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Sinorhizobium meliloti forms a robust N₂-fixing root-nodule symbiosis with Medicago sativa. We are interested in identifying the minimal symbiotic genome of the model strain S. meliloti Rm1021. This gene set refers to the minimal genetic determinants required to form a robust N₂-fixing symbiosis. Many symbiotic genes are located on the 1,354 kb pSymA megaplasmid of S. meliloti Rm1021. We recently constructed a minimalized pSymA, minSymA2.1, that lacked over 90% of the pSymA genes. Relative to the wild-type, minSymA2.1 showed a reduction in M. sativa shoot biomass production and nodule size with an increase in total nodule number. Here we show that the addition of either the stachydrine (stc) or trigonelline (trc) catabolism genes from pSymA to minSymA2.1 restores nodule size and total nodule number to levels indistinguishable from the wild-type but does not restore reduced shoot biomass production. In the context of the complete Rm1021 genome, removing the stc genes reduced nodule size and increased total nodule number while removal of the trc genes alone had no apparent effect. Together, these observations implicate stachydrine catabolism as an important determinant of root nodule symbiosis between S. meliloti and M. sativa while trigonelline catabolism seems to contribute in a more conditional manner, in the context of the minimized genome. These findings highlight the minimal symbiotic genome as a tool for investigating the impact individual genetic determinants have in conferring an optimal symbiosis. Factors whose impact, in the context of a complete genome, may be hidden or dampened due to redundancies. 

Abstract Biodiversity has experienced tremendous shifts in community, species, and genetic diversity during the Anthropocene. Understanding temporal diversity shifts is especially critical in biodiversity hotspots, i.e., regions that are exceptionally biodiverse and threatened. Here, we use museomics and temporal genomics approaches to quantify temporal shifts in genomic diversity in an assemblage of eight generalist highland bird species from the Ethiopian Highlands (part of the Eastern Afromontane Biodiversity Hotspot). With genomic data from contemporary and historical samples, we demonstrate an assemblage-wide trend of increased genomic diversity through time, potentially due to improved habitat connectivity within highland regions. Genomic diversity shifts in these generalist species contrast with general trends of genomic diversity declines in specialist or imperiled species. In addition to genetic diversity shifts, we found an assemblage-wide trend of decreased realized mutational load, indicative of overall trends for potentially deleterious variation to be masked or selectively purged. Across this avian assemblage, we also show that shifts in population genomic structure are idiosyncratic, with species-specific trends. These results are in contrast with other charismatic and imperiled African taxa that have largely shown strong increases in population genetic structure over the recent past. This study highlights that not all taxa respond the same to environmental change, and generalists, in some cases, may even respond positively. Future comparative conservation genomics assessments on species groups or assemblages with varied natural history characteristics would help us better understand how diverse taxa respond to anthropogenic landscape changes. 

This study addresses the challenges of efficient, large-scale production of flexible transparent conducting electrodes (TCEs). We fabricate TCEs on polyethylene terephthalate (PET) substrates using a high-speed roll-to-roll (R2R) compatible method that combines gravure printing and photonic curing. The hybrid TCEs consist of Ag metal bus lines (Ag MBLs) coated with silver nanowires (AgNWs) and indium zinc oxide (IZO) layers. All materials are solutions deposited at speeds exceeding 10 m/min using gravure printing. We conduct a systematic study to optimize coating parameters and tune solvent composition to achieve a uniform AgNW network. The entire stack undergoes photonic curing, a low-energy annealing method that can be completed at high speeds and will not damage the plastic substrates. The resulting hybrid TCEs exhibit a transmittance of 92% averaged from 400 nm to 1100 nm and a sheet resistance of 11 Ω/sq. Mechanical durability is tested by bending the hybrid TCEs to a strain of 1% for 2000 cycles. The results show a minimal increase (<5%) in resistance. The high-throughput potential is established by showing that each hybrid TCE fabrication step can be completed at 30 m/min. We further fabricate methylammonium lead iodide solar cells to demonstrate the practical use of these TCEs, achieving an average power conversion efficiency (PCE) of 13%. The high-performance hybrid TCEs produced using R2R-compatible processes show potential as a viable choice for replacing vacuum-deposited indium tin oxide films on PET. 

Abstract We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers. 

Abstract MotivationJBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and inspecting genome annotations. Historically they have been deployed at the end of bioinformatics pipelines, typically decoupled from the analysis itself. However, emerging technologies such as Jupyter notebooks enable a more rapid iterative cycle of development, analysis and visualization. ResultsWe have developed a package that provides a Python interface to JBrowse 2’s suite of embeddable components, including the primary Linear Genome View. The package enables users to quickly set up, launch and customize JBrowse views from Jupyter notebooks. In addition, users can share their data via Google’s Colab notebooks, providing reproducible interactive views. Availability and implementationJBrowse Jupyter is released under the Apache License and is available for download on PyPI. Source code and demos are available on GitHub at https://github.com/GMOD/jbrowse-jupyter. 

Abstract The support structures required in many forms of additive manufacturing are often seen as waste that is tolerated as necessary. In metal additive processes, cost is frequently reduced by minimizing the amount of support structures needed to produce a part so that in turn, material use is decreased. However, there still exists the challenge of generating parts that are not deformed by the stresses created in the process. In this case study, support structures were leveraged to address deformation. A part was printed via direct metal laser melting with supports with a high grouping density in areas of high anticipated deformation in order to stiffen the part to prevent deformation. Then, they were printed again with a low grouping density to allow the part to relax and reduce stress. Combinations of support strategy and leaving supports on during post processing were used to investigate the effects of keeping or removing the supports in post-print operations such as surface treatment. The two optimized support strategies saw a lower deformation than the baseline approach to supports, and the releasing strategy was closest to the reference solid model with a 26% reduction in average deformation. The results suggest that the support structures in additively manufactured parts have a different impact on the part than the original intent of the supports to simply alleviate a process requirement. The support structures should be used to impact the final part geometry.