65 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 2019/07/25

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.

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"systems biology"

These pubmed results were generated on 2019/07/24

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.

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"systems biology"

These pubmed results were generated on 2019/07/23

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.

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"systems biology"

These pubmed results were generated on 2019/07/22

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.

13 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 2019/07/22

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.

Integrating three comprehensive datasets shows that mitochondrial DNA variation is linked to species traits and paleogeographic events in European butterflies.

Mol Ecol Resour. 2019 Jul 20;:

Authors: Dapporto L, Cini A, Vodă R, Dincă V, Wiemers M, Menchetti M, Magini G, Talavera G, Shreeve T, Bonelli S, Casacci LP, Balletto E, Scalercio S, Vila R

Abstract
Understanding the dynamics of biodiversity, including the spatial distribution of genetic diversity, is critical for predicting responses to environmental changes, as well as for effective conservation measures. This task requires tracking changes in biodiversity at large spatial scales and correlating with species functional traits. We provide three comprehensive resources to understand the determinants for mitochondrial DNA differentiation represented by i) 15,609 COI sequences and ii) 14 traits belonging to 307 butterfly species occurring in Western-Central Europe and iii) the first multi-locus phylogenetic tree of all European butterfly species. By applying phylogenetic regressions we show that mitochondrial DNA spatial differentiation (as measured with Gst, G'st, D and Dst) is negatively correlated with species traits determining dispersal capability and colonization ability. Thanks to the high spatial resolution of the COI data, we also provide the first zoogeographic regionalization maps based on intraspecific genetic variation. The overall pattern obtained by averaging the spatial differentiation of all Western-Central European butterflies shows that the paradigm of long-term glacial isolation followed by rapid pulses of post-glacial expansion has been a pervasive phenomenon in European butterflies. The results and the extensive datasets we provide here constitute the basis for genetically-informed conservation plans for a charismatic group in a continent where flying insects are under alarming decline. This article is protected by copyright. All rights reserved.

PMID: 31325412 [PubMed - as supplied by publisher]

Gains and losses of metabolic function inferred from a phylotranscriptomic analysis of algae.

Sci Rep. 2019 Jul 19;9(1):10482

Authors: Goh FQY, Jeyakani J, Tipthara P, Cazenave-Gassiot A, Ghosh R, Bogard N, Yeo Z, Wong GK, Melkonian M, Wenk MR, Clarke ND

Abstract
Hidden Markov models representing 167 protein sequence families were used to infer the presence or absence of homologs within the transcriptomes of 183 algal species/strains. Statistical analyses of the distribution of HMM hits across major clades of algae, or at branch points on the phylogenetic tree of 98 chlorophytes, confirmed and extended known cases of metabolic loss and gain, most notably the loss of the mevalonate pathway for terpenoid synthesis in green algae but not, as we show here, in the streptophyte algae. Evidence for novel events was found as well, most remarkably in the recurrent and coordinated gain or loss of enzymes for the glyoxylate shunt. We find, as well, a curious pattern of retention (or re-gain) of HMG-CoA synthase in chlorophytes that have otherwise lost the mevalonate pathway, suggesting a novel, co-opted function for this enzyme in select lineages. Finally, we find striking, phylogenetically linked distributions of coding sequences for three pathways that synthesize the major membrane lipid phosphatidylcholine, and a complementary phylogenetic distribution pattern for the non-phospholipid DGTS (diacyl-glyceryl-trimethylhomoserine). Mass spectrometric analysis of lipids from 25 species was used to validate the inference of DGTS synthesis from sequence data.

PMID: 31324835 [PubMed - in process]

Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings.

Nat Commun. 2019 Jul 19;10(1):3244

Authors: Stewart TA, Liang C, Cotney JL, Noonan JP, Sanger TJ, Wagner GP

Abstract
In crown group tetrapods, individual digits are homologized in relation to a pentadactyl ground plan. However, testing hypotheses of digit homology is challenging because it is unclear whether digits represent distinct and conserved gene regulatory states. Here we show dramatic evolutionary dynamism in the gene expression profiles of digits, challenging the notion that five digits have conserved developmental identities across amniotes. Transcriptomics shows diversity in the patterns of gene expression differentiation of digits, although the anterior-most digit of the pentadactyl limb has a unique, conserved expression profile. Further, we identify a core set of transcription factors that are differentially expressed among the digits of amniote limbs; their spatial expression domains, however, vary between species. In light of these results, we reevaluate the frame shift hypothesis of avian wing evolution and conclude only the identity of the anterior-most digit has shifted position, suggesting a 1,3,4 digit identity in the bird wing.

PMID: 31324809 [PubMed - in process]

Patronus is the elusive plant securin, preventing chromosome separation by antagonizing separase.

Proc Natl Acad Sci U S A. 2019 Jul 19;:

Authors: Cromer L, Jolivet S, Singh DK, Berthier F, De Winne N, De Jaeger G, Komaki S, Prusicki MA, Schnittger A, Guérois R, Mercier R

Abstract
Chromosome distribution at anaphase of mitosis and meiosis is triggered by separase, an evolutionarily conserved protease. Separase must be tightly regulated to prevent the untimely release of chromatid cohesion and disastrous chromosome distribution defects. Securin is the key inhibitor of separase in animals and fungi, but has not been identified in other eukaryotic lineages. Here, we identified PATRONUS1 and PATRONUS2 (PANS1 and PANS2) as the Arabidopsis homologs of securin. Disruption of PANS1 is known to lead to the premature separation of chromosomes at meiosis, and the simultaneous disruption of PANS1 and PANS2 is lethal. Here, we show that PANS1 targeting by the anaphase-promoting complex is required to trigger chromosome separation, mirroring the regulation of securin. We showed that PANS1 acts independently from Shugosins. In a genetic screen for pans1 suppressors, we identified SEPARASE mutants, showing that PANS1 and SEPARASE have antagonistic functions in vivo. Finally, we showed that the PANS1 and PANS2 proteins interact directly with SEPARASE. Altogether, our results show that PANS1 and PANS2 act as a plant securin. Remote sequence similarity was identified between the plant patronus family and animal securins, suggesting that they indeed derive from a common ancestor. Identification of patronus as the elusive plant securin illustrates the extreme sequence divergence of this central regulator of mitosis and meiosis.

PMID: 31324745 [PubMed - as supplied by publisher]

Simultaneous quantification of six indicator compounds in Wen-Qing-Yin by high-performance liquid chromatography-diode array detection.

J Food Drug Anal. 2019 Jul;27(3):749-757

Authors: Yeh CC, Huang SS, Liu PY, Wang BC, Tsai CF, Wang DY, Cheng HF

Abstract
A simple gradient high-performance liquid chromatography with diode array detection (HPLC-DAD) method was used to simultaneously to analyze characteristics of six indicator compounds in the traditional Chinese medicine (TCM) formulation Wen-Qing-Yin (WQY). Separate optimization was performed using a Cosmosil C18 column gradient method with 0.1% formic acid in both mobile phases of aqueous and acetonitrile (ACN), at a flow rate, detection wavelength, and sample volume of 1.8 mL/min, 268 nm, and 10 μL, respectively. The linear regression of six active compounds berberine (BER), baicalin (BAI), ferulic acid (FER), geniposide (GEN), hydorxymethoxylfurfural (HMF), and paeoniflorin (PAE) was produced at the concentration range of 10-2000 μg/mL. The method validation revealed an acceptable precision (intra- and inter-day precision < 3.39% and 4.11%, respectively) and recovery (85.60-110.45% and 86.58-110.90%), a recovery range of 86.61-109.42%, and sensitivity (limit of detection [LOD] and limit of quantification [LOQ] values were in the range of 0.03-3.13, and 0.08-9.38 μg/mL, respectively) while the calibration curves were linear with a correlation coefficient (R2) ranging from 0.9966 to 0.9989. The qualitative and quantitative analyses were performed by direct comparison of the peaks of the WCY extract to retention times of reference standards. Additionally, principal component analysis (PCA) successfully discriminated four purchased commercial samples of all six indicator constituents, and the present results indicate their comprehensive potential usefulness for qualitative and quantitative analyses of the WQY decoction and its commercial products.

PMID: 31324290 [PubMed - in process]

Absence of an embryonic stem cell DNA methylation signature in human cancer.

BMC Cancer. 2019 Jul 19;19(1):711

Authors: Zhang Z, Wiencke JK, Koestler DC, Salas LA, Christensen BC, Kelsey KT

Abstract
BACKGROUND: Differentiated cells that arise from stem cells in early development contain DNA methylation features that provide a memory trace of their fetal cell origin (FCO). The FCO signature was developed to estimate the proportion of cells in a mixture of cell types that are of fetal origin and are reminiscent of embryonic stem cell lineage. Here we implemented the FCO signature estimation method to compare the fraction of cells with the FCO signature in tumor tissues and their corresponding nontumor normal tissues.
METHODS: We applied our FCO algorithm to discovery data sets obtained from The Cancer Genome Atlas (TCGA) and replication data sets obtained from the Gene Expression Omnibus (GEO) data repository. Wilcoxon rank sum tests, linear regression models with adjustments for potential confounders and non-parametric randomization-based tests were used to test the association of FCO proportion between tumor tissues and nontumor normal tissues. P-values of < 0.05 were considered statistically significant.
RESULTS: Across 20 different tumor types we observed a consistently lower FCO signature in tumor tissues compared with nontumor normal tissues, with 18 observed to have significantly lower FCO fractions in tumor tissue (total n = 6,795 tumor, n = 922 nontumor, P < 0.05). We replicated our findings in 15 tumor types using data from independent subjects in 15 publicly available data sets (total n = 740 tumor, n = 424 nontumor, P < 0.05).
CONCLUSIONS: The results suggest that cancer development itself is substantially devoid of recapitulation of normal embryologic processes. Our results emphasize the distinction between DNA methylation in normal tightly regulated stem cell driven differentiation and cancer stem cell reprogramming that involves altered methylation in the service of great cell heterogeneity and plasticity.

PMID: 31324166 [PubMed - in process]

Arachidonic Acid Evokes an Increase in Intracellular Ca2+ Concentration and Nitric Oxide Production in Endothelial Cells from Human Brain Microcirculation.

Cells. 2019 Jul 09;8(7):

Authors: Berra-Romani R, Faris P, Negri S, Botta L, Genova T, Moccia F

Abstract
It has long been known that the conditionally essential polyunsaturated arachidonic acid (AA) regulates cerebral blood flow (CBF) through its metabolites prostaglandin E2 and epoxyeicosatrienoic acid, which act on vascular smooth muscle cells and pericytes to vasorelax cerebral microvessels. However, AA may also elicit endothelial nitric oxide (NO) release through an increase in intracellular Ca2+ concentration ([Ca2+]i). Herein, we adopted Ca2+ and NO imaging, combined with immunoblotting, to assess whether AA induces intracellular Ca2+ signals and NO release in the human brain microvascular endothelial cell line hCMEC/D3. AA caused a dose-dependent increase in [Ca2+]i that was mimicked by the not-metabolizable analogue, eicosatetraynoic acid. The Ca2+ response to AA was patterned by endoplasmic reticulum Ca2+ release through type 3 inositol-1,4,5-trisphosphate receptors, lysosomal Ca2+ mobilization through two-pore channels 1 and 2 (TPC1-2), and extracellular Ca2+ influx through transient receptor potential vanilloid 4 (TRPV4). In addition, AA-evoked Ca2+ signals resulted in robust NO release, but this signal was considerably delayed as compared to the accompanying Ca2+ wave and was essentially mediated by TPC1-2 and TRPV4. Overall, these data provide the first evidence that AA elicits Ca2+-dependent NO release from a human cerebrovascular endothelial cell line, but they seemingly rule out the possibility that this NO signal could acutely modulate neurovascular coupling.

PMID: 31323976 [PubMed - in process]

Diachasmimorpha longicaudata Parasitism Response to Medfly Host Fruit and Fruit Infestation Age.

Insects. 2019 Jul 18;10(7):

Authors: Harbi A, de Pedro L, Ferrara FAA, Tormos J, Chermiti B, Beitia F, Sabater-Munoz B

Abstract
The parasitoid Diachasmimorpha longicaudata (Ashmead) (Hymenoptera: Braconidae) is increasingly being used in integrated pest management (IPM) programs as a biological control agent in order to suppress tephritid fruit flies of economic importance. Innate and acquired behavioral responses-such as pest host fruit preference-of parasitoids can modulate their efficiency in the field and should be taken into consideration prior to parasitoid species' selection for mass-rearing. We have assessed the influence of medfly-infested (two infestation ages, 1 and 4-d-old) and uninfested fruit species on host preference and efficiency of D. longicaudata by using a multistep assay including olfactory, laboratory and semi-field trials. We found that D. longicaudata was significantly more attracted to medfly-infested apples for both infestation ages, with the oldest being the most preferred. D. longicaudata exhibited a significant preference among the four fruits tested. The implications of these behavioral responses of D. longicaudata to medfly host fruits and infestation age are discussed in relationship to its use in IPM programs in the Mediterranean basin area.

PMID: 31323827 [PubMed]

Clinical Applications of Circulating Tumour DNA in Pancreatic Adenocarcinoma.

J Pers Med. 2019 Jul 18;9(3):

Authors: Loft M, Lee B, Tie J, Gibbs P

Abstract
Pancreatic adenocarcinoma remains one of the most aggressive cancers with an ongoing dismal survival rate despite some recent advances in treatment options. This is largely due to the typically late presentation and limited effective therapeutic options in advanced disease. There are numerous circulating biomarkers that have potential clinical application as tumour markers, including circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), cell-free RNA (cfRNA), exosomes and circulating tumour proteins. This review will focus on the development of ctDNA as a non-invasive liquid biopsy, with its high sensitivity and specificity having potential clinical applications in pancreatic cancer. These include a role in screening, prognostication via the detection of minimal residual disease, early detection of recurrence, and for patients with advanced disease; tumour genotyping and monitoring treatment response. Prospective randomised adjuvant clinical trials are currently underway, exploring the impact of ctDNA-guided adjuvant therapy decisions. In this review, we provide perspectives on the current literature and considerations of future directions.

PMID: 31323810 [PubMed]

Separating the Wheat from the Chaff: RNA Editing and Selection of Translatable mRNA in Trypanosome Mitochondria.

Pathogens. 2019 Jul 18;8(3):

Authors: Maslov DA

Abstract
In the mitochondria of trypanosomes and related kinetoplastid protists, most mRNAs undergo a long and sophisticated maturation pathway before they can be productively translated by mitochondrial ribosomes. Some of the aspects of this pathway (identity of the promotors, transcription initiation, and termination signals) remain obscure, and some (post-transcriptional modification by U-insertion/deletion, RNA editing, 3'-end maturation) have been illuminated by research during the last decades. The RNA editing creates an open reading frame for a productive translation, but the fully edited mRNA often represents a minor fraction in the pool of pre-edited and partially edited precursors. Therefore, it has been expected that the final stages of the mRNA processing generate molecular hallmarks, which allow for the efficient and selective recognition of translation-competent templates. The general contours and several important details of this process have become known only recently and represent the subject of this review.

PMID: 31323762 [PubMed]

27 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 2019/07/20

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.

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 2019/07/20

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.

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 2019/07/19

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.

29 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 2019/07/18

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 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.