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McSNAC:A software to approximate first-order signaling networks from mass cytometry data

Quantitative Biology 2023年第1期11卷 59-71页

作者： Darren Wethington Sayak Mukherjee Jayajit Das steve and cindy rasmussen institute for genomic medicine Abigail Wexner Research InstituteNationwide Children’s HospitalColumbusOhio 43205United States Biomedical Sciences Graduate Program College of MedicineThe Ohio State UniversityColumbusOhio 43210United States Department of Pediatrics College of MedicineThe Ohio State UniversityColumbusOhio 43210United States Pelotonia institute for Immuno-Oncology College of MedicineThe Ohio State UniversityColumbusOhio 43210United States DepartmentofBiomedicalInformatics CollegeofMedicineTheOhioStateUniversityColumbusOhio43210United States Biophysics Graduate Program The Ohio State UniversityColumbusOhio 43210United States Battelle Memorial institute ColumbusOhio 43201United States

Background:Mass cytometry(CyTOF)gives unprecedented opportunity to simultaneously measure up to 40 proteins in single cells,with a theoretical potential to reach 100 *** high-dimensional single-cell information can be very useful in dissecting mechanisms of cellular *** particular,measuring abundances of signaling proteins like phospho-proteins can provide detailed information on the dynamics of single-cell signaling ***,computational analysis is required to reconstruct such networks with a mechanistic ***:We propose our Mass cytometry Signaling Network Analysis Code(McSNAC),a new software capable of reconstructing signaling networks and estimating their kinetic parameters from CyTOF *** approximates signaling networks as a network of first-order reactions between *** assumption often breaks down as signaling reactions can involve binding and unbinding,enzymatic reactions,and other nonlinear ***,McSNAC may be limited to approximating indirect interactions between protein species,as cytometry experiments are only able to assay a small fraction of protein species involved in ***:We carry out a series of in silico experiments here to show(1)McSNAC is capable of accurately estimating the ground-truth model in a scalable manner when given data originating from a first-order system;(2)McSNAC is capable of qualitatively predicting outcomes to perturbations of species abundances in simple second-order reaction models and in a complex in silico nonlinear signaling network in which some proteins are ***:These findings demonstrate that McSNAC can be a valuable screening tool for generating models of signaling networks from time-stamped CyTOF data.

关键词： single-cell CyTOF data signaling network kinetics ODE McSNAC

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Insecticidal Potential of α-Pinene and β-Caryophyllene against Myzus persicae and Their Impacts on Gene Expression

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Phyton-International Journal of Experimental Botany 2023年第7期92卷 1943-1954页

作者： Talha Ali Chohan Tahir Ali Chohan Muhammad Zahid Mumtaz Muhammad Waqar Alam Salah ud Din Iqra Naseer Ayesha Riaz Tayyeba Naseem Areeba Iftikhar Dur ENajaf Ali Mubashir Hassan Hayssam M.Ali institute of Molecular Biology and Biotechnology(IMBB) The University of LahoreLahore54000Pakistan institute of Pharmaceutical Sciences University of Veterinary and Animal SciencesLahore54000Pakistan Deparment of Plant Pathology University of OkaraOkara56300Pakistan Deparment of Bioinformatics University of OkaraOkara56300Pakistan Department of Soil Science The Islamia University of BahawalpurBahawalpur63100Pakistan Department of Zoology The Islamia University of BahawalpurBahawalpur(Bahawalnagar Campus)63100Pakistan The steve and cindy rasmussen institute for genomic medicine Nationwide Children’s HospitalColumbusOhio43205USA Department of Botany and Microbiology College of ScienceKing Saud UniversityRiyadh11451Saudi Arabia

Myzus persicae(***)is now considered a threat to agricultural crops due to economic *** synthetic insecticides applied every year against ***,are reported to be unsafe for environment,humans,and beneficial ***,several species of Myzus have been found to develop resistance due to over application of these ***,it is required to find some novel insecticide that would be safe for the environment as well as for *** the current study,two major pure constituentsα-pinene andβ-caryophyllene were evaluated for their insecticidal potential against *** using a fumigant toxicity ***,impact ofα-pinene andβ-caryophyllene on expression of five different genes,e.g.,HSP 60,FPPS I,OSD,TOL and ANT responsible for reproduction,dispersion,and growth of *** has also been *** perform fumigant toxicity assay,five different concentrations(3.5,4,4.5,5 and 6μL L−1)ofα-pinene andβ-caryophyllene were *** concentration(LC)was calculated,and gene expression studies were executed through qRT PCR at LC30 ofα-pinene andβ-*** constituents demonstrated excellent fumigant toxicity effects against *** at all five ***,α-pinene shows significantly better results(98%)as compared toβ-caryophyllene(80%)after 72 h at 6μL L−1 of *** highest upregulation in expression was demonstrated at LC30 dose ofα-pinene in five in three out of five genes understudy(TOL,ANT,and FPPS I).Conversely,two genes HSP 60 and OSD demonstrated downregulation at LC30 dose ofβ-***,our results highlighted the promising insecticidal potential of both compoundsα-pinene andβ-caryophylleneby interfering with the reproduction and development related processes in ***,allowing us to recommend the phytoconstituents under investigation as an ecofriendly alternative to synthetic insecticides.

关键词： Fumigation M.persicae gene expression real time PCR α-pinene β-caryophyllene

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