Self-Incompatibility & Modelling
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Principal Component Analysis explained visually

Principal Component Analysis explained visually | Self-Incompatibility & Modelling | Scoop.it

Via Neelima Sinha
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The evolution of selfing from outcrossing ancestors in Brassicaceae: what have we learned from variation at the S-locus? - Vekemans - 2014 - Journal of Evolutionary Biology - Wiley Online Library

The evolution of selfing from outcrossing ancestors in Brassicaceae: what have we learned from variation at the S-locus? - Vekemans - 2014 - Journal of Evolutionary Biology - Wiley Online Library | Self-Incompatibility & Modelling | Scoop.it

Evolutionary transitions between mating systems have occurred repetitively and independently in flowering plants. One of the most spectacular advances of the recent empirical literature in the field was the discovery of the underlying genetic machinery, which provides the opportunity to retrospectively document the scenario of the outcrossing to selfing transitions in a phylogenetic perspective. In this review, we explore the literature describing patterns of polymorphism and molecular evolution of the locus controlling self-incompatibility (S-locus) in selfing species of the Brassicaceae family in order to document the transition from outcrossing to selfing, a retrospective approach that we describe as the ‘mating system genes approach'. The data point to strikingly contrasted scenarios of transition from outcrossing to selfing. We also perform original analyses of the fully sequenced genomes of four species showing self-compatibility, to compare the orthologous S-locus region with that of functional S-locus haplotypes. Phylogenetic analyses suggest that all species we investigated evolved independently towards loss of self-incompatibility, and in most cases almost intact sequences of either of the two S-locus genes suggest that these transitions occurred relatively recently. The S-locus region in Aethionema arabicum, representing the most basal lineage of Brassicaceae, showed unusual patterns so that our analysis could not determine whether self-incompatibility was lost secondarily, or evolved in the core Brassicaceae after the split with this basal lineage. Although the approach we detail can only be used when mating system genes have been identified in a clade, we suggest that its integration with phylogenetic and population genetic approaches should help determine the main routes of this predominant mating system shift in plants.

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BRASSINOSTEROID INSENSITIVE2 Interacts with ABSCISIC ACID INSENSITIVE5 to Mediate the Antagonism of Brassinosteroids to Abscisic Acid during Seed Germination in Arabidopsis

BRASSINOSTEROID INSENSITIVE2 Interacts with ABSCISIC ACID INSENSITIVE5 to Mediate the Antagonism of Brassinosteroids to Abscisic Acid during Seed Germination in Arabidopsis | Self-Incompatibility & Modelling | Scoop.it
Seed germination and postgerminative growth are regulated by a delicate hormonal balance. Abscisic acid (ABA) represses Arabidopsis thaliana seed germination and postgerminative growth, while brassinosteroids (BRs) antagonize ABA-mediated inhibition and promote these processes. However, the molecular mechanism underlying BR-repressed ABA signaling remains largely unknown. Here, we show that the Glycogen Synthase Kinase 3-like kinase BRASSINOSTEROID INSENSITIVE2 (BIN2), a critical repressor of BR signaling, positively regulates ABA responses during seed germination and postgerminative growth. Mechanistic investigation revealed that BIN2 physically interacts with ABSCISIC ACID INSENSITIVE5 (ABI5), a bZIP transcription factor. Further genetic analysis demonstrated that the ABA-hypersensitive phenotype of BIN2-overexpressing plants requires ABI5. BIN2 was found to phosphorylate and stabilize ABI5 in the presence of ABA, while application of epibrassinolide (the active form of BRs) inhibited the regulation of ABI5 by BIN2. Consistently, the ABA-induced accumulation of ABI5 was affected in BIN2-related mutants. Moreover, mutations of the BIN2 phosphorylation sites on ABI5 made the mutant protein respond to ABA improperly. Additionally, the expression of several ABI5 regulons was positively modulated by BIN2. These results provide evidence that BIN2 phosphorylates and stabilizes ABI5 to mediate ABA response during seed germination, while BRs repress the BIN2-ABI5 cascade to antagonize ABA-mediated inhibition.
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Investigate this-- any connection to self/nonself recognition?

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OpenSUNY textbook: Introduction to the Modeling and Analysis of Complex Systems - Hiroki Sayama

OpenSUNY textbook: Introduction to the Modeling and Analysis of Complex Systems - Hiroki Sayama | Self-Incompatibility & Modelling | Scoop.it

Introduction to the Modeling and Analysis of Complex Systems will introduce students to the concepts and techniques of mathematical/computational modeling and analysis developed in the emerging interdisciplinary field of Complex Systems Science. Introduction to the Modeling and Analysis of Complex Systems"

 

 

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Self-Incompatibility-induced Programmed Cell Death in Papaver pollen involves dramatic acidification of the incompatible pollen tube cytosol - PubMed - NCBI

"Self-incompatibility (SI) is an important genetically controlled mechanism to prevent inbreeding in higher plants. SI involves highly specific interactions during pollination, resulting in the rejection of incompatible ("self") pollen. Programmed cell death (PCD) is an important mechanism for destroying cells in a precisely regulated manner... Here we provide evidence demonstrating the physiological relevance of the cytosolic acidification and identify key targets of this major physiological alteration."

 

Plant Physiol. 2015 Jan 28. pii: pp.114.252742.Wilkins, Bosch, Haque, Teng, Poulter, Franklin-Tong.

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Quantitative and logic modelling of molecular and gene networks : Nature Reviews Genetics : Nature Publishing Group

Quantitative and logic modelling of molecular and gene networks : Nature Reviews Genetics : Nature Publishing Group | Self-Incompatibility & Modelling | Scoop.it
NEW! Review in @NatureRevGenet by Nicolas Le Novère: Quantitative and logic modelling of molecular and gene networks http://t.co/vecaGFcJNN
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Rescooped by Hanna Schempf from Plant Biology Teaching Resources (Higher Education)
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Academic writing, publishing, reviewing, ethics

Slides from a workshop on academic writing and publishing, including discussions of the peer review process and ethics

Via Mary Williams
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Analysis of a Plant Complex Resistance Gene Locus Underlying Immune-Related Hybrid Incompatibility and Its Occurrence in Nature

Analysis of a Plant Complex Resistance Gene Locus Underlying Immune-Related Hybrid Incompatibility and Its Occurrence in Nature | Self-Incompatibility & Modelling | Scoop.it
Author Summary In plants, naturally evolving disease resistance ( R ) genes can cause autoimmunity when combined with different genetic backgrounds.
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Robust Self-Incompatibility in the Absence of a Functional ARC1 Gene in Arabidopsis thaliana

"Here, we review results demonstrating that S-locus genes are necessary and sufficient for SI signaling and for restoration of a strong and developmentally stable SI phenotype in several accessions of A. thaliana. The data indicate that introduction of a functional E3 ligase-encoding ARC1 gene, which is deleted in all accessions that have been analyzed to date, is not required for SI signaling leading to inhibition of self pollen or for reversion of A. thaliana to its fully self-incompatible ancestral state."

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Inheritance of Hetero-Diploid Pollen S-Haplotype in Self-Compatible Tetraploid Chinese Cherry (Prunus pseudocerasus Lindl)

Inheritance of Hetero-Diploid Pollen  S-Haplotype in Self-Compatible Tetraploid Chinese Cherry (Prunus pseudocerasus  Lindl) | Self-Incompatibility & Modelling | Scoop.it
The breakdown of self-incompatibility, which could result from the accumulation of non-functional S -haplotypes or competitive interaction between two different functional S -haplotypes, has been studied extensively at the molecular level in...

Via Plant Breeding and Genomics News
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An Online Bioinformatics Curriculum

An Online Bioinformatics Curriculum | Self-Incompatibility & Modelling | Scoop.it

Online learning initiatives over the past decade have become increasingly comprehensive in their selection of courses and sophisticated in their presentation, culminating in the recent announcement of a number of consortium and startup activities that promise to make a university education on the internet, free of charge, a real possibility. At this pivotal moment it is appropriate to explore the potential for obtaining comprehensive bioinformatics training with currently existing free video resources. This article presents such a bioinformatics curriculum in the form of a virtual course catalog, together with editorial commentary, and an assessment of strengths, weaknesses, and likely future directions for open online learning in this field.


Via Niklaus Grunwald
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Read later.

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Programming tools: Adventures with R

Programming tools: Adventures with R | Self-Incompatibility & Modelling | Scoop.it
A guide to the popular, free statistics and visualization software that gives scientists control of their own data analysis.

Via Niklaus Grunwald
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I really do need to learn R at some point...

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PLOS Computational Biology: A Quick Guide to Organizing Computational Biology Projects

PLOS Computational Biology: A Quick Guide to Organizing Computational Biology Projects | Self-Incompatibility & Modelling | Scoop.it

Most bioinformatics coursework focuses on algorithms, with perhaps some components devoted to learning programming skills and learning how to use existing bioinformatics software. Unfortunately, for students who are preparing for a research career, this type of curriculum fails to address many of the day-to-day organizational challenges associated with performing computational experiments. In practice, the principles behind organizing and documenting computational experiments are often learned on the fly, and this learning is strongly influenced by personal predilections as well as by chance interactions with collaborators or colleagues.

The purpose of this article is to describe one good strategy for carrying out computational experiments. I will not describe profound issues such as how to formulate hypotheses, design experiments, or draw conclusions. Rather, I will focus on relatively mundane issues such as organizing files and directories and documenting progress. These issues are important because poor organizational choices can lead to significantly slower research progress. I do not claim that the strategies I outline here are optimal. These are simply the principles and practices that I have developed over 12 years of bioinformatics research, augmented with various suggestions from other researchers with whom I have discussed these issues.

 


Via Niklaus Grunwald
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Possibly useful in my SI modelling; read later.

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Contemporary evolution of plant reproductive strategies under global change is revealed by stored seeds

Contemporary evolution of plant reproductive strategies under global change is revealed by stored seeds | Self-Incompatibility & Modelling | Scoop.it

Global change is expected to impose new selection pressures on natural populations. Phenotypic responses, such as earlier phenology in response to climate warming, have been repeatedly observed in the field. The recent pollinator decline is also expected to change selection on reproductive traits in flowering plants. However, it remains unclear whether short-term adaptation of plant reproductive strategies occurs in response to global change. In this study, we report the evolution of some important reproductive traits of the annual self-incompatible weed Centaurea cyanus. In a common garden experiment we germinated stored seeds, sampled 18 years apart from the same location, in a region where warmer springs and indices of pollinator decline have been reported. Compared to the ancestral population (1992), our results showed that plants of the descendant population (2010) flowered earlier and also produced larger capitula with longer receptivity and a larger floral display. QST -FST comparisons indicated that natural selection has likely contributed to the evolution of some of the traits investigated. Lower FST within temporal samples than among spatial samples further suggests a limited role of gene flow from neighboring populations. We therefore propose that trait shifts could partly be due to adaptation to global change.

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Genome Editing with Engineered Nucleases in Plants

Genome Editing with Engineered Nucleases in Plants | Self-Incompatibility & Modelling | Scoop.it

Osakabe & Osakabe 2014

"Numerous examples of successful ‘genome editing’ now exist. Genome editing uses engineered nucleases as powerful tools to target specific DNA sequences to edit genes precisely in the genomes of both model and crop plants, as well as a variety of other organisms. The DNA-binding domains of zinc finger (ZF) proteins were the first to be used as genome editing tools, in the form of designed ZF nucleases (ZFNs). More recently, transcription activator-like effector nucleases (TALENs), as well as the clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) system, which utilizes RNA–DNA interactions, have proved useful. A key step in genome editing is the generation of a double-stranded DNA break that is specific to the target gene. This is achieved by custom-designed endonucleases, which enable site-directed mutagenesis via a non-homologous end-joining (NHEJ) repair pathway and/or gene targeting via homologous recombination (HR) to occur efficiently at specific sites in the genome. This review provides an overview of recent advances in genome editing technologies in plants, and discusses how these can provide insights into current plant molecular biology research and molecular breeding technology."

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 Some potential here for experimental research... Not useful to me now, but maybe later.
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The Genetics of Self-Incompatibility - US National Science Foundation (NSF)

The Genetics of Self-Incompatibility - US National Science Foundation (NSF) | Self-Incompatibility & Modelling | Scoop.it

"It turns out that the mechanisms behind petunia inbreeding prevention are very similar to those in an immune response. Just like vertebrates have many types of T-cell receptors that specialize in fighting different antigens, petunia pollen proteins are encoded by different types of related genes that all collaborate together to help fight destructive enzymes in the petunia pistil. Through this complicated system, only correct pollen (pollen produced by a plant genetically different from the pistil) will thrive, grow and complete fertilization."

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A nice little summary of SI in petunias, with a very nice figure and a comparison to the more widely known vertebrate immune system.

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Introducing the Research Resource Identification Initiative at PLOS Biology & PLOS Genetics

Introducing the Research Resource Identification Initiative at PLOS Biology & PLOS Genetics | Self-Incompatibility & Modelling | Scoop.it

"Reproducibility is one of the holy grails of effective, open biomedical literature. But too often resources (e.g. model organisms, software, antibodies) are not reported with sufficient detail to ensure others can replicate or expand upon the results. Today sees PLOS Biology and PLOS Genetics linking in with an exciting pilot study using the principles set out by a Force11 group, the Research Resource Identification Initiative (#RII). Through the use of unique Resource Identifiers (RRIDs), authors will be able to cite the resources that they use in their manuscripts."

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Supercomputing And Botany Team Up To Study Plant Evolution At UT Austin - BioNews Texas

Supercomputing And Botany Team Up To Study Plant Evolution At UT Austin - BioNews Texas | Self-Incompatibility & Modelling | Scoop.it
In an off-the-beaten-path conjunction of botany and genetic investigation with big data, scientists at The University of Texas at Austin are focusing the power of the iPlant, Stampede, Lonestar and Ranger supercomputers of the Texas Advanced...
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101 Innovations in Scholarly Communication

101 Innovations in Scholarly Communication | Self-Incompatibility & Modelling | Scoop.it

This is fascinating - how the processes of writing, reviewing, publishing and citing are changing. Which tools do you use? Modern? Traditional? Experimental? Or do you Follow the crowd? There are links to all of the new tools to help you explore your many options.
Prepared by Bianca Kramer and Jeroen Bosman at Utrecht University Library.


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Evolutionary Dynamics of Microsatellite Distribution in Plants: Insight from the Comparison of Sequenced Brassica , Arabidopsis and Other Angiosperm Species

Evolutionary Dynamics of Microsatellite Distribution in Plants: Insight from the Comparison of Sequenced  Brassica ,  Arabidopsis  and Other Angiosperm Species | Self-Incompatibility & Modelling | Scoop.it
Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information.
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This isn't SI exactly, but it does bear on the evolutionary history of SI lineages.

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How petunias avoid self-fertilization - Science Codex

How petunias avoid self-fertilization - Science Codex | Self-Incompatibility & Modelling | Scoop.it
The ability of many plant species to recognize and their own pollen enables them to avoid inbreeding and the genetic defects that brings. Plants recognize their own pollen by a molecular mechanism, known as 'self-incompatibility' or 'SI'.
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The ARC1 E3 Ligase Promotes a Strong and Stable Self-Incompatibility Response in Arabidopsis Species: Response to the Nasrallah and Nasrallah Commentary

"Here, we discuss our findings on the role of ARC1 in reconstructing a strong and stable A. thaliana self- incompatibility phenotype, in the context of the putative issues outlined in a commentary by Nasrallah and Nasrallah. Additionally, with their proposed standardized strategy for studying self-incompatibility in A. thaliana, we offer our perspective on what constitutes a strong and stable self-incompatibility phenotype in A. thaliana and how this should be investigated and reported to the greater community."

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Dominance hierarchy arising from the evolution of a complex small RNA regulatory network

"The prevention of fertilization through self-pollination (or pollination by a close relative) in the Brassicaceae plant family is determined by the genotype of the plant at the self-incompatibility locus (S locus). The many alleles at this locus exhibit a dominance hierarchy that determines which of the two allelic specificities of a heterozygous genotype is expressed at the phenotypic level. Here, we uncover the evolution of how at least 17 small RNA (sRNA)–producing loci and their multiple target sites collectively control the dominance hierarchy among alleles within the gene controlling the pollen S-locus phenotype in a self-incompatibleArabidopsis species. Selection has created a dynamic repertoire of sRNA-target interactions by jointly acting on sRNA genes and their target sites, which has resulted in a complex system of regulation among alleles."

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A New Online Computational Biology Curriculum

A New Online Computational Biology Curriculum | Self-Incompatibility & Modelling | Scoop.it

A recent proliferation of Massive Open Online Courses (MOOCs) and other web-based educational resources has greatly increased the potential for effective self-study in many fields. This article introduces a catalog of several hundred free video courses of potential interest to those wishing to expand their knowledge of bioinformatics and computational biology. The courses are organized into eleven subject areas modeled on university departments and are accompanied by commentary and career advice.


Via Niklaus Grunwald
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This is very intriguing-- something to look into!

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A population genetic R-evolution

A population genetic R-evolution | Self-Incompatibility & Modelling | Scoop.it

… I stumbled across the R package poppr (Kamvar et al. 2014) and it became an important leap in my personal R-evolution. … Though perhaps not revolutionary in and of themselves, this package is an important milestone in the population genetic analyses in R. ... Likely this is a case of preaching to the converted, but the ease with which one can manipulate data while simultaneously reproducing said analyses is making popgen a lot easier. poppr represents an important advance for popgen analyses, from sexual to clonal.


Via Niklaus Grunwald
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Investigate!

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