Publications

A High-Throughput, Seedling Screen for Plant Immunity

Posted by on Apr 27, 2020 in Publications | Comments Off on A High-Throughput, Seedling Screen for Plant Immunity

Alexandre Martel, Timothy Lo, Darrell Desveaux, and David S. Guttman MPMI 2020 33(3):394-401. 10.1094/MPMI-10-19-0295-TA PMID:31851574
Abstract: An understanding of how biological diversity affects plant-microbe interactions is becoming increasingly important, particularly with respect to components of the pathogen effector arsenal and the plant immune system. Although technological improvements have greatly advanced our ability to examine molecular sequences and interactions, relatively few advances have been made that facilitate high-throughput, in vivo pathology screens. Here,...

Read More

Generation of Transgenic Self-Incompatible Arabidopsis thaliana Shows a Genus-Specific Preference for Self-Incompatibility Genes

Posted by on Apr 27, 2020 in Publications | Comments Off on Generation of Transgenic Self-Incompatible Arabidopsis thaliana Shows a Genus-Specific Preference for Self-Incompatibility Genes

Zhang T, Zhou G, Goring DR, Liang X, Macgregor S, Dai C, Wen J, Yi B, Shen J, Tu J, Fu T, Ma C. Plants 2019 8(12):570. 10.3390/plants8120570 PMID:31817214
Abstract: Brassicaceae species employ both self-compatibility and self-incompatibility systems to regulate post-pollination events. Arabidopsis halleri is strictly self-incompatible, while the closely related Arabidopsis thaliana has transitioned to self-compatibility with the loss of functional S-locus genes during evolution. The downstream signaling protein, ARC1, is also required for the...

Read More

Convergent patterns of evolution of mitochondrial oxidative phosphorylation (OXPHOS) genes in electric fishes.

Posted by on Apr 27, 2020 in Publications | Comments Off on Convergent patterns of evolution of mitochondrial oxidative phosphorylation (OXPHOS) genes in electric fishes.

Elbassiouny AA, Lovejoy NR, Chang BSW Philios Trans R Soc Lond B Biol Sci 2020 375(1790):20190179. 10.1098/rstb.2019.0179 PMID:31787042
Abstract: The ability to generate and detect electric fields has evolved in several groups of fishes as a means of communication, navigation and, occasionally, predation. The energetic burden required can account for up to 20% of electric fishes’ daily energy expenditure. Despite this, molecular adaptations that enable electric fishes to meet the metabolic demands of bioelectrogenesis remain unknown. Here, we investigate the molecular...

Read More

Multiple Modes of Convergent Adaptation in the Spread of Glyphosate-Resistant Amaranthus tuberculatus

Posted by on Apr 27, 2020 in Publications | Comments Off on Multiple Modes of Convergent Adaptation in the Spread of Glyphosate-Resistant Amaranthus tuberculatus

Kreiner JM, Giacomini DA, Bemm F, Waithaka B, Regalado J, Lanz C, Hildebrandt J, Sikkema PH, Tranel PJ, Weigel D, Stinchcombe JR, Wright SI. Proc Natl Acad Sci USA 2019 116(42):21076-21084. 10.1073/pnas.1900870116 PMID:31570613
Abstract: The selection pressure exerted by herbicides has led to the repeated evolution of herbicide resistance in weeds. The evolution of herbicide resistance on contemporary timescales in turn provides an outstanding opportunity to investigate key questions about the genetics of adaptation, in particular the relative importance of adaptation from new...

Read More

Screening of Chemical Libraries Using a Yeast Model of Retinal Disease

Posted by on Apr 27, 2020 in Publications | Comments Off on Screening of Chemical Libraries Using a Yeast Model of Retinal Disease

Scott BM, Wybenga-Groot LE, McGlade CJ, Heon E, Peisajovich SG, Chang BSW SLAS Discovery 2019 24(10):969-977. 10.1177/2472555219875934 PMID:31556794
Abstract: Retinitis pigmentosa (RP) is a degenerative retinal disease, often caused by mutations in the G-protein-coupled receptor rhodopsin. The majority of pathogenic rhodopsin mutations cause rhodopsin to misfold, including P23H, disrupting its crucial ability to respond to light. Previous screens to discover pharmacological chaperones of rhodopsin have primarily been based on rescuing rhodopsin trafficking and localization to the...

Read More

Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting.

Posted by on Apr 27, 2020 in Publications | Comments Off on Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting.

Lu AX, Kraus OZ, Cooper S, Moses AM PLoS Comput Biol 2019 15(9):e1007348. 10.1371/journal.pcbi.1007348 PMID:31479439
Abstract: Cellular microscopy images contain rich insights about biology. To extract this information, researchers use features, or measurements of the patterns of interest in the images. Here, we introduce a convolutional neural network (CNN) to automatically design features for fluorescence microscopy. We use a self-supervised method to learn feature representations of single cells in microscopy images without labelled training data. We train CNNs on a simple task...

Read More

Gut-associated IgA+ immune cells regulate obesity-related insulin resistance.

Posted by on Apr 27, 2020 in Publications | Comments Off on Gut-associated IgA+ immune cells regulate obesity-related insulin resistance.

Luck H, Khan S, Kim JH, Copeland JK, Revelo XS, Tsai S, Chakraborty M, Cheng K, Tao Chan Y, Nøhr MK, Clemente-Casares X, Perry MC, Ghazarian M, Lei H, Lin YH, Coburn B, Okrainec A, Jackson T, Poutanen S, Gaisano H, Allard JP, Guttman DS, Conner ME, Winer S, Winer DA Nature Communications 2019 10(1):3650. 10.1038/s41467-019-11370-y PMID:31409776
Abstract: The intestinal immune system is emerging as an important contributor to obesity-related insulin resistance, but the role of intestinal B cells in this context is unclear. Here, we show that high fat diet (HFD) feeding alters...

Read More

An ‘eFP‐Seq Browser’ for visualizing and exploring RNA sequencing data

Posted by on Apr 27, 2020 in Publications | Comments Off on An ‘eFP‐Seq Browser’ for visualizing and exploring RNA sequencing data

Alexander Sullivan, Priyank K. Purohit, Nowlan H. Freese, Asher Pasha, Eddi Esteban, Jamie Waese, Alison Wu, Michelle Chen, Chih Y. Chin, Richard Song, Sneha R. Watharkar, Agnes P. Chan, Vivek Krishnakumar, Matthew W. Vaughn, Chris Town, Ann E. Loraine, Nicholas J. Provart The Plant Journal 2019 100(3):641-654. 10.1111/tpj.14468 PMID:31350781
Abstract: Improvements in next-generation sequencing technologies have resulted in dramatically reduced sequencing costs. This has led to an explosion of ‘-seq’-based methods, of which RNA sequencing (RNA-seq) for...

Read More

Evolutionary signatures of photoreceptor transmutation in geckos reveal potential adaptation and convergence with snakes

Posted by on Apr 27, 2020 in Publications | Comments Off on Evolutionary signatures of photoreceptor transmutation in geckos reveal potential adaptation and convergence with snakes

Ryan K. Schott  Nihar Bhattacharyya  Belinda S.W. Chang Evolution 2019 73(9):1958-1971. 10.1111/evo.13810 PMID:31339168
Abstract: Most vertebrates use a combination of rod and cone photoreceptors to enable vision in conditions ranging from starlight to direct sunlight. Nocturnal geckos, however, have simplex retinas that contain only rods in terms of morphology and physiology, but these rods are thought to be derived from cones through an evolutionary process known as photoreceptor transmutation. To investigate this, we generated eye transcriptomes and analyzed patterns of...

Read More

Population Genomics of the Facultatively Asexual Duckweed Spirodela Polyrhiza.

Posted by on Apr 27, 2020 in Publications | Comments Off on Population Genomics of the Facultatively Asexual Duckweed Spirodela Polyrhiza.

Eddie K H Ho , Magdalena Bartkowska, Stephen I Wright , Aneil F Agrawal  New Phytol 2019 224(3):1361-1371.  10.1111/nph.16056  PMID:31298732
Abstract: Clonal propagation allows some plant species to achieve massive population sizes quickly but also reduces the evolutionary independence of different sites in the genome. We examine genome-wide genetic diversity in Spirodela polyrhiza, a duckweed that reproduces primarily asexually. We find that this geographically widespread and numerically abundant species has very low levels of genetic diversity. Diversity at nonsynonymous sites...

Read More