scholarly journals Identification of important interacting proteins (IIPs) in Plasmodium falciparum using large-scale interaction network analysis and in-silico knock-out studies

2015 ◽  
Vol 14 (1) ◽  
Author(s):  
Madhumita Bhattacharyya ◽  
Saikat Chakrabarti
2021 ◽  
Author(s):  
Jack Adderley ◽  
Finn O'Donoghue ◽  
Christian Doerig ◽  
Stephen Davis

Phosphorylation based signalling is a complicated and intertwined series of pathways critical to all domains of life. This interconnectivity, though essential to life, makes understanding and decoding the interactions difficult. Large datasets of phosphorylation interactions through the activity of kinases on their numerous effectors are now being generated, however interpretation of the network environment remains challenging. In humans, many phosphorylation interactions have been identified across published works to form the known phosphorylation interaction network. We overlayed phosphorylation datasets onto this network which provided information to each of the connections. To analyse the datasets now mapped into a network, we designed a pathway analysis that uses random walks to identify chains of phosphorylation events occurring much more or much less frequently than expected. This analysis highlights pathways of phosphorylation that work synergistically, providing a rapid interpretation of the most critical pathways in a given dataset. Here we used datasets of human red blood cells infected with the notable stages of Plasmodium falciparum asexual development. The analysis identified several known signalling interactions, and additional interactions which could form the basis of numerous future studies. The network analysis designed here is widely applicable to any comparative phosphorylation dataset across infection and disease and can provide a rapid and reliable analysis to guide validation studies.


Author(s):  
Mark S. Granovetter

A fundamental weakness of current sociological theory is that it does not relate micro level interactions to macro level patterns in any convincing way. Large-scale statistical, as well as qualitative, studies offer a good deal of insight into such macro phenomena as social mobility, community organization, and political structure. At the micro level, a large and increasing body of data and theory offers useful and illuminating ideas about what transpires within the confines of the small group. But how interaction in small groups aggregates to form large-scale patterns eludes us in most cases. I will argue in this paper that the analysis of processes in interpersonal networks provides the most fruitful micro-macro bridge. In one way or another, it is through these networks that small-scale interaction becomes translated into large-scale patterns and that these, in turn, feed back into small groups. Sociometry, the precursor of network analysis, has always been curiously peripheral—invisible, really—in sociological theory. This is partly because it has usually been studied and applied only as a branch of social psychology; it is also because of the inherent complexities of precise network analysis. We have had neither the theory nor the measurement and sampling techniques to move sociometry from the usual small-group level to that of larger structures. While a number of stimulating and suggestive studies have recently moved in this direction (Bott 1957; Mayer 1961; Milgram 1967; Boissevain 1968; Mitchell 1969), they do not treat structural issues in much theoretical detail. Studies which do so usually involve a level of technical complexity appropriate to such forbidding sources as the Bulletin of Mathematical Biophysics, where the original motivation for the study of networks was that of developing a theory of neural, rather than social, interaction (see the useful review of this literature by Coleman 1960; also Rapoport 1963). The strategy of the present paper is to choose a rather limited aspect of small-scale interaction—the strength of interpersonal ties—and to show, in some detail, how the use of network analysis can relate this aspect to such varied macro phenomena as diffusion, social mobility, political organization, and social cohesion in general.


2019 ◽  
Vol 52 (6) ◽  
pp. 1027-1031 ◽  
Author(s):  
Timothy Prestby ◽  
Joseph App ◽  
Yuhao Kang ◽  
Song Gao

Hidden biases of racial and socioeconomic preferences shape residential neighborhoods throughout the USA. Thereby, these preferences shape neighborhoods composed predominantly of a particular race or income class. However, the assessment of spatial extent and the degree of isolation outside the residential neighborhoods at large scale is challenging, which requires further investigation to understand and identify the magnitude and underlying geospatial processes. With the ubiquitous availability of location-based services, large-scale individual-level location data have been widely collected using numerous mobile phone applications and enable the study of neighborhood isolation at large scale. In this research, we analyze large-scale anonymized smartphone users’ mobility data in Milwaukee, Wisconsin, to understand neighborhood-to-neighborhood spatial interaction patterns of different racial classes. Several isolated neighborhoods are successfully identified through the mobility-based spatial interaction network analysis.


2019 ◽  
Author(s):  
Tarun Kumar ◽  
Leo Blondel ◽  
Cassandra G. Extavour

AbstractUnderstanding the genetic regulation of organ structure is a fundamental problem in developmental biology. Here, we use egg-producing structures of insect ovaries, called ovarioles, to deduce systems-level gene regulatory relationships from quantitative functional genetic analysis. We previously showed that Hippo signalling, a conserved regulator of animal organ size, regulates ovariole number in Drosophila melanogaster. To comprehensively determine how Hippo signalling interacts with other pathways in this regulation, we screened all known signalling pathway genes, and identified Hpo-dependent and Hpo-independent signalling requirements. Network analysis of known protein-protein interactions among screen results identified independent gene regulatory sub-networks regulating one or both of ovariole number and egg laying. These sub-networks predict involvement of previously uncharacterised genes with higher accuracy than the original candidate screen. This shows that network analysis combining functional genetic and large-scale interaction data can predict function of novel genes regulating development.


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bashir A. Akhoon ◽  
Shishir K. Gupta ◽  
Sudeep Tiwari ◽  
Laxmi Rathor ◽  
Aakanksha Pant ◽  
...  

Abstract Protein-protein interaction (PPI) studies are gaining momentum these days due to the plethora of various high-throughput experimental methods available for detecting PPIs. Proteins create complexes and networks by functioning in harmony with other proteins and here in silico network biology hold the promise to reveal new functionality of genes as it is very difficult and laborious to carry out experimental high-throughput genetic screens in living organisms. We demonstrate this approach by computationally screening C. elegans conserved homologs of already reported human tumor suppressor and aging associated genes. We select by this nhr-6, vab-3 and gst-23 as predicted longevity genes for RNAi screen. The RNAi results demonstrated the pro-longevity effect of these genes. Nuclear hormone receptor nhr-6 RNAi inhibition resulted in a C. elegans phenotype of 23.46% lifespan reduction. Moreover, we show that nhr-6 regulates oxidative stress resistance in worms and does not affect the feeding behavior of worms. These findings imply the potential of nhr-6 as a common therapeutic target for aging and cancer ailments, stressing the power of in silico PPI network analysis coupled with RNAi screens to describe gene function.


2009 ◽  
Vol 9 (3) ◽  
pp. 351-358 ◽  
Author(s):  
Segun Fatumo ◽  
Kitiporn Plaimas ◽  
Jan-Philipp Mallm ◽  
Gunnar Schramm ◽  
Ezekiel Adebiyi ◽  
...  

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Tarun Kumar ◽  
Leo Blondel ◽  
Cassandra G Extavour

Understanding the genetic regulation of organ structure is a fundamental problem in developmental biology. Here, we use egg-producing structures of insect ovaries, called ovarioles, to deduce systems-level gene regulatory relationships from quantitative functional genetic analysis. We previously showed that Hippo signalling, a conserved regulator of animal organ size, regulates ovariole number in Drosophila melanogaster. To comprehensively determine how Hippo signalling interacts with other pathways in this regulation, we screened all known signalling pathway genes, and identified Hpo-dependent and Hpo-independent signalling requirements. Network analysis of known protein-protein interactions among screen results identified independent gene regulatory sub-networks regulating one or both of ovariole number and egg laying. These sub-networks predict involvement of previously uncharacterised genes with higher accuracy than the original candidate screen. This shows that network analysis combining functional genetic and large-scale interaction data can predict function of novel genes regulating development.


Gene Reports ◽  
2016 ◽  
Vol 5 ◽  
pp. 134-139
Author(s):  
Siddhant S Sahoo ◽  
Chinmoy Mishra ◽  
Mangalika Rout ◽  
Gangadhar Nayak ◽  
Stuti T Mohanty ◽  
...  

2018 ◽  
Vol 15 (3) ◽  
pp. 517-527
Author(s):  
Ritu Saxena ◽  
Prakash Chandra Mishra

Plasmodium falciparum is a causative agent of one of the most devastating disease, cerebral malaria. Absence of suitable vaccine and the emergence of multi drug resistant parasites hinder prevention of malaria disease worldwide. One of the most reliable approaches to control this disease is to develop antimalarial against drug targets which are specific for ubiquitous and necessary enzymes such as helicases. Helicases work in ATP dependent manner and help in unwinding of nucleic acids during replication, transcription and repair mechanism. In this study, in silico analysis and homology modeling method were used to characterize the physicochemical properties and 3D structure of PfBrr2 helicase. Suitable structure of different domains was validated using in silico tools and used for docking studies to understand protein-ligand interactions. Protein-protein interaction network of PfBrr2 was investigated to understand its function inside the parasite.


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