Magnetosome Gene Duplication as an Important Driver in the Evolution of Magnetotaxis in the Alphaproteobacteria

The evolution of microbial magnetoreception (or magnetotaxis) is of great interest in the fields of microbiology, evolutionary biology, biophysics, geomicrobiology, and geochemistry. Current genomic data from magnetotactic bacteria (MTB), the only prokaryotes known to be capable of sensing the Earth’s geomagnetic field, suggests an ancient origin of magnetotaxis in the domain Bacteria. Vertical inheritance, followed by multiple independent magnetosome gene cluster loss, is considered to be one of the major forces that drove the evolution of magnetotaxis at or above the class or phylum level, although the evolutionary trajectories at lower taxonomic ranks (e.g., within the class level) remain largely unstudied. Here we report the isolation, cultivation, and sequencing of a novel magnetotactic spirillum belonging to the genus Terasakiella (Terasakiella sp. strain SH-1) within the class Alphaproteobacteria. The complete genome sequence of Terasakiella sp. strain SH-1 revealed an unexpected duplication event of magnetosome genes within the mamAB operon, a group of genes essential for magnetosome biomineralization and magnetotaxis. Intriguingly, further comparative genomic analysis suggests that the duplication of mamAB genes is a common feature in the genomes of alphaproteobacterial MTB. Taken together, with the additional finding that gene duplication appears to have also occurred in some magnetotactic members of the Deltaproteobacteria, our results indicate that gene duplication plays an important role in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria

Effective Data Sampling Strategies and Boundary Condition Constraints of Physics-Informed Neural Networks for Identifying Material Properties in Solid Mechanics

Material identification is critical for understanding the relationship between mechanical properties and the associated mechanical functions. However, material identification is a challenging task, especially when the characteristic of the material is highly nonlinear in nature, as is common in biological tissue. In this work, we identify unknown material properties in continuum solid mechanics via physics-informed neural networks (PINNs). To improve the accuracy and efficiency of PINNs, we developed efficient strategies to nonuniformly sample observational data. We also investigated different approaches to enforce Dirichlet boundary conditions as soft or hard constraints. Finally, we apply the proposed methods to a diverse set of time-dependent and time-independent solid mechanic examples that span linear elastic and hyperelastic material space. The estimated material parameters achieve relative errors of less than 1%. As such, this work is relevant to diverse applications, including optimizing structural integrity and developing novel materials

Nanodisc-cell fusion: Control of fusion pore nucleation and lifetimes by SNARE protein transmembrane domains

The initial, nanometer-sized connection between the plasma membrane and a hormone- or neurotransmitter-filled vesicle-the fusion pore- can flicker open and closed repeatedly before dilating or resealing irreversibly. Pore dynamics determine release and vesicle recycling kinetics, but pore properties are poorly known because biochemically defined single-pore assays are lacking. We isolated single flickering pores connecting v-SNARE-reconstituted nanodiscs to cells ectopically expressing cognate, "flipped" t-SNAREs. Conductance through single, voltage-clamped fusion pores directly reported sub-millisecond pore dynamics. Pore currents fluctuated, transiently returned to baseline multiple times, and disappeared ∼6 s after initial opening, as if the fusion pore fluctuated in size, flickered, and resealed. We found that interactions between v- and t-SNARE transmembrane domains (TMDs) promote, but are not essential for pore nucleation. Surprisingly, TMD modifications designed to disrupt v- and t-SNARE TMD zippering prolonged pore lifetimes dramatically. We propose that the post-fusion geometry of the proteins contribute to pore stability.Fil: Wu, Zhenyong. University of Yale; Estados Unidos. University of Yale. School of Medicine; Estados UnidosFil: Auclair, Sarah M.. University of Yale. School of Medicine; Estados Unidos. University of Yale; Estados UnidosFil: Bello, Oscar Daniel. University of Yale. School of Medicine; Estados Unidos. University of Yale; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Vennekate, Wensi. University of Yale. School of Medicine; Estados Unidos. University of Yale; Estados UnidosFil: Dudzinski, Natasha R.. University of Yale; Estados Unidos. University of Yale. School of Medicine; Estados UnidosFil: Krishnakumar, Shyam S.. University of Yale. School of Medicine; Estados Unidos. University of Yale; Estados UnidosFil: Karatekin, Erdem. University of Yale; Estados Unidos. University of Yale. School of Medicine; Estados Unidos. Universite Paris Descartes; Francia. Centre National de la Recherche Scientifique; Franci

Dilation of fusion pores by crowding of SNARE proteins

Hormones and neurotransmitters are released through fluctuating exocytotic fusion pores that can flicker open and shut multiple times. Cargo release and vesicle recycling depend on the fate of the pore, which may reseal or dilate irreversibly. Pore nucleation requires zippering between vesicle-associated v-SNAREs and target membrane t-SNAREs, but the mechanisms governing the subsequent pore dilation are not understood. Here, we probed the dilation of single fusion pores using v-SNARE-reconstituted ~23-nm-diameter discoidal nanolipoprotein particles (vNLPs) as fusion partners with cells ectopically expressing cognate, ’flipped’ t-SNAREs. Pore nucleation required a minimum of two v-SNAREs per NLP face, and further increases in v-SNARE copy numbers did not affect nucleation rate. By contrast, the probability of pore dilation increased with increasing v-SNARE copies and was far from saturating at 15 v-SNARE copies per face, the NLP capacity. Our experimental and computational results suggest that SNARE availability may be pivotal in determining whether neurotransmitters or hormones are released through a transient (’kiss and run’) or an irreversibly dilating pore (full fusion).Fil: Wu, Zhenyong. University of Yale; Estados Unidos. University of Yale. School of Medicine; Estados UnidosFil: Bello, Oscar Daniel. University of Yale. School of Medicine; Estados Unidos. University of Yale; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Thiyagarajan, Sathish. Columbia University; Estados UnidosFil: Auclair, Sarah Marie. University of Yale. School of Medicine; Estados Unidos. University of Yale; Estados UnidosFil: Vennekate, Wensi. University of Yale; Estados Unidos. University of Yale. School of Medicine; Estados UnidosFil: Krishnakumar, Shyam S. University of Yale; Estados Unidos. University of Yale. School of Medicine; Estados UnidosFil: O'Shaughnessy, Ben. Columbia University; Estados UnidosFil: Karatekin, Erdem. University of Yale; Estados Unidos. Universite Paris Descartes; Francia. University of Yale. School of Medicine; Estados Unido

Identification of Cassava MicroRNAs under Abiotic Stress

Edwardsiella ictaluri (E. ictaluri) is one of the main bacterial pathogens in catfish which has caused serious economic loss to yellow catfish (Pelteobagrus fulvidraco) in China. In our previous work, we demonstrated that CypA was up-regulated at the early stage of E. ictaluri infection in yellow catfish and displayed strong chemotactic activity for leukocytes in vitro. However, the effect of CypA on E. ictaluri is unknown in vivo. Therefore, two homozygous transgenic zebrafish lines expressing yellow catfish CypA (TG-CypA-1 and TG-CypA-2) were generated. After challenged with E. ictaluri at a dose of 1.0 x 10(4) CFU per adult fish, both two transgenic lines exhibited a higher resistance to bacterial infection than the wildtype zebrafish. Herein, CypA gene in E. ictalurichallenged yellow catfish was screened for presence of polymorphisms by sequencing and six single nucleotide polymorphisms (SNPs) were identified. SNP association analysis revealed that 528T/C SNP in the first intron was significantly different in disease-susceptible and-resistant groups, which was confirmed in two independent populations of yellow catfish. Moreover, the relative expression of CypA in the resistant group (CC genotype in 528T/C SNP) was significantly higher than that in the susceptible group (TT genotype in 528T/C SNP) in different immune organs of yellow catfish including spleen, head kidney, body kidney and liver. Our results reveal the potential function of CypA in host defense to bacterial infection and suggest the SNP marker in CypA gene associated with the resistance to E. ictaluri may facilitate the selective breeding of disease-resistant yellow catfish in the future

The effects of leaflet material properties on the simulated function of regurgitant mitral valves

Advances in three-dimensional imaging provide the ability to construct and analyze finite element (FE) models to evaluate the biomechanical behavior and function of atrioventricular valves. However, while obtaining patient-specific valve geometry is now possible, non-invasive measurement of patient-specific leaflet material properties remains nearly impossible. Both valve geometry and tissue properties play a significant role in governing valve dynamics, leading to the central question of whether clinically relevant insights can be attained from FE analysis of atrioventricular valves without precise knowledge of tissue properties. As such we investigated 1) the influence of tissue extensibility and 2) the effects of constitutive model parameters and leaflet thickness on simulated valve function and mechanics. We compared metrics of valve function (e.g., leaflet coaptation and regurgitant orifice area) and mechanics (e.g., stress and strain) across one normal and three regurgitant mitral valve (MV) models with common mechanisms of regurgitation (annular dilation, leaflet prolapse, leaflet tethering) of both moderate and severe degree. We developed a novel fully-automated approach to accurately quantify regurgitant orifice areas of complex valve geometries. We found that the relative ordering of the mechanical and functional metrics was maintained across a group of valves using material properties up to 15% softer than the representative adult mitral constitutive model. Our findings suggest that FE simulations can be used to qualitatively compare how differences and alterations in valve structure affect relative atrioventricular valve function even in populations where material properties are not precisely known

Supplementing Vitamin E to the Ration of Beef Cattle Increased the Utilization Efficiency of Dietary Nitrogen

The objectives of the trial were to investigate the effects of supplementing vitamin E (VE) on nutrient digestion, nitrogen (N) retention and plasma parameters of beef cattle in feedlot. Four growing Simmental bulls, fed with a total mixed ration composed of corn silage and concentrate mixture as basal ration, were used as the experimental animals. Four levels of VE product, i.e. 0, 150, 300, 600 mg/head/d (equivalent to 0, 75, 150, 300 IU VE/head/d), were supplemented to the basal ration (VE content 38 IU/kg dry matter) in a 4×4 Latin square design as experimental treatments I, II, III and IV, respectively. Each experimental period lasted 15 days, of which the first 12 days were for pretreatment and the last 3 days for sampling. The results showed that supplementing VE did not affect the nutrient digestibility (p>0.05) whereas decreased the urinary N excretion (p0.05). It was concluded that supplementing VE up to 300 IU/head/d did not affect the nutrient digestibility whereas supplementing VE at 150 or 300 IU/head/d increased the N retention and the plasma concentrations of VE and TG (p<0.05) of beef cattle

ARNOLD: A Benchmark for Language-Grounded Task Learning With Continuous States in Realistic 3D Scenes

Understanding the continuous states of objects is essential for task learning and planning in the real world. However, most existing task learning benchmarks assume discrete(e.g., binary) object goal states, which poses challenges for the learning of complex tasks and transferring learned policy from simulated environments to the real world. Furthermore, state discretization limits a robot's ability to follow human instructions based on the grounding of actions and states. To tackle these challenges, we present ARNOLD, a benchmark that evaluates language-grounded task learning with continuous states in realistic 3D scenes. ARNOLD is comprised of 8 language-conditioned tasks that involve understanding object states and learning policies for continuous goals. To promote language-instructed learning, we provide expert demonstrations with template-generated language descriptions. We assess task performance by utilizing the latest language-conditioned policy learning models. Our results indicate that current models for language-conditioned manipulations continue to experience significant challenges in novel goal-state generalizations, scene generalizations, and object generalizations. These findings highlight the need to develop new algorithms that address this gap and underscore the potential for further research in this area. See our project page at: https://arnold-benchmark.github.ioComment: The first two authors contributed equally; 20 pages; 17 figures; project availalbe: https://arnold-benchmark.github.io

NOIR: Neural Signal Operated Intelligent Robots for Everyday Activities

We present Neural Signal Operated Intelligent Robots (NOIR), a general-purpose, intelligent brain-robot interface system that enables humans to command robots to perform everyday activities through brain signals. Through this interface, humans communicate their intended objects of interest and actions to the robots using electroencephalography (EEG). Our novel system demonstrates success in an expansive array of 20 challenging, everyday household activities, including cooking, cleaning, personal care, and entertainment. The effectiveness of the system is improved by its synergistic integration of robot learning algorithms, allowing for NOIR to adapt to individual users and predict their intentions. Our work enhances the way humans interact with robots, replacing traditional channels of interaction with direct, neural communication. Project website: https://noir-corl.github.io/