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Square beams for optimal tiling in TEM.

ABSTRACT: Imaging large fields-of-view at a high magnification requires tiling. Transmission electron microscopes typically have round beam profiles; therefore, tiling across a large field-of-view is either imperfect or results in uneven exposures, which is a problem on dose-sensitive samples. Here we introduce a square electron beam that can be easily retrofitted in existing microscopes and demonstrate its application showing it can tile nearly perfectly and deliver cryo-EM imaging with resolution comparable to conventional setups.

SUBMITTER: Chua EY

PROVIDER: S-EPMC10441458 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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Square beams for optimal tiling in TEM.

Chua Eugene Yd EY Alink Lambertus M LM Kopylov Mykhailo M de Marco Alex A

Research square 20230809

Imaging large fields-of-view at a high magnification requires tiling. Transmission electron microscopes typically have round beam profiles; therefore, tiling across a large field-of-view is either imperfect or results in uneven exposures, which is a problem on dose-sensitive samples. Here we introduce a square electron beam that can be easily retrofitted in existing microscopes and demonstrate its application showing it can tile nearly perfectly and deliver cryo-EM imaging with resolution compar ...[more]

PMID: 37609243

Similar Datasets

Square beams for optimal tiling in TEM.

Project description:Imaging large fields of view at a high magnification requires tiling. Transmission electron microscopes typically have round beam profiles; therefore, tiling across a large area is either imperfect or results in uneven exposures, a problem on dose-sensitive samples. Here, we introduce a square electron beam that can be easily retrofitted in existing microscopes and demonstrate its application, showing it can tile nearly perfectly and deliver cryo-EM imaging with a resolution comparable to conventional setups.

| S-EPMC10592621 | biostudies-literature

Thermodynamically optimal whole-genome tiling microarray design and validation.

Project description:Microarray is an efficient apparatus to interrogate the whole transcriptome of species. Microarray can be designed according to annotated gene sets, but the resulted microarrays cannot be used to identify novel transcripts and this design method is not applicable to unannotated species. Alternatively, a whole-genome tiling microarray can be designed using only genomic sequences without gene annotations, and it can be used to detect novel RNA transcripts as well as known genes. The difficulty with tiling microarray design lies in the tradeoff between probe-specificity and coverage of the genome. Sequence comparison methods based on BLAST or similar software are commonly employed in microarray design, but they cannot precisely determine the subtle thermodynamic competition between probe targets and partially matched probe nontargets during hybridizations.Using the whole-genome thermodynamic analysis software PICKY to design tiling microarrays, we can achieve maximum whole-genome coverage allowable under the thermodynamic constraints of each target genome. The resulted tiling microarrays are thermodynamically optimal in the sense that all selected probes share the same melting temperature separation range between their targets and closest nontargets, and no additional probes can be added without violating the specificity of the microarray to the target genome.This new design method was used to create two whole-genome tiling microarrays for Escherichia coli MG1655 and Agrobacterium tumefaciens C58 and the experiment results validated the design.

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Assessing the deviation from the inverse square law for orthovoltage beams with closed-ended applicators.

Project description:In this report, we quantify the divergence from the inverse square law (ISL) of the beam output as a function of distance (standoff) from closed-ended applicators for a modern clinical orthovoltage unit. The divergence is clinically significant exceeding 3% at a 1.2 cm distance for 4 × 4 and 10 × 10 cm2 closed-ended applicators. For all investigated cases, the measured dose falloff is more rapid than that predicted by the ISL and, therefore, causes a systematic underdose when using the ISL for dose calculations at extended SSD. The observed divergence from the ISL in closed-ended applicators can be explained by the end-plate scattering contribution not accounted for in the ISL calculation. The standoff measurements were also compared to the predictions from a home-built kV dose computation algorithm, kVDoseCalc. The kVDoseCalc computation predicted a more rapid falloff with distance than observed experimentally. The computation and measurements agree to within 1.1% for standoff distances of 3 cm or less for 4 × 4 cm2 and 10 × 10 cm2 field sizes. The overall agreement is within 2.3% for all field sizes and standoff distances measured. No significant deviation from the ISL was observed for open-ended applicators for standoff distances up to 10 cm.

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The Optimal Locomotion of a Self-Propelled Worm Actuated by Two Square Waves.

Project description:Worm-like locomotion at small scales induced by propagating a series of extensive or contraction waves has exhibited enormous possibilities in reproducing artificial mobile soft robotics. However, the optimal relation between locomotion performance and some important parameters, such as the distance between two adjacent waves, wave width, and body length, is still not clear. To solve this problem, this paper studies the optimal problem of a worm's motion induced by two peristalsis waves in a viscous medium. Inspired by a worm's motion, we consider that its body consists of two segments which can perform the respective shape change. Next, a quasi-static model describing the worm-like locomotion is used to investigate the relationship between its average velocity over the period and these parameters. Through the analysis of the relationship among these parameters, we find that there exist four different cases which should be addressed. Correspondingly, the average velocity in each case can be approximately derived. After that, optimization is carried out on each case to maximize the average velocity according to the Kuhn?Tucker Conditions. As a result, the optimal conditions of all of the cases are obtained. Finally, numerical and experimental verifications are carried out to demonstrate the correctness of the obtained results.

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GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition.

Project description:BackgroundCalculation of the root mean square deviation (RMSD) between the atomic coordinates of two optimally superposed structures is a basic component of structural comparison techniques. We describe a quaternion based method, GPU-Q-J, that is stable with single precision calculations and suitable for graphics processor units (GPUs). The application was implemented on an ATI 4770 graphics card in C/C++ and Brook+ in Linux where it was 260 to 760 times faster than existing unoptimized CPU methods. Source code is available from the Compbio website http://software.compbio.washington.edu/misc/downloads/st_gpu_fit/ or from the author LHH.FindingsThe Nutritious Rice for the World Project (NRW) on World Community Grid predicted de novo, the structures of over 62,000 small proteins and protein domains returning a total of 10 billion candidate structures. Clustering ensembles of structures on this scale requires calculation of large similarity matrices consisting of RMSDs between each pair of structures in the set. As a real-world test, we calculated the matrices for 6 different ensembles from NRW. The GPU method was 260 times faster that the fastest existing CPU based method and over 500 times faster than the method that had been previously used.ConclusionsGPU-Q-J is a significant advance over previous CPU methods. It relieves a major bottleneck in the clustering of large numbers of structures for NRW. It also has applications in structure comparison methods that involve multiple superposition and RMSD determination steps, particularly when such methods are applied on a proteome and genome wide scale.

| S-EPMC3087690 | biostudies-literature

Sequences of the genes for the TEM-20, TEM-21, TEM-22, and TEM-29 extended-spectrum beta-lactamases.

Project description:The sequences of the blaTEM genes encoding TEM-20, TEM-21, TEM-22, and TEM-29 extended-spectrum beta-lactamases were determined. Analysis of the deduced amino acid sequences indicated that TEM-20 and TEM-29 were derived from TEM-1 and that TEM-21 and TEM-22 were derived from TEM-2. The substitutions involved were Ser-238 and Thr-182 for TEM-20; His-164 for TEM-29; Lys-104, Arg-153, and Ser-238 for TEM-21; and Lys-104, Gly-237, and Ser-238 for TEM-22. The promoter region of the blaTEM-22 gene was identical to that of blaTEM-3. High-level production of TEM-20 could result from a 135-bp deletion which combined the -35 region of the Pa promoter with the -10 region of the P3 promoter and a G-->T transition in the latter motif.

| S-EPMC89239 | biostudies-literature

PARP1-tiling

Project description:Focused PARP1 mutagenesis screen for talazoparib resistance in HeLa-PARP1-GFP and SUM149-GFP cells

| PRJEB24332 | ENA

Evolution of TEM-type enzymes: biochemical and genetic characterization of two new complex mutant TEM enzymes, TEM-151 and TEM-152, from a single patient.

Project description:Two clinical isolates of Escherichia coli, CF1179 and CF1295, were isolated from a patient hospitalized in the hematology unit of the University Hospital of Clermont-Ferrand, Clermont-Ferrand, France. They were resistant to penicillin-clavulanate combinations and to ceftazidime. The double-disk synergy test was positive only for isolate CF1179. Molecular comparison of the isolates showed that they were clonally related. E. coli recombinant strains exhibiting the resistance phenotype of the clinical strains were obtained by cloning. The clones corresponding to strains CF1179 and CF1295 produced TEM-type beta-lactamases with pI values of 5.7 and 5.3, respectively. Sequencing analysis revealed two novel blaTEM genes encoding closely related complex mutant TEM enzymes, designated TEM-151 (pI 5.3) and TEM-152 (pI 5.7). These two genes also harbored a new promoter region which presented a 9-bp deletion. The two novel beta-lactamases differed from the parental enzyme, TEM-1, by the substitution Arg164His, previously observed in extended-spectrum beta-lactamases (ESBLs), and by the substitutions Met69Val and Asn276Asp, previously observed in the inhibitor-resistant penicillinase TEM-36/IRT-7. They differed by two amino acid substitutions: TEM-152 harbored a Glu240Lys ESBL-type substitution and TEM-151 had an Ala284Gly substitution. Functional analysis of TEM-151 and TEM-152 showed that both enzymes had hydrolytic activity against ceftazidime (kcat, 5 and 16 s-1, respectively). TEM-152 was more resistant than TEM-151 to the inhibitor clavulanic acid (50% inhibitory concentrations, 1 versus 0.17 microM). These results confirm the evolution of TEM-type enzymes toward complex enzymes harboring the two kinds of substitutions which confer an extended spectrum of action against beta-lactam antibiotics and resistance to inhibitors.

| S-EPMC1855492 | biostudies-literature

Infections with nontyphoidal Salmonella species producing TEM-63 or a novel TEM enzyme, TEM-131, in South Africa.

Project description:Salmonella spp. producing extended-spectrum beta-lactamases (ESBLs) have been reported in many countries, but there is no information on their prevalence in Africa. ESBL-producing Salmonella enterica serotype Isangi and S. enterica serotype Typhimurium strains have been noted in South Africa since 2001. A total of 160 consecutive isolates of Salmonella spp. were collected from 13 hospitals located in different cities in South Africa over a 5-month period from December 2002 to April 2003. All strains were screened for production of ESBLs by the double disk diffusion test and for AmpC production by assessing resistance to cefoxitin. bla(SHV), bla(TEM), bla(CTX-M), and bla(CMY-2) were sought from all ESBL-positive and cefoxitin-resistant isolates. A total of 15.6% (25 of 160) isolates produced SHV or TEM ESBLs, and 1.9% (3 of 160) produced CMY-2. Nine S. enterica serotype Typhimurium, eight S. enterica serotype Isangi, and three S. enterica serotype Muenchen strains produced either TEM-63 or a derivative of TEM-63 designated TEM-131. Both TEM-63 and TEM-131 have an isoelectric point of 5.6, and their sequences have the following amino acid substitutions compared to the TEM-1 sequence: Leu21Phe, Glu104Lys, Arg164Ser, and Met182Thr. Additionally, TEM-131 has an Ala237Thr substitution. ESBL-producing Salmonella spp. have become a significant public health problem in South Africa with particular implications for the treatment of serious nontyphoidal Salmonella infections in children, for whom extended-spectrum cephalosporins were the preferred treatment.

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Rhodoplanes sp. TEM

Project description:Rhodoplanes sp. TEM Genome sequencing and assembly

| PRJNA930462 | ENA