30 research outputs found
Changepoint problem with angular data using a measure of variation based on the intrinsic geometry of torus
In many temporally ordered data sets, it is observed that the parameters of
the underlying distribution change abruptly at unknown times. The detection of
such changepoints is important for many applications. While this problem has
been studied substantially in the linear data setup, not much work has been
done for angular data. In this article, we utilize the intrinsic geometry of a
torus to introduce the notion of the `square of an angle' and use it to propose
a new measure of variation, called the `curved variance', of an angular random
variable. Using the above ideas, we propose new tests for the existence of
changepoint(s) in the concentration, mean direction, and/or both of these. The
limiting distributions of the test statistics are derived and their powers are
obtained using extensive simulation. It is seen that the tests have better
power than the corresponding existing tests. The proposed methods have been
implemented on three real-life data sets revealing interesting insights. In
particular, our method when used to detect simultaneous changes in mean
direction and concentration for hourly wind direction measurements of the
cyclonic storm `Amphan' identified changepoints that could be associated with
important meteorological events
Learning Microbial Interaction Networks from Metagenomic Count Data
Abstract Many microbes associate with higher eukaryotes and impact their vitality. To engineer microbiomes for host benefit, we must understand the rules of community assembly and maintenance that, in large part, demand an understanding of the direct interactions among community members. Toward this end, we have developed a Poisson-multivariate normal hierarchical model to learn direct interactions from the count-based output of standard metagenomics sequencing experiments. Our model controls for confounding predictors at the Poisson layer and captures direct taxon–taxon interactions at the multivariate normal layer using an ℓ1 penalized precision matrix. We show in a synthetic experiment that our method handily outperforms state-of-the-art methods such as SparCC and the graphical lasso (glasso). In a real in planta perturbation experiment of a nine-member bacterial community, we show our model, but not SparCC or glasso, correctly resolves a direct interaction structure among three community members that ..
The molecular basis of host specialization in bean pathovars of Pseudomonas syringae
Biotrophic phytopathogens are typically limited to their
adapted host range. In recent decades, investigations have
teased apart the general molecular basis of intraspecific
variation for innate immunity of plants, typically involving
receptor proteins that enable perception of pathogen-associated
molecular patterns or avirulence elicitors from the
pathogen as triggers for defense induction. However, general
consensus concerning evolutionary and molecular factors
that alter host range across closely related phytopathogen
isolates has been more elusive. Here, through genome
comparisons and genetic manipulations, we investigate the
underlying mechanisms that structure host range across
closely related strains of Pseudomonas syringae isolated
from different legume hosts. Although type III secretionindependent
virulence factors are conserved across these
three strains, we find that the presence of two genes encoding
type III effectors (hopC1 and hopM1) and the absence
of another (avrB2) potentially contribute to host range differences
between pathovars glycinea and phaseolicola.
These findings reinforce the idea that a complex genetic
basis underlies host range evolution in plant pathogens.
This complexity is present even in host–microbe interactions
featuring relatively little divergence among both hosts
and their adapted pathogens
Pseudomonas syringae Type III Effector HopBB1 Promotes Host Transcriptional Repressor Degradation to Regulate Phytohormone Responses and Virulence
Independently evolved pathogen effectors from three branches of life (ascomycete, eubacteria, and oomycete) converge onto the Arabidopsis TCP14 transcription factor to manipulate host defense. However, the mechanistic basis for defense control via TCP14 regulation is unknown. We demonstrate that TCP14 regulates the plant immune system by transcriptionally repressing a subset of the jasmonic acid (JA) hormone signaling outputs. A previously unstudied Pseudomonas syringae (Psy) type III effector, HopBB1, interacts with TCP14 and targets it to the SCFCOI1 degradation complex by connecting it to the JA signaling repressor JAZ3. Consequently, HopBB1 de-represses the TCP14-regulated subset of JA response genes and promotes pathogen virulence. Thus, HopBB1 fine-tunes host phytohormone crosstalk by precisely manipulating part of the JA regulon to avoid pleiotropic host responses while promoting pathogen proliferation
Phytochromes function as thermosensors in Arabidopsis
Plants are responsive to temperature, and can distinguish differences of 1ºC. In Arabidopsis, warmer temperature accelerates flowering and increases elongation growth hermomorphogenesis). The mechanisms of temperature perception are however largely unknown. We describe a major thermosensory role for the phytochromes (red light receptors) during the night. Phytochrome null plants display a constitutive warm temperature response, and consistent with this, we show in this background that the warm temperature transcriptome becomes de-repressed at low temperatures. We have discovered phytochrome B (phyB) directly associates with the promoters of key target genes in a temperature dependent manner. The rate of phyB inactivation is proportional to temperature in the dark, enabling phytochromes to function as thermal timers, integrating temperature information over the course of the night
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Variable Suites of Non-effector Genes Are Co-regulated in the Type III Secretion Virulence Regulon across the Pseudomonas syringae Phylogeny
Pseudomonas syringae is a phylogenetically diverse species of Gram-negative bacterial plant pathogens responsible for crop diseases around the world. The HrpL sigma factor drives expression of the major P. syringae virulence regulon. HrpL controls expression of the genes encoding the structural and functional components of the type III secretion system (T3SS) and the type three secreted effector proteins (T3E) that are collectively essential for virulence. HrpL also regulates expression of an under-explored suite of non-type III effector genes (non-T3E), including toxin production systems and operons not previously associated with virulence. We implemented and refined genome-wide transcriptional analysis methods using cDNA-derived high-throughput sequencing (RNA-seq) data to characterize the HrpL regulon from six isolates of P. syringae spanning the diversity of the species. Our transcriptomes, mapped onto both complete and draft genomes, significantly extend earlier studies. We confirmed HrpL-regulation for a majority of previously defined T3E genes in these six strains. We identified two new T3E families from P. syringae pv. oryzae 1_6, a strain within the relatively underexplored phylogenetic Multi-Locus Sequence Typing (MLST) group IV. The HrpL regulons varied among strains in gene number and content across both their T3E and non-T3E gene suites. Strains within MLST group II consistently express the lowest number of HrpL-regulated genes. We identified events leading to recruitment into, and loss from, the HrpL regulon. These included gene gain and loss, and loss of HrpL regulation caused by group-specific cis element mutations in otherwise conserved genes. Novel non-T3E HrpL-regulated genes include an operon that we show is required for full virulence of P. syringae pv. phaseolicola 1448A on French bean. We highlight the power of integrating genomic, transcriptomic, and phylogenetic information to drive concise functional experimentation and to derive better insight into the evolution of virulence across an evolutionarily diverse pathogen species