scholarly journals Cryo-EM Structures of Two Bacteriophage Portal Proteins Provide Insights for Antimicrobial Phage Engineering

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2532
Author(s):  
Abid Javed ◽  
Hugo Villanueva ◽  
Shadikejiang Shataer ◽  
Sara Vasciaveo ◽  
Renos Savva ◽  
...  
Keyword(s):  
Structural Engineering ◽  
Bacillus Pumilus ◽  
Structural Diversity ◽  
Broad Host Range ◽  
Protein Fold ◽  
Structural Elements ◽  
Portal Protein ◽  
Core Elements ◽  
Genomic Editing ◽  
Human Infections

Widespread antibiotic resistance has returned attention to bacteriophages as a means of managing bacterial pathogenesis. Synthetic biology approaches to engineer phages have demonstrated genomic editing to broaden natural host ranges, or to optimise microbicidal action. Gram positive pathogens cause serious pastoral animal and human infections that are especially lethal in newborns. Such pathogens are targeted by the obligate lytic phages of the Salasmaviridae and Guelinviridae families. These phages have relatively small ~20 kb linear protein-capped genomes and their compact organisation, relatively few structural elements, and broad host range, are appealing from a phage-engineering standpoint. In this study, we focus on portal proteins, which are core elements for the assembly of such tailed phages. The structures of dodecameric portal complexes from Salasmaviridae phage GA1, which targets Bacillus pumilus, and Guelinviridae phage phiCPV4 that infects Clostridium perfringens, were determined at resolutions of 3.3 Å and 2.9 Å, respectively. Both are found to closely resemble the related phi29 portal protein fold. However, the portal protein of phiCPV4 exhibits interesting differences in the clip domain. These structures provide new insights on structural diversity in Caudovirales portal proteins and will be essential for considerations in phage structural engineering.

scholarly journals Hierarchical mechanical metamaterials built with scalable tristable elements for ternary logic operation and amplitude modulation

2021 ◽  
Vol 7 (9) ◽  
pp. eabf1966
Author(s):  
Hang Zhang ◽  
Jun Wu ◽  
Daining Fang ◽  
Yihui Zhang
Keyword(s):  
Structural Diversity ◽  
Cell Number ◽  
Structural Elements ◽  
Ternary Logic ◽  
Stable States ◽  
One Dimensional ◽  
Logic Operation ◽  
Artificial Materials ◽  
Mechanical Metamaterials ◽  
Unit Cells

Multistable mechanical metamaterials are artificial materials whose microarchitectures offer more than two different stable configurations. Existing multistable mechanical metamaterials mainly rely on origami/kirigami-inspired designs, snap-through instability, and microstructured soft mechanisms, with mostly bistable fundamental unit cells. Scalable, tristable structural elements that can be built up to form mechanical metamaterials with an extremely large number of programmable stable configurations remains illusive. Here, we harness the elastic tensile/compressive asymmetry of kirigami microstructures to design a class of scalable X-shaped tristable structures. Using these structure as building block elements, hierarchical mechanical metamaterials with one-dimensional (1D) cylindrical geometries, 2D square lattices, and 3D cubic/octahedral lattices are designed and demonstrated, with capabilities of torsional multistability or independent controlled multidirectional multistability. The number of stable states increases exponentially with the cell number of mechanical metamaterials. The versatile multistability and structural diversity allow demonstrative applications in mechanical ternary logic operators and amplitude modulators with unusual functionalities.

The Properties of Welded Joints Made by 6082-T6 Aluminium Alloy and their Behaviour under Cyclic Loading Conditions

2015 ◽  
Vol 812 ◽  
pp. 375-380 ◽  
Author(s):  
D. Pósalaky ◽  
János Lukács
Keyword(s):  
Cyclic Loading ◽  
Automotive Industry ◽  
Welded Joints ◽  
Structural Engineering ◽  
Physical Simulation ◽  
Base Material ◽  
Point Of View ◽  
Test Results ◽  
Structural Elements ◽  
Effective Use

The magnitude of different aluminium alloys, especially the ones with higher strength, are increasing in the structural engineering, not just the usual applications (like the aerospace industry) but more likely in the automotive industry. There are more assumptions of the effective use of aluminium; we should highlight two important factors, the technological and the applicability criterions. The technological criterion is the joining of structural elements, frequently with welding thus the technological criterion ultimately is the weldability. The assumption of applicability comes from the loading capability of these structures, which is typically cyclic loading so the key issue from the point of view of applicability is the resistance to fatigue. This article represents physical simulation and fatigue test results both on the base material and on the welded joints.

scholarly journals Self-Regulation and Rubrics Assessment in Structural Engineering Subjects

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
María Consuelo Sáiz Manzanares ◽  
Miguel Ángel Sánchez Báez ◽  
Vanesa Ortega-López ◽  
Juan M. Manso Villalaín
Keyword(s):  
Structural Engineering ◽  
Procedural Knowledge ◽  
Self Regulation ◽  
Expert Assessment ◽  
Control Group ◽  
Structural Elements ◽  
Self Assessment ◽  
Perceptions Of Students ◽  
University Systems ◽  
Experimental Group

Present-day university systems need to educate graduates who are confident and highly independent, attributes that are especially relevant to engineering. We need to develop active methods that can analyze the prior knowledge of students and that impart teaching based on self-regulation and self-assessment by the student. In this study, we work with a sample of 116 students of architecture following a Structural Engineering subject module (61 in the experimental group and 55 in the control group). The objectives of the investigation are (1) to test whether significant differences exist in the knowledge of students after a training program in self-regulation and (2) to test whether the use of rubrics will improve the perceptions of students with regard to their own knowledge. We found that students trained in self-regulation methodologies improved their procedural knowledge in the field of structural engineering. Likewise, student self-perceptions of their own knowledge increased in relation to the design and expert assessment of structural elements and the graphic representation of constructive elements.

scholarly journals Pseudomonas aeruginosa PAO1 KillsCaenorhabditis elegans by Cyanide Poisoning

2001 ◽  
Vol 183 (21) ◽  
pp. 6207-6214 ◽  
Author(s):  
Larry A. Gallagher ◽  
Colin Manoil
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Hydrogen Cyanide ◽  
Insertion Mutation ◽  
Broad Host Range ◽  
Toxic Factor ◽  
Gene Encoding ◽  
Transposon Insertion ◽  
A Subunit ◽  
Human Infections ◽  
Mitochondrial Cytochrome Oxidase

ABSTRACT In this report we describe experiments to investigate a simple virulence model in which Pseudomonas aeruginosaPAO1 rapidly paralyzes and kills the nematode Caenorhabditis elegans. Our results imply that hydrogen cyanide is the sole or primary toxic factor produced by P. aeruginosa that is responsible for killing of the nematode. Four lines of evidence support this conclusion. First, a transposon insertion mutation in a gene encoding a subunit of hydrogen cyanide synthase (hcnC) eliminated nematode killing. Second, the 17 avirulent mutants examined all exhibited reduced cyanide synthesis, and the residual production levels correlated with killing efficiency. Third, exposure to exogenous cyanide alone at levels comparable to the level produced by PAO1 killed nematodes with kinetics similar to those observed with bacteria. The killing was not enhanced ifhcnC mutant bacteria were present during cyanide exposure. And fourth, a nematode mutant (egl-9) resistant to P. aeruginosa was also resistant to killing by exogenous cyanide in the absence of bacteria. A model for nematode killing based on inhibition of mitochondrial cytochrome oxidase is presented. The action of cyanide helps account for the unusually broad host range of virulence of P. aeruginosa and may contribute to the pathogenesis in opportunistic human infections due to the bacterium.

scholarly journals High-efficiency multi-site genomic editing (HEMSE) of Pseudomonas putida through thermoinducible ssDNA recombineering

2019 ◽  
Author(s):  
Tomas Aparicio ◽  
Akos Nyerges ◽  
Esteban Martínez-García ◽  
Víctor de Lorenzo
Keyword(s):  
Genome Engineering ◽  
High Efficiency ◽  
Broad Host Range ◽  
Single Stranded Dna ◽  
Genetic Construct ◽  
Genomic Changes ◽  
Broad Host Range Plasmid ◽  
Set Up ◽  
Genomic Editing ◽  
Powerful Strategy

SUMMARYWhile single-stranded DNA recombineering is a powerful strategy for higher-scale genome editing, its application to species other than enterobacteria is typically limited by the efficiency of the recombinase and the action of native mismatch repair (MMR) systems. By building on [i] availability of the Erf-like single-stranded DNA-annealing protein Rec2, [ii] adoption of tightly-regulated thermoinducible device and [iii] transient expression of a MMR-supressing mutL allele, we have set up a coherent genetic platform for entering multiple changes in the chromosome of Pseudomononas putida with an unprecedented efficacy and reliability. The key genetic construct to this end is a broad host range plasmid encoding co-transcription of rec2 and P. putida’s mutLE36KPP at high levels under the control of the PL/cI857 system. Cycles of short thermal shifts of P. putida cells followed by transformation with a suite of mutagenic oligos delivered different types of high-fidelity genomic changes at frequencies up to 10% per single change—that can be handled without selection. The same approach was instrumental to super-diversify short chromosomal portions for creating libraries of functional genomic segments—as shown in this case with ribosomal binding sites. These results enable the multiplexing of genome engineering of P. putida, as required for metabolic engineering of this important biotechnological chassis.

scholarly journals RAG: RNA-As-Graphs database—concepts, analysis, and features

1987 ◽  
Vol 5 (1-2) ◽  
pp. 1285-1291 ◽  
Author(s):  
Hin Hark Gan ◽  
Daniela Fera ◽  
Julie Zorn ◽  
Nahum Shiffeldrim ◽  
Michael Tang ◽  
...  
Keyword(s):  
Structural Diversity ◽  
Secondary Structures ◽  
Sequence Length ◽  
Structural Elements ◽  
Rna Structures ◽  
Rna Motifs ◽  
Rna Secondary Structures ◽  
Vertex Number ◽  
Dual Graphs ◽  
Tree Graphs

Motivation Understanding RNA's structural diversity is vital for identifying novel RNA structures and pursuing RNA genomics initiatives. By classifying RNA secondary motifs based on correlations between conserved RNA secondary structures and functional properties, we offer an avenue for predicting novel motifs. Although several RNA databases exist, no comprehensive schemes are available for cataloguing the range and diversity of RNA's structural repertoire. Results Our RNA-As-Graphs (RAG) database describes and ranks all mathematically possible (including existing and candidate) RNA secondary motifs on the basis of graphical enumeration techniques. We represent RNA secondary structures as two-dimensional graphs (networks), specifying the connectivity between RNA secondary structural elements, such as loops, bulges, stems and junctions. We archive RNA tree motifs as ‘tree graphs’ and other RNAs, including pseudoknots, as general ‘dual graphs’. All RNA motifs are catalogued by graph vertex number (a measure of sequence length) and ranked by topological complexity. The RAG inventory immediately suggests candidates for novel RNA motifs, either naturally occurring or synthetic, and thereby might stimulate the prediction and design of novel RNA motifs. Availability The database is accessible on the web at http://monod.biomath.nyu.edu/rna Contact [email protected]

Preliminary observations of the 2010 Darfield (Canterbury) earthquakes

2010 ◽  
Vol 43 (4) ◽  
pp. i-iv ◽  
Author(s):  
Peter Wood ◽  
Philip Robins ◽  
John Hare
Keyword(s):  
New Zealand ◽  
Earthquake Engineering ◽  
Structural Engineering ◽  
Structural Elements ◽  
Science And Engineering ◽  
Engineering Society ◽  
Introductory Paper ◽  
Ground Structures

This Bulletin of the New Zealand Society for Earthquake Engineering (NZSEE) is a collaboration with the New Zealand Geotechnical Society (NZGS) and the Structural Engineering Society New Zealand (SESOC), with papers on the preliminary observations of the 2010 September 4, 04:35 (NZST; September 3, 16:35 UTC) Darfield (Canterbury) earthquakes. This Introductory paper summarises preliminary observations of the earthquakes and the performance of ground, structures, non-structural elements, and lifelines; the assessments of usability; and the communication of information amongst the science and engineering communities.

scholarly journals Sensitive Assays for Isolation and Detection of Simian Foamy Retroviruses

1999 ◽  
Vol 37 (8) ◽  
pp. 2678-2686 ◽  
Author(s):  
Arifa S. Khan ◽  
Johnna F. Sears ◽  
Jacqueline Muller ◽  
Teresa A. Galvin ◽  
Muhammad Shahabuddin
Keyword(s):  
Rhesus Macaques ◽  
Prototype Strain ◽  
Immunofluorescence Assay ◽  
Macaca Nemestrina ◽  
Primate Species ◽  
Laboratory Research ◽  
Broad Host Range ◽  
Highly Sensitive ◽  
Human Infections ◽  
Retrovirus Infection

Simian foamy viruses (SFVs) are highly prevalent in a variety of nonhuman primate species ranging from prosimians to apes. SFVs possess a broad host range, and human infections can occur by cross-species transfer (W. Heneine et al., Nat. Med. 4:403–407, 1998). Retrovirus screening of potential sources of infection, such as laboratory research animals and simian-derived biological products, could minimize human exposure to SFVs by reducing the risk of potential retrovirus infection in humans. We describe a variety of sensitive assays for SFV isolation and detection which were developed with a prototype strain of SFV serotype 2. The Mus dunni cell line (M. R. Lander and S. K. Chattopadhyay, J. Virol. 52:695–698, 1984) was found to be highly sensitive for SFV production on the basis of various general and specific retrovirus detection assays such as reverse transcriptase assay, transmission electron microscopy, immunofluorescence assay, and Western blotting. A highly sensitive PCR assay was developed on the basis of the sequences in primary SFV isolates obtained from pig-tailed macaques (Macaca nemestrina) and rhesus macaques (Macaca mulatta). Analysis of naturally occurring SFV infection in macaques indicated that analysis by a combination of assays, including both highly sensitive, specific assays and less sensitive, broadly reactive assays, is important for evaluation of retrovirus infection.

scholarly journals Structures of TOG1 and TOG2 From the Human Microtubule Dynamics Regulator CLASP1

2018 ◽  
Author(s):  
Jonathan B. Leano ◽  
Kevin C. Slep
Keyword(s):  
Crystal Structures ◽  
Family Members ◽  
Structural Diversity ◽  
Binding Activity ◽  
Structure And Function ◽  
Microtubule Dynamics ◽  
Structural Elements ◽  
X Ray ◽  
Tubulin Binding ◽  
And Function

AbstractTubulin-binding TOG domains are found arrayed in a number of proteins that regulate microtubule dynamics. While much is known about the structure and function of TOG domains in the XMAP215 microtubule polymerase family, less in known about the TOG domain array found in the CLASP family. The CLASP TOG array promotes microtubule pause, potentiates rescue, and limits catastrophe. How distinct the TOG domains of CLASP are from one another, from XMAP215 TOG domains, and whether they are positionally conserved across CLASP family members is poorly understood. We present the x-ray crystal structures of human CLASP1 TOG1 and TOG2. The structures of CLASP1 TOG1 and TOG2 are distinct from each other, from CLASP TOG3, and are positionally conserved across species. While studies have failed to detect CLASP TOG1 tubulin-binding activity, TOG1 is structurally similar to the free-tubulin binding TOG domains of XMAP215. In contrast, though CLASP TOG2 and TOG3 have tubulin binding activity, they are structurally distinct from the free-tubulin binding TOG domains of XMAP215. CLASP TOG2 has a convex architecture, predicted to engage a hyper-curved tubulin state. CLASP TOG3 has unique structural elements in the C-terminal half of its α-solenoid domain that modeling studies implicate in binding to laterally-associated tubulin subunits in the microtubule lattice in a mode similar to, yet distinct from XMAP215 TOG4. These findings highlight the structural diversity of TOG domains within the CLASP TOG array and provide a molecular foundation for understanding CLASP-dependent effects on microtubule dynamics.

scholarly journals Thermo-mechano-chemical modeling and computation of thermosetting polymers used in post-installed fastening systems in concrete structures

2020 ◽  
Author(s):  
Bilen Emek Abali ◽  
Jan Vorel ◽  
Roman Wan-Wendner
Keyword(s):  
Structural Engineering ◽  
Careful Analysis ◽  
Chemical Processes ◽  
Structural Elements ◽  
Material Models ◽  
Chemical Modeling ◽  
Source Codes ◽  
Thermosetting Polymers ◽  
Computational Implementation ◽  
Adhesive Anchors

Abstract As thermoset polymers find frequent implementation in engineering design, their application in structural engineering is rather limited. One key reason relies on the ongoing curing process in typical applications such as post-installed adhesive anchors, joints by structural elements or surface-mounted laminates glued by adhesive polymers. Mechanochemistry including curing and aging under thermal as well as mechanical loading causes a multiphysics problem to be discussed. For restricting the variety of material models based on empirical observations, we aim at a thermodynamically sound strategy for modeling thermosets. By providing a careful analysis and clearly identifying the assumptions and simplifications, we present the general framework for modeling and computational implementation of thermo-mechano-chemical processes by using open-source codes.

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