ActuAtor, a Listeria-inspired molecular tool for physical manipulation of intracellular organizations through de novo actin polymerization

細胞の中のものを「押す」方法を開発 --細胞内構造体の“かたち”と機能の関係を明らかに--. 京都大学プレスリリース. 2023-09-25.Form and function are often interdependent throughout biology. Inside cells, mitochondria have particularly attracted attention since both their morphology and functionality are altered under pathophysiological conditions. However, directly assessing their causal relationship has been beyond reach due to the limitations of manipulating mitochondrial morphology in a physiologically relevant manner. By engineering a bacterial actin regulator, ActA, we developed tools termed “ActuAtor” that inducibly trigger actin polymerization at arbitrary subcellular locations. The ActuAtor-mediated actin polymerization drives striking deformation and/or movement of target organelles, including mitochondria, Golgi apparatus, and nucleus. Notably, ActuAtor operation also disperses non-membrane-bound entities such as stress granules. We then implemented ActuAtor in functional assays, uncovering the physically fragmented mitochondria being slightly more susceptible to degradation, while none of the organelle functions tested are morphology dependent. The modular and genetically encoded features of ActuAtor should enable its application in studies of the form-function interplay in various intracellular contexts

Effect of Grain Coalescence on Dislocation and Stress Evolution of GaN Films Grown on Nanoscale Patterned Sapphire Substrates

Two types of nucleation layers (NLs), including in-situ low-temperature grown GaN (LT-GaN) and ex-situ sputtered physical vapor deposition AlN (PVD-AlN), are applied on cone-shaped nanoscale patterned sapphire substrate (NPSS). The initial growth process of GaN on these two NLs is comparably investigated by a series of growth interruptions. The coalescence process of GaN grains is modulated by adjusting the three-dimensional (3D) temperatures. The results indicate that higher 3D temperatures reduce the edge dislocation density while increasing the residual compressive stress in GaN films. Compared to the LT-GaN NLs, the PVD-AlN NLs effectively resist Ostwald ripening and facilitate the uniform growth of GaN grains on NPSS. Furthermore, GaN films grown on NPSS with PVD-AlN NLs exhibit a reduction of over 50% in both screw and edge dislocation densities compared to those grown on LT-GaN NLs. Additionally, PVD-AlN NLs result in an increase of about 0.5 GPa in the residual compressive stress observed in GaN films

Functional immune responses against SARS-CoV-2 variants of concern after fourth COVID-19 vaccine dose or infection in patients with blood cancer

Summary Patients with blood cancer continue to have a greater risk of inadequate immune responses following three COVID-19 vaccine doses and risk of severe COVID-19 disease. In the context of the CAPTURE study (NCT03226886) we report immune responses in 80 patients with blood cancer who received a fourth dose of BNT162b2. We measured neutralising antibody titres (NAbT) using a live virus microneutralization assay against wild-type (WT), Delta, Omicron BA.1 and BA.2 and T cell responses against WT and Omicron BA.1 using an activation-induced marker (AIM) assay. The proportion of patients with detectable NAb titres and T cell responses after the fourth vaccine dose increases compared to those after the third vaccine dose. Patients who received B cell-depleting therapies within 12 months before vaccination have the greatest risk of not having detectable NAbT. In addition, we report immune responses in 57 patients with breakthrough infections after vaccination

Hybrid Underwater Vehicle: ARV Design and Development

The development of SMU-I, a new autonomous & remotely-operated vehicle (ARV) is described. Since it has both the characteristics of autonomous underwater vehicle (AUV) and remote operated underwater vehicle (ROV), it is able to achieve precision fix station operation and manual timely intervention. In the paper the initial design of basic components, such as vehicle, propulsion, batteries etc. and the control design of motion are introduced and analyzed. ROV’s conventional cable is replaced by a fiber optic cable, which makes it available for high-bandwidth real-time video, data telemetry and high-quality teleoperation. Furthermore, with the aid of the manual real-time remote operation and ranging sonar, it also resolves the AUV’s conflicting issue, which can absolutely adapt the actual complex sea environment and satisfy the unknown mission need. The whole battery system is designed as two-battery banks, whose voltages and temperatures are monitored through CAN (controller area network) bus to avoid battery fire and explosion. A fuzzy-PID controller is designed for its motion control, including depth control and direction control. The controller synthesizes the advantage of fuzzy control and PID control, utilizes the fuzzy rules to on-line tune the parameters of PID controller, and achieves a better control effect. Experiment results demonstrate to show the effectiveness of the test-bed

Electrochemical CO2 reduction catalyzed by organic/inorganic hybrids

Electroreduction of CO2 into value-added chemicals and fuels utilizing renewable electricity offers a sustainable way to meet the carbon-neutral goal and a viable solution for the storage of intermittent green energy sources. At the core of this technology is the development of electrocatalysts to accelerate the redox kinetics of CO2 reduction reactions (CO2RR) toward high targeted-product yield at minimal energy input. This perspective focuses on a unique category of CO2RR electrocatalysts embodying both inorganic and organic components to synergistically promote the reaction activity, selectivity and stability. First, we summarize recent progress on the design and fabrication of organic/inorganic hybrids CO2RR electrocatalysts, with special attention to the assembly protocols and structural configurations. We then carry out a comprehensive discussion on the mechanistic understanding of CO2RR processes tackled jointly by the inorganic and organic phases, with respect to the regulation of mass and charge transport, modification of double-layer configuration, tailoring of intermediates adsorption, and establishment of tandem pathways. At the end, we outline future challenges in the rational design of organic/inorganic hybrids for CO2RR and further extend the scope to the device level. We hope this work could incentivize more research interests to construct organic/inorganic hybrids for mobilizing electrocatalytic CO2RR towards industrialization

Upregulation of MetC Is Essential for d-Alanine-Independent Growth of an alr/dadX-Deficient Escherichia coli Strain ▿

d-Alanine is a central component of the cell wall in most prokaryotes. d-Alanine synthesis in Escherichia coli is carried out by two different alanine racemases encoded by the alr and dadX genes. Deletion of alr and dadX from the E. coli genome results in a d-alanine auxotrophic phenotype. However, we have observed growth of prototrophic phenotypic revertants during routine culturing of a d-alanine auxotrophic strain. We present a detailed comparison of the proteome and transcriptome profiles of the d-alanine auxotroph and a prototrophic revertant strain. Most noticeably, a general upregulation of genes involved in methionine synthesis in the revertant strain was detected. The appearance of the revertant phenotype was genetically linked to point mutations in the methionine repressor gene (metJ). Our results reveal an alternative metabolic pathway which can supply essential d-alanine for peptidoglycan synthesis of alr- and dadX-deficient E. coli mutants and provide evidence for significant alanine racemase coactivity of the E. coli cystathionine beta-lyase (MetC)

ActuAtor, a Listeria-inspired molecular tool for physical manipulation of intracellular organizations through de novo actin polymerization.

Form and function are often interdependent throughout biology. Inside cells, mitochondria have particularly attracted attention since both their morphology and functionality are altered under pathophysiological conditions. However, directly assessing their causal relationship has been beyond reach due to the limitations of manipulating mitochondrial morphology in a physiologically relevant manner. By engineering a bacterial actin regulator, ActA, we developed tools termed ActuAtor that inducibly trigger actin polymerization at arbitrary subcellular locations. The ActuAtor-mediated actin polymerization drives striking deformation and/or movement of target organelles, including mitochondria, Golgi apparatus, and nucleus. Notably, ActuAtor operation also disperses non-membrane-bound entities such as stress granules. We then implemented ActuAtor in functional assays, uncovering the physically fragmented mitochondria being slightly more susceptible to degradation, while none of the organelle functions tested are morphology dependent. The modular and genetically encoded features of ActuAtor should enable its application in studies of the form-function interplay in various intracellular contexts

CIGAR‐seq, a CRISPR/Cas‐based method for unbiased screening of novel mRNA modification regulators

Abstract Cellular RNA is decorated with over 170 types of chemical modifications. Many modifications in mRNA, including m6A and m5C, have been associated with critical cellular functions under physiological and/or pathological conditions. To understand the biological functions of these modifications, it is vital to identify the regulators that modulate the modification rate. However, a high‐throughput method for unbiased screening of these regulators is so far lacking. Here, we report such a method combining pooled CRISPR screen and reporters with RNA modification readout, termed CRISPR integrated gRNA and reporter sequencing (CIGAR‐seq). Using CIGAR‐seq, we discovered NSUN6 as a novel mRNA m5C methyltransferase. Subsequent mRNA bisulfite sequencing in HAP1 cells without or with NSUN6 and/or NSUN2 knockout showed that NSUN6 and NSUN2 worked on non‐overlapping subsets of mRNA m5C sites and together contributed to almost all the m5C modification in mRNA. Finally, using m1A as an example, we demonstrated that CIGAR‐seq can be easily adapted for identifying regulators of other mRNA modification