A. Levy

CryoDRGN-AI: Neural ab initio reconstruction of challenging cryo-EM and cryo-ET datasets

The paper introduces cryoDRGN-AI, a method for ab initio 3D reconstruction of cryo-EM and cryo-ET datasets, revealing new conformational states and unresolved motions.

NONEXPRESSOR OF PATHOGENESIS-RELATED GENES control Huanglongbing tolerance by regulating immune balance in citrus plants

This study shows that overexpressing AtNPR1 or silencing AtNPR3/AtNPR4 orthologs in citrus enhances HLB tolerance by regulating immune balance and reducing callose and ROS accumulation.

Multiplexed gene editing with a multi-intron containing Cas9 gene in citrus

This paper introduces a multiplex gene editing system in citrus using a multi-intron Cas9 gene and gRNA-tRNA arrays to target the PDS gene, improving editing efficiency in Carrizo citrange and Duncan grapefruit.

Toxinome - The Bacterial Protein Toxin Database

The paper introduces Toxinome, a comprehensive database of bacterial protein toxins and antitoxins, revealing their distribution, depletion in extreme temperature bacteria, and identification of toxin-rich genomic regions called Toxin Islands.

A genomic and structural bioinformatic pipeline identifies candidate type VI secretion antibacterial effector-immunity pairs

The paper develops a genomic and AlphaFold2-based pipeline to identify T6SS effector-immunity pairs, validates four effector proteins and their cognate immunity genes, and explores their mechanisms using bioinformatics and fluorescence microscopy.

Widespread horizontal gene transfer between plants and their microbiota

The paper identifies 180 horizontally transferred genes between plants and their microbiota, showing functional complementarity and suggesting gene transfer shapes host-microbe interactions.

Accurate prediction of transition metal ion location via deep learning

This paper introduces two tools, Metal3D and Metal1D, for predicting metal ion locations in protein structures, with Metal3D showing superior accuracy.

Candidatus Liberibacter asiaticus reduces callose and reactive oxygen species production in the phloem

This study shows that Candidatus Liberibacter asiaticus reduces callose and reactive oxygen species in the phloem, suggesting it manipulates host metabolism to evade defenses.

Genome sequences of the five Sitopsis species of Aegilops and the origin of polyploid wheat B-subgenome

This paper reports chromosome-level genome assemblies of five Sitopsis species and identifies the B-subgenome donor of bread wheat as an extinct species closely related to Ae. speltoides.

Systematic Discovery of Antibacterial and Antifungal Bacterial Toxins

The paper identifies novel bacterial toxins and their immunity genes, showing antifungal activity and enzymatic function.

Large-scale discovery of candidate type VI secretion effectors with antibacterial activity

The paper identifies candidate type VI secretion effectors with antibacterial activity using bioinformatics and experimental validation across diverse bacterial species.

Canopy health, but not Candidatus Liberibacter asiaticus Ct values, are correlated with fruit yield in Huanglongbing affected sweet orange trees.

The paper identifies canopy health metrics as better predictors of fruit yield than CLas Ct values in HLB-affected sweet orange trees.

Transcriptome profiling of Candidatus Liberibacter asiaticus in citrus and psyllids

This study profiles the transcriptome of Candidatus Liberibacter asiaticus in citrus and psyllids, identifying gene expression patterns and differentially expressed genes between hosts.

Phloem transport limitation in Huanglongbing affected sweet orange is dependent on phloem-limited bacteria and callose

This study shows that callose accumulation and CLas infection interact to limit phloem transport in HLB-affected sweet orange, with rootstock genotype modulating the extent of this limitation.

Increased susceptibility to Chrysanthemum Yellows phytoplasma infection in Atcals7 ko plants is accompanied by enhanced expression of carbohydrate transporters.

This study shows that AtCALS7 deficiency in Arabidopsis increases susceptibility to phytoplasma infection by altering carbohydrate transporter expression and sieve-pore structure.

The spatial-temporal dynamics of respiratory syncytial virus infections across the east-west coasts of Australia during 2016-17

This study analyzes RSV genome sequences from eastern and western Australia to understand spatial-temporal dynamics and transmission patterns during 2016-17.

The extracellular contractile injection system is enriched in environmental microbes and associates with numerous toxins

The paper identifies eCIS loci in environmental microbes, shows their association with toxins, and presents an eCIS repository.

Continuous administration of the p38α inhibitor neflamapimod during the subacute phase after transient ischemia-induced stroke in the rat promotes dose-dependent functional recovery accompanied by increase in brain BDNF protein level

This study shows that neflamapimod, a p38 inhibitor, improves functional recovery and increases BDNF levels in rats after stroke when administered during the subacute phase.