scholarly journals Time-resolved mapping of genetic interactions to model rewiring of signaling pathways

2018 ◽  
Author(s):  
Florian Heigwer ◽  
Christian Scheeder ◽  
Thilo Miersch ◽  
Barbara Schmitt ◽  
Claudia Blass ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Genetic Interactions ◽  
Ras Signaling ◽  
Multiple Time ◽  
Time Resolved ◽  
External Stresses ◽  
Cellular Pathways ◽  
Context Dependent ◽  
Multiple Time Points ◽  
Over Time

AbstractContext-dependent changes in genetic vulnerabilities are important to understand the wiring of cellular pathways and variations in different environmental conditions. However, methodological frameworks to investigate the plasticity of genetic networks over time or in response to external stresses are lacking. To analyze the plasticity of genetic interactions, we performed an arrayed combinatorial RNAi screen in Drosophila cells at multiple time points and after pharmacological inhibition of Ras signaling activity. Using an image-based morphology assay to capture a broad range of phenotypes, we assessed the effect of 12768 pairwise RNAi perturbations in six different conditions. We found that genetic interactions form in different trajectories and developed an algorithm, termed MODIFI, to analyze how genetic interactions rewire over time. Using this framework, we identified more statistically significant interactions compared to endpoints assays and further observed several examples of context-dependent crosstalk between signaling pathways such as an interaction between Ras and Rel which is dependent on MEK activity.

scholarly journals Time-resolved mapping of genetic interactions to model rewiring of signaling pathways

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Florian Heigwer ◽  
Christian Scheeder ◽  
Thilo Miersch ◽  
Barbara Schmitt ◽  
Claudia Blass ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Genetic Interaction ◽  
Genetic Interactions ◽  
Editorial Note ◽  
Ras Signaling ◽  
Multiple Time ◽  
Time Resolved ◽  
Context Dependent ◽  
Multiple Time Points ◽  
Over Time

Context-dependent changes in genetic interactions are an important feature of cellular pathways and their varying responses under different environmental conditions. However, methodological frameworks to investigate the plasticity of genetic interaction networks over time or in response to external stresses are largely lacking. To analyze the plasticity of genetic interactions, we performed a combinatorial RNAi screen in Drosophila cells at multiple time points and after pharmacological inhibition of Ras signaling activity. Using an image-based morphology assay to capture a broad range of phenotypes, we assessed the effect of 12768 pairwise RNAi perturbations in six different conditions. We found that genetic interactions form in different trajectories and developed an algorithm, termed MODIFI, to analyze how genetic interactions rewire over time. Using this framework, we identified more statistically significant interactions compared to end-point assays and further observed several examples of context-dependent crosstalk between signaling pathways such as an interaction between Ras and Rel which is dependent on MEK activity.Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (<xref ref-type="decision-letter" rid="SA1">see decision letter</xref>).

scholarly journals Author response: Time-resolved mapping of genetic interactions to model rewiring of signaling pathways

2018 ◽  
Author(s):  
Florian Heigwer ◽  
Christian Scheeder ◽  
Thilo Miersch ◽  
Barbara Schmitt ◽  
Claudia Blass ◽  
...  
Keyword(s):  
Response Time ◽  
Signaling Pathways ◽  
Genetic Interactions ◽  
Author Response ◽  
Time Resolved

scholarly journals Motivation-achievement cycle in learning: an intensive longitudinal latent change study

2019 ◽  
Author(s):  
Tuong-Van Vu ◽  
Martijn Meeter ◽  
Abe Dirk Hofman ◽  
Brenda Jansen ◽  
Lucía Magis-Weinberg ◽  
...  
Keyword(s):  
Simulated Data ◽  
Change Score ◽  
Multiple Time ◽  
Main Question ◽  
Modeling Framework ◽  
Data Set ◽  
Latent Change Score ◽  
Multiple Time Points ◽  
Over Time ◽  
Motivation And Achievement

The present research investigates the relations between motivation belief, motivational behaviors and academic achievement in educational contexts. The first main question is whether motivational belief is reciprocally related to achievement and whether a cyclic loop of motivation and achievement is formed over time. The second objective is to study the mediating pathway between motivation and achievement by measuring actual effort spent on learning (i.e. motivational behaviors). Third, we examine the causality of these relations by investigating how they are affected when achievement is experimentally manipulated. We design an intensive longitudinal experiment in which participants will learn new English vocabulary and their motivational belief, effort, and achievement are measured at multiple time points. In the second half of the experiment, participants receive rigged feedback that their achievement has dropped which is expected to influence their subsequent motivation, effort, and actual achievement. To study these dynamics, the changes in one construct are related to changes in other constructs over time, and will be analyzed within a latent change score modeling framework. Planned analyses, expected (narrative) results, and a simulated data set are provided.

scholarly journals Temporal variation in lymphocyte proteomics

2021 ◽  
Author(s):  
Michaela A McCown ◽  
Carolyn Allen ◽  
Daniel D Machado ◽  
Hannah Boekweg ◽  
Yiran Liang ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Small Sample ◽  
Lymphocytic Leukemia ◽  
Small Samples ◽  
Tumor Evolution ◽  
Multiple Time ◽  
Time Points ◽  
Asymptomatic Stage ◽  
Multiple Time Points ◽  
Over Time

Chronic Lymphocytic Leukemia (CLL) is a slow progressing disease, characterized by a long asymptomatic stage followed by a symptomatic stage during which patients receive treatment. While proteomic studies have discovered differential pathways in CLL, the proteomic evolution of CLL during the asymptomatic stage has not been studied. In this pilot study, we show that by using small sample sizes comprising ~145 cells, we can detect important features of CLL necessary for studying tumor evolution. Our small samples are collected at two time points and reveal large proteomic changes in healthy individuals over time. A meta-analysis of two CLL proteomic papers showed little commonality in differentially expressed proteins and demonstrates the need for larger control populations sampled over time. To account for proteomic variability between time points and individuals, large control populations sampled at multiple time points are necessary for understanding CLL progression. Data is available via ProteomeXchange with identifier PXD027429.

Loss of Stress Sensor GADD45a and GADD45b Accelerates BCR-ABL-Driven Leukemogenesis Via Distinct Signaling and Cellular Pathways.

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 1217-1217
Author(s):  
Xiaojin Sha ◽  
Barbara Hoffman ◽  
Dan Liebermann
Keyword(s):  
Bone Marrow ◽  
Cell Proliferation ◽  
Signaling Pathways ◽  
Conflicts Of Interest ◽  
Multiple Stressors ◽  
Myelogenous Leukemia ◽  
Ras Signaling ◽  
Wild Type ◽  
Cellular Pathways ◽  
Myeloid Progenitors

Abstract Abstract 1217 The bcr/abl oncogene causes chronic myelogenous leukemia (CML) in humans. BCR/ABL is known to localize to the cytoskeleton and to display a constitutively active tyrosine kinase activity that leads to the recruitment of downstream effectors of cell proliferation and survival. This is accomplished via several adapter proteins and signaling pathways, including Ras, PI3K-AKT, PkD2-NFkB and JAK-STAT5, all of which are believed to participate in the pathogenesis of CML. The complex nature of these signaling pathways and how they contribute to the initiation and progression of CML is only partially understood. The Gadd45 family of genes (Gadd45a, Gadd45b & Gadd45g) encode for small (18 kd) nuclear proteins that are rapidly induced by multiple stressors, including genotoxic and oncogenic stress. They are involved in G2/M cell cycle arrest and apoptosis in response to exogenous stress stimuli through MAPK and JNK/SAPK pathways. Furthermore Gadd45a has been identified as a mediator of oncogenic Ras signaling. GADD45 proteins are upregulated during myeloid lineage terminal differentiation. To investigate if and how GADD45A and GADD45B play a role in the development of CML, syngeneic wild type lethally irradiated mice were reconstituted with wild type, gadd45a or gadd45b null myeloid progenitors transduced with a retrovirally expressed 210-kD BCR/ABL fusion oncoprotein. It was observed that loss of gadd45a or gadd45b accelerates the development of BCR/ABL driven leukemia in wild type recipients. BCR/ABL transformed gadd45a or gadd45b deficient progenitor recipients exhibited significantly accelerated kinetics of increase in the number of WBC and percentage of myeloid blasts in blood compared to mice reconstituted with the same number of wild type bone marrow cells transduced with BCR/ABL. There was also increase in the rate of accumulation of CD11b+Gr1+ cells in the bone marrow and spleen. Using in vitro and in vivo BrdU assays, enhanced proliferation capacity was observed for BCR/ABL transduced gadd45a, but not gadd45b, deficient myeloid progenitors. However, impaired apoptosis was observed both in BCR/ABL transduced gadd45a and gadd45b deficient myeloid progenitors. These results indicate that both gadd45a and gadd45b function as suppressors of the development of BCR/ABL driven CML, where gadd45a appears to suppress CML via a mechanism involving both inhibition of cell proliferation and enhancement of apoptosis, whereas gadd45b appears to effect only apoptosis. Enhanced JNK signaling was observed in both gadd45a and gadd45b deficient progenitors, whereas enhanced p38 and AKT signaling was observed only in gadd45a deficient myeloid progenitors. Taken together, these data indicate that loss of either gadd45a or gadd45b accelerates BCR-ABL driven CML via distinct signaling and cellular pathways. Further elucidating the role Gadd45 stress sensors play in suppressing the development of leukemia should increase understanding of the molecular/cellular pathology BCR/ABL mediated leukemogenesis, and has the potential to lead to the development of new/improved modalities for treatment of leukemia. Disclosures: No relevant conflicts of interest to declare.

scholarly journals An evaluation of the implementation of a UK school-based running programme

2020 ◽  
Author(s):  
Anna Chalkley ◽  
Ash C. Routen ◽  
Jo P. Harris ◽  
Lorraine A. Cale ◽  
Trish Gorely ◽  
...  
Keyword(s):  
Primary Schools ◽  
Average Distance ◽  
Multiple Time ◽  
School Year ◽  
School Based ◽  
Before And After ◽  
Multiple Time Points ◽  
High Level ◽  
Academic Year ◽  
Over Time

Abstract Background The adoption of school-based running programmes has rapidly increased in recent years. However, there is a lack of information on how these initiatives are implemented, and how generalisable and sustainable they are. This study evaluated the implementation of a school-based running programme, Marathon Kids (MK), over 7 months. The aim was to understand the context within which MK was implemented in each of the schools and the key elements of implementation including reach, fidelity and dose. Methods This study used a mixed method, single group before-and-after design strengthened by multiple interim measurements. Five state-funded primary schools in Leicestershire, UK participated, with 17 teachers and 189 (81 boys (47.4%) and 90 girls (52.6%)) Year 5 pupils (aged 9–10 years) from eight classes. During the 2016/2017 academic year, data were collected via measures at multiple levels (i.e. school and individual) and at multiple time points during implementation. Follow up qualitative data were also collected during 2017/2018. Results Marathon Kids achieved good reach, with all pupils opting to participate at some point during the academic year. All schools implemented MK with good fidelity, although the level of implementation varied between schools and over time. The average number of MK sessions held per week ranged from 0.94–3.89 with the average distance accumulated per pupil per week ranging from 0.02 to 2.91 kilometres and boys being more likely than girls to be classed as high-level participators. Despite an initial drop off in participation over time, all schools remained engaged in the programme and continued to implement MK until the end of the school year. Contextual features (e.g., staff capacity and resources) differed between schools and influenced the quality of implementation of MK and the frequency of delivery. Conclusions Marathon Kids is a simple, inexpensive and versatile physical activity programme which can be implemented by schools with relative at ease. However, schools are diverse settings, with unique challenges to ongoing delivery. Thus, planned adaptations, specific to each school’s context, is likely necessary to sustain participation in the longer term.

scholarly journals Advanced understanding of prokaryotic biofilm formation using a cost-effective and versatile multi-panel adhesion (mPAD) mount

2021 ◽  
Author(s):  
Stefan Schulze ◽  
Heather Schiller ◽  
Jordan Solomonic ◽  
Orkan Telhan ◽  
Kyle Costa ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Cost Effective ◽  
Flow Chamber ◽  
Culture Conditions ◽  
Multiple Time ◽  
Wild Type ◽  
Flowing Liquid ◽  
External Stresses ◽  
Multiple Time Points ◽  
Static Conditions

AbstractMost microorganisms exist in biofilms, which comprise aggregates of cells surrounded by an extracellular matrix that provides protection from external stresses. Based on the conditions under which they form, biofilm structures vary in significant ways. For instance, biofilms that develop when microbes are incubated under static conditions differ from those formed when microbes encounter the shear forces of a flowing liquid. Moreover, biofilms develop dynamically over time. Here, we describe a cost-effective, 3D-printed coverslip holder that facilitates surface adhesion assays under a broad range of standing and shaking culture conditions. This multi-panel adhesion (mPAD) mount further allows cultures to be sampled at multiple time points, ensuring consistency and comparability between samples and enabling analyses of the dynamics of biofilm formation. As a proof of principle, using the mPAD mount for shaking, oxic cultures, we confirm previous flow chamber experiments showing that Pseudomonas aeruginosa wild type and a phenazine deletion mutant (Δphz) form similar biofilms. Extending this analysis to anoxic conditions, we reveal that microcolony and biofilm formation can only be observed under shaking conditions and are decreased in the Δphz mutant compared to wild-type cultures, indicating that phenazines are crucial for the formation of biofilms if oxygen as an electron acceptor is not available. Furthermore, while the model archaeon Haloferax volcanii does not require archaella for attachment to surfaces under static conditions, we demonstrate that H. volcanii mutants that lack archaella are negatively affected in their early stages of biofilm formation under shaking conditions.ImportanceDue to the versatility of the mPAD mount, we anticipate that it will aid the analysis of biofilm formation in a broad range of bacteria and archaea. Thereby, it contributes to answering critical biological questions about the regulatory and structural components of biofilm formation and understanding this process in a wide array of environmental, biotechnological, and medical contexts.

Normative Values for Potential Necrotizing Enterocolitis Biomarkers Across Gestational Ages

2020 ◽  
Author(s):  
Darla Shores ◽  
Jennifer Fundora ◽  
Mitzi Go ◽  
Fauzia Shakeel ◽  
Sandra Brooks ◽  
...  
Keyword(s):  
Necrotizing Enterocolitis ◽  
Premature Infants ◽  
Normative Values ◽  
Multiple Time ◽  
Term Infants ◽  
Fatty Acid Binding ◽  
Calprotectin Level ◽  
Low Levels ◽  
Multiple Time Points ◽  
Over Time

Abstract Background: Necrotizing enterocolitis (NEC) is associated with significant morbidity and mortality. Serum biomarkers to aid diagnosis, such as intestinal fatty acid binding protein (IFABP) and calprotectin, are actively being investigated; however, the normative values of these markers among healthy premature and term infants remains unknown.Aims: We sought to identify normative values for the serum concentrations of IFABP and calprotectin across gestational (GA) and post-menstrual age.Methods: We collected serum from infants (24-40 weeks GA) in the first week of life and at multiple time points in a sub-cohort of premature infants (24-29 weeks GA), excluding sepsis or known intestinal disease. IFABP and calprotectin were measured using ELISA. Groups were compared with descriptive statistics and mixed effects linear regression.Results: 112 infants had specimens in the first week of life, and 19 premature infants had longitudinal specimens. IFABP concentration in the first week of life was low and did not differ across gestational ages. Longitudinally, IFABP increased 4% per day (P<0.001). Calprotectin concentration in the first week of life was more variable. An inverse relationship between day of life and calprotectin level was found in the longitudinal cohort (P <0.001).Conclusions: Serum IFABP and calprotectin fluctuate over time. Infants had low levels of IFABP during the first week of life, independent of gestational age, and levels increased longitudinally in premature infants. Calprotectin levels generally declined over time. Normative data for infants is necessary to establish meaningful cut-off levels for clinical use.

scholarly journals Transcriptome Analysis and RNA Interference Reveal GhGDH2 Regulating Cotton Resistance to Verticillium Wilt by JA and SA Signaling Pathways

2021 ◽  
Vol 12 ◽  
Author(s):  
Xian-Peng Xiong ◽  
Shi-Chao Sun ◽  
Qian-Hao Zhu ◽  
Xin-Yu Zhang ◽  
Feng Liu ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Verticillium Wilt ◽  
Molecular Mechanisms ◽  
Functional Characterization ◽  
Lignin Biosynthesis ◽  
Differentially Expressed ◽  
Multiple Time ◽  
Virus Induced Gene Silencing ◽  
Network Modules ◽  
Multiple Time Points

Verticillium wilt, caused by Verticillium dahliae, is one of the most damaging and widespread soil-borne cotton diseases. The molecular mechanisms underlying the cotton defense against V. dahliae remain largely elusive. Here, we compared the transcriptional differences between Upland cotton cultivars: one highly resistant (HR; Shidalukang 1) and one highly susceptible (HS; Junmian 1). This was done at multiple time points after V. dahliae inoculation, which identified 2010 and 1275 differentially expressed genes (DEGs) in HR and HS, respectively. Plant hormone signal transduction-related genes were enriched in HR, whereas genes related to lignin biosynthesis were enriched in both HR and HS. Weighted gene co-expression network analysis (WGCNA) using the 2868 non-redundant genes differentially expressed between the V. dahliae infected and uninfected samples in HR or HS identified 10 different gene network modules and 22 hub genes with a potential role in regulating cotton defense against V. dahliae infection. GhGDH2, encoding glutamate dehydrogenase (GDH), was selected for functional characterization. Suppressing the expression level of GhGDH2 by virus-induced gene silencing (VIGS) in HS led to inhibition of the salicylic acid (SA) biosynthesis/signaling pathways and activation of the jasmonic acid (JA) biosynthesis/signaling pathways, which resulted in an increase of 42.1% JA content and a reduction of 78.9% SA content in cotton roots, and consequently enhanced V. dahliae resistance. Our finding provides new insights on the molecular mechanisms of cotton resistance to V. dahliae infection and candidate genes for breeding V. dahliae resistance cotton cultivars by genetic modification.

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