Information-based methods for predicting gene function from systematic gene knock-downs

<p>Abstract</p> <p>Background</p> <p>The rapid annotation of genes on a genome-wide scale is now possible for several organisms using high-throughput RNA interference assays to knock down the expression of a specific gene. To date, dozens of RNA interference phenotypes have been recorded for the nematode <it>Caenorhabditis elegans</it>. Although previous studies have demonstrated the merit of using knock-down phenotypes to predict gene function, it is unclear how the data can be used most effectively. An open question is how to optimally make use of phenotypic observations, possibly in combination with other functional genomics datasets, to identify genes that share a common role.</p> <p>Results</p> <p>We compared several methods for detecting gene-gene functional similarity from phenotypic knock-down profiles. We found that information-based measures, which explicitly incorporate a phenotype's genomic frequency when calculating gene-gene similarity, outperform non-information-based methods. We report the presence of newly predicted modules identified from an integrated functional network containing phenotypic congruency links derived from an information-based measure. One such module is a set of genes predicted to play a role in regulating body morphology based on their multiply-supported interactions with members of the TGF-<it>β </it>signaling pathway.</p> <p>Conclusion</p> <p>Information-based metrics significantly improve the comparison of phenotypic knock-down profiles, based upon their ability to enhance gene function prediction and identify novel functional modules.</p

Single-cell morphological data reveals signaling network architecture

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2010.Cataloged from PDF version of thesis.Includes bibliographical references.Metastasis, the migration of cancer cells from the primary site of tumorigenesis and the subsequent invasion of secondary tissues, causes the vast majority of cancer deaths. To spread, metastatic cells dramatically rearrange their shape in complex, dynamic fashions. Genes encoding signaling proteins that regulate cell shape in normal cells are often mutated in cancer, especially in highly metastatic disease. To study these key signaling proteins in locomotion and metastasis, we develop and validate statistical methods to extract information from highthroughput morphological data from genetic screens. Our contributions fall into three major categories. 1) To define and apply robust statistical measures to identify genes regulating morphological variability. We develop and thoroughly test methods for measuring morphological variability of single-cells populations, and apply these metrics to genetic screens in yeast and fly. We further apply these techniques to subsets of genes involved in cellular processes to study genetic contributions to variability in these processes. We propose new roles for genes as suppressors or enhancers of morphological noise. We validate our findings on the basis of known gene function and network architecture. 2) To perform inference of protein signaling relationships by utilizing high-throughput morphological data. We apply machine-learning techniques to systematically identify genetic interactions between proteins on the basis of image-based data from double-knockout screens.(cont.) Next, we focus on RhoGTPases and RhoGTPase Activating Proteins (RhoGAPs) in Drosophila., where by using basic knowledge of network architecture we apply our techniques to detect signaling relationships. 3) To integrate expression data with high-throughput morphological data to study the mechanisms for determination of cell morphology. We utilize morphological and microarray data from fly screens. By comparing expression data between control treatment conditions and treatment conditions displaying morphological phenotypes (e.g. high population variability), we identify genes and pathways correlated with this class distinction, thereby validating our previous studies and providing further insight into the determination of morphology. A key challenge in systems biology is to analyze emerging high-throughput image-based data to understand how cellular phenotypes are genetically encoded. Our work makes significant contributions to the literature on high-throughput morphological study and describes a path for future investigation.by Oaz Nir.Ph.D

Arabidopsis inositol phosphate kinases, IPK1 and ITPK1, constitute a metabolic pathway in maintaining phosphate homeostasis

Emerging studies have implicated a close link between inositol phosphate (InsP) metabolism and cellular phosphate (Pi) homeostasis in eukaryotes; however, whether a common InsP species is deployed as an evolutionarily conserved metabolic messenger to mediate Pi signaling remains unknown. Here, using genetics and InsP profiling combined with Pi starvation response (PSR) analysis in Arabidopsis thaliana, we showed that the kinase activity of inositol pentakisphosphate 2‐kinase (IPK1), an enzyme required for phytate (inositol hexakisphosphates; InsP6) synthesis, is indispensable for maintaining Pi homeostasis under Pi‐replete conditions, and inositol 1,3,4‐trisphosphate 5/6‐kinase 1 (ITPK1) plays an equivalent role. Although both ipk1‐1 and itpk1 mutants exhibited decreased levels of InsP6 and diphosphoinositol pentakisphosphate (PP‐InsP5; InsP7), disruption of another ITPK family enzyme, ITPK4, which correspondingly caused depletion of InsP6 and InsP7, did not display similar Pi‐related phenotypes, which precludes these InsP species as effectors. Notably, the level of D/L‐Ins(3,4,5,6)P4 was concurrently elevated in both ipk1‐1 and itpk1 mutants, which showed a specific correlation to the misregulated Pi phenotypes. However, the level of D/L‐Ins(3,4,5,6)P4 is not responsive to Pi starvation that instead manifests a shoot‐specific increase in InsP7 level. This study demonstrates a more nuanced picture of the intersection of InsP metabolism and Pi homeostasis and PSR than has previously been elaborated and additionally establishes intermediate steps to phytate biosynthesis in plant vegetative tissues

XXI Fungal Genetics Conference Abstracts

XXI Fungal Genetics Conference Abstract

Inactivation of pathogens on food and contact surfaces using ozone as a biocidal agent

This study focuses on the inactivation of a range of food borne pathogens using ozone as a biocidal agent. Experiments were carried out using Campylobacter jejuni, E. coli and Salmonella enteritidis in which population size effects and different treatment temperatures were investigate

Colorectal Cancer Through Simulation and Experiment

Colorectal cancer has continued to generate a huge amount of research interest over several decades, forming a canonical example of tumourigenesis since its use in Fearon and Vogelstein’s linear model of genetic mutation. Over time, the field has witnessed a transition from solely experimental work to the inclusion of mathematical biology and computer-based modelling. The fusion of these disciplines has the potential to provide valuable insights into oncologic processes, but also presents the challenge of uniting many diverse perspectives. Furthermore, the cancer cell phenotype defined by the ‘Hallmarks of Cancer’ has been extended in recent times and provides an excellent basis for future research. We present a timely summary of the literature relating to colorectal cancer, addressing the traditional experimental findings, summarising the key mathematical and computational approaches, and emphasising the role of the Hallmarks in current and future developments. We conclude with a discussion of interdisciplinary work, outlining areas of experimental interest which would benefit from the insight that mathematical and computational modelling can provide

White Paper 2: Origins, (Co)Evolution, Diversity & Synthesis Of Life

Publicado en Madrid, 185 p. ; 17 cm.How life appeared on Earth and how then it diversified into the different and currently existing forms of life are the unanswered questions that will be discussed this volume. These questions delve into the deep past of our planet, where biology intermingles with geology and chemistry, to explore the origin of life and understand its evolution, since “nothing makes sense in biology except in the light of evolution” (Dobzhansky, 1964). The eight challenges that compose this volume summarize our current knowledge and future research directions touching different aspects of the study of evolution, which can be considered a fundamental discipline of Life Science. The volume discusses recent theories on how the first molecules arouse, became organized and acquired their structure, enabling the first forms of life. It also attempts to explain how this life has changed over time, giving rise, from very similar molecular bases, to an immense biological diversity, and to understand what is the hylogenetic relationship among all the different life forms. The volume further analyzes human evolution, its relationship with the environment and its implications on human health and society. Closing the circle, the volume discusses the possibility of designing new biological machines, thus creating a cell prototype from its components and whether this knowledge can be applied to improve our ecosystem. With an effective coordination among its three main areas of knowledge, the CSIC can become an international benchmark for research in this field

Thermal relations and molecular measures in salmonidae gene expression

Arctic, boreal and temperate latitudes are characterised by conspicuous shifts in photoperiod and temperature, which restricts ecosystem productivity and compels resident taxa to anticipate and coordinate physiological processes to the cyclic variability of environmental conditions. The increase in temperature of high latitude habitats due to climate change is likewise complicit in asserting a progressive phenological incongruence between photoperiod and temperature, the repercussions of which on circadian and seasonal rhythms remain veiled in uncertainty. An organism’s capacity to physiologically adjust to a changing environment relies upon the induction of gene expression programmes quantifiable through steady-state mRNA level, which has long served as a proxy for transcription and functional inferences in ecophysiological studies, although it is ultimately determined by the integrated processes of nuclear transcription and nucleocytoplasmic degradation. There is consequently an inadequate appreciation of upstream and downstream regulatory elements that finely control gene expression. Pursuant to these considerations is the molecular regulation of heat shock proteins, which presents a suitable system to evaluate temperature inducible gene expression and the thermal and temporal relations in transcription, steady-state mRNA level and translation upon temperature acclimation and heat shock of ecologically and economically valuable salmonids. The studies comprising this thesis revealed temperature acclimation manifests in the alteration of whole organism upper thermal tolerance and ventricle morphology (I), which at the cellular level involved modifications to inducible hsp70 expression during chronic and acute temperature exposure (II). Although not directly measured, evidence for post-transcriptional regulation in the acclimation process and hsp70 expression is presented and discussed (II & III), whilst gaining fundamental insights in the final study (IV) assessing the effect of elevated temperature on gene transcription and its temporal relationship with steady-state mRNA level in a thermally sensitive salmonid at the forefront of climate change effects. These studies provide a detailed perspective on the capacity of salmonids to acclimate to novel habitat temperatures, and the potential practical application of molecular level measures that could be beneficial in the management and conservation of vulnerable wild and domesticated fish populations

Polyphasic taxonomy of thermophilic actinomycetes

PhD ThesisMolecular systematic methods were applied in a series of studies designed to resolve the taxonomic relationships of thermophilic actinomycetes known to be difficult to classify using standard taxonomic procedures. The test strains included representatives of clusters defined in an extensiven umerical phenetic survey of thermophilic streptomycetesa nd twelve marker strains. The resultant genotypic data together with the results of corresponding phenotypic studies were used to highlight novel taxa and to improve the circumscription of validly described species. The most comprehensive study was undertaken to clarify relationships within and between representative alkalitolerant, thermophilic and neutrophilic, thermophilic streptomycetes isolated from soil and appropriate marker strains. The resultant data, notably those from DNA: DNA relatedness studies, supported the taxonomic integrity of the validly described species Streptomyces thermodiastaticus, Streptomyces thermoviolaceus and Streptomyces thermovulgaris. However, the genotypic and phenotypic data clearly show that Streptomyces thermonitrificans Desai and Dhala 1967 and Streptomyces thermovulgaris (Henssen 1957) Goodfellow et al. 1987 represent a single species. On the basis of the priority, Streptomyces thermonitrificans is a later subjective synonym of Streptomyces thermovulgaris. Similarly, eight out of eleven representative alkalitolerant, thermophilic isolates and three out of sixteen representative neutrophilic, thermophilic isolates had a combination of properties consistent with their classification as Streptomyces thermovulgaris. One of the remaining alkalitolerant, thermophilic isolate, Streptomyces strain TA56, merited species status. The name Streptomyces thermoalcalitolerans sp. nov. is proposed for this strain. A neutrophilic, thermophilic isolate, Streptomyces strain NAR85, was identified as Streptomyces thermodiastaticus. Four other neutrophilic thermophilic isolates assigned to a numerical phenetic cluster and a thermophilic isolates from poultry faeces were also considered to warrant species status; the names Streptomyces eurythermophilus sp. nov. and Streptomyces thermocoprophilus sp. nov. are proposed to accommodate these strains. It was also concluded that additional comparative taxonomic studies are required to clarify the relationships between additional thermophilic streptomycete strains included in the present investigation. A corresponding polyphasic approach was used to clarify the taxonomy of six thermophilic isolates provisionally assigned to either the genera Amycolatopsis or Excellospora. Two of the isolates, strain NT202 and NT303, had properties consistent with their classification in the genus Amycolatopsis. However, the genotypic and phenotypic data also showed that these strains formed a new centre of taxonomic variation for which the name Amycolatopsis eurythermus sp. nov. is proposed. Similarly, the four remaining strains formed two new centre of taxonomic variation within the genus Excellospora. It is proposed that isolates TA113 and TA114 be designated Excellospora alcalithermophilus sp. nov. Similarly, the name Excellospora thermoalcalitolerans sp. nov. is proposed for strains TA86 and TA111. An emended description is also given for the genus Excellospora.Overseas Research Student Award