scholarly journals Higher order analysis of gene correlations by tensor decomposition

2019 ◽  
Author(s):  
Farzane Yahyanejad
Keyword(s):  
Tensor Decomposition ◽  
Receptor Activation ◽  
Higher Order ◽  
Cellular System ◽  
Signaling Proteins ◽  
Tensor Order ◽  
Gene Correlation ◽  
Data Signal ◽  
Multiple Signaling ◽  
First Time

AbstractThis study advances our understanding of inter- and intra-pathways higher order signaling in the cellular system and it leads to new discovery of multiple intracellular structures in signal transduction pathways in yeast Saccharomyces. We present a new tensor decomposition algorithm in reconstructing the pathways based on higher correlations among genes that compose a cellular system. The higher order gene correlation (HOGC) analysis has the power to elucidate gene’s higher interaction dependencies which has been barely understood. Recent studies i.e. [24] have experimentally revealed that multiple signaling proteins, yet sometimes infinite, may assemble to meaningful structure to transmit a receptor activation information. In this paper we reveal 3-order genomic correlations among significant component of the cellular system. This is the first time such a systematic and computational model provided for analysis of higher order correlations among genes. We use new fast algorithm to formulate a genes × genes × genes × decorrelated rank-1 sub-tensors (complexes) which can be associated with functionally independent pathways. Then we model higher order tensor decomposition which is constructed by K tensors of genes × genes × genes. Each new tensor is constructed by an orthogonal projection of data signal onto a designated basis signal to keep common sub-tensors in both signals. Our model for decomposing tensor order-4 approximates series of tensors as linear components of deccorelated rank-1 sub-tensors over tensor of order-3 and rank-3 triplings among sub-tensors. The linear components represent intra-pathway in cell signaling and triplings implicate inter-pathways higher order signaling. Through structural studies of inter- and intra-higher order signaling pathways, we uncover different scenario that involves triple formation of signaling proteins into higher order signaling machines for transmission of receptor activation information to cellular responses.

Free Vibration of Moderately Thick Conical Shells Using a Higher Order Shear Deformable Theory

2014 ◽  
Vol 136 (5) ◽  
Author(s):  
R. D. Firouz-Abadi ◽  
M. Rahmanian ◽  
M. Amabili
Keyword(s):  
Free Vibration ◽  
Boundary Conditions ◽  
Equations Of Motion ◽  
Free Vibration Analysis ◽  
Higher Order ◽  
Arbitrary Boundary ◽  
Conical Shells ◽  
First Time ◽  
Circumferential Wave ◽  
Shear Deformable

The present study considers the free vibration analysis of moderately thick conical shells based on the Novozhilov theory. The higher order governing equations of motion and the associate boundary conditions are obtained for the first time. Using the Frobenius method, exact base solutions are obtained in the form of power series via general recursive relations which can be applied for any arbitrary boundary conditions. The obtained results are compared with the literature and very good agreement (up to 4%) is achieved. A comprehensive parametric study is performed to provide an insight into the variation of the natural frequencies with respect to thickness, semivertex angle, circumferential wave numbers for clamped (C), and simply supported (SS) boundary conditions.

scholarly journals Characterisation of Glucose-Dependent Insulinotropic Polypeptide Receptor Antagonists in Rodent Pancreatic Beta Cells and Mice

2019 ◽  
Vol 12 ◽  
pp. 117955141987545 ◽  
Author(s):  
RA Perry ◽  
SL Craig ◽  
MT Ng ◽  
VA Gault ◽  
PR Flatt ◽  
...  
Keyword(s):  
Insulin Secretion ◽  
Pancreatic Beta Cells ◽  
Receptor Activation ◽  
Contributing Factors ◽  
Glucose Lowering ◽  
Incretin Hormone ◽  
Glucose Levels ◽  
First Time ◽  
Gip Receptor

Hypersecretion and alterations in the biological activity of the incretin hormone, glucose-dependent insulinotropic polypeptide (GIP), have been postulated as contributing factors in the development of obesity-related diabetes. However, recent studies also point to weight-reducing effects of GIP receptor activation. Therefore, generating precise experimental tools, such as specific and effective GIP receptor (GIPR) antagonists, is of key significance to better understand GIP physiology. Thus, the primary aim of the current study was to uncover improved GIPR antagonists for use in rodent studies, using human and mouse GIP sequences with N- and C-terminal deletions. Initial in vitro studies revealed that the GIPR agonists, human (h) GIP(1-42), hGIP(1-30) and mouse (m) GIP(1-30), stimulated ( P < 0.01 to P < 0.001) insulin secretion from rat BRIN-BD11 cells. Analysis of insulin secretory effects of the N- and C-terminally cleaved GIP peptides, including hGIP(3-30), mGIP(3-30), h(Pro3)GIP(3-30), hGIP(5-30), hGIP(3-42) and hGIP(5-42), revealed that these peptides did not modulate insulin secretion. More pertinently, only hGIP(3-30), mGIP(3-30) and h(Pro3)GIP(3-30) were able to significantly ( P < 0.01 to P < 0.001) inhibit hGIP(1-42)-stimulated insulin secretion. The human-derived GIPR agonist sequences, hGIP(1-42) and hGIP(1-30), reduced ( P < 0.05) glucose levels in mice following conjoint injection with glucose, but mGIP(1-30) was ineffective. None of the N- and C-terminally cleaved GIP peptides affected glucose homeostasis when injected alone with glucose. However, hGIP(5-30) and mGIP(3-30) significantly ( P < 0.05 to P < 0.01) impaired the glucose-lowering action of hGIP(1-42). Further evaluation of these most effective sequences demonstrated that mGIP(3-30), but not hGIP(5-30), effectively prevented GIP-induced elevations of plasma insulin concentrations. These data highlight, for the first time, that mGIP(3-30) represents an effective molecule to inhibit GIPR activity in mice.

scholarly journals Formyl-Peptide Receptor Activation Enhances Phagocytosis of Community-Acquired Methicillin-Resistant Staphylococcus aureus

2019 ◽  
Author(s):  
Elisabeth Weiß ◽  
Katja Schlatterer ◽  
Christian Beck ◽  
Andreas Peschel ◽  
Dorothee Kretschmer
Keyword(s):  
Staphylococcus Aureus ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Receptor Activation ◽  
Formyl Peptide Receptor ◽  
Peptide Receptors ◽  
Highly Pathogenic ◽  
Methicillin Resistant ◽  
Formyl Peptide Receptors ◽  
Formyl Peptide ◽  
First Time

Abstract Background Formyl-peptide receptors (FPRs) are important pattern recognition receptors that sense specific bacterial peptides. Formyl-peptide receptors are highly expressed on neutrophils and monocytes, and their activation promotes the migration of phagocytes to sites of infection. It is currently unknown whether FPRs may also influence subsequent processes such as bacterial phagocytosis and killing. Staphylococcus aureus, especially highly pathogenic community-acquired methicillin-resistant S aureus strains, release high amounts of FPR2 ligands, the phenol-soluble modulins. Methods We demonstrate that FPR activation leads to upregulation of complement receptors 1 and 3 as well as FCγ receptor I on neutrophils and, consequently, increased opsonic phagocytosis of S aureus and other pathogens. Results Increased phagocytosis promotes killing of S aureus and interleukin-8 release by neutrophils. Conclusions We show here for the first time that FPRs govern opsonic phagocytosis. Manipulation of FPR2 activation could open new therapeutic opportunities against bacterial pathogens.

Vibration control of magnetostrictive plate under multi- physical loads via trigonometric higher order shear deformation theory

2015 ◽  
Vol 23 (19) ◽  
pp. 3057-3070 ◽  
Author(s):  
Ali Ghorbanpour Arani ◽  
Z Khoddami Maraghi ◽  
H Khani Arani
Keyword(s):  
Elastic Medium ◽  
Shear Deformation ◽  
Deformation Theory ◽  
Differential Quadrature Method ◽  
Equations Of Motion ◽  
Shear Deformation Theory ◽  
Higher Order ◽  
Feedback Gain ◽  
First Time ◽  
Free Vibration Response

For the first time in this research, a feedback control system is used to study the free vibration response of rectangular plate made of magnetostrictive material. In this regard, magnetostrictive plate (MsP) is analyzed by trigonometric higher order shear deformation theory that involved six unknown displacement functions and does not require shear correction factor. The MsP is supported by elastic medium as Pasternak foundation which considers both normal and shears modules. Also the MsP undergoes in-plane forces in x and y directions. Considering simply supported boundary condition, six equations of motion are derived using Hamilton’s principle and solved by differential quadrature method. Results indicate the effect of aspect ratio, thickness ratio, elastic medium, compression and tension loads on vibration behavior of MsP. Also, findings show the controller effect of velocity feedback gain to minimize the frequency as far as other parameters become ineffective. These findings can be used to active noise and vibration cancellation systems in many structures.

scholarly journals CHIP promotes the activation of NF-κB signaling through enhancing the K63-linked ubiquitination of TAK1

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Yuchun Liu ◽  
Yao Sun ◽  
Shaoming Han ◽  
Yanan Guo ◽  
Qingnan Tian ◽  
...  
Keyword(s):  
Neurological Disorders ◽  
Autosomal Recessive ◽  
Opposite Effect ◽  
Nuclear Factor Κb ◽  
Nuclear Factor ◽  
Interacting Protein ◽  
Pathological Conditions ◽  
Extracellular Stimuli ◽  
Multiple Signaling ◽  
First Time

AbstractTranscriptional factor nuclear factor κB (NF-κB) can be activated by various intracellular or extracellular stimuli and its dysregulation leads to pathological conditions, such as neurodegenerative disorders, infection, and cancer. The carboxyl terminus of HSC70-interacting protein (CHIP), a pathogenic gene of spinocerebellar autosomal recessive 16 (SCAR16), plays an important roles in protein degradation, trafficking, and multiple signaling transductions. It has been reported that CHIP participates in the regulation of NF-κB signaling, and the mutant of CHIP (p.T246M) leads to the occurrence of SCAR16. However, the detailed mechanism of CHIP and CHIP (p.T246M) in the regulation of NF-κB signaling in neurological disorders remains unclear. Here, we found that CHIP promoted the activation of NF-κB signaling, while the knockdown had the opposite effect. Furthermore, CHIP interacted with TAK1 and targeted it for K63-linked ubiquitination. Finally, CHIP enhanced the interaction between TAK1 and NEMO. However, CHIP (p.T246M) couldn’t upregulate NF-κB signaling, potentiate the ubiquitination of TAK1, and enhance the interactions. Taken together, our study demonstrated for the first time that CHIP positively regulates NF-κB signaling by targeting TAK1 and enhancing its K63-linked ubiquitination.

scholarly journals Occurrence of CCR5 Heterozygous 32 bp Deletion in Nepali Ethnic Groups

2015 ◽  
Vol 19 (2) ◽  
pp. 105-108
Author(s):  
Nanda Bahadur Singh
Keyword(s):  
Ethnic Groups ◽  
Population Level ◽  
Asia Pacific ◽  
Signaling Proteins ◽  
Asia Pacific Region ◽  
Ccr5 Gene ◽  
Pcr Rflp ◽  
The World ◽  
First Time ◽  
Hiv 1

The Chemokine (C-C) receptor 5 (CCR5) as one of the small signaling proteins, is a HIV-1 resistant gene. The major boosting to the study of CCR5 gene among ethnic groups in the world is the detection of 32 bp deletion in its heterozygous and homozygous condition which is responsible for relative or absolute resistance to HIV-1 infection. A total of 456 samples belonging to six Nepalese ethnic groups were subjected to genotyping by the use of PCR-RFLP for detecting 32 bp deletion on exon 3 of CCR5 gene. Finally, allele frequencies of 32 bp deletion among Nepalese ethnic groups were calculated by the use of Hardy-Weinberg formula for analysis and interpretation. Chidimar ethnic group, for the first time, showed heterozygous 32 bp deletion at the population level in Asia-pacific region is an excitement in which Chidimar might have conferred resistance against HIV-1 infection in Nepal.Journal of Institute of Science and Technology, 2014, 19(2): 105-108

scholarly journals Constitutive activation of leucine-rich repeat receptor kinase signaling pathways by BAK1-interacting receptor-like kinase 3 chimera

2020 ◽  
Author(s):  
Ulrich Hohmann ◽  
Priya Ramakrishna ◽  
Kai Wang ◽  
Laura Lorenzo-Orts ◽  
Joel Nicolet ◽  
...  
Keyword(s):  
Receptor Activation ◽  
Activation Mechanism ◽  
Signaling Proteins ◽  
Receptor Kinase ◽  
Leucine Rich Repeat ◽  
Protein Ligands ◽  
Receptor Like Kinase ◽  
Transgenic Lines ◽  
Receptor Kinase Signaling ◽  
Membrane Signaling

AbstractReceptor kinases with extracellular leucine-rich repeat domains (LRR-RKs) form the largest group of membrane signaling proteins in plants. LRR-RKs can sense small molecule, peptide or protein ligands, and may be activated by ligand-induced interaction with a shape complementary SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK) co-receptor kinase. We have previously shown that SERKs can also form constitutive, ligand-independent complexes with the LRR ectodomains of BAK1-interacting receptor-like kinase 3 (BIR3) receptor pseudokinases, negative regulators of LRR-RK signaling. Here we report that receptor chimaera in which the extracellular LRR domain of BIR3 is fused to the cytoplasmic kinase domains of the SERK-dependent LRR-RKs BRASSINOSTEROID INSENSITIVE1, HAESA and ERECTA form tight complexes with endogenous SERK co-receptors in the absence of ligand stimulus. Expression of these chimaera under the control of the endogenous promoter of the respective LRR-RK leads to strong gain-of-function brassinosteroid, floral abscission and stomatal patterning phenotypes, respectively. Importantly, a BIR3-GSO1/SGN3 chimera can partially complement sgn3 Casparian strip formation phenotypes, suggesting that GSO1/SGN3 receptor activation is also mediated by SERK proteins. Collectively, our protein engineering approach may be used to elucidate the physiological functions of orphan LRR-RKs and to identify their receptor activation mechanism in single transgenic lines.

scholarly journals Magnetization of magnetically inhomogeneous Sr2FeMoO6-δ nanoparticles

2021 ◽  
Vol 7 (3) ◽  
pp. 85-90
Author(s):  
Gunnar Suchaneck
Keyword(s):  
Curie Temperature ◽  
Temperature Dependence ◽  
Magnetic Materials ◽  
Spin Wave ◽  
Analytical Description ◽  
Higher Order ◽  
Ferromagnetic Behavior ◽  
Double Perovskites ◽  
Langevin Function ◽  
First Time

Magnetization is a key property of magnetic materials. Nevertheless, a satisfactory, analytical description of the temperature dependence of magnetization in double perovskites such as strontium ferromolybdate is still missing. In this work, we develop, for the very first time, a model of the magnetization of nanosized, magnetically inhomogeneous Sr2FeMoO6-δ nanoparticles. The temperature dependence of magnetization was approximated by an equation consisting of a Bloch-law spin wave term, a higher order spin wave correction, both taking into account the temperature dependence of the spin-wave stiffness, and a superparamagnetic term including the Langevin function. In the limit of pure ferromagnetic behavior, the model is applicable also to SFMO ceramics. In the vicinity of the Curie temperature (T/TC &gt; 0.85), the model fails.

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