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 2020/02/09

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.

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 2020/02/09

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.

34 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 2020/02/08

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.

34 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 2020/02/08

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.

36 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 2020/02/07

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.

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 2020/02/07

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.

112 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 2020/02/06

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.

86 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 2020/02/05

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.

Reconstruction, verification and in-silico analysis of a genome-scale metabolic model of bacterial cellulose producing Komagataeibacter xylinus.

Bioprocess Biosyst Eng. 2020 Feb 01;:

Authors: Rezazadeh M, Babaeipour V, Motamedian E

Abstract
In this study, a comprehensive genome-scale metabolic network of Komagataeibacter xylinus as the model microorganism was reconstructed based on genome annotation, for better understanding of metabolic growth and biosynthesis of bacterial cellulose (BC). The reconstructed network included 640 genes, 783 metabolic reactions and 865 metabolites. The model was completely successful to predict the lack of growth under anaerobic conditions. Model validation by the data for the growth of acetic acid bacteria with ethanol-limited chemostat cultures showed that there is a good agreement for the O2 and CO2 fluxes with actual growth conditions. Then the model was used to forecast the simultaneous production of BC and by-products. The obtained data showed that the rate of BC production is consistent with experimental data with an accuracy of 93.7%. Finally, the study of flux balance analysis (FBA) data showed that the pentose phosphate pathway and the TCA cycle play an important role in growth-promoting metabolism in K. xylinus and have a close relationship with BC biosynthesis. By integrating this model with various metabolic engineering and systems biology tools in the future, it is possible to overcome the common challenges in the large-scale BC production, such as low yield and productivity.

PMID: 32008096 [PubMed - as supplied by publisher]

Evaluating climate change impacts on mountain lakes by applying the new silicification value to paleolimnological samples.

Sci Total Environ. 2020 Jan 25;715:136913

Authors: Kuefner W, Hofmann AM, Geist J, Raeder U

Abstract
The evaluation of climate change impact on lakes typically relies on statistical methods like the reorganisation of organism communities (beta diversity) or transfer functions. A new method uses the silicification of diatoms that correlates with temperature and nutrients. The so-called silicification value (SiVa) overcomes problems of descriptive statistics or absent indicator species. Averaged over diatom communities, it related inversely to lake surface temperatures in mountain lakes. Hence, its change over time (δ SiVa) in a lake was hypothesised to reflect global change-driven lake warming quantitatively, which supposedly climaxes in shallow lakes. Sixteen different δ SiVa calculation approaches were tested. They (1) included or excluded planktic diatoms, (2) integrated fixed or variable time series referring to climate data or changes in diatom assemblages, (3) employed a top-bottom or regression approach and (4) expressed the δ SiVa as relative or absolute values. Subfossil diatom assemblages from 24 sediment cores from Bavarian and north Tyrolian mountain lakes served as sample set. All possible approaches were evaluated for their explanatory power for lake characteristics using GLMs. The top-bottom benthic approach with fixed climate data-based time series appeared to be the best model based on AIC and the extent of variable integration. In line with the hypothesis, the strongest decrease of δ SiVa was evident in most shallow lakes. Segmented regression further highlighted a positive correlation with depth if shallower than 10 m. By referring to the negative SiVa-summer temperature relation, δ SiVa also enabled the quantification of lake warming within the last decades, which ranged mainly between 0.1 °C and 1.1 °C per decade, consistent with existing literature. Additionally, a 100 year temperature reconstruction from a varved sediment core successfully validated the approach. Further studies may focus and extend its application to deeper lakes, but it can already serve as a powerful tool in palaeolimnological studies of shallow lakes like hard-water mountain lakes.

PMID: 32007888 [PubMed - as supplied by publisher]

A genetic toolbox for metabolic engineering of Issatchenkia orientalis.

Metab Eng. 2020 Jan 30;:

Authors: Cao M, Fatma Z, Song X, Hsieh PH, Tran VG, Lyon WL, Sayadi M, Shao Z, Yoshikuni Y, Zhao H

Abstract
The nonconventional yeast Issatchenkia orientalis can grow under highly acidic conditions and has been explored for production of various organic acids. However, its broader application is hampered by the lack of efficient genetic tools to enable sophisticated metabolic manipulations. We recently constructed an episomal plasmid based on the autonomously replicating sequence (ARS) from Saccharomyces cerevisiae (ScARS) in I. orientalis and developed a CRISPR/Cas9 system for multiplex gene deletions. Here we report three additional genetic tools including: (1) identification of a 0.8 kb centromere-like (CEN-L) sequence from the I. orientalis genome by using bioinformatics and functional screening; (2) discovery and characterization of a set of constitutive promoters and terminators under different culture conditions by using RNA-Seq analysis and a fluorescent reporter; and (3) development of a rapid and efficient in vivo DNA assembly method in I. orientalis, which exhibited ∼100% fidelity when assembling a 7 kb-plasmid from seven DNA fragments ranging from 0.7 kb to 1.7 kb. As proof of concept, we used these genetic tools to rapidly construct a functional xylose utilization pathway in I. orientalis.

PMID: 32007615 [PubMed - as supplied by publisher]

Peptide retention time prediction in hydrophilic interaction liquid chromatography: Zwitter-ionic sulfoalkylbetaine and phosphorylcholine stationary phases.

J Chromatogr A. 2020 Jan 22;:460909

Authors: Yeung D, Klaassen N, Mizero B, Spicer V, Krokhin OV

Abstract
Peptide retention time prediction models have been developed for zwitter-ionic ZIC-HILIC and ZIC-cHILIC stationary phases (pH 4.5 eluents) using proteomics-derived retention datasets of ~30 thousand tryptic peptides each. Overall, hydrophilicity of these stationary phases was found to be similar to the previously studied Amide HILIC phase, but lower compared to bare silicas. Peptide retention is driven by interactions of all charged (hydrophilic) residues at pH 4.5 (Asp, Glu, Arg, Lys, His), but shows specificity according to orientation of functional groups in zwitter-ionic pair. Thus, ZIC-cHILIC exhibits an increased contribution of negatively charged Asp and Glu due to the distal positioning of positively charged quaternary amines on the stationary phase. These findings confirm that HILIC interactions are driven by both peptide distribution between water layer adsorbed on the stationary phase and by interactions specific to functional groups of the packing material. Sequence-Specific Retention Calculator HILIC models were optimized for these columns showing 0.967-0.976 R2-values between experimental and predicted retention values. ZIC-HILIC separations represent a good choice as a first dimension in 2D LC-MS of peptide mixtures with correlations between retention values of ZIC-HILIC against RPLC found at 0.197 (ZIC-HILIC) and 0.137 (ZIC-cHILIC) R2-values, confirming a good orthogonality.

PMID: 32007221 [PubMed - as supplied by publisher]

Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription.

Mol Cell. 2020 Jan 27;:

Authors: Cossa G, Roeschert I, Prinz F, Baluapuri A, Silveira Vidal R, Schülein-Völk C, Chang YC, Ade CP, Mastrobuoni G, Girard C, Wortmann L, Walz S, Lührmann R, Kempa S, Kuster B, Wolf E, Mumberg D, Eilers M

Abstract
Deregulated expression of MYC induces a dependence on the NUAK1 kinase, but the molecular mechanisms underlying this dependence have not been fully clarified. Here, we show that NUAK1 is a predominantly nuclear protein that associates with a network of nuclear protein phosphatase 1 (PP1) interactors and that PNUTS, a nuclear regulatory subunit of PP1, is phosphorylated by NUAK1. Both NUAK1 and PNUTS associate with the splicing machinery. Inhibition of NUAK1 abolishes chromatin association of PNUTS, reduces spliceosome activity, and suppresses nascent RNA synthesis. Activation of MYC does not bypass the requirement for NUAK1 for spliceosome activity but significantly attenuates transcription inhibition. Consequently, NUAK1 inhibition in MYC-transformed cells induces global accumulation of RNAPII both at the pause site and at the first exon-intron boundary but does not increase mRNA synthesis. We suggest that NUAK1 inhibition in the presence of deregulated MYC traps non-productive RNAPII because of the absence of correctly assembled spliceosomes.

PMID: 32006464 [PubMed - as supplied by publisher]

Tissue mechanics drives regeneration of a mucociliated epidermis on the surface of Xenopus embryonic aggregates.

Nat Commun. 2020 Jan 31;11(1):665

Authors: Kim HY, Jackson TR, Stuckenholz C, Davidson LA

Abstract
Injury, surgery, and disease often disrupt tissues and it is the process of regeneration that aids the restoration of architecture and function. Regeneration can occur through multiple strategies including stem cell expansion, transdifferentiation, or proliferation of differentiated cells. We have identified a case of regeneration in Xenopus embryonic aggregates that restores a mucociliated epithelium from mesenchymal cells. Following disruption of embryonic tissue architecture and assembly of a compact mesenchymal aggregate, regeneration first restores an epithelium, transitioning from mesenchymal cells at the surface of the aggregate. Cells establish apico-basal polarity within 5 hours and a mucociliated epithelium within 24 hours. Regeneration coincides with nuclear translocation of the putative mechanotransducer YAP1 and a sharp increase in aggregate stiffness, and regeneration can be controlled by altering stiffness. We propose that regeneration of a mucociliated epithelium occurs in response to biophysical cues sensed by newly exposed cells on the surface of a disrupted mesenchymal tissue.

PMID: 32005801 [PubMed - in process]

Cholecystokinin-expressing Interneurons of the Medial Prefrontal Cortex Mediate Working Memory Retrieval.

J Neurosci. 2020 Jan 29;:

Authors: Nguyen R, Venkatesan S, Binko M, Yoon Bang J, Cajanding JD, Briggs C, Sargin D, Imayoshi I, Lambe EK, Chul Kim J

Abstract
Distinct components of working memory are co-ordinated by different classes of inhibitory interneurons in the prefrontal cortex, but the role of CCK-positive interneurons remains enigmatic. In humans, this major population of interneurons shows histological abnormalities in schizophrenia, an illness in which deficient working memory is a core defining symptom and the best predictor of long-term functional outcome. Yet, CCK interneurons as a molecularly distinct class have proved intractable to examination by typical molecular methods due to widespread expression of CCK in the pyramidal neuron population. Using an intersectional approach in mice of both sexes, we have succeeded in labeling, interrogating, and manipulating CCK interneurons in the medial prefrontal cortex. Here, we describe the anatomical distribution, electrophysiological properties, and postsynaptic connectivity of CCK interneurons, and evaluate their role in cognition. We found that CCK interneurons comprise a larger proportion of the mPFC interneurons compared to PV interneurons, targeting a wide range of neuronal subtypes with a distinct connectivity pattern. Phase-specific optogenetic inhibition revealed that CCK, but not PV, interneurons play a critical role in the retrieval of working memory. These findings shine new light on the relationship between cortical CCK interneurons and cognition and offer a new set of tools to investigate interneuron dysfunction and cognitive impairments associated with schizophrenia.SIGNIFICANCE STATEMENTCholecystokinin (CCK)-expressing interneurons outnumber other interneuron populations in key brain areas involved in cognition and memory, including the medial prefrontal cortex (mPFC). However, they have proved intractable to examination as experimental techniques have lacked the necessary selectivity. To the best of our knowledge, the present study is the first to report detailed properties of cortical CCK interneurons, revealing their anatomical organization, electrophysiological properties, postsynaptic connectivity, and behavioural function in working memory.

PMID: 32005764 [PubMed - as supplied by publisher]

The Protein Phosphatase PP2A-B'γ Takes Control over Salicylic Acid to Suppress Defense and Premature Senescence.

Plant Physiol. 2020 Feb;182(2):681-682

Authors: Mhamdi A

PMID: 32005741 [PubMed - in process]

5Gs for crop genetic improvement.

Curr Opin Plant Biol. 2020 Jan 28;:

Authors: Varshney RK, Sinha P, Singh VK, Kumar A, Zhang Q, Bennetzen JL

Abstract
Here we propose a 5G breeding approach for bringing much-needed disruptive changes to crop improvement. These 5Gs are Genome assembly, Germplasm characterization, Gene function identification, Genomic breeding (GB), and Gene editing (GE). In our view, it is important to have genome assemblies available for each crop and a deep collection of germplasm characterized at sequencing and agronomic levels for identification of marker-trait associations and superior haplotypes. Systems biology and sequencing-based mapping approaches can be used to identify genes involved in pathways leading to the expression of a trait, thereby providing diagnostic markers for target traits. These genes, markers, haplotypes, and genome-wide sequencing data may be utilized in GB and GE methodologies in combination with a rapid cycle breeding strategy.

PMID: 32005553 [PubMed - as supplied by publisher]

The extended recovery ring-stage survival assay provides a superior association with patient clearance half-life and increases throughput.

Malar J. 2020 Jan 31;19(1):54

Authors: Davis SZ, Singh PP, Vendrely KM, Shoue DA, Checkley LA, McDew-White M, Button-Simons KA, Cassady Z, Sievert MAC, Foster GJ, Nosten FH, Anderson TJC, Ferdig MT

Abstract
BACKGROUND: Tracking and understanding artemisinin resistance is key for preventing global setbacks in malaria eradication efforts. The ring-stage survival assay (RSA) is the current gold standard for in vitro artemisinin resistance phenotyping. However, the RSA has several drawbacks: it is relatively low throughput, has high variance due to microscopy readout, and correlates poorly with the current benchmark for in vivo resistance, patient clearance half-life post-artemisinin treatment. Here a modified RSA is presented, the extended Recovery Ring-stage Survival Assay (eRRSA), using 15 cloned patient isolates from Southeast Asia with a range of patient clearance half-lives, including parasite isolates with and without kelch13 mutations.
METHODS: Plasmodium falciparum cultures were synchronized with single layer Percoll during the schizont stage of the intraerythrocytic development cycle. Cultures were left to reinvade to early ring-stage and parasitaemia was quantified using flow cytometry. Cultures were diluted to 2% haematocrit and 0.5% parasitaemia in a 96-well plate to start the assay, allowing for increased throughput and decreased variability between biological replicates. Parasites were treated with 700 nM of dihydroartemisinin or 0.02% dimethyl sulfoxide (DMSO) for 6 h, washed three times in drug-free media, and incubated for 66 or 114 h, when samples were collected and frozen for PCR amplification. A SYBR Green-based quantitative PCR method was used to quantify the fold-change between treated and untreated samples.
RESULTS: 15 cloned patient isolates from Southeast Asia with a range of patient clearance half-lives were assayed using the eRRSA. Due to the large number of pyknotic and dying parasites at 66 h post-exposure (72 h sample), parasites were grown for an additional cell cycle (114 h post-exposure, 120 h sample), which drastically improved correlation with patient clearance half-life compared to the 66 h post-exposure sample. A Spearman correlation of - 0.8393 between fold change and patient clearance half-life was identified in these 15 isolates from Southeast Asia, which is the strongest correlation reported to date.
CONCLUSIONS: eRRSA drastically increases the efficiency and accuracy of in vitro artemisinin resistance phenotyping compared to the traditional RSA, which paves the way for extensive in vitro phenotyping of hundreds of artemisinin resistant parasites.

PMID: 32005233 [PubMed - in process]

52 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 2020/02/01

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.

51 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 2020/02/01

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.