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1. Beam theory predicts muscle deformation and vertebral curvature during feeding in rainbow trout ( Oncorhynchus mykiss )

   https://doi.org/10.1242/jeb.245788  

   Jimenez, Yordano E; Camp, Ariel L (October 2023, Journal of Experimental Biology)

   ABSTRACT Muscle shortening underpins most skeletal motion and ultimately animal performance. Most animal muscle generates its greatest mechanical output over a small, homogeneous range of shortening magnitudes and speeds. However, homogeneous muscle shortening is difficult to achieve for swimming fish because the whole body deforms like a bending beam: as the vertebral column flexes laterally, longitudinal muscle strain increases along a medio-lateral gradient. Similar dorsoventral strain gradients have been identified as the vertebral column flexes dorsally during feeding in at least one body location in one fish. If fish bodies also deform like beams during dorsoventral feeding motions, this would suggest the dorsal body (epaxial) muscles must homogenize both dorsoventral and mediolateral strain gradients. We tested this hypothesis by measuring curvature of the anterior vertebral column with XROMM and muscle shortening in 14 epaxial subregions with fluoromicrometry during feeding in rainbow trout (Oncorhynchus mykiss). We compared measured strain with the predicted strain based on beam theory's curvature–strain relationship. Trout flexed the vertebrae dorsally and laterally during feeding strikes, yet when flexion in both planes was included, the strain predicted by beam theory was strongly and significantly correlated with measured strain (P<0.01, R2=0.60). Beam theory accurately predicted strain (slope=1.15, compared with ideal slope=1) across most muscle subregions, confirming that epaxial muscles experience dorsoventral and mediolateral gradients in longitudinal strain. Establishing this deformation–curvature relationship is a crucial step to understanding how these muscles overcome orthogonal strain gradients to produce powerful feeding and swimming behaviours. 

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2. Draft Genome Sequence of the Plant Growth-Promoting Sphingobium sp. Strain AEW4, Isolated from the Rhizosphere of the Beachgrass Ammophila breviligulata

   https://doi.org/10.1128/genomeA.00410-18  

   Wanees, Abanoub E.; Zaslow, Shari J.; Potter, Savannah J.; Hsieh, Brandon P.; Boss, Brianna L.; Izquierdo, Javier A. (May 2018, Genome Announcements)

   ABSTRACT Sphingobium sp. strain AEW4 is a novel isolate from rhizosphere soil attached to the root of the American beachgrass Ammophila breviligulata . The genomic sequence consisted of 4,678,518 bp and 4,428 protein-coding sequences. Here we report the draft genome sequence of this strain and some initial insights on its plant growth-promoting capabilities. 

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3. Draft genome sequences of Arthrobacter sp. AZCC_0090 and Mycobacterium sp. AZCC_0083 isolated from oligotrophic subsurface forest soil in the Santa Catalina mountains of Southern Arizona

   https://doi.org/10.1128/mra.01089-23  

   Kridler, Melanie R; Viney, Isabella A; Custer, Joy M; Schlottman, Bradley; Bartelme, Ryan; Carini, Paul (March 2024, Microbiology Resource Announcements)

   Becket, Elinne (Ed.)

   ABSTRACT Here, we present the genomes of two soil actinobacteria:Arthrobactersp. strain AZCC_0090 andMycobacteriumsp. strain AZCC_0083, isolated from oligotrophic subsurface soils in Southern Arizona, USA. 

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4. Understanding muscle function during perturbed in vivo locomotion using a muscle avatar approach

   https://doi.org/10.1242/jeb.244721  

   Rice, Nicole; Bemis, Caitlin M.; Daley, Monica A.; Nishikawa, Kiisa (July 2023, Journal of Experimental Biology)

   ABSTRACT The work loop technique has provided key insights into in vivo muscle work and power during steady locomotion. However, for many animals and muscles, ex vivo experiments are not feasible. In addition, purely sinusoidal strain trajectories lack variations in strain rate that result from variable loading during locomotion. Therefore, it is useful to develop an ‘avatar’ approach in which in vivo strain and activation patterns from one muscle are replicated in ex vivo experiments on a readily available muscle from an established animal model. In the present study, we used mouse extensor digitorum longus (EDL) muscles in ex vivo experiments to investigate in vivo mechanics of the guinea fowl lateral gastrocnemius (LG) muscle during unsteady running on a treadmill with obstacle perturbations. In vivo strain trajectories from strides down from obstacle to treadmill, up from treadmill to obstacle, strides with no obstacle and sinusoidal strain trajectories at the same amplitude and frequency were used as inputs in work loop experiments. As expected, EDL forces produced with in vivo strain trajectories were more similar to in vivo LG forces (R2=0.58–0.94) than were forces produced with the sinusoidal trajectory (average R2=0.045). Given the same stimulation, in vivo strain trajectories produced work loops that showed a shift in function from more positive work during strides up from treadmill to obstacle to less positive work in strides down from obstacle to treadmill. Stimulation, strain trajectory and their interaction had significant effects on all work loop variables, with the interaction having the largest effect on peak force and work per cycle. These results support the theory that muscle is an active material whose viscoelastic properties are tuned by activation, and which produces forces in response to deformations of length associated with time-varying loads. 

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5. Average nucleotide identity-based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome

   https://doi.org/10.1128/msystems.00143-24  

   Raghuram, Vishnu; Petit, Robert A; Karol, Zach; Mehta, Rohan; Weissman, Daniel B; Read, Timothy D (July 2024, mSystems)

   Hayer, Juliette (Ed.)

   Staphylococcus aureus causes both hospital- and community-acquired infections in humans worldwide. Due to the high incidence of infection, S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding resource to understand variation at the bacterial subspecies level. We processed and downsampled 83,383 public S. aureus Illumina whole-genome shotgun sequences and 1,263 complete genomes to produce 7,954 representative substrains. Pairwise comparison of average nucleotide identity revealed a natural boundary of 99.5% that could be used to define 145 distinct strains within the species. We found that intermediate frequency genes in the pangenome (present in 10%–95% of genomes) could be divided into those closely linked to strain background (“strain-concentrated”) and those highly variable within strains (“strain-diffuse”). Non-core genes had different patterns of chromosome location. Notably, strain-diffuse genes were associated with prophages; strain-concentrated genes were associated with the vSaβ genome island and rare genes (<10% frequency) concentrated near the origin of replication. Antibiotic resistance genes were enriched in the strain-diffuse class, while virulence genes were distributed between strain-diffuse, strain-concentrated, core, and rare classes. This study shows how different patterns of gene movement help create strains as distinct subspecies entities and provide insight into the diverse histories of important S. aureus functions. 

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