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Pneumatic artificial muscles (PAMs), also known as McKibben artificial muscles, are used in a variety of applications owing to its many positive features, such as simple and lightweight structure and high force to weight ratio. Sensing is essential to precisely control PAMs. Previous studies have proposed various embeddings of PAMs with sensors. However, these often require sophisticated fabrication processes and dedicated setups, which can cause production to be laborious and costly. This letter presents a method to create sensorized PAMs using a dielectric elastomer sensor (DES). In these self-sensing actuators, which we call PAM-DES, the sensor is consisting of a thin, highly compliant dielectric and conductive membranes, which allow the length of the actuator to be detected by reading the capacitance. The sensor directly wraps around the inner tube of the actuator. Therefore, the entire structure remains simple. This feature allows the fabrication of actuators to be relatively effortless and inexpensive. As a proof of concept, a PAM-DES with a length of 100 mm and diameter of 9 mm is fabricated. An analytical model is constructed to design and predict the sensor response. Characterization results show that the sensor properly detects actuator deformation, and low hysteresis and high robustness are observed. The prediction model shows good agreement with the experimental data. Furthermore, the presence of the sensor has almost no influence on the actuator performance. These results validate the concept and suggest that PAM-DES is a highly effective strategy to sensorize actuators of the same type.

The mildly thermophilic purple phototrophic bacterium Allochromatium tepidum provides a unique model for investigating various intermediate phenotypes observed between those of thermophilic and mesophilic counterparts. The core light-harvesting (LH1) complex from A. tepidum exhibits an absorption maximum at 890 nm and mildly enhanced thermostability, both of which are Ca

The light-harvesting-reaction center (LH1-RC) core complex of purple photosynthetic bacterium Rhodobacter (Rba.) sphaeroides is characterized by the presence of both a dimeric form and a monomeric form. Following structure determination of the monomeric LH1-RC including its previously unrecognized component designated protein-U (Nat. Commun. 12, 6300, 2021), here we present cryo-EM structures of the dimeric LH1-RC from native Rba. sphaeroides IL106 at 2.75 Å resolution and from an LH1-RC monomer lacking protein-U (ΔU) at 2.64 Å resolution. The native dimeric core complex reveals many asymmetric features in the arrangement of its two monomeric components including the structural integrity of protein-U, the overall LH1 organization, and the rigidities of the proteins and pigments that form the complex. PufX polypeptides play a critical role in connecting two monomers, with one PufX interacting at its N-terminus with another PufX and an LH1 β-polypeptide in another monomer, in good agreement with biochemical analyses. One of the proteins-U was only partially identified in the dimeric structure, signaling significantly different degrees of disorder in the two monomers. The ΔU LH1-RC monomer revealed a half-moon-shaped structure containing 11 α- and 10 β-polypeptides (compared with 14 of each in the wild type), indicating a critical role for protein-U in controlling the number of αβ-subunits required for correct assembly and stabilization of the LH1-RC dimer. The structural features are discussed in relation to the unusual topology of intracytoplasmic photosynthetic membranes and an assembly model proposed for the native Rba. sphaeroides dimeric LH1-RC complex in membranes of wild-type cells.

Dielectric elastomer actuators (DEAs) are a promising actuator technology for soft robotics. As a configuration of this technology, stacked DEAs afford a muscle-like contraction that is useful to build soft robotic systems. In stacked DEAs, dielectric and electrode layers are alternately stacked. Thus, often a dedicated setup with complicated processes or sometimes laborious manual stacking of the layers is required to fabricate stacked actuators. In this study, we propose a method to monolithically fabricate stacked DEAs without alternately stacking the dielectric and electrode layers. In this method, the actuators are fabricated mainly through two steps: 1) molding of an elastomeric matrix containing free-form microfluidic channels and 2) injection of a liquid conductive material that acts as an electrode. The feasibility of our method is investigated via the fabrication and characterization of simple monolithic DEAs with multiple electrodes (2, 4, and 10). The fabricated actuators are characterized in terms of actuation stroke, output force, and frequency response. In the actuators, polydimethylsiloxane (PDMS) and eutectic gallium–indium (EGaIn) are used for the elastomeric matrix and electrode material, respectively. Microfluidic channels are realized by dissolving a three-dimensional printed part suspended in the elastomeric structure. The experimental results show the successful implementation of the proposed method and the good agreement between the measured data and theoretical predication, validating the feasibility of the proposed method.

We present a cryo-EM structure of the monomeric light-harvesting-reaction center (LH1-RC) core complex from photosynthetic purple bacterium Rhodobacter (Rba.) sphaeroides at 2.9 Å resolution. The LH1 complex forms a C-shaped structure composed of 14 αβ-polypeptides around the RC with a large ring opening. From the cryo-EM density map, a previously unrecognized integral membrane protein, referred to as protein-U, was identified. Protein-U has a U-shaped conformation near the LH1-ring opening and was annotated as a hypothetical protein in the Rba. sphaeroides genome. Deletion of protein-U resulted in a mutant strain that expressed a much-reduced amount of the dimeric LH1-RC, indicating an important role for protein-U in dimerization of the LH1-RC complex. PufX was located opposite protein-U on the LH1-ring opening, and both its position and conformation differed from that of previous reports of dimeric LH1-RC structures obtained at low-resolution. Twenty-six molecules of the carotenoid spheroidene arranged in two distinct configurations were resolved in the Rba. sphaeroides LH1 and were positioned within the complex to block its pores. Our findings offer a new view of the core photocomplex of Rba. sphaeroides and the connections between structure and function in bacterial photocomplexes in general.

Rhodospirillum (Rsp.) rubrum is one of the most widely used model organisms in bacterial photosynthesis. This purple phototroph is characterized by the presence of both rhodoquinone (RQ) and ubiquinone as electron carriers and bacteriochlorophyll (BChl) a esterified at the propionic acid side chain by geranylgeraniol (BChl aG) instead of phytol. Despite intensive efforts, the structure of the light-harvesting-reaction center (LH1-RC) core complex from Rsp. rubrum remains at low resolutions. Using cryo-EM, here we present a robust new view of the Rsp. rubrum LH1-RC at 2.76 A resolution. The LH1 complex forms a closed, slightly elliptical ring structure with 16 αβ-polypeptides surrounding the RC. Our biochemical analysis detected RQ molecules in the purified LH1-RC, and the cryo-EM density map specifically positions RQ at the QA site in the RC. The geranylgeraniol side chains of BChl aG coordinated by LH1 β-polypeptides exhibit a highly homologous tail-up conformation that allows for interactions with the bacteriochlorin rings of nearby LH1 α-associated BChls aG. The structure also revealed key protein-protein interactions in both N- and C-terminal regions of the LH1 αβ-polypeptides, mainly within a face-to-face structural subunit. Our high-resolution Rsp. rubrum LH1-RC structure provides new insight for evaluating past experimental and computational results obtained with this old organism over many decades and lays the foundation for more detailed exploration of light-energy conversion, quinone transport, and structure-function relationships in this pigment-protein complex.

We report on pneumatic artificial muscles (PAMs), also known as McKibben artificial muscles, that are integrated with a tubular dielectric elastomer sensor (DES). PAMs are usually composed of a rubber tube surrounded by a sleeve. When pressurized, the deformations of the rubber tube are conformed by the sleeve such that the actuator shrinks in the length direction and expands in the radial direction. To precisely control PAMs, a sensor is required to detect the deformations. DES is suitable for this purpose because it is highly compliant and thin, minimizing the influence on the configuration and performance of the actuators. In order to prove the concept, a sensorized PAM is fabricated by adhering a tubular DES onto the outside of the rubber tube, followed by placing the sleeve. A natural rubber tube with an outer diameter of 6 mm is employed. DES is made of an acrylic elastomer (3M, VHB4905) sandwiched between two compliant electrodes (Adhesives Research, ARcare 90366). When injecting air, the surface of the actuator increases therefore the capacitance of DES. This relationship enables the sensing of the actuator length by measuring the change in capacitance. We characterize the actuators in terms of capacitance as a function of the actuator displacement at different applied pressure.

Rhodobacter (Rba.) sphaeroides is the most widely used model organism in bacterial photosynthesis. The light-harvesting-reaction center (LH1-RC) core complex of this purple phototroph is characterized by the co-existence of monomeric and dimeric forms, the presence of the protein PufX, and approximately two carotenoids per LH1 αβ-polypeptides. Despite many efforts, structures of the Rba. sphaeroides LH1-RC have not been obtained at high resolutions. Here we report a cryo-EM structure of the monomeric LH1-RC from Rba. sphaeroides strain IL106 at 2.9 Å resolution. The LH1 complex forms a C-shaped structure composed of 14 αβ-polypeptides around the RC with a large ring opening. From the cryo-EM density map, a previously unrecognized integral membrane protein, referred to as protein-U, was identified. Protein-U has a U-shaped conformation near the LH1-ring opening and was annotated as a hypothetical protein in the Rba. sphaeroides genome. Deletion of protein-U resulted in a mutant strain that expressed a much-reduced amount of the dimeric LH1-RC, indicating an important role for protein-U in dimerization of the LH1-RC complex. PufX was located opposite protein-U on the LH1-ring opening, and both its position and conformation differed from that of previous reports of dimeric LH1-RC structures obtained at low-resolution. Twenty-six molecules of the carotenoid spheroidene arranged in two distinct configurations were resolved in the Rba. sphaeroides LH1 and were positioned within the complex to block its channels. Our findings offer an exciting new view of the core photocomplex of Rba. sphaeroides and the connections between structure and function in bacterial photocomplexes in general., Rhodobacter (Rba.) sphaeroides is a model organism for studying bacterial photosynthesis. Here, the authors present the 2.9 Å cryo-EM structure of the monomeric light-harvesting-reaction center core complex from Rba. sphaeroides strain IL106, which revealed the position and conformation of PufX and the presence of an additional component protein-U, an integral membrane protein.

BackgroundThe structural abnormalities in chromosomes are important issues in cancer genomics. Next generation sequencing technologies have big potentials to detect the structural variations precisely and comprehensively. Nevertheless, it is still difficult problem to detect large structural variations from short read sequence data. Major efforts have been achieved with paired-end reads, since discordant pairs directly reflect the existence of large rearrangement. Furthermore, approaches to detect structural variations from single-end reads are still worthwhile challenge because they allow wide choices of sequencing platforms.ResultWe present ReALLEN, a series of tools to detect genomic rearrangement with base-pair resolution from single-end reads provided by next generation sequencing. We examined the performance of ReALLEN using simulated dataset and real dataset sequenced by Ion Torrent systems. In most cases on the simulated dataset, ReALLEN showed nearly 100% precision and better sensitivity than other major tools. Notably, ReALLEN showed stable scores even if it was on some unfavorable conditions, for example, low coverage or small variant size. On the real dataset sequenced by Ion Torrent systems, ReALLEN accurately found an insertional translocation that was crucial for the diagnosis of chronic myeloid leukemia.ConclusionReALLEN is useful to researchers in finding genomic rearrangements. It will contribute to discovery of cancer-specific fusion proteins, precise diagnosis of known types of cancers, and understanding of genetic diseases caused by abnormal chromosomes.

Mutation burden in a tumor, presumably involving neo-antigens in the tumor tissue, is also thought to be one of the better predictors for the efficacy of immune checkpoint inhibitors. However, it is difficult to analyze the mutation burden routinely in the clinic. Here, we describe more convenient factors that can be used as surrogate markers of mutation burden. Ninety-four patients with NSCLC who underwent resection in our institution were recruited for this study. Mutation burden and major gene alterations were analyzed by using next generation sequencing. Several immunological parameters were also assessed using immunohistochemistry. Statistical analysis was performed on mutation burden, major gene alternations, immunohistochemistry, and clinical parameters. The median mutation load was 54 mutations(range, 10-363 mutations). Squamous cell carcinoma, EGFRmutation -negativity, and TP53 alteration-positivity were closely connected with higher mutation burden. Multiple regression analysis showed that mutation burden in the tumor could be associated with EGFRmutation and TP53 alteration status.

Continuous presentation of the odorant diacetyl to the nematode Caenorhabditis elegans causes a decrease in the level of chemotactic response to diacetyl. This decline in response is caused by diacetyl adaptation. When wild-type nematodes were maintained at 15°C after pre-exposure to diacetyl, diacetyl adaptation did not continue up to 2 hr. Adaptation continued up to 6 hr in nematodes bred at 20°C, and it continued beyond 12 hr in nematodes bred at 25°C. These results indicate that the retention time of diacetyl adaptation is dependent on the environmental breeding temperature and suggest that moderate oxygen signals are required for maintaining the attenuated response to diacetyl because of the correlation between breeding temperature and production of oxygen intermediates. When isp-1 and clk-1 mutants, which show reduced rates of oxygen intermediate production, were maintained at 20 and 25°C after pre-exposure to diacetyl, the mutants showed a shorter retention time of diacetyl adaptation compared with that of wild-type nematodes. When gas-1 and mev-1 mutants, which have a hypersensitive response to oxidative stress, were maintained at 15 and 20°C, they showed a longer retention time of adaptation, that is, adaptation continued beyond 2 and 12 hr, respectively. When wild-type nematodes were maintained on plates that included 0.05% α-lipoic acid, which suppresses production of oxygen intermediates, the retention time of adaptation did not continue up to 6 hr in nematodes bred at 20°C and up to 12 hr in nematodes bred at 25°C. These results support the possibility that oxygen intermediates contribute to retention time for diacetyl adaptation in the nematode C. elegans.

The retention time of attenuated chemotactic response to continuous presentation of odorant diacetyl was investigated in the nematode Caenorhabditis elegans. The level of chemotactic response of nematodes pre-exposed to diacetyl for 90 min was significantly smaller than that of nonexposed control nematodes. In this study, wild-type (N2) nematodes were maintained at 15, 20 and 25 degrees C after pre-exposure to diacetyl. At 20 degrees C, there was a decrease in response to diacetyl continuing for up to 6 hr after pre-exposure to the chemical, but not up to 12 hr. Interestingly, the decrease in response to diacetyl did not continue up to 2 hr in nematodes bred at 15 degrees C, although it continued beyond 12 hr in nematodes bred at 25 degrees C. These results indicate that the retention time of attenuated chemotactic response to diacetyl is dependent on the environmental breeding temperature of nematodes. The breeding temperature correlated with aging speed of nematodes, suggesting that a short life span (higher aging speed) prolongs the retention time of attenuated chemotactic response to diacetyl after pre-exposure to diacetyl. In the long-lived daf-2, age-1, clk-1 and isp-1 mutants, the effect of diacetyl did not continue up to 2 hr. The short-lived daf-16, daf-18, mev-1 and gas-1 mutants showed a longer duration of decrease in response to diacetyl, that is, the retention time of attenuated chemotactic response to diacetyl continued beyond 12 hr. There is a possibility that the duration of decrease in response to diacetyl after pre-exposure to diacetyl was inversely related to the length of nematodes' life span.

SummaryThe chaperonin GroEL interacts with various proteins, leading them to adopt their correct conformations with the aid of GroES and ATP. The actual mechanism is still being debated. In this study, by use of cryo-electron microscopy, we determined the solution structure of the Thermus thermophilus GroEL-GroES complex encapsulating its substrate proteins. We observed the averaged density of substrate proteins in the center of the GroEL-GroES cavity. The position of the averaged substrate density in the cavity suggested a repulsive interaction between a majority of the substrate proteins and the interior wall of the cavity, which is suitable for substrate release. In addition, we observed a distortion of the cis-GroEL ring, especially at the position near the substrate, which indicated that the interaction between the encapsulated proteins and the GroEL ring results in an adjustment in the cavity's shape to accommodate the substrate.

Continuous presentation of the odorant diacetyl to the nematode Caenorhabditis elegans causes a decrease in the level of chemotactic response to diacetyl. This decline in response is caused by diacetyl adaptation. When wild-type nematodes were maintained at 15°C after pre-exposure to diacetyl, diacetyl adaptation did not continue up to 2 hr. Adaptation continued up to 6 hr in nematodes bred at 20°C, and it continued beyond 12 hr in nematodes bred at 25°C. These results indicate that the retention time of diacetyl adaptation is dependent on the environmental breeding temperature and suggest that moderate oxygen signals are required for maintaining the attenuated response to diacetyl because of the correlation between breeding temperature and production of oxygen intermediates. When isp-1 and clk-1 mutants, which show reduced rates of oxygen intermediate production, were maintained at 20 and 25°C after pre-exposure to diacetyl, the mutants showed a shorter retention time of diacetyl adaptation compared with that of wild-type nematodes. When gas-1 and mev-1 mutants, which have a hypersensitive response to oxidative stress, were maintained at 15 and 20°C, they showed a longer retention time of adaptation, that is, adaptation continued beyond 2 and 12 hr, respectively. When wild-type nematodes were maintained on plates that included 0.05% α-lipoic acid, which suppresses production of oxygen intermediates, the retention time of adaptation did not continue up to 6 hr in nematodes bred at 20°C and up to 12 hr in nematodes bred at 25°C. These results support the possibility that oxygen intermediates contribute to retention time for diacetyl adaptation in the nematode C. elegans.

e20040Background: ICIs have been widely developing in the field of NSCLC. Several kinds of biomarkers predicting the efficacy of ICIs, such as PD-L1 expression, frequency of tumor infiltrating lymp...