NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats

Whole-genome sequencing (WGS) of bacterial isolates has become standard practice in many laboratories. Applications for WGS analysis include phylogeography and molecular epidemiology, using single nucleotide polymorphisms (SNPs) as the unit of evolution. NASP was developed as a reproducible method that scales well with the hundreds to thousands of WGS data typically used in comparative genomics applications. In this study, we demonstrate how NASP compares with other tools in the analysis of two real bacterial genomics datasets and one simulated dataset. Our results demonstrate that NASP produces similar, and often better, results in comparison with other pipelines, but is much more flexible in terms of data input types, job management systems, diversity of supported tools and output formats. We also demonstrate differences in results based on the choice of the reference genome and choice of inferring phylogenies from concatenated SNPs or alignments including monomorphic positions. NASP represents a source-available, version-controlled, unit-tested method and can be obtained from tgennorth.github.io/NASP

Stability of bulk Ba2YCu3O(7-x) in a variety of environments

Small bars of ceramic Ba2YCu3O(7-x) were fabricated and subjected to environments similar to those that might be encountered during some NASA missions. These conditions include ambient conditions, high humidity, vacuum, and high fluences of electrons and protrons. The normal state resistivity or critical current density (J sub c) were monitored during these tests to assess the stability of the material. When normal state resistivity is used as a criterion, the ambient stability of these samples was relatively good, exhibiting only a 2 percent degradation over a 3 month period. The humidity stability was shown to be very poor, and to be a steep function of temperature. Samples stored at 50 C for 40 min increased in normal state resistivity by four orders of magnitude. Kinetic analysis indicates that the degradation reaction is second order with water vapor concentration. It is suspected that humidity degradation also accounts for the ambient instability. The samples were stable to vacuum over a period of at least 3 months. Degradation of J sub c in a 1 MeV electron fluence of 9.7 x 10 to the 14th e(-)/sq cm was determined to be no more than about 2 percent. Degradation of J sub c in a 8.7 x 10 to the 14th p(+)/sq cm of 42 MeV protons was found to be grain size dependent. Samples with smaller grain size and initial J sub c of about 240 A/sq cm showed no degradation. while that with larger grain size and an initial J sub c of about 30 A/sq cm degraded to 37 percent of its original value

Converting Tall Spindle Apple Trees to Narrow Walls with Summer and Dormant Hedging Plus Root Pruning

Recently, some commercial apple growers have been adopting hedging as an alternative or supplement to hand-pruning. With increasing labor costs across the United States, alternatives to hand-pruning and current training systems are being considered. One management strategy involves transitioning tall spindle trees to a narrow tree wall and simplifying labor-intensive activities of apple production, such as pruning, harvesting, and fruit thinning. The objective is to form the orchard system into a “fruiting wall” that makes fruit more visible and accessible, thus facilitating harvesting. Four management practices (tall spindle; narrow tree wall with manual pruning; narrow tree wall with dormant and summer hedging; and narrow tree wall with dormant hedging, summer hedging, and root pruning) were used to convert 12-year-old ‘Brak Fuji’ apple trees from the tall spindle training system to a narrow tree wall. Photosynthetically active radiation (PAR) and ultraviolet light levels within the canopies were improved by summer hedging, but they were still low for all treatments. Light within the canopy was improved most when root pruning was included. Specific leaf weight was not significantly impacted by hedging or root pruning. Detailed spur sampling showed that treatments had no effect on vegetative or reproductive growth on 2- to 3-year-old wood. Although dormant plus summer hedging alone did not affect shoot length, the combination of hedging and root pruning caused a significant reduction in terminal shoot length. Red fruit color was only improved with dormant hedging plus summer hedging plus root pruning. Compared with dormant plus summer hedging, dormant plus summer hedging plus root pruning improved fruit set and yield, but it reduced fruit size. Without root pruning, hedging had little effect on light, specific leaf weight, flower initiation, fruit set, and fruit quality. Conversion to narrow tree walls by manual pruning resulted in more poorly colored fruit and less highly colored fruit compared with maintaining the trees as tall spindles with manual pruning

A telecom-wavelength quantum repeater node based on a trapped-ion processor

A quantum repeater node is presented based on trapped ions that act as single photon emitters, quantum memories and an elementary quantum processor. The node's ability to establish entanglement across two 25 km-long optical fibers independently, then to swap that entanglement efficiently to extend it over both fibers, is demonstrated. The resultant entanglement is established between telecom-wavelength photons at either end of the 50 km channel. The system improvements to allow for repeater-node chains to establish stored entanglement over 800 km at Hertz rates are calculated, revealing a near-term path to distributed networks of entangled sensors, atomic clocks and quantum processors.Comment: 5 pages and 4 figures main text plus supplementar

Molecular typing of mycobacterium tuberculosis by using nine novel variable-number tandem repeats across the Beijing family and low-copy-number IS6110 isolates

Molecular epidemiological tools for genotyping clinical isolates of Mycobacterium tuberculosis have been developed and used to help track and contain transmission of tuberculosis. We identified 87 short sequence repeat loci within the genome of the M. tuberculosis H37Rv strain. Nine tandem repeats were found to be variable (variable-number tandem repeats (VNTRs)) in a set of 91 isolates. Fifty-seven of the isolates had only four IS6110 bands. The other 34 isolates were members of the Beijing strain family. The number of alleles of each these nine VNTRs was determined by examining each isolate. Six of the loci (Mtb-v1, -v4, -v10, -v15, -v18, and -v20) were able to differentiate the Beijing spoligotype identical isolates into seven distinct genotypes. Five of the loci (Mtb-v3, -v5, -v6, -v10, and -v15) were informative in discriminating the four-band IS6110 restriction fragment length polymorphism isolates from each other. The Nei's diversity values of each marker ranged from 0.02 to 0.59, with the number of alleles ranging from two to eight across the entire strain set. These nine loci provide a useful, discriminatory extension of VNTR typing methods for application to molecular epidemiologic studies of M. tuberculosis

Evolution of a pathogen: a comparative genomics analysis identifies a genetic pathway to pathogenesis in acinetobacter.

Acinetobacter baumannii is an emergent and global nosocomial pathogen. In addition to A. baumannii, other Acinetobacter species, especially those in the Acinetobacter calcoaceticus-baumannii (Acb) complex, have also been associated with serious human infection. Although mechanisms of attachment, persistence on abiotic surfaces, and pathogenesis in A. baumannii have been identified, the genetic mechanisms that explain the emergence of A. baumannii as the most widespread and virulent Acinetobacter species are not fully understood. Recent whole genome sequencing has provided insight into the phylogenetic structure of the genus Acinetobacter. However, a global comparison of genomic features between Acinetobacter spp. has not been described in the literature. In this study, 136 Acinetobacter genomes, including 67 sequenced in this study, were compared to identify the acquisition and loss of genes in the expansion of the Acinetobacter genus. A whole genome phylogeny confirmed that A. baumannii is a monophyletic clade and that the larger Acb complex is also a well-supported monophyletic group. The whole genome phylogeny provided the framework for a global genomic comparison based on a blast score ratio (BSR) analysis. The BSR analysis demonstrated that specific genes have been both lost and acquired in the evolution of A. baumannii. In addition, several genes associated with A. baumannii pathogenesis were found to be more conserved in the Acb complex, and especially in A. baumannii, than in other Acinetobacter genomes; until recently, a global analysis of the distribution and conservation of virulence factors across the genus was not possible. The results demonstrate that the acquisition of specific virulence factors has likely contributed to the widespread persistence and virulence of A. baumannii. The identification of novel features associated with transcriptional regulation and acquired by clades in the Acb complex presents targets for better understanding the evolution of pathogenesis and virulence in the expansion of the genus

Local Population Structure and Patterns of Western Hemisphere Dispersal for Coccidioides spp., the Fungal Cause of Valley Fever.

UnlabelledCoccidioidomycosis (or valley fever) is a fungal disease with high morbidity and mortality that affects tens of thousands of people each year. This infection is caused by two sibling species, Coccidioides immitis and C. posadasii, which are endemic to specific arid locales throughout the Western Hemisphere, particularly the desert southwest of the United States. Recent epidemiological and population genetic data suggest that the geographic range of coccidioidomycosis is expanding, as new endemic clusters have been identified in the state of Washington, well outside the established endemic range. The genetic mechanisms and epidemiological consequences of this expansion are unknown and require better understanding of the population structure and evolutionary history of these pathogens. Here we performed multiple phylogenetic inference and population genomics analyses of 68 new and 18 previously published genomes. The results provide evidence of substantial population structure in C. posadasii and demonstrate the presence of distinct geographic clades in central and southern Arizona as well as dispersed populations in Texas, Mexico, South America, and Central America. Although a smaller number of C. immitis strains were included in the analyses, some evidence of phylogeographic structure was also detected in this species, which has been historically limited to California and Baja, Mexico. Bayesian analyses indicated that C. posadasii is the more ancient of the two species and that Arizona contains the most diverse subpopulations. We propose a southern Arizona-northern Mexico origin for C. posadasii and describe a pathway for dispersal and distribution out of this region.ImportanceCoccidioidomycosis, or valley fever, is caused by the pathogenic fungi Coccidioides posadasii and C. immitis The fungal species and disease are primarily found in the American desert southwest, with spotted distribution throughout the Western Hemisphere. Initial molecular studies suggested a likely anthropogenic movement of C. posadasii from North America to South America. Here we comparatively analyze eighty-six genomes of the two Coccidioides species and establish local and species-wide population structures to not only clarify the earlier dispersal hypothesis but also provide evidence of likely ancestral populations and patterns of dispersal for the known subpopulations of C. posadasii

Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus

Staphylococcus aureus is an important clinical pathogen worldwide and understanding this organism\u27s phylogeny and, in particular, the role of recombination, is important both to understand the overall spread of virulent lineages and to characterize outbreaks. To further elucidate the phylogeny of S. aureus, 35 diverse strains were sequenced using whole genome sequencing. In addition, 29 publicly available whole genome sequences were included to create a single nucleotide polymorphism (SNP)-based phylogenetic tree encompassing 11 distinct lineages. All strains of a particular sequence type fell into the same clade with clear groupings of the major clonal complexes of CC8, CC5, CC30, CC45 and CC1. Using a novel analysis method, we plotted the homoplasy density and SNP density across the whole genome and found evidence of recombination throughout the entire chromosome, but when we examined individual clonal lineages we found very little recombination. However, when we analyzed three branches of multiple lineages, we saw intermediate and differing levels of recombination between them. These data demonstrate that in S. aureus, recombination occurs across major lineages that subsequently expand in a clonal manner. Estimated mutation rates for the CC8 and CC5 lineages were different from each other. While the CC8 lineage rate was similar to previous studies, the CC5 lineage was 100-fold greater. Fifty known virulence genes were screened in all genomes in silico to determine their distribution across major clades. Thirty-three genes were present variably across clades, most of which were not constrained by ancestry, indicating horizontal gene transfer or gene loss

Resilience and Resistance of Sagebrush Ecosystems: Implications for State and Transition Models and Management Treatments

In sagebrush ecosystems invasion of annual exotics and expansion of piñon (Pinus monophylla Torr. and Frem.) and juniper (Juniperus occidentalis Hook., J. osteosperma [Torr.] Little) are altering fire regimes and resulting in large-scale ecosystem transformations. Management treatments aim to increase resilience to disturbance and enhance resistance to invasive species by reducing woody fuels and increasing native perennial herbaceous species. We used Sagebrush Steppe Treatment Evaluation Project data to test predictions on effects of fire vs. mechanical treatments on resilience and resistance for three site types exhibiting cheatgrass (Bromus tectorum L.) invasion and/or piñon and juniper expansion: 1) warm and dry Wyoming big sagebrush (WY shrub); 2) warm and moist Wyoming big sagebrush (WY PJ); and 3) cool and moist mountain big sagebrush (Mtn PJ). Warm and dry (mesic/aridic) WY shrub sites had lower resilience to fire (less shrub recruitment and native perennial herbaceous response) than cooler and moister (frigid/xeric) WY PJ and Mtn PJ sites. Warm (mesic) WY Shrub and WY PJ sites had lower resistance to annual exotics than cool (frigid to cool frigid) Mtn PJ sites. In WY shrub, fire and sagebrush mowing had similar effects on shrub cover and, thus, on perennial native herbaceous and exotic cover. In WY PJ and Mtn PJ, effects were greater for fire than cut-and-leave treatments and with high tree cover in general because most woody vegetation was removed increasing resources for other functional groups. In WY shrub, about 20% pretreatment perennial native herb cover was necessary to prevent increases in exotics after treatment. Cooler and moister WY PJ and especially Mtn PJ were more resistant to annual exotics, but perennial native herb cover was still required for site recovery. We use our results to develop state and transition models that illustrate how resilience and resistance influence vegetation dynamics and management options

‘Bell’ Pear

‘Bell’ (Pyrus communis L.) is an early-season pear variety that combines fire blight resistance with exceptional flavor and high productivity. Fire blight, caused by the bacterial pathogen Erwinia amylovora, is a devastating disease for pear growers in the mid-Atlantic region and other pear production areas prone to hot and humid climates. ‘Bell’ has exhibited strong resistance to natural infection by Erwinia compared with the susceptible, industry-standard ‘Bartlett’. ‘Bell’ also exhibits a “balanced” sugar and acidity content that is desirable and preferred by pear consumers. The US Department of Agriculture and Pennsylvania State University released ‘Bell’ in 2022 as a fresh-market pear for commercial, direct-to-market, and home production