Targeted exome sequencing of unselected heavy‐ion beam‐irradiated populations reveals less‐biased mutation characteristics in the rice genome

Heavy‐ion beams have been widely utilized as a novel and effective mutagen for mutation breeding in diverse plant species, but the induced mutation spectrum is not fully understood at the genome scale. We describe the development of a multiplexed and cost‐efficient whole‐exome sequencing procedure in rice, and its application to characterize an unselected population of heavy‐ion beam‐induced mutations. The bioinformatics pipeline identified single‐nucleotide mutations as well as small and large (>63 kb) insertions and deletions, and showed good agreement with the results obtained with conventional polymerase chain reaction (PCR) and sequencing analyses. We applied the procedure to analyze the mutation spectrum induced by heavy‐ion beams at the population level. In total, 165 individual M₂ lines derived from six irradiation conditions as well as eight pools from non‐irradiated ‘Nipponbare’ controls were sequenced using the newly established target exome sequencing procedure. The characteristics and distribution of carbon‐ion beam‐induced mutations were analyzed in the absence of bias introduced by visual mutant selections. The average (±SE) number of mutations within the target exon regions was 9.06 ± 0.37 induced by 150 Gy irradiation of dry seeds. The mutation frequency changed in parallel to the irradiation dose when dry seeds were irradiated. The total number of mutations detected by sequencing unselected M₂ lines was correlated with the conventional mutation frequency determined by the occurrence of morphological mutants. Therefore, mutation frequency may be a good indicator for sequencing‐based determination of the optimal irradiation condition for induction of mutations.     

Using focus ion beam to prepare crystal lamella for electron diffraction

Electron diffraction provides a powerful tool to solve the structures of small protein crystals. However, strong interactions between the electrons and the materials limit the application of the electron crystallographic method on large protein crystals with micrometer or larger sizes. Here, we used the focused ion beam (FIB) equipped on the scanning electron microscope (SEM) to mill a large crystal to thin lamella. The influences of the milling on the crystal lamella were observed and investigated, including radiation damage on the crystal surface during the FIB imaging, deformation of the thin crystal lamella, and variation in the diffraction intensities under electron radiation. These observations provide important information to optimize the FIB milling, and hence is important to obtain high-quality crystal samples for routine structure determination of protein crystals using the electron cryo-microscope.     

Axial resolution enhancement of light‐sheet microscopy by double scanning of Bessel beam and its complementary beam

The side lobes of Bessel beam will create significant out‐of‐focus background when scanned in light‐sheet fluorescence microscopy (LSFM), limiting the axial resolution of the imaging system. Here, we propose to overcome this issue by scanning the sample twice with zeroth‐order Bessel beam and another type of propagation‐invariant beam, complementary to the zeroth‐order Bessel beam, which greatly reduces the out‐of‐focus background created in the first scan. The axial resolution can be improved from 1.68 μm of the Bessel light‐sheet to 1.07 μm by subtraction of the two scanned images across a whole field‐of‐view of up to 300 μm × 200 μm × 200 μm. The optimization procedure to create the complementary beam is described in detail and it is experimentally generated with a spatial light modulator. The imaging performance is validated experimentally with fluorescent beads as well as eGFP‐labeled mouse brain neurons.      

电子束辐照在农产品贮藏保鲜中的应用

对电子束辐照保鲜机理和特性进行了阐述,并对近年来电子束辐照技术在水果、食用菌、蔬菜、肉类、谷物等农产品保鲜中应用情况进行了评述。与钴源辐照相比,电子束辐照具有杀菌作用强、方便快捷、安全环保等优势,因此该技术在农产品保鲜应用上具有广阔的前景。     

Growth and Characterization of Epitaxial Insulating CaF2 Layers on Silicon by MBE

In the course of the present work CaF₂ epitaxialfilms were grown on Si(111) substrates by means ofMBE. The Si substrates were chemically cleaned priorto insertion into the system. The final volatile oxidewas desorbed in situ by heating to 850. CaF₂ was evaporated from aKnudsen-type cell by use of a graphite crucible, whilethe growth temperature was held at 650 .RHEED (Reflection High Energy Electron Diffraction)has been used to monitor the film growth in situand to study the epitaxial quality. Also we have usedthe MeV He⁺ RBS channeling technique to look atdefects and to measure strain in the CaF₂ layer.Usually good crystallographic properties are achievedunder optimum growth conditions, with values of_min < 5%. Electrical properties aremeasured by use of a special MIS structure.     

碳离子束辐照对质粒DNA的损伤效应

为了证明DNA双链断裂(DSB)片段分布与DNA序列有关的假设,采用32keV／μm的^12C^6 离子和45ke V／μm的^13C^6 离子分别辐照pUCl8质粒,结合限制性内切酶处理,进行琼脂糖凝胶电泳,分析DNA断裂和片段分布。结果表明,除了由一个DSB导致的线性DNA带外,还出现了一条新的、小分子量线性DNA带;限制性内切酶处理后,有另一条线性DNA带产生。证明重离子辐照诱导的DSB是非随机分布的,DNA分子上存在对电离辐射相对敏感的位点。     

低能氮离子注入同源四倍体水稻的生物学效应

以低能氮离子束为诱变源,对同源四倍体水稻进行注入处理后,对其生物学效应进行了研究。研究结果表明,同源四倍体水稻比二倍体水稻对低能氮离子束注入处理更敏感。在注入离子剂量为3×1017N+/cm2时,同源四倍体水稻所受到的损伤比二倍体水稻所受到的损伤更严重。4份同源四倍体水稻(即IR36(4)、IR28(4)、紫血稻(4)、明恢63(4))的成苗率分别是2.0%、3.5%、3.0%和4.0%,致死率非常高。在同样条件下,4份相应的二倍体水稻(即IR36(2)、IR28(2)、紫血稻(2)、明恢63(2))的成苗率分别是33.0%、31.5%、29.0%和24.5%,致死率也比较高。在经过注入处理后的当代群体内,4份同源四倍体水稻的平均变异频率为32.5%,而4份相应的二倍体水稻的平均变异频率为9.5%。在同源四倍体水稻IR36(4)和IR28(4)的变异群体内分别发现22株和14株结实率均达到75.0%以上的单株,其中在IR36(4)群体内有1单株的结实率高达91.89%;在紫血稻(4)的变异群体内发现2株具有双胚苗性状的单株;在二倍体水稻明恢63(2)的变异群体内发现1株具有红心米性状的单株。在第二代群体中,除了叶鞘变异和米质变异这两个变异性状能稳定遗传之外,其它变异性状在群体内都发生了明显的性状分离现象。同源四倍体水稻的高结实率特性和双胚苗特性表现出一定的可遗传性。     

Actomyosin motility on nanostructured surfaces

We have here, for the first time, used nanofabrication techniques to reproduce aspects of the ordered actomyosin arrangement in a muscle cell. The adsorption of functional heavy meromyosin (HMM) to five different resist polymers was first assessed. One group of resists (MRL-6000.1XP and ZEP-520) consistently exhibited high quality motility of actin filaments after incubation with HMM. A second group (PMMA-200, PMMA-950, and MRI-9030) generally gave low quality of motility with only few smoothly moving filaments. Based on these findings electron beam lithography was applied to a bi-layer resist system with PMMA-950 on top of MRL-6000.1XP. Grooves (100-200nm wide) in the PMMA layer were created to expose the MRL-6000.1XP surface for adsorption of HMM and guidance of actin filament motility. This guidance was quite efficient allowing no U-turns of the filaments and approximately 20 times higher density of moving filaments in the grooves than on the surrounding PMMA.     

Surface Enhanced Raman Spectroscopy Detection of Biomolecules Using EBL Fabricated Nanostructured Substrates

Fabrication and characterization of conjugate nano-biological systems interfacing metallic nanostructures on solid supports with immobilized biomolecules is reported. The entire sequence of relevant experimental steps is described, involving the fabrication of nanostructured substrates using electron beam lithography, immobilization of biomolecules on the substrates, and their characterization utilizing surface-enhanced Raman spectroscopy (SERS). Three different designs of nano-biological systems are employed, including protein A, glucose binding protein, and a dopamine binding DNA aptamer. In the latter two cases, the binding of respective ligands, D-glucose and dopamine, is also included. The three kinds of biomolecules are immobilized on nanostructured substrates by different methods, and the results of SERS imaging are reported. The capabilities of SERS to detect vibrational modes from surface-immobilized proteins, as well as to capture the protein-ligand and aptamer-ligand binding are demonstrated. The results also illustrate the influence of the surface nanostructure geometry, biomolecules immobilization strategy, Raman activity of the molecules and presence or absence of the ligand binding on the SERS spectra acquired.     

Fabrication and Operation of a Nano-Optical Conveyor Belt

The technique of using focused laser beams to trap and exert forces on small particles has enabled many pivotal discoveries in the nanoscale biological and physical sciences over the past few decades. The progress made in this field invites further study of even smaller systems and at a larger scale, with tools that could be distributed more easily and made more widely available. Unfortunately, the fundamental laws of diffraction limit the minimum size of the focal spot of a laser beam, which makes particles smaller than a half-wavelength in diameter hard to trap and generally prevents an operator from discriminating between particles which are closer together than one half-wavelength. This precludes the optical manipulation of many closely-spaced nanoparticles and limits the resolution of optical-mechanical systems. Furthermore, manipulation using focused beams requires beam-forming or steering optics, which can be very bulky and expensive. To address these limitations in the system scalability of conventional optical trapping our lab has devised an alternative technique which utilizes near-field optics to move particles across a chip. Instead of focusing laser beams in the far-field, the optical near field of plasmonic resonators produces the necessary local optical intensity enhancement to overcome the restrictions of diffraction and manipulate particles at higher resolution. Closely-spaced resonators produce strong optical traps which can be addressed to mediate the hand-off of particles from one to the next in a conveyor-belt-like fashion. Here, we describe how to design and produce a conveyor belt using a gold surface patterned with plasmonic C-shaped resonators and how to operate it with polarized laser light to achieve super-resolution nanoparticle manipulation and transport. The nano-optical conveyor belt chip can be produced using lithography techniques and easily packaged and distributed.