The Complete Genome Sequence of ‘Candidatus Liberibacter solanacearum’, the Bacterium Associated with Potato Zebra Chip Disease

Zebra Chip (ZC) is an emerging plant disease that causes aboveground decline of potato shoots and generally results in unusable tubers. This disease has led to multi-million dollar losses for growers in the central and western United States over the past decade and impacts the livelihood of potato farmers in Mexico and New Zealand. ZC is associated with ‘Candidatus Liberibacter solanacearum’, a fastidious alpha-proteobacterium that is transmitted by a phloem-feeding psyllid vector, Bactericera cockerelli Sulc. Research on this disease has been hampered by a lack of robust culture methods and paucity of genome sequence information for ‘Ca. L. solanacearum’. Here we present the sequence of the 1.26 Mbp metagenome of ‘Ca. L. solanacearum’, based on DNA isolated from potato psyllids. The coding inventory of the ‘Ca. L. solanacearum’ genome was analyzed and compared to related Rhizobiaceae to better understand ‘Ca. L. solanacearum’ physiology and identify potential targets to develop improved treatment strategies. This analysis revealed a number of unique transporters and pathways, all potentially contributing to ZC pathogenesis. Some of these factors may have been acquired through horizontal gene transfer. Taxonomically, ‘Ca. L. solanacearum’ is related to ‘Ca. L. asiaticus’, a suspected causative agent of citrus huanglongbing, yet many genome rearrangements and several gene gains/losses are evident when comparing these two Liberibacter. species. Relative to ‘Ca. L. asiaticus’, ‘Ca. L. solanacearum’ probably has reduced capacity for nucleic acid modification, increased amino acid and vitamin biosynthesis functionalities, and gained a high-affinity iron transport system characteristic of several pathogenic microbes

Comparison of Absolute Thresholds Derived from an Adaptive Forced-Choice Procedure and from Reaction Probabilities and Reaction Times in a Simple Reaction Time Paradigm

An understanding of the auditory system's operation requires knowledge of the mechanisms underlying thresholds. In this work we compare detection thresholds obtained with a three-interval-three-alternative forced-choice paradigm with reaction thresholds extracted from both reaction probabilities (RP) and reaction times (RT) in a simple RT paradigm from the same listeners under otherwise nearly identical experimental conditions. Detection thresholds, RP, and RT to auditory stimuli exhibited substantial variation from session to session. Most of the intersession variation in RP and RT could be accounted for by intersession variation in a listener's absolute sensitivity. The reaction thresholds extracted from RP were very similar, if not identical, to those extracted from RT. On the other hand, reaction thresholds were always higher than detection thresholds. The difference between the two thresholds can be considered as the additional amount of evidence required by each listener to react to a stimulus in an unforced design on top of that necessary for detection in the forced-choice design. This difference is inversely related to the listener's probability of producing false alarms. We found that RT, once corrected for some irreducible minimum RT, reflects the time at which a given stimulus reaches the listener's reaction threshold. This suggests that the relationships between simple RT and loudness (reported in the literature) are probably caused by a tight relationship between temporal summation at threshold and temporal summation of loudness

Multiple Single-Cell Genomes Provide Insight into Functions of Uncultured Deltaproteobacteria in the Human Oral Cavity

Campbell AG, Campbell JH, Schwientek P, et al. Multiple Single-Cell Genomes Provide Insight into Functions of Uncultured Deltaproteobacteria in the Human Oral Cavity. PLoS ONE. 2013;8(3): e59361.Despite a long history of investigation, many bacteria associated with the human oral cavity have yet to be cultured. Studies that correlate the presence or abundance of uncultured species with oral health or disease highlight the importance of these community members. Thus, we sequenced several single-cell genomic amplicons from Desulfobulbus and Desulfovibrio (class Deltaproteobacteria) to better understand their function within the human oral community and their association with periodontitis, as well as other systemic diseases. Genomic data from oral Desulfobulbus and Desulfovibrio species were compared to other available deltaproteobacterial genomes, including from a subset of host-associated species. While both groups share a large number of genes with other environmental Deltaproteobacteria genomes, they encode a wide array of unique genes that appear to function in survival in a host environment. Many of these genes are similar to virulence and host adaptation factors of known human pathogens, suggesting that the oral Deltaproteobacteria have the potential to play a role in the etiology of periodontal disease