Skip to main content

Li Wan’s publication appears in “Science”

August 22, 2019

Congratulations to current Dangl lab post-doc co-first author Li Wan (pictured), who along with former Dangl lab post-docs Ryan Anderson, Freddy Monteiro, and Eui Hwan Chung and co-corresponding Marc Nishimura published this week paper in Science titled ‘TIR domains of plant immune receptors are NAD+ cleaving enzymes tat promote cell death’. This work was a collaboration with Jeff Milbrant’s lab at Washington University, St. Louis. The paper demonstrates that a major class of plant intracellular immune receptors, called NLRs, feature an N-terminal signaling domain, called TIR, that, instead of functioning as a scaffold as predicted from animal innate immunity studies, instead function as an enzyme that cleaves a common cellular energy storing molecule and likely generates a small molecule signal required for downstream activation of cell death and immune response. This work will re-orient ongoing studies of TIR domain function in plant innate immunity and contribute to development of sustainable agriculture. READ MORE >>

Oliver Furzer’s paper is published in “Cell”

August 22, 2019

Congratulations to current Dangl lab post-doc co-first author Oliver Furzer (pictured), who along with former Dangl lab post-doc and co-first author Freddy Monteiro and co-author Marc Nishimura published this week paper in Cell titled ‘A species-wide inventory of NLR gene alleles in Arabidopsis thaliana.’ This work was a collaboration with Detlef Weigel’s lab in Tuebingen, Germany, and Jonathan Jones’ lab in Norwich, UK. The paper defined a near saturation set of the key intracellular immune receptors, called NLRs, across the genetic diversity of the key reference plant species. Their results will provide a blueprint for functional studies of existing receptors and rational design of novel receptors, as well as a blueprint for similar studies in crops and management of dangerous crop diseases by rational deployment of naturally evolved receptor alleles. READ MORE >>

Bloom lab’s New Publication in “PLOS Computational Biology”

August 15, 2019

Josh Lawrimore (right) and Kerry Bloom (left) with their colleagues in Applied Math-Benjamin Walker, David Adalsteinsson, Greg Forest, Dane Taylor, and Caitlin Hult have a new publication in PLOS Computational Biology. The publication is titled: “Transient crosslinking kinetics optimize gene cluster interactions”.

Abstract:  The spatiotemporal organization of the genome plays an important role in cellular processes involving DNA, but remains poorly understood, especially in the nucleolus, which does not facilitate conventional techniques. We consider here a polymer bead-chain model of the full yeast genome, featuring special dynamic crosslinking to model the effects of condensin in the nucleolus, and investigate how the kinetic timescale on which the crosslinks bind and unbind affects the resulting dynamics inside the nucleolus. When this timescale is sufficiently short, large, stable clusters appear, but when it is long, there is no resulting structure. We find that there additionally exists a range of timescales for which flexible clusters appear, in which beads frequently enter and leave clusters. These flexible clusters maximize the cross-communication between beads in the nucleolus. We apply network temporal community detection algorithms to identify what beads are in what communities at what times, in a way that is more robust and objective in comparison to conventional visual-based methods.

Kerry Bloom Receives New NSF Grant Award

August 15, 2019

Congratulations to Kerry Bloom, whose lab received a new National Science Foundation (NSF) grant award of $900,000. This grant will be active from Sept. 2019-Aug. 2023 and is titled: “Exploring the Interplay between DNA Replication Kinetics and Macromolecular Protein Assembly at the Centromere”.

Abstract: Centromeres are essential for kinetochore assembly and chromosome segregation during the eukaryotic cell division. Despite extensive studies, little is known regarding the interplay between replisome progression through centromeric regions and the assembly of functional kinetochore at these sites. In this proposal we will combine genetics, cell biology, live-cell microscopy, and computational methods to study the relationship between DNA replication, centromere establishment, kinetochore assembly, and chromosome segregation during mitosis. Specifically, we will apply our recently developed live-cell imaging approach for monitoring replication fork progression through active and inactive centromeric regions, investigate how transcription of centromeric regions affects kinetochore assembly and utilize computer simulations to investigate the importance of DNA configurations to centromere assembly. This integrative approach, applied to a variety of mutant strains and conditions, will enable us to shed new light on different aspects of centromeric DNA replication, genome stability, chromosome segregation and cell division. This research program requires strong collaboration between labs that share the expertise in centromere biology and DNA replication using yeast as a model organism. The proposed collaboration is ideal, as the infrastructure and methodologies required to pursue the suggested proposal are well implemented in the Bloom and Aharoni labs.

Alain Laederach coauthors a “Nature Microbiology” paper

July 30, 2019

Congratulations to Alain Laederach who coauthored a paper in Nature Microbiology titled “The structure of the influenza A virus genome,” in collaboration with Ervin Fodor’s laboratory at the University of Oxford. This paper presents a complete structure of the in virio genome of Influenza virus. Importantly, this paper captures both intra and inter-segment interactions and reveals RNA mediated mechanisms by which the virus genome segments. The paper can be read here >>

Lela Lackey receives an Alpha-1 Foundation Grant

July 30, 2019

Congratulations to Lela Lackey (postdoc, Alain Laederach’s lab) for receiving a grant from “Alpha-1 Foundation” to study the effects of non-coding mutations on the expression of the Alpha-1-antitrypsin protein. Dr. Lackey will investigate novel variants in the UTRs of the messenger RNA coding for Alpha-1-antitrypsin protein that lower its expression and lead to a wide range of pathologies including liver cirrhosis and chronic obstructive pulmonary disease. The Alpha-1 Foundation promotes the research and the development of new therapies for improving the quality of life for those diagnosed with Alpha-1-antitrypsin deficiency. Read more about the foundation > >

Gregory Copenhaver co-authors “Plant Cell” paper

July 18, 2019

Dr. Gregory P. Copenhaver co-authored a paper in Plant Cell with his collaborators at The University of Vienna that is titled “Meiotic DNA Repair in the Nucleolus Employs a Non-homologous End Joining Mechanism”. This paper shows how plants repair chromosomal breaks during meiosis in regions of the genome that contain large repetitive arrays. The arrays, which encode the RNA used to build ribosomes, form a unique compartment in the nucleus that processes meiotic breaks differently to ensure genome stability. You can read more here >>