Week 6 Flashcards
What crosstalk signaling pathways entail?
Crosstalk occurs between two signaling pathways A and B when the stimulation at the receptors of pathway A causes a cellular response downstream of pathway B, usually carried out by the TFs in B.
What is nuclear receptor crosstalk?
The interplay between different nuclear receptors or between their overlapping signalling pathways
Where do toll-like receptors (TLRs) 4, 5, 7 and 9 belong to?
A family of proteins that recognize mainly conserved microbial motifs
What does Kaposi’s sarcoma-associated herpesvirus interact with?
Cell surface receptors, such as heparan sulfate, integrins (α3β1, αVβ3, and αVβ5), and EphrinA2 (EphA2), and activates focal adhesion kinase (FAK), Src, phosphoinositol 3-kinase (PI3-K), c-Cbl, and RhoA GTPase signal molecules early during lipid raft (LR)-dependent productive macropinocytic entry into human dermal microvascular endothelial cells
What are two types of crosstalk?
The two types of crosstalk are near-end and far-end crosstalk, both of which create unwanted interference between signals on different interconnects
What are some limitations of a graph?
No more than two measurement types can be displayed on a graph
What is a central issue in systems biology?
Understanding signal transduction in cellular systems
What can discrete dynamic modeling, combined with network analysis provide?
An effective way to integrate fragmentary knowledge of regulatory interactions into a predictive mathematical model which is able to describe the time evolution of the system without the requirement for kinetic parameters
What is the advantages of dynamic model?
Although some complex systems may be difficult to model accurately, dynamic modeling provides extra product performance data from virtual prototypes
What is a critical challenge for cancer therapy?
Prediction of drug combinations that effectively target cancer cells
What can the analysis of signalling network activity and crosstalk predict?
Potent drug combinations and rational stratification of patients, thus bringing therapeutic and prognostic values. We have previously showed that the non-receptor tyrosine kinase PYK2 is a downstream effector of EGFR and c-Met and demonstrated their crosstalk signalling in basal-like TNBC
How does the iterative modeling approach work?
The same logical steps may be repeated by using different software, or different versions of the same software, with or without additional data
What models are used in biology?
After reflecting on the types of models we use in our daily work as biological researchers, we have identified three main categories of models used regularly in scientific practice: concrete, conceptual, and mathematical
What are the major computational approaches used to study signaling networks?
Graph theory and dynamical modeling
What is network theory?
A network can be defined as a graph in which nodes and/or edges have attributes
What are the different types of signalling?
There are four basic categories of chemical signaling found in multicellular organisms: paracrine signaling, autocrine signaling, endocrine signaling, and signaling by direct contact.
What are hubs?
They represent proteins with a large number of interactions
What are clusters?
Tightly linked sets of mostly non-homologous genes participating in a common, discrete metabolic pathway
What is a path?
A step by step series of interconnected biochemical reactions in which each step is catalyzed by a specific enzyme
Where does Ras activates it’s effectors?
At the membrane
Where does active PI3K-alpha assemble?
At membrane regions enriched in signaling lipids
Where does the the Raf kinase domain localise?
It extends into the cytoplasm and its assembly is away from the crowded membrane surface
What is network visualisation?
Network visualization, graph visualization or link analysis is the process of visually presenting networks of connected entities as links and nodes
What is network clustering?
Network clustering (or graph clustering) refers to both a computational problem to extract densely connected but relatively isolated subnetworks from a network and a set of algorithms and methods to solve this problem
What is crucial in treating the signal flow of complex diseases?
Identifying control targets that can most effectively block such unwanted signal flow
What are examples of spatial information?
Data includes spatial information such as spatial coordinates for land boundaries, area or size, road and street names, names of waterways, codes for local government.
What are regulatory motifs?
Short nucleotide sequences typically upstream of genes that are used to control the expression of genes
What are positive and negative feedback loops?
Common regulatory elements in biological signaling systems
What is Hippo YAP?
A complex network of proteins that controls organ size via regulation of cellular proliferation, survival and differentiation
What does PI3K-Akt do?
Promotes metabolism, proliferation, cell survival, growth and angiogenesis in response to extracellular signals
What does Ras do in the MAPK pathway?
Transduce signals from the extracellular milieu to the cell nucleus where specific genes are activated for cell growth, division and differentiation
