scholarly journals RFCM-PALM: In-Silico Prediction of S-Palmitoylation Sites in the Synaptic Proteins for Male/Female Mouse Data

2021 ◽  
Vol 22 (18) ◽  
pp. 9901
Author(s):  
Soumyendu Sekhar Bandyopadhyay ◽  
Anup Kumar Halder ◽  
Monika Zaręba-Kozioł ◽  
Anna Bartkowiak-Kaczmarek ◽  
Aviinandaan Dutta ◽  
...  
Keyword(s):  
Female Mouse ◽  
Critical Role ◽  
Synaptic Proteins ◽  
Post Translational Modification ◽  
Knock Out ◽  
Heuristic Strategy ◽  
Physicochemical Features ◽  
Consensus Strategy ◽  
Reversible Covalent ◽  
The Individual

S-palmitoylation is a reversible covalent post-translational modification of cysteine thiol side chain by palmitic acid. S-palmitoylation plays a critical role in a variety of biological processes and is engaged in several human diseases. Therefore, identifying specific sites of this modification is crucial for understanding their functional consequences in physiology and pathology. We present a random forest (RF) classifier-based consensus strategy (RFCM-PALM) for predicting the palmitoylated cysteine sites on synaptic proteins from male/female mouse data. To design the prediction model, we have introduced a heuristic strategy for selection of the optimum set of physicochemical features from the AAIndex dataset using (a) K-Best (KB) features, (b) genetic algorithm (GA), and (c) a union (UN) of KB and GA based features. Furthermore, decisions from best-trained models of the KB, GA, and UN-based classifiers are combined by designing a three-star quality consensus strategy to further refine and enhance the scores of the individual models. The experiment is carried out on three categorized synaptic protein datasets of a male mouse, female mouse, and combined (male + female), whereas in each group, weighted data is used as training, and knock-out is used as the hold-out set for performance evaluation and comparison. RFCM-PALM shows ~80% area under curve (AUC) score in all three categories of datasets and achieve 10% average accuracy (male—15%, female—15%, and combined—7%) improvements on the hold-out set compared to the state-of-the-art approaches. To summarize, our method with efficient feature selection and novel consensus strategy shows significant performance gains in the prediction of S-palmitoylation sites in mouse datasets.

scholarly journals N-Cadherin Is Critical for the Survival of Germ Cells, the Formation of Steroidogenic Cells, and the Architecture of Developing Mouse Gonads

Cells ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 1610 ◽  
Author(s):  
Rafal P. Piprek ◽  
Michal Kolasa ◽  
Dagmara Podkowa ◽  
Malgorzata Kloc ◽  
Jacek Z. Kubiak
Keyword(s):  
Germ Cells ◽  
Hormonal Regulation ◽  
Critical Role ◽  
Somatic Cells ◽  
Gonad Development ◽  
Knock Out ◽  
Gonad Differentiation ◽  
Steroidogenic Cells ◽  
The Individual ◽  
And Function

Normal gonad development assures the fertility of the individual. The properly functioning gonads must contain a sufficient number of the viable germ cells, possess a correct architecture and tissue structure, and assure the proper hormonal regulation. This is achieved by the interplay between the germ cells and different types of somatic cells. N-cadherin coded by the Cdh2 gene plays a critical role in this interplay. To gain an insight into the role of N-cadherin in the development of mouse gonads, we used the Cre-loxP system to knock out N-cadherin separately in two cell lines: the SF1+ somatic cells and the OCT4+ germ cells. We observed that N-cadherin plays a key role in the survival of both female and male germ cells. However, the N-cadherin is not necessary for the differentiation of the Sertoli cells or the initiation of the formation of testis cords or ovigerous cords. In the later stages of gonad development, N-cadherin is important for the maintenance of testis cord structure and is required for the formation of steroidogenic cells. In the ovaries, N-cadherin is necessary for the formation of the ovarian follicles. These results indicate that N-cadherin plays a major role in gonad differentiation, structuralization, and function.

Pathogenesis of Age-related Cataract: a systematic review of proteomic studies

2020 ◽  
Vol 17 ◽  
Author(s):  
Christina Karakosta ◽  
Argyrios Tzamalis ◽  
Michalis Aivaliotis ◽  
Ioannis Tsinopoulos
Keyword(s):  
Systematic Review ◽  
Oxidant Stress ◽  
Critical Role ◽  
Human Lens ◽  
Nuclear Cataract ◽  
Cataract Formation ◽  
Post Translational Modification ◽  
Ability To Act ◽  
Age Related

Background/Objective:: The aim of this systematic review is to identify all the available data on human lens proteomics with a critical role to age-related cataract formation in order to elucidate the physiopathology of the aging lens. Materials and Methods:: We searched on Medline and Cochrane databases. The search generated 328 manuscripts. We included nine original proteomic studies that investigated human cataractous lenses. Results:: Deamidation was the major age-related post-translational modification. There was a significant increase in the amount of αA-crystallin D-isoAsp58 present at all ages, while an increase in the extent of Trp oxidation was apparent in cataract lenses when compared to aged normal lenses. During aging, enzymes with oxidized cysteine at critical sites included GAPDH, glutathione synthase, aldehyde dehydrogenase, sorbitol dehydrogenase, and PARK7. Conclusion:: D-isoAsp in αA crystallin could be associated with the development of age-related cataract in human, by contributing to the denaturation of a crystallin, and decreasing its ability to act as a chaperone. Oxidation of Trp may be associated with nuclear cataract formation in human, while the role of oxidant stress in age-related cataract formation is dominant.

scholarly journals The p47phox mouse knock-out model of chronic granulomatous disease.

1995 ◽  
Vol 182 (3) ◽  
pp. 751-758 ◽  
Author(s):  
S H Jackson ◽  
J I Gallin ◽  
S M Holland
Keyword(s):  
Nadph Oxidase ◽  
Chronic Granulomatous Disease ◽  
Fungal Infections ◽  
Critical Role ◽  
Granulomatous Inflammation ◽  
Mammalian Host ◽  
Granulomatous Disease ◽  
Knock Out ◽  
Phagocyte Nadph Oxidase ◽  
Life Threatening

Chronic granulomatous disease (CGD) is caused by a congenital defect in phagocyte reduced nicotinamide dinucleotide phosphate (NADPH) oxidase production of superoxide and related species. It is characterized by recurrent life-threatening bacterial and fungal infections and tissue granuloma formation. We have created a mouse model of CGD by targeted disruption of p47phox, one of the genes in which mutations cause human CGD. Identical to the case in human CGD, leukocytes from p47phox-/- mice produced no superoxide and killed staphylococci ineffectively. p47phox-/- mice developed lethal infections and granulomatous inflammation similar to those encountered in human CGD patients. This model mirrors human CGD and confirms a critical role for the phagocyte NADPH oxidase in mammalian host defense.

Affine Versus Non-Affine Fibril Kinematics in Collagen Networks: Theoretical Studies of Network Behavior

2005 ◽  
Vol 128 (2) ◽  
pp. 259-270 ◽  
Author(s):  
Preethi L. Chandran ◽  
Victor H. Barocas
Keyword(s):  
Network Model ◽  
Constitutive Modeling ◽  
Load Transfer ◽  
Critical Role ◽  
Affine Model ◽  
Tissue Equivalents ◽  
Scale Models ◽  
Macroscopic Deformation ◽  
The Individual ◽  
Open Question

The microstructure of tissues and tissue equivalents (TEs) plays a critical role in determining the mechanical properties thereof. One of the key challenges in constitutive modeling of TEs is incorporating the kinematics at both the macroscopic and the microscopic scale. Models of fibrous microstructure commonly assume fibrils to move homogeneously, that is affine with the macroscopic deformation. While intuitive for situations of fibril-matrix load transfer, the relevance of the affine assumption is less clear when primary load transfer is from fibril to fibril. The microstructure of TEs is a hydrated network of collagen fibrils, making its microstructural kinematics an open question. Numerical simulation of uniaxial extensile behavior in planar TE networks was performed with fibril kinematics dictated by the network model and by the affine model. The average fibril orientation evolved similarly with strain for both models. The individual fibril kinematics, however, were markedly different. There was no correlation between fibril strain and orientation in the network model, and fibril strains were contained by extensive reorientation. As a result, the macroscopic stress given by the network model was roughly threefold lower than the affine model. Also, the network model showed a toe region, where fibril reorientation precluded the development of significant fibril strain. We conclude that network fibril kinematics are not governed by affine principles, an important consideration in the understanding of tissue and TE mechanics, especially when load bearing is primarily by an interconnected fibril network.

scholarly journals Nonlinear visuoauditory integration in the mouse superior colliculus

2021 ◽  
Author(s):  
Shinya Ito ◽  
Yufei Si ◽  
Alan M. Litke ◽  
David A. Feldheim
Keyword(s):  
Superior Colliculus ◽  
Sensory Integration ◽  
Large Scale ◽  
Temporal Dynamics ◽  
Critical Role ◽  
Sensory Information ◽  
Population Level ◽  
Object Identification ◽  
Response Properties ◽  
The Individual

AbstractSensory information from different modalities is processed in parallel, and then integrated in associative brain areas to improve object identification and the interpretation of sensory experiences. The Superior Colliculus (SC) is a midbrain structure that plays a critical role in integrating visual, auditory, and somatosensory input to assess saliency and promote action. Although the response properties of the individual SC neurons to visuoauditory stimuli have been characterized, little is known about the spatial and temporal dynamics of the integration at the population level. Here we recorded the response properties of SC neurons to spatially restricted visual and auditory stimuli using large-scale electrophysiology. We then created a general, population-level model that explains the spatial, temporal, and intensity requirements of stimuli needed for sensory integration. We found that the mouse SC contains topographically organized visual and auditory neurons that exhibit nonlinear multisensory integration. We show that nonlinear integration depends on properties of auditory but not visual stimuli. We also find that a heuristically derived nonlinear modulation function reveals conditions required for sensory integration that are consistent with previously proposed models of sensory integration such as spatial matching and the principle of inverse effectiveness.

scholarly journals Immune regulation of neuronal injury and repair by observing T cell activation

2018 ◽  
Vol 1 (1) ◽  
Author(s):  
Eric J. Regele ◽  
Elizabeth M. Runge ◽  
Felicia M. Kennedy ◽  
Virginia M. Sanders ◽  
Kathryn J. Jones
Keyword(s):  
T Cells ◽  
T Cell Activation ◽  
Cd4 T Cells ◽  
Cell Activation ◽  
Critical Role ◽  
Cd4 Cells ◽  
Knock Out ◽  
Facial Motoneuron ◽  
Injury And Repair ◽  
Antigen Presenting

Background and Hypothesis:  It is unknown how the immune system maintains the majority of facial motoneuron (FMN) survival after axotomy. IL-10 cytokine is necessary for FMN survival and CD4+ T cells are activated and play a critical role in survival, but do not produce IL-10. It was proposed that the source of IL-10 resides in the CNS; however, it is possible that antigen presenting cells (APC) produce IL-10 which activate CD4+ T cells to a neuroprotective phenotype. The regulation of IL-10 receptors (IL-10R) in immunodeficient compared to wild-type (WT) mice in the facial nucleus was studied in this experiment, as well as the possibility of the PNS producing IL-10.  Experimental Design or Project Methods:  To study APC’s role in motoneuron survival, we transferred WT whole splenocytes into global IL-10 knock out (KO) mice prior to axotomy. To study IL-10R gene expression, immunodeficient RAG-2 KO mice received WT or IL-10R-/- CD4+ T cells prior to axotomy.   Results:  qPCR revealed that WT mice upregulate IL-10R after axotomy, whereas RAG-2 KO mice had decreased expression comparatively. RAG-2 mice who received WT CD4+ T cells transfer restored IL-10R comparable to WT values.IL-10R was rescued in RAG-2 mice after the adoptive transfer of WT CD4+T cells. When IL-10R-/- CD4+ cells were transferred into RAG-2 mice, IL-10R values were restored; however, these T cells were unable to rescue FMN survival.   Conclusion and Potential Impact:  If WT whole splenocytes transferred into global IL-10 KO mice rescue FMN survival, it implies that APC play a role in producing IL-10. If they cannot mediate rescue, then peripheral IL-10 is unlikely sufficient for FMN survival. CD4+ T cells regulate central IL-10R response and must respond to IL-10 to mediate FMN survival. The transfer of whole splenocytes provides APCs capable of producing IL-10 and CD4+ T cells capable of responding to IL-10. 

Potential Role of Darvyadi Kwatha in the Management of Diabetes

The Healer ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 80-86
Author(s):  
Shankar Gautam ◽  
Abhishek Upadhyay ◽  
Rashmi Mutha ◽  
BINOD KUMAR SINGH ◽  
Ram Kishor Joshi
Keyword(s):  
Causes Of Death ◽  
Potential Role ◽  
Critical Role ◽  
Animal Experiments ◽  
Safety Evaluation ◽  
New Drugs ◽  
Effective Management ◽  
The Individual ◽  
Glucose 6 Phosphate Dehydrogenase

Diabetes is a clinical condition characterized by a spike in blood glucose in plasma. It is one of the 21st century's greatest public health crises and is among the top 10 causes of death worldwide. Although new drugs and therapeutics are emerging for its management but the prevalence is increasing at an alarming pace; thus, every system must contribute for effective management. An effort is made to review the efficacy and safety evaluation of the individual herbs of Darvyadi Kwatha (DK), an Ayurvedic formulation mentioned in Charaka Samhita. The constituents of the DK has some strong efficient antidiabetic/hypoglycaemic chemical principle having insulin-triggering and insulin-like behaviors which increases the activity of glucose-6-phosphate dehydrogenase (G6PD) and glucokinase and decreases glucose-6-phosphatase activity, reduce oxidative stress and prevention of glutathione reductase, superoxide dismutase, and catalase activity play a critical role in glucose homeostasis. DK also improve biochemical parameters such as SGPT, SGOT, cholesterol and triglycerides and is found to be safe in animal experiments. The various evidences clearly indicates that DK has definite hypoglycemic potential as well as anti-diabetic activity.

Cochlear Implants and Mobile Wireless Connectivity

2016 ◽  
pp. 65-80
Author(s):  
Panteleimon Chriskos ◽  
Orfeas Tsartsianidis
Keyword(s):  
Cochlear Implants ◽  
Critical Role ◽  
Sensory Systems ◽  
Human Communication ◽  
Mobile Wireless ◽  
The Individual ◽  
Significant Distance ◽  
Wireless Connectivity

Human senses enable humans to perceive and interact with their environment, through a set of sensory systems or organs which are mainly dedicated to each sense. From the five main senses in humans hearing plays a critical role in many aspects of our lives. Hearing allows the perception not only of the immediate visible environment but also parts of the environment that are obstructed from view and/or that are a significant distance from the individual. One of the most important and sometimes overlooked aspects of hearing is communication, since most human communication is accomplished through speech and hearing. Hearing does not only convey speech but also conveys more complex messages in the form of music, singing and storytelling.

SUSTAINABLE DESIGN IN PROJECT DELIVERY: A DISCUSSION ON CURRENT AND FUTURE TRENDS

2016 ◽  
Vol 11 (2) ◽  
pp. 39-56 ◽  
Author(s):  
Karno Widjaja
Keyword(s):  
Construction Projects ◽  
Sustainable Design ◽  
Current System ◽  
Critical Role ◽  
Project Delivery ◽  
Starting Point ◽  
New Construction ◽  
Communication And Coordination ◽  
The Individual ◽  
Sustainability Principles

INTRODUCTION Sustainability principles have become an integral part of the design and construction process for many new construction projects. The selection of the project delivery method (PDM) is extremely important in the effective execution of the project, and plays a critical role in establishing communication and coordination between the key entities: owner, architect, and contractor. The goal of this paper is to hopefully serve as a starting point for further discussion to improve on the AEC industry's current integration of sustainability principles in PDMs. The first step consists of an assessment of current project delivery systems from a sustainable design perspective. This is followed by a determination of the current limitations, and examination of the various disruptions in the industry. Various literature sources are analyzed to form a framework to discuss improvements and optimization strategies beyond the current system. Thereafter, proposed solutions are introduced at both stakeholders, as well as PDM scales. In this paper, the focus for the conducted analysis and proposed methodologies is predicated on new construction projects instead of retrofits due to the resources available. However, the principles can similarly be applied to retrofit scenarios as well, depending on the specific requirements of the individual project at play.

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