthogonal translation systems provide the means to overcome many of these limitations by enabling site-specific incorporation of phosphorylated amino acids into recombinantly expressed proteins. Site-by-site, combinatorial assessment of phosphorylation site function is unique to orthogonal translation system based approaches and offers unmatched precision in the study of PTM-enzymology, extending well beyond the scope of kinase biology.

PMID: 31606090 [PubMed - in process]

Utilizing intein trans-splicing for in vivo generation of site-specifically modified proteins.

Methods Enzymol. 2019;626:203-222

Authors: Maksimovic I, Ray D, Zheng Q, David Y

Abstract
Many cellular processes as well as their associated pathologies are regulated by protein post-translational modifications (PTMs). Understanding the precise roles of these adducts hinges on the development of methods to robustly and site-specifically manipulate proteins in their physiological environments. Recently, ultrafast intein protein trans-splicing (PTS) was harnessed to incorporate site-specific modifications on cellular chromatin in live cells. In this chapter, we present the protocols for the generation of synthetic modifications on native chromatin as well as highlight the capabilities of this methodology.

PMID: 31606075 [PubMed - in process]

Metabolic profiling of seminal plasma from teratozoospermia patients.

J Pharm Biomed Anal. 2019 Oct 03;178:112903

Authors: Mehrparvar B, Chashmniam S, Nobakht F, Amini M, Javidi A, Minai-Tehrani A, Arjmand B, Gilany K

Abstract
Teratozoospermia is one of conditions that can cause male infertility. The mechanism of teratozoospermia remains unclear. The knowledge of the metabolites in human seminal plasma (HSP) is meaningful for the pathological study of teratozoospermia. Analysis of changed metabolites in HSP can help understand the cellular mechanism, find the novel biomarkers and subsequently design a diagnosis test. In this study, the analysis of samples performed by proton nuclear magnetic resonance spectroscopy (1H NMR spectroscopy) to identify the various metabolites, with the aim of finding metabolic profiles and biomarkers related to male infertility. Eighteen de-regulated metabolites were identified in fertile men compared to teratozoospermia patients. These changes illustrate the deficiencies in absorption or metabolism of these metabolites in teratozoospermia. Furthermore, metabolic profiling showed that it is not possible to classify teratozoospermia based on teratozoospermia index (TZI). To the best of our knowledge, this is the first metabolic profiling analysis of HSP described the metabolic features of teratozoospermia in a holistic view.

PMID: 31605879 [PubMed - as supplied by publisher]

Identification of the sirohaem biosynthesis pathway in Staphylococcus aureus.

FEBS J. 2019 Oct 12;:

Authors: Videira MAM, Lobo SAL, Sousa FL, Saraiva LM

Abstract
Sirohaem is a modified tetrapyrrole and a key prosthetic group of several enzymes involved in nitrogen and sulfur metabolisms. This work shows that Staphylococcus aureus produces sirohaem through a pathway formed by three independent enzymes. Of the two putative sirohaem synthases encoded in the S. aureus genome and annotated as cysG, one is herein shown to be a uroporphyrinogen III methyltransferase that converts uroporphyrinogen III to precorrin-2, and was renamed as UroM. The second cysG gene encodes a precorrin-2 dehydrogenase that converts precorrin-2 to sirohydrochlorin, and was designated as P2D. The last step was found to be performed by the gene nirR that, in fact, codes for a protein with sirohydrochlorin ferrochelatase activity, labeled as ShfC. Additionally, site-directed mutagenesis studies of S. aureus ShfC revealed that residues H22 and H87, which are predicted by homology modelling to be located at the active site, control the ferrochelatase activity. Within bacteria, sirohaem synthesis may occur via one, two or three enzymes, and we propose to name the correspondent pathways as Type 1, 2 and 3, respectively. A phylogenetic analysis revealed that Type 1 is the most used pathway in Gammaproteobacteria and Streptomycetales, Type 2 predominates in Fibriobacteres and Vibrionales, and Type 3 in Firmicutes of the Baciliales order. Altogether, we concluded that the current distribution of sirohaem pathways within bacteria, that changes at the genus or species level and within taxa, seems to be the result of evolutionary multiple fusion/fission events.

PMID: 31605669 [PubMed - as supplied by publisher]

Bacterial variability in the mammalian gut captured by a single-cell synthetic oscillator.

Nat Commun. 2019 Oct 11;10(1):4665

Authors: Riglar DT, Richmond DL, Potvin-Trottier L, Verdegaal AA, Naydich AD, Bakshi S, Leoncini E, Lyon LG, Paulsson J, Silver PA

Abstract
Synthetic gene oscillators have the potential to control timed functions and periodic gene expression in engineered cells. Such oscillators have been refined in bacteria in vitro, however, these systems have lacked the robustness and precision necessary for applications in complex in vivo environments, such as the mammalian gut. Here, we demonstrate the implementation of a synthetic oscillator capable of keeping robust time in the mouse gut over periods of days. The oscillations provide a marker of bacterial growth at a single-cell level enabling quantification of bacterial dynamics in response to inflammation and underlying variations in the gut microbiota. Our work directly detects increased bacterial growth heterogeneity during disease and differences between spatial niches in the gut, demonstrating the deployment of a precise engineered genetic oscillator in real-life settings.

PMID: 31604953 [PubMed - in process]

HCMV-encoded US7 and US8 act as antagonists of innate immunity by distinctively targeting TLR-signaling pathways.

Nat Commun. 2019 Oct 11;10(1):4670

Authors: Park A, Ra EA, Lee TA, Choi HJ, Lee E, Kang S, Seo JY, Lee S, Park B

Abstract
The mechanisms by which many human cytomegalovirus (HCMV)-encoded proteins help the virus to evade immune surveillance remain poorly understood. In particular, it is unknown whether HCMV proteins arrest Toll-like receptor (TLR) signaling pathways required for antiviral defense. Here, we report that US7 and US8 as key suppressors that bind both TLR3 and TLR4, facilitating their destabilization by distinct mechanisms. US7 exploits the ER-associated degradation components Derlin-1 and Sec61, promoting ubiquitination of TLR3 and TLR4. US8 not only disrupts the TLR3-UNC93B1 association but also targets TLR4 to the lysosome, resulting in rapid degradation of the TLR. Accordingly, a mutant HCMV lacking the US7-US16 region has an impaired ability to hinder TLR3 and TLR4 activation, and the impairment is reversed by the introduction of US7 or US8. Our findings reveal an inhibitory effect of HCMV on TLR signaling, which contributes to persistent avoidance of the host antiviral response to achieve viral latency.

PMID: 31604943 [PubMed - in process]

Proteomic atlas of organ vasculopathies triggered by Staphylococcus aureus sepsis.

Nat Commun. 2019 Oct 11;10(1):4656

Authors: Toledo AG, Golden G, Campos AR, Cuello H, Sorrentino J, Lewis N, Varki N, Nizet V, Smith JW, Esko JD

Abstract
Sepsis is a life-threatening condition triggered by a dysregulated host response to microbial infection resulting in vascular dysfunction, organ failure and death. Here we provide a semi-quantitative atlas of the murine vascular cell-surface proteome at the organ level, and how it changes during sepsis. Using in vivo chemical labeling and high-resolution mass spectrometry, we demonstrate the presence of a vascular proteome that is perfusable and shared across multiple organs. This proteome is enriched in membrane-anchored proteins, including multiple regulators of endothelial barrier functions and innate immunity. Further, we automated our workflows and applied them to a murine model of methicillin-resistant Staphylococcus aureus (MRSA) sepsis to unravel changes during systemic inflammatory responses. We provide an organ-specific atlas of both systemic and local changes of the vascular proteome triggered by sepsis. Collectively, the data indicates that MRSA-sepsis triggers extensive proteome remodeling of the vascular cell surfaces, in a tissue-specific manner.

PMID: 31604940 [PubMed - in process]

Taste receptor function.

Handb Clin Neurol. 2019;164:173-185

Authors: Töle JC, Behrens M, Meyerhof W

Abstract
This chapter summarizes the available data about taste receptor functions and their role in perception of food with emphasis on the human system. In addition we illuminate the widespread presence of these receptors throughout the body and discuss some of their extraoral functions. Finally, we describe clinical aspects where taste receptor signaling could be relevant.

PMID: 31604546 [PubMed - in process]

Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm.

BMC Bioinformatics. 2019 Oct 11;20(1):494

Authors: Karki R, Kodamullil AT, Hoyt CT, Hofmann-Apitius M

Abstract
BACKGROUND: Literature derived knowledge assemblies have been used as an effective way of representing biological phenomenon and understanding disease etiology in systems biology. These include canonical pathway databases such as KEGG, Reactome and WikiPathways and disease specific network inventories such as causal biological networks database, PD map and NeuroMMSig. The represented knowledge in these resources delineates qualitative information focusing mainly on the causal relationships between biological entities. Genes, the major constituents of knowledge representations, tend to express differentially in different conditions such as cell types, brain regions and disease stages. A classical approach of interpreting a knowledge assembly is to explore gene expression patterns of the individual genes. However, an approach that enables quantification of the overall impact of differentially expressed genes in the corresponding network is still lacking.
RESULTS: Using the concept of heat diffusion, we have devised an algorithm that is able to calculate the magnitude of regulation of a biological network using expression datasets. We have demonstrated that molecular mechanisms specific to Alzheimer (AD) and Parkinson Disease (PD) regulate with different intensities across spatial and temporal resolutions. Our approach depicts that the mitochondrial dysfunction in PD is severe in cortex and advanced stages of PD patients. Similarly, we have shown that the intensity of aggregation of neurofibrillary tangles (NFTs) in AD increases as the disease progresses. This finding is in concordance with previous studies that explain the burden of NFTs in stages of AD.
CONCLUSIONS: This study is one of the first attempts that enable quantification of mechanisms represented as biological networks. We have been able to quantify the magnitude of regulation of a biological network and illustrate that the magnitudes are different across spatial and temporal resolution.

PMID: 31604427 [PubMed - in process]

Effects of depression, dementia and delirium on activities of daily living in elderly patients after discharge.

BMC Geriatr. 2019 Oct 11;19(1):261

Authors: Weng CF, Lin KP, Lu FP, Chen JH, Wen CJ, Peng JH, Tseng AH, Chan DC

Abstract
BACKGROUND: The three geriatric conditions, depression, dementia and delirium (3D's), are common among hospitalized older patients and often lead to impairments of activities of daily living. The aim of this study is to explore the impact of depression, dementia and delirium on activities of daily living (ADLs) during and after hospitalization.
METHODS: A prospective cohort study was conducted between 2012 and 2013 in a tertiary medical center in Taiwan. Patients who aged over 65 years and admitted to the geriatric ward were invited to this study. Geriatric Depression Scale Short Form, Mini-Mental State and Confusion Assessment Method were used to identify patients with depression, dementia and delirium on admission, respectively. Barthel Index (BI) was used to evaluate patients' functional status on admission, at discharge, 30-day, 90-day and 180-day after discharge. Generalized Estimating Equation (GEE) was used to calculate the associations between 3 D's and BI.
RESULTS: One-hundred-and-forty-nine patients were included in this study. Twenty-seven patients (18.1%) had depression, 37 (24.8%) had dementia, and 85 (57.0%) had delirium. The study demonstrated that all the geriatric patients with functional decline presented gradual improvements of physical function up to 180 days after discharge. Whether depression exists did not substantially affect functional recovery after discharge, whilst either dementia or delirium could impede elder people functional status. The recovery of functional improvement in delirium or dementia was relatively irreversible when comparing with depression. Once delirium or dementia was diagnosed, poorer functional restore was expected. In brief, intensive work and strategies on modifying delirium or dementia should be put more effort as early as possible.
CONCLUSIONS: Old hospitalized patients with depression can recover well after adequate intervention. We emphasize that early detection of dementia and delirium is imperative in subsequent functional outcome, even if at or before admission. Comprehensive plan must be implemented timely.

PMID: 31604425 [PubMed - in process]

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 2019/10/12

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.

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 2019/10/11

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.

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 2019/10/11

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.