16 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 2019/06/28

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.

54 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 2019/06/27

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.

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 2019/06/27

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.

47 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 2019/06/25

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.

Delayed complication of tracheocutaneous fistula closure with severe compromising subcutaneous emphysema.

BMJ Case Rep. 2019 Jun 22;12(6):

Authors: Lewis RJ, Mandler AG, Perez G, Mudd PA

Abstract
We report a significant complication after tracheocutaneous fistula (TCF) excision with closure by secondary intention in a 4-year-old boy who had been tracheostomy dependent since infancy. He had a persistent 3 mm TCF one year after decannulation. On postoperative day 2 the patient developed profound subcutaneous emphysema and pneumomediastinum. He was extubated after 2 days and discharged from the hospital on postoperative day 7. At follow up he had complete resolution of subcutaneous emphysema and complete closure of the TCF. The main methods of TCF closure and management of subcutaneous emphysema are discussed along with the lessons learned from this case.

PMID: 31229983 [PubMed - in process]

Natural ACE inhibitory peptides discovery from Spirulina (Arthrospira platensis) strain C1.

Peptides. 2019 Jun 20;:170107

Authors: Anekthanakul K, Senachak J, Hongsthong A, Charoonratana T, Ruengjitchatchawalya M

Abstract
Bioactive peptides from natural sources are utilized as food supplements for disease prevention and are increasingly becoming targets for drug discovery due to their specificity, efficacy and the absence of undesirable side effects, among others. Hence, the 'SpirPep' platform was developed to facilitate the in silico-based bioactive peptide discovery of these highly sought-after biomolecules from Spirulina (Arthrospira platensis) and to select the protease (thermolysin) used for in vitro digestion. Analysis of the predicted and experimentally-derived peptides suggested that they were mainly involved in ACE inhibition; thus, an ACEi assay was used to study the ACE inhibitory activity of five candidate peptides (SpirPep1-5), chosen from common peptides with multifunctional bioactivity and 100% bioactive peptide coverage, originating from phycobiliproteins. Results showed that SpirPep1 inhibited the activity of ACE with IC50 of 1.748 mM and was non-toxic to fibroblasts of African green monkey kidney and human dermal skin. The molecular docking and MD simulation analysis revealed SpirPep1 had significantly lower binding scores than others and showed greater specificity to ACE. The non-bonded interaction energy of SpirPep1 and ACE was -883 kJ/mol. The SpirPep1 indirectly bound to ACE via the ACE substrate binding sites residues (D121, E123, S516, and S517) found in natural ACE inhibitory peptides (angiotensin II and bradykinin potentiating peptides). In addition, two unreported substrate binding sites including R124 and S219 were found. These results indicate that 'SpirPep' platform could increase the success rate for natural bioactive peptide discovery.

PMID: 31229668 [PubMed - as supplied by publisher]

Effect of epigallocatechin gallate on the body composition and lipid profile of down syndrome individuals: Implications for clinical management.

Clin Nutr. 2019 Jun 08;:

Authors: Xicota L, Rodríguez J, Langohr K, Fitó M, Dierssen M, de la Torre R, TESDAD study group

Abstract
BACKGROUND & AIMS: Individuals with Down syndrome (DS) have higher rates of obesity. In the general population green tea extracts, and in particular epigallocatechin gallate (EGCG), have been studied for their antiobesogenic effects. The aim of this study is to elucidate the effect of EGCG on body weight in young DS adults and whether it could be related to changes in lipid profile.
METHODS: In the context of a double-blind phase II clinical trial comparing the effect of EGCG to that of placebo, the body composition of 77 young adults with DS was analyzed through bioelectrical impedance analysis. Lipids were analyzed using standard laboratory procedures. The factors tested in the ANCOVA model for the differences from baseline were treatment, sex as well as their interaction as independent variables. Baseline values were included in the models as covariates.
RESULTS: Individuals receiving placebo showed an increase in body weight and body mass index (BMI) that was not detected in those with EGCG treatment. EGCG effect on body composition was mainly observed in males, with significant differences between the EGCG and the placebo group after 12 months for weight (estimated adjusted mean difference (AMD) = -2.34, 95% CI = [-4.21, -0.48]; p = 0.015) and body fat (estimated AMD = -1.23, 95% CI = [-2.43,-0.04], p = 0.043). The changes detected in body composition were associated with changes in lipid profile.
CONCLUSIONS: Our results suggest that EGCG could have a modest beneficial effect on weight management in DS. Furthermore, EGCG has also a sex-dependent effect on lipid profile that is related to changes in body mass and composition.

PMID: 31229326 [PubMed - as supplied by publisher]

Trimerization of dopamine transporter triggered by AIM-100 binding: Molecular mechanism and effect of mutations.

Neuropharmacology. 2019 Jun 19;:107676

Authors: Cheng MH, Ponzoni L, Sorkina T, Lee JY, Zhang S, Sorkin A, Bahar I

Abstract
Recent work demonstrated the propensity of dopamine transporters (DATs) to form trimers or higher oligomers, enhanced upon binding a furopyrimidine, AIM-100. AIM-100 binding promotes DAT endocytosis and thereby moderates dopaminergic transmission. Despite the neurobiological significance of these events, the molecular mechanisms that underlie the stabilization of DAT trimer and the key interactions that modulate the trimerization of DAT, and not serotonin transporter SERT, remain unclear. In the present study, we determined three structural models, termed trimer-W238, -C306 and -Y303, for possible trimerization of DATs using structural data resolved for DAT and its paralogs and structural homologs that share the LeuT fold in advanced computational modeling and simulations, site-directed mutagenesis experiments and live-cell imaging assays. The models are in accord with the versatility of LeuT fold to stabilize dimeric or higher order constructs. Selected residues show a high propensity to occupy interfacial regions. Among them, D231-W238 in the extracellular loop EL2, including the intersubunit salt-bridge forming pair D231/D232-R237 (not present in SERT) (in trimer-W238), the loop EL3 (trimers-C306 and -Y303), and W497 on the intracellularly exposed IL5 loop (trimer-C306) and its spatial neighbors (e.g. K525) near the C-terminus are computationally predicted and experimentally confirmed to play important roles in enabling the correct folding and/or oligomerization of DATs in the presence of AIM-100. The study suggests the possibility of controlling the effective transport of dopamine by altering the oligomerization state of DAT upon small molecule binding, as a possible intervention strategy to modulate dopaminergic signaling.

PMID: 31228486 [PubMed - as supplied by publisher]

DEUS: an R package for accurate small RNA profiling based on differential expression of unique sequences.

Bioinformatics. 2019 Jun 22;:

Authors: Jeske T, Huypens P, Stirm L, Höckele S, Wurmser CM, Böhm A, Weigert C, Staiger H, Klein C, Beckers J, Hastreiter M

Abstract
SUMMARY: Despite their fundamental role in various biological processes, the analysis of small RNA sequencing data remains a challenging task. Major obstacles arise when short RNA sequences map to multiple locations in the genome, align to regions that are not annotated or underwent post-transcriptional changes which hamper accurate mapping. In order to tackle these issues, we present a novel profiling strategy that circumvents the need for read mapping to a reference genome by utilizing the actual read sequences to determine expression intensities. After differential expression analysis of individual sequence counts, significant sequences are annotated against user defined feature databases and clustered by sequence similarity. This strategy enables a more comprehensive and concise representation of small RNA populations without any data loss or data distortion.
AVAILABILITY: Code and documentation of our R package at http://ibis.helmholtz-muenchen.de/deus/.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID: 31228198 [PubMed - as supplied by publisher]

CaPSSA: Visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data.

Bioinformatics. 2019 Jun 22;:

Authors: Jang Y, Seo J, Kim S, Lee S

Abstract
SUMMARY: Predictive biomarkers for patient stratification play critical roles in realizing the paradigm of precision medicine. Molecular characteristics such as somatic mutations and expression signatures represent the primary source of putative biomarker genes for patient stratification. However, evaluation of such candidate biomarkers is still cumbersome and requires multistep procedures especially when using massive public omics data. Here, we present an interactive web application that divides patients from large cohorts (e.g. TCGA) dynamically into two groups according to the mutation, copy number variation, or gene expression of query genes. It further supports users to examine the prognostic value of resulting patient groups based on survival analysis and their association with the clinical features as well as the previously annotated molecular subtypes, facilitated with a rich and interactive visualization. Importantly, we also support custom omics data with clinical information.
AVAILABILITY AND IMPLEMENTATION: CaPSSA (Cancer Patient Stratification and Survival Analysis) runs on a web-browser and is freely available without restrictions at http://capssa.ewha.ac.kr. The source code is available on https://github.com/yjjang/capssa.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID: 31228188 [PubMed - as supplied by publisher]

Networking in Biology: The Hybrid Rat Diversity Panel.

Methods Mol Biol. 2019;2018:213-231

Authors: Tabakoff B, Smith H, Vanderlinden LA, Hoffman PL, Saba LM

Abstract
One of the most fruitful resources for systems genetic studies of nonhuman mammals is a panel of inbred strains that exhibits significant genetic diversity between strains but genetic stability (isogenicity) within strains. These characteristics allow for fine mapping of complex phenotypes (QTLs) and provide statistical power to identify loci which contribute nominally to the phenotype. This type of resource also allows the planning and performance of investigations using the same genetic backgrounds over several generations of the test animals. Often, rats are preferred over mice for physiologic and behavioral studies because of their larger size and more distinguishable anatomy (particularly for their central nervous system). The Hybrid Rat Diversity Panel (HRDP) is a panel of inbred rat strains, which combines two recombinant inbred panels (the HXB/BXH, 30 strains; the LEXF/FXLE, 34 strains and 35 more strains of inbred rats which were selected for genetic diversity, based on their fully sequenced genomes and/or thorough genotyping). The genetic diversity and statistical power of this panel for mapping studies rivals or surpasses currently available panels in mouse. The genetic stability of this panel makes it particularly suitable for collection of high-throughput omics data as relevant technology becomes available for engaging in truly integrative systems biology. The PhenoGen website ( http://phenogen.org ) is the repository for the initial transcriptome data, making the raw data, the processed data, and the analysis results, e.g., organ-specific protein coding and noncoding transcripts, isoform analysis, expression quantitative trait loci, and co-expression networks, available to the research public. The data sets and tools being developed will complement current efforts to analyze the human transcriptome and its genetic controls (the Genotype-Tissue Expression Project (GTEx)) and allow for dissection of genetic networks that predispose to particular phenotypes and gene-by-environment interactions that are difficult or even impossible to study in humans. The HRDP is an essential population for exploring truly integrative systems genetics.

PMID: 31228159 [PubMed - in process]

Crystal structures and protein engineering of three different penicillin G acylases from Gram-positive bacteria with different thermostability.

Appl Microbiol Biotechnol. 2019 Jun 21;:

Authors: Mayer J, Pippel J, Günther G, Müller C, Lauermann A, Knuuti T, Blankenfeldt W, Jahn D, Biedendieck R

Abstract
Penicillin G acylase (PGA) catalyzes the hydrolysis of penicillin G to 6-aminopenicillanic acid and phenylacetic acid, which provides the precursor for most semisynthetic penicillins. Most applications rely on PGAs from Gram-negative bacteria. Here we describe the first three crystal structures for PGAs from Gram-positive Bacilli and their utilization in protein engineering experiments for the manipulation of their thermostability. PGAs from Bacillus megaterium (BmPGA, Tm = 56.0 °C), Bacillus thermotolerans (BtPGA, Tm = 64.5 °C), and Bacillus sp. FJAT-27231 (FJAT-PGA, Tm = 74.3 °C) were recombinantly produced with B. megaterium, secreted, purified to apparent heterogeneity, and crystallized. Structures with resolutions of 2.20 Å (BmPGA), 2.27 Å (BtPGA), and 1.36 Å (FJAT-PGA) were obtained. They revealed high overall similarity, reflecting the high identity of up to approx. 75%. Notably, the active center displays a deletion of more than ten residues with respect to PGAs from Gram-negatives. This enlarges the substrate binding site and may indicate a different substrate spectrum. Based on the structures, ten single-chain FJAT-PGAs carrying artificial linkers were produced. However, in all cases, complete linker cleavage was observed. While thermostability remained in the wild-type range, the enzymatic activity dropped between 30 and 60%. Furthermore, four hybrid PGAs carrying subunits from two different enzymes were successfully produced. Their thermostabilities mostly lay between the values of the two mother enzymes. For one PGA increased, enzyme activity was observed. Overall, the three novel PGA structures combined with initial protein engineering experiments provide the basis for establishment of new PGA-based biotechnological processes.

PMID: 31227867 [PubMed - as supplied by publisher]

EcoFABs: advancing microbiome science through standardized fabricated ecosystems.

Nat Methods. 2019 Jun 21;:

Authors: Zengler K, Hofmockel K, Baliga NS, Behie SW, Bernstein HC, Brown JB, Dinneny JR, Floge SA, Forry SP, Hess M, Jackson SA, Jansson C, Lindemann SR, Pett-Ridge J, Maranas C, Venturelli OS, Wallenstein MD, Shank EA, Northen TR

PMID: 31227812 [PubMed - as supplied by publisher]

Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors.

BMC Immunol. 2019 Jun 21;20(1):19

Authors: Chu ND, Bi HS, Emerson RO, Sherwood AM, Birnbaum ME, Robins HS, Alm EJ

Abstract
BACKGROUND: The adaptive immune system maintains a diversity of T cells capable of recognizing a broad array of antigens. Each T cell's specificity for antigens is determined by its T cell receptors (TCRs), which together across all T cells form a repertoire of millions of unique receptors in each individual. Although many studies have examined how TCR repertoires change in response to disease or drugs, few have explored the temporal dynamics of the TCR repertoire in healthy individuals.
RESULTS: Here we report immunosequencing of TCR β chains (TCRβ) from the blood of three healthy individuals at eight time points over one year. TCRβ repertoires of all peripheral-blood T cells and sorted memory T cells clustered clearly by individual, systematically demonstrating that TCRβ repertoires are specific to individuals across time. This individuality was absent from TCRβs from naive T cells, suggesting that the differences resulted from an individual's antigen exposure history, not genetic background. Many characteristics of the TCRβ repertoire (e.g., diversity, clonality) were stable across time, although we found evidence of T cell expansion dynamics even within healthy individuals. We further identified a subset of "persistent" TCRβs present across all time points. These receptors were rich in clonal and highly public receptors and may play a key role in immune system maintenance.
CONCLUSIONS: Our results highlight the importance of longitudinal sampling of the immune system, providing a much-needed baseline for TCRβ dynamics in healthy individuals. Such a baseline will improve interpretation of changes in the TCRβ repertoire during disease or treatment.

PMID: 31226930 [PubMed - in process]

Molecular Diversity and Network Complexity in Growing Protocells.

Life (Basel). 2019 Jun 20;9(2):

Authors: Kamimura A, Kaneko K

Abstract
A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address the essential role of the huge diversity of cellular components, we studied a model of protocells that convert resources into catalysts with the aid of a catalytic reaction network. As the resources were limited, the diversity in the intracellular components was found to be increased to allow the use of diverse resources for cellular growth. A scaling relation was demonstrated between resource abundances and molecular diversity. In the present study, we examined how the molecular species diversify and how complex catalytic reaction networks develop through an evolutionary course. At some generations, molecular species first appear as parasites that do not contribute to the replication of other molecules. Later, the species turn into host species that contribute to the replication of other species, with further diversification of molecular species. Thus, a complex joint network evolves with this successive increase in species. The present study sheds new light on the origin of molecular diversity and complex reaction networks at the primitive stage of a cell.

PMID: 31226813 [PubMed]

35 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 2019/06/22

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.

30 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 2019/06/22

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.

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 2019/06/21

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.

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 2019/06/21

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.

28 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 2019/06/20

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.