Whole genome sequences reveal the Xanthomonas perforans population is shaped by the tomato production system

Modern agricultural practices increase the potential for plant pathogen spread, while the advent of affordable whole genome sequencing enables in-depth studies of pathogen movement. Population genomic studies may decipher pathogen movement and population structure as a result of complex agricultural production systems. We used whole genome sequences of 281 Xanthomonas perforans strains collected within one tomato production season across Florida and southern Georgia fields to test for population genetic structure associated with tomato production system variables. We identified six clusters of X. perforans from core gene SNPs that corresponded with phylogenetic lineages. Using whole genome SNPs, we found genetic structure among farms, transplant facilities, cultivars, seed producers, grower operations, regions, and counties. Overall, grower operations that produced their own transplants were associated with genetically distinct and less diverse populations of strains compared to grower operations that received transplants from multiple sources. The degree of genetic differentiation among components of Florida’s tomato production system varied between clusters, suggesting differential dispersal of the strains, such as through seed or contaminated transplants versus local movement within farms. Overall, we showed that the genetic variation of a bacterial plant pathogen is shaped by the structure of the plant production system.Subject terms: Applied microbiology, Population genetics, Microbial ecology, Microbial ecology     

Molecular Evolution across Mouse Spermatogenesis

Genes involved in spermatogenesis tend to evolve rapidly, but we lack a clear understanding of how protein sequences and patterns of gene expression evolve across this complex developmental process. We used fluorescence-activated cell sorting (FACS) to generate expression data for early (meiotic) and late (postmeiotic) cell types across 13 inbred strains of mice (Mus) spanning ∼7 My of evolution. We used these comparative developmental data to investigate the evolution of lineage-specific expression, protein-coding sequences, and expression levels. We found increased lineage specificity and more rapid protein-coding and expression divergence during late spermatogenesis, suggesting that signatures of rapid testis molecular evolution are punctuated across sperm development. Despite strong overall developmental parallels in these components of molecular evolution, protein and expression divergences were only weakly correlated across genes. We detected more rapid protein evolution on the X chromosome relative to the autosomes, whereas X-linked gene expression tended to be relatively more conserved likely reflecting chromosome-specific regulatory constraints. Using allele-specific FACS expression data from crosses between four strains, we found that the relative contributions of different regulatory mechanisms also differed between cell types. Genes showing cis-regulatory changes were more common late in spermatogenesis, and tended to be associated with larger differences in expression levels and greater expression divergence between species. In contrast, genes with trans-acting changes were more common early and tended to be more conserved across species. Our findings advance understanding of gene evolution across spermatogenesis and underscore the fundamental importance of developmental context in molecular evolutionary studies.     

Sex‐specific aging in animals: Perspective and future directions

Sex differences in aging occur in many animal species, and they include sex differences in lifespan, in the onset and progression of age‐associated decline, and in physiological and molecular markers of aging. Sex differences in aging vary greatly across the animal kingdom. For example, there are species with longer‐lived females, species where males live longer, and species lacking sex differences in lifespan. The underlying causes of sex differences in aging remain mostly unknown. Currently, we do not understand the molecular drivers of sex differences in aging, or whether they are related to the accepted hallmarks or pillars of aging or linked to other well‐characterized processes. In particular, understanding the role of sex‐determination mechanisms and sex differences in aging is relatively understudied. Here, we take a comparative, interdisciplinary approach to explore various hypotheses about how sex differences in aging arise. We discuss genomic, morphological, and environmental differences between the sexes and how these relate to sex differences in aging. Finally, we present some suggestions for future research in this area and provide recommendations for promising experimental designs.     

Rapid directed molecular evolution of fluorescent proteins in mammalian cells

In vivo imaging of model organisms is heavily reliant on fluorescent proteins with high intracellular brightness. Here we describe a practical method for rapid optimization of fluorescent proteins via directed molecular evolution in cultured mammalian cells. Using this method, we were able to perform screening of large gene libraries containing up to 2 × 10⁷ independent random genes of fluorescent proteins expressed in HEK cells, completing one iteration of directed evolution in a course of 8 days. We employed this approach to develop a set of green and near‐infrared fluorescent proteins with enhanced intracellular brightness. The developed near‐infrared fluorescent proteins demonstrated high performance for fluorescent labeling of neurons in culture and in vivo in model organisms such as Caenorhabditis elegans, Drosophila, zebrafish, and mice. Spectral properties of the optimized near‐infrared fluorescent proteins enabled crosstalk‐free multicolor imaging in combination with common green and red fluorescent proteins, as well as dual‐color near‐infrared fluorescence imaging. The described method has a great potential to be adopted by protein engineers due to its simplicity and practicality. We also believe that the new enhanced fluorescent proteins will find wide application for in vivo multicolor imaging of small model organisms.     

A peplomycin-supersensitive cell line lacking activation of poly(adenosine diphosphate ribose) synthetase by peplomycin

In peplomycin-supersensitive Chinese hamster lung cells, the increase in poly(ADP-ribose) synthesizing activity following peplomycin treatment was significantly reduced as compared with the parental lung cells, suggesting that peplomycin-supersensitive lung cells may have some deficiency in DNA repair. On the contrary, peplomycin-supersensitive ovary cells, which undergo increased DNA damage induced by peplomycin, showed normally increased poly(ADP-ribose) polymerizing activity compared with the parental ovary cells. Relationship between poly(ADP-ribose) polymerase and peplomycin sensitivity was discussed.     

Mechanism of proteolytic activation of rat liver protein kinase C generating Ca2(+)-phospholipid-independent form with apparent molecular mass of 80,000

1. New Ca2(+)-phospholipid-independent form of protein kinase C was produced by limited proteolysis with trypsin. 2. The molecular mass of this active enzyme was slightly smaller than that of original protein kinase C. 3. The active enzyme cross-reacted with antibody against the pseudosubstrate region on amino-terminal end of protein kinase C. 4. The active enzyme was inhibited by the peptide inhibitor derived from the pseudosubstrate region. 5. These results suggest that the limited proteolysis at or near the pseudosubstrate region made protein kinase C active without Ca2+ and phospholipid.     

Exercise-induced lipid peroxidation and leakage of enzymes before and after vitamin E supplementation

1. The purpose of this study was to investigate the effects of vitamin E on serum levels of malondialdehyde following the acute exhaustive exercise in human, and to determine whether the magnitude of leakage of enzyme would be affected by vitamin E supplementation. 2. Increase of malondialdehyde after exercise before vitamin E supplementation was slight (but statistically significant), however after supplementation with vitamin E, malondialdehyde level after exercise was significantly decreased. 3. Leakage of enzyme was significantly increased after exercise before vitamin E supplementation, but it was lower following exercise after vitamin E supplementation. 4. Lipid peroxidation following a bout of acute heavy exercise can be inhibited by vitamin E supplementation.     

Cellular hydrophobicity of Listeria monocytogenes involves initial attachment and biofilm formation on the surface of polyvinyl chloride

Aims: To clarify the cellular properties of Listeria monocytogenes involved in adhesion to and biofilm formation on polyvinyl chloride, a widely used material in the food manufacturing process. Methods and Results: A significant correlation between the ability of initial adherence to and biofilm formation on PVC was observed for 24 L. monocytogenes strains (Spearman rank‐correlation coefficient, r_s = 0·89). The swimming motility assay revealed no relationship between initial adherence and motility of L. monocytogenes. The microbial adhesion to solvent assay revealed an interaction of L. monocytogenes cells with nonpolar solvents, and a significant correlation was also observed between the degree of interaction with nonpolar solvents and initial adherence to PVC (r_s = 0·87 and r_s = 0·84, between initial adherence and affinities to decane and hexadecane, respectively). Conclusions: Results indicate that cellular hydrophobicity of L. monocytogenes is an important property involved in the initial adherence to and biofilm formation on PVC. Significance and Impact of Study: This study clarified the factors involved in the adherence to and biofilm formation ability of L. monocytogenes strains with PVC.