A General Mechanism of Differentiation Based on Morphogenetic Studies in Ciliates

Paul B. Weisz

doi:10.1086/281681

Further Evidence for Energy Landscape Flattening in the Superionic Argyrodites Li6+xP1−xMxS5I (M = Si, Ge, Sn)

10.26434/chemrxiv.8109506.v2 ◽

2019 ◽

Author(s):

Saneyuki Ohno ◽

Bianca Helm ◽

Till Fuchs ◽

Georg Dewald ◽

Marvin Kraft ◽

...

Keyword(s):

Solid State ◽

Activation Barrier ◽

Energy Landscape ◽

General Mechanism ◽

Ionic Conductors ◽

Energy Storage Devices ◽

Ion Conductor ◽

Storage Devices ◽

Open Questions ◽

Sudden Decrease

All-solid-state batteries are promising candidates for next-generation energy storage devices. Although the list of candidate materials for solid electrolytes has grown in the past decade, there are still many open questions concerning the mechanisms behind ionic migration in materials. In particular, the lithium thiophosphate family of materials has shown very promising properties for solid-state battery applications. Recently, the Ge-substituted Li6PS5I argyrodite was shown to be a very fast Li-ion conductor, despite the poor ionic conductivity of the unsubstituted Li6PS5I. Therein, the conductivity was enhanced by over three orders of magnitude due to the emergence of I−/S2−exchange, i.e.site-disorder, which led to a sudden decrease of the activation barrier with a concurrent flattening of the energy landscapes. Inspired by this work, two series of elemental substitutions in Li6+xP1−xMxS5I (M= Si and Sn) were investigated in this study and compared to the Ge-analogue. A sharp reduction in the activation energy was observed at the same M4+/P5+composition as previously found in the Ge-analogue, suggesting a more general mechanism at play. Furthermore, structural analyses with X-ray and neutron diffraction indicate that similar changes in the Li-sublattice occur despite a significant variation in the size of the substituents, suggesting that in the argyrodites, the lithium substructure is most likely influenced by the occurring Li+– Li+interactions. This work provides further evidence that the energy landscape of ionic conductors can be tailored by inducing local disorder.

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Faculty Opinions recommendation of Physical transfer of membrane and cytoplasmic components as a general mechanism of cell-cell communication.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1158017.618100 ◽

2009 ◽

Author(s):

Vivian Tang

Keyword(s):

Cell Communication ◽

General Mechanism ◽

Cell Cell

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A general mechanism of grain growth-Ⅱ: Experimental

Journal of Materiomics ◽

10.1016/j.jmat.2021.02.008 ◽

2021 ◽

Author(s):

Jianfeng Hu ◽

Junzhan Zhang ◽

Xianhao Wang ◽

Jun Luo ◽

Zhijun Zhang ◽

...

Keyword(s):

Grain Growth ◽

General Mechanism

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Peculiarities of promiscuous l-threonine transaldolases for enantioselective synthesis of β-hydroxy-α-amino acids

Applied Microbiology and Biotechnology ◽

10.1007/s00253-021-11288-w ◽

2021 ◽

Author(s):

Shan Wang ◽

Hai Deng

Keyword(s):

Amino Acids ◽

Organic Molecules ◽

Stereoselective Synthesis ◽

Enantioselective Synthesis ◽

General Mechanism ◽

Future Developments ◽

Key Points ◽

Biomaterial Science ◽

One Step ◽

Harsh Conditions

Abstract The introduction of β-hydroxy-α-amino acids (βHAAs) into organic molecules has received considerable attention as these molecules have often found widespread applications in bioorganic chemistry, medicinal chemistry and biomaterial science. Despite innovation of asymmetric synthesis of βHAAs, stereoselective synthesis to control the two chiral centres at Cα and Cβ positions is still challenging, with poor atomic economy and multi protection and deprotection steps. These syntheses are often operated under harsh conditions. Therefore, a biotransformation approach using biocatalysts is needed to selectively introduce these two chiral centres into structurally diverse molecules. Yet, there are few ways that enable one-step synthesis of βHAAs. One is to extend the substrate scope of the existing enzyme inventory. Threonine aldolases have been explored to produce βHAAs. However, the enzymes have poor controlled installation at Cβ position, often resulting in a mixture of diastereoisomers which are difficult to be separated. In this respect, l-threonine transaldolases (LTTAs) offer an excellent potential as the enzymes often provide controlled stereochemistry at Cα and Cβ positions. Another is to mine LTTA homologues and engineer the enzymes using directed evolution with the aim of finding engineered biocatalysts to accept broad substrates with enhanced conversion and stereoselectivity. Here, we review the development of LTTAs that incorporate various aldehyde acceptors to generate structurally diverse βHAAs and highlight areas for future developments. Key points • The general mechanism of the transaldolation reaction catalysed by LTTAs • Recent advances in LTTAs from different biosynthetic pathways • Applications of LTTAs as biocatalysts for production of βHAAs

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LncRNA:DNA triplex-forming sites are positioned at specific areas of genome organization and are predictors for Topologically Associated Domains

BMC Genomics ◽

10.1186/s12864-021-07727-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Benjamin Soibam ◽

Ayzhamal Zhamangaraeva

Keyword(s):

Genome Organization ◽

Chromatin Organization ◽

Ctcf Binding ◽

General Mechanism ◽

Promoter Regions ◽

Cellular Processes ◽

A Genome ◽

Topologically Associated Domains ◽

Multiple Cell ◽

Genomic Regions

Abstract Background Chromosomes are organized into units called topologically associated domains (TADs). TADs dictate regulatory landscapes and other DNA-dependent processes. Even though various factors that contribute to the specification of TADs have been proposed, the mechanism is not fully understood. Understanding the process for specification and maintenance of these units is essential in dissecting cellular processes and disease mechanisms. Results In this study, we report a genome-wide study that considers the idea of long noncoding RNAs (lncRNAs) mediating chromatin organization using lncRNA:DNA triplex-forming sites (TFSs). By analyzing the TFSs of expressed lncRNAs in multiple cell lines, we find that they are enriched in TADs, their boundaries, and loop anchors. However, they are evenly distributed across different regions of a TAD showing no preference for any specific portions within TADs. No relationship is observed between the locations of these TFSs and CTCF binding sites. However, TFSs are located not just in promoter regions but also in intronic, intergenic, and 3’UTR regions. We also show these triplex-forming sites can be used as predictors in machine learning models to discriminate TADs from other genomic regions. Finally, we compile a list of important “TAD-lncRNAs” which are top predictors for TADs identification. Conclusions Our observations advocate the idea that lncRNA:DNA TFSs are positioned at specific areas of the genome organization and are important predictors for TADs. LncRNA:DNA triplex formation most likely is a general mechanism of action exhibited by some lncRNAs, not just for direct gene regulation but also to mediate 3D chromatin organization.

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A general mechanism of grain growth ─Ⅰ. Theory

Journal of Materiomics ◽

10.1016/j.jmat.2021.02.007 ◽

2021 ◽

Author(s):

Jianfeng Hu ◽

Xianhao Wang ◽

Junzhan Zhang ◽

Jun Luo ◽

Zhijun Zhang ◽

...

Keyword(s):

Grain Growth ◽

General Mechanism

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Research on Knowledge Discovery and Stock Forecasting of Financial News Based on Domain Ontology

International Journal of Information Technology & Decision Making ◽

10.1142/s0219622019500160 ◽

2019 ◽

Vol 18 (03) ◽

pp. 953-979 ◽

Cited By ~ 1

Author(s):

Lingling Zhang ◽

Minghui Zhao ◽

Zili Feng

Keyword(s):

Knowledge Acquisition ◽

Knowledge Discovery ◽

Tacit Knowledge ◽

Explicit Knowledge ◽

Academic Research ◽

Online News ◽

Domain Ontology ◽

General Mechanism ◽

Financial News ◽

Knowledge Reasoning

In the era of big data, how to obtain useful knowledge from online news and utilize it as an important basis to make investment decision has become the hotspot of industrial and academic research. At present, there have been research and practice on explicit knowledge acquisition from news, but tacit knowledge acquisition is still under exploration. Based on the general mechanism of domain knowledge, knowledge reasoning, and knowledge discovery, this paper constructs a framework for discovering tacit knowledge from news and applying the knowledge to stock forecasting. The concrete work is as follows: First, according to the characteristics of financial field and the conceptual cube, the conceptual structure of industry–company–product is constructed, and the framework of domain ontology is put forward. Second, with the construction of financial field ontology, the financial news knowledge management framework is proposed. Besides, with the application of attributes in ontology and domain rules extracted from news text, the knowledge reasoning mechanism of financial news is constructed to achieve financial news knowledge discovery. Finally, news knowledge that reflects important information about stock changes is integrated into the traditional stock price forecasting model and the newly proposed model performs well in the empirical analysis of polyester industry.

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Downregulation of c-kit (Stem Cell Factor Receptor) in Transformed Hematopoietic Precursor Cells by Stroma Cells

Blood ◽

10.1182/blood.v93.2.554 ◽

1999 ◽

Vol 93 (2) ◽

pp. 554-563 ◽

Cited By ~ 5

Author(s):

Christoph Heberlein ◽

Jutta Friel ◽

Christine Laker ◽

Dorothee von Laer ◽

Ulla Bergholz ◽

...

Keyword(s):

Stem Cell ◽

Cell Line ◽

Stem Cell Factor ◽

Progenitor Cell ◽

Receptor Expression ◽

General Mechanism ◽

Ligand Interaction ◽

Kit Ligand ◽

Kit Receptor ◽

Progenitor Cell Line

Abstract We show a dramatic downregulation of the stem cell factor (SCF) receptor in different hematopoietic cell lines by murine stroma. Growth of the human erythroid/macrophage progenitor cell line TF-1 is dependent on granulocyte-macrophage colony-stimulating factor (GM-CSF) or interleukin-3 (IL-3). However, TF-1 cells clone and proliferate equally well on stroma. Independent stroma-dependent TF-1 clones (TF-1S) were generated on MS-5 stroma. Growth of TF-1S and TF-1 cells on stroma still requires interaction between c-kit (SCF receptor) and its ligand SCF, because antibodies against c-kit inhibit growth to less than 2%. Surprisingly, c-kit receptor expression (RNA and protein) was downregulated by 2 to 3 orders of magnitude in TF-1S and TF-1 cells grown on stroma. This stroma-dependent regulation of the kit receptor in TF-1 was also observed on exposure to kit ligand-negative stroma, thus indicating the need for heterologous receptor ligand interaction. Removal of stroma induced upregulation by 2 to 4 orders of magnitude. Downregulation and upregulation of c-kit expression could also be shown for the megakaryocytic progenitor cell line M-07e and was comparable to that of TF-1, indicating that stroma-dependent regulation of c-kit is a general mechanism. Downregulation may be an economic way to compensate for the increased sensitivity of the c-kit/ligand interaction on stroma. The stroma-dependent c-kit regulation most likely occurs at the transcriptional level, because mechanisms, such as splicing, attenuation, differential promoter usage, or mRNA stability, could be excluded.

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A GENERAL MECHANISM FOR LUPUS ANTICOAGULANTS

10.1055/s-0038-1643660 ◽

1987 ◽

Author(s):

V Pengo ◽

M J Heine ◽

P Thiagarajan ◽

s s Shapiro

Keyword(s):

Lupus Anticoagulant ◽

Anticoagulant Activity ◽

Protein A ◽

Coagulation Factors ◽

Phosphatidyl Serine ◽

General Mechanism ◽

Factor X ◽

Lupus Anticoagulants ◽

Calcium Dependent ◽

Anionic Phospholipids

Although- a number of observations have implied that lupus anticoagulants have immunologic specificity towards anionic. phospholipids, thereby prolonging phospholipid-dependent coagulation tests, this assumption has been directly demonstrated in only one patient with a monoclonal IgM paraprotein. We have tested the generality of this hypothesis directly by isolating five IgG lupus anticoagulants from patients with lupus-like syndromes and/or thrombosis. IgG lupus anticoagulant fractions were isolated free of other plasma proteins and free of contaminating phospholipid by adsorption to and elution from cardiolipin-cholesterol-dicetylphosphate liposomes , followed by chromatography on protein A-Sepharose. Cardiolipin liposomes, but not phosphatidylcholine liposomes, were capable of removing all, or nearly all, lupus anticoagulant activity from patient plasma. Anticardiolipin and lupus anticoagulant activity were both present in acidic fractions on isoelectric focusing. F(ab’)2 fragments retained lupus anti coagulant activity and bound to cardiolipin in an ELISA assay. The affinity-purified IgG preparations reacted with cardiolipin, phosphatidyl serine , phosphatidylinositol and phosphatidic acid, but not with phosphatidylcholine or phosphatidyl ethanol amine, and inhibited calcium-dependent binding of prothrombin and of factor X to phosphatidy1serine-coated surfaces. These data demonstrate a general mechanism for the action of lupus anticoagulants: antibodies that have immunologic specificity towards anionic phospholipids, thereby blocking the calcium-mediated binding of vitamin K-dependent coagulation factors to coagulation-active phospholipid surfaces.

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