Multiple Displacement Research Articles

Preimplantation High-Resolution HLA Sequencing Using Next Generation Sequencing

Hematopoietic stem cell transplantation (SCT) is the only therapeutic option in a number of heritable hematologic disorders and hematologic cancers. Many parents and families fail to find an HLA-identical donor for their affected family member. In such cases, conceiving for a “savior baby” remains the only option, especially in countries without access to national registries. By means of next generation sequencing (NGS) techniques, in a single experiment on single-cell products of in vitro fertilization, a healthy HLA-identical embryo can be implanted in the uterus of a concerned mother. The patient can therefore benefit from cord blood SCT along with confirming that the fetuses are not suffering from the heritable disorder. This study is an attempt to study the feasibility of preimplantation HLA sequencing on single blastomeres using NGS. Two couples who had previously undergone preimplantation genetic diagnosis of β-thalassemia and their overall 10 embryos were studied and their 5 HLA loci were typed in high resolution through multiple displacement amplification and NGS of single cells. For 88.9% of the 90 HLA alleles, conclusive HLA typing in 4 digit sets was made. HLA alleles were typed; 1 ambiguity in the allelic group and 4 ambiguities in the protein level were observed that were then unraveled by haplotype analysis. Amplification efficiency was 93.3% with an allele drop-out (ADO) rate of 22.2% (6 alleles dropped from a maximum of 27 possible ADOs). In this study the feasibility of a new method of preimplantation HLA sequencing via combining the state-of-the-art techniques used in single-cell whole genome amplification, preimplantation genetic diagnosis, and high-resolution HLA typing by NGS has been shown. This method can make preimplantation HLA sequencing a practicable technique in families desperate for an HLA-matched donor.

Reducing inherent biases introduced during DNA viral metagenome analyses of municipal wastewater.

Metagenomics is a powerful tool for characterizing viral composition within environmental samples, but sample and molecular processing steps can bias the estimation of viral community structure. The objective of this study is to understand the inherent variability introduced when conducting viral metagenomic analyses of wastewater and provide a bioinformatic strategy to accurately analyze sequences for viral community analyses. A standard approach using a combination of ultrafiltration, membrane filtration, and DNase treatment, and multiple displacement amplification (MDA) produced DNA preparations without any bacterial derived genes. Results showed recoveries in wastewater matrix ranged between 60–100%. A bias towards small single stranded DNA (ssDNA; polyomavirus) virus types vs larger double stranded DNA (dsDNA; adenovirus) viruses was also observed with a total estimated recovery of small circular viruses to be as much as 173-fold higher. Notably, ssDNA abundance decreased with sample dilution while large dsDNA genomes (e.g., Caudovirales) initially increased in abundance with dilution before gradually decreasing with further dilution in wastewater samples. The present study revealed the inherent biases associated with different components of viral metagenomic methods applied to wastewater. Overall, these results provide a well-characterized approach for effectively conducting viral metagenomics analysis of wastewater and reveal that dilution can effectively mitigate MDA bias.

Limited reverse transcriptase activity of phi29 DNA polymerase.

Phi29 (Φ29) DNA polymerase is an enzyme commonly used in DNA amplification methods such as rolling circle amplification (RCA) and multiple strand displacement amplification (MDA), as well as in DNA sequencing methods such as single molecule real time (SMRT) sequencing. Here, we report the ability of phi29 DNA polymerase to amplify RNA-containing circular substrates during RCA. We found that circular substrates with single RNA substitutions are amplified at a similar amplification rate as non-chimeric DNA substrates, and that consecutive RNA pyrimidines were generally preferred over purines. We observed RCA suppression with higher number of ribonucleotide substitutions, which was partially restored by interspacing RNA bases with DNA. We show that supplementing manganese ions as cofactor supports replication of RNAs during RCA. Sequencing of the RCA products demonstrated accurate base incorporation at the RNA base with both Mn2+ and Mg2+ as cofactors during replication, proving reverse transcriptase activity of the phi29 DNA polymerase. In summary, the ability of phi29 DNA polymerase to accept RNA-containing substrates broadens the spectrum of applications for phi29 DNA polymerase-mediated RCA. These include amplification of chimeric circular probes, such as padlock probes and molecular inversion probes.

Motion laws synthesis for cam mechanisms with multiple follower displacement

The research discusses the cam mechanisms design. The analysis of specialized literature indicates that the synthesis of the cam mechanisms laws of motion is currently done mainly by a standard set of acceleration curves. In some cases, the designer needs to synthesize a new acceleration law which should be task-specific and enforce a certain production step. The values of the technological loads and inertia forces loads generated by the mechanism are calculated to analyze the slay mechanism behavior in the production of closely woven fabrics. Mathematical packages MathCad and SolidWorks are used in calculations. As a result of the research, the authors propose the methodology for synthesizing the slay mechanism with multiple follower displacements for the point of contact between the reed and the fabric edge. Theoretical studies have been tested on a specific machine model (STB loom). The authors have synthesized the motion law of the filling threads beat-up mechanism for the production of strong fabrics. New basic and closing cam profiles are proposed. The results are designed to enhance the possibilities of the looms and to recommend the most efficient equipment operation modes for the producers.

DNA Computing Boosted by a Cationic Copolymer

AbstractThe huge information storage capability of DNA and its ability to self‐assemble can be harnessed to enable massively parallel computing in a small space. DNA‐based logic gates are designed that rely on DNA strand displacement reactions; however, computation is slow due to time‐consuming DNA reassembly processes and prone to failure as DNA is susceptible to degradation by nucleases and under certain solution conditions. Here, it is shown that the presence of a cationic copolymer boosts the speed of DNA logic gate operations that involve multiple and parallel strand displacement reactions. Two kinds of DNA molecular operations, one based on a translator gate and one on a seesaw gate, are successfully enhanced by the copolymer without tuning of computing conditions or DNA sequences. The copolymer markedly reduces operation times from hours to minutes. Moreover, the copolymer enhances nuclease resistance.

Systematic assessment of the performance of whole-genome amplification for SNP/CNV detection and β-thalassemia genotyping

In this study, we aimed to assess the performance of two whole-genome amplification methods, multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycle (MALBAC), for β-thalassemia genotyping and single-nucleotide polymorphism (SNP)/copy-number variant (CNV) detection using two DNA sequencing assays. We collected peripheral blood, cell lines, and discarded embryos, and carried out MALBAC and MDA on single-cell and five-cell samples. We detected and statistically analyzed differences in the amplification efficiency, positive predictive value, sensitivity, allele dropout (ADO) rate, SNPs, and CV values between the two methods. Through Sanger sequencing at the single-cell and five-cell levels, we showed that both the amplification rate and ADO rate of MDA were better than those using MALBAC, and the sensitivity and positive predictive value obtained from MDA were higher than those from MALBAC for β-thalassemia genotyping. Using next-generation sequencing (NGS) at the single-cell level, we confirmed that MDA has better properties than MALBAC for SNP detection. However, MALBAC was more stable and homogeneous than MDA using low-depth NGS at the single-cell level for CNV detection. We conclude that MALBAC is the better option for CNV detection, while MDA is better suited for SNV detection.

Bioreactor virome metagenomics sequencing using DNA spike-ins

With the emergence of Next Generation Sequencing, major advances were made with regard to identifying viruses in natural environments. However, bioinformatical research on viruses is still limited because of the low amounts of viral DNA that can be obtained for analysis. To overcome this limitation, DNA is often amplified with multiple displacement amplification (MDA), which may cause an unavoidable bias. Here, we describe a case study in which the virome of a bioreactor is sequenced using Ion Torrent technology. DNA-spiking of samples is compared with MDA-amplified samples. DNA for spiking was obtained by amplifying a bacterial 16S rRNA gene. After sequencing, the 16S rRNA gene reads were removed by mapping to the Silva database. Three samples were tested, a whole genome from Enterobacteria P1 Phage and two viral metagenomes from an infected bioreactor. For one sample, the new DNA-spiking protocol was compared with the MDA technique. When MDA was applied, the overall GC content of the reads showed a bias towards lower GC%, indicating a change in composition of the DNA sample. Assemblies using all available reads from both MDA and the DNA-spiked samples resulted in six viral genomes. All six genomes could be almost completely retrieved (97.9%–100%) when mapping the reads from the DNA-spiked sample to those six genomes. In contrast, 6.3%–77.7% of three viral genomes was covered by reads obtained using the MDA amplification method and only three were nearly fully covered (97.4%–100%). This case study shows that DNA-spiking could be a simple and inexpensive alternative with very low bias for sequencing of metagenomes for which low amounts of DNA are available.

Microfluidic Device for Aptamer-Based Cancer Cell Capture and Genetic Mutation Detection.

We present a microfluidic device for specifically capturing cancer cells and isolating their genomic DNA (gDNA) for specific amplification and sequence analysis. To capture cancer cells within the device, nucleic acid aptamers that specifically bind to cancer cells were immobilized within a channel containing micropillars designed to increase capture efficiency. The captured cells were lysed in situ, and their gDNA was isolated by physical entanglement within a second smaller-dimensioned micropillar array. This type of isolation allows the gDNA to be retained and purified within the channel and enables amplification and analysis to be performed on the gDNA without the loss of the original template. We developed a technique for selectively amplifying genes from whole gDNA using multiple displacement amplification. The amplified gene samples were sequenced, and the resulting sequence information was compared against the known wild-type gene to identify any mutations. We have tested cervical and ovarian cancer cells for mutations in the TP53 gene using this technology. This approach offers a way to monitor multiple genetic mutations in the same small population of cells, which is beneficial given the wide diversity in cancer cells, and therefore it requires very few cells to be extracted from a patient sample.

Quasimetagenomics-Based and Real-Time-Sequencing-Aided Detection and Subtyping of Salmonella enterica from Food Samples.

Metagenomics analysis of food samples promises isolation-independent detection and subtyping of foodborne bacterial pathogens in a single workflow. The selective concentration of Salmonella genomic DNA by immunomagnetic separation (IMS) and multiple displacement amplification (MDA) shortened the time for culture enrichment of Salmonella-spiked raw chicken breast samples by over 12 h while permitting serotyping and high-fidelity single nucleotide polymorphism (SNP) typing of the pathogen using short shotgun sequencing reads. The herein-termed quasimetagenomics approach was evaluated on Salmonella-spiked lettuce and black peppercorn samples as well as retail chicken parts naturally contaminated with different serotypes of Salmonella Culture enrichment of between 8 and 24 h was required for detecting and subtyping naturally occurring Salmonella from unspiked chicken parts compared with 4- to 12-h culture enrichment when Salmonella-spiked food samples were analyzed, indicating the likely need for longer culture enrichment to revive low levels of stressed or injured Salmonella cells in food. A further acceleration of the workflow was achieved by real-time nanopore sequencing. After 1.5 h of analysis on a potable sequencer, sufficient data were generated from sequencing the IMS-MDA products of a cultured-enriched lettuce sample to enable serotyping and robust phylogenetic placement of the inoculated isolate.IMPORTANCE Both culture enrichment and next-generation sequencing remain time-consuming processes for food testing, whereas rapid methods for pathogen detection are widely available. Our study demonstrated a substantial acceleration of these processes by the use of immunomagnetic separation (IMS) with multiple displacement amplification (MDA) and real-time nanopore sequencing. In one example, the combined use of the two methods delivered a less than 24-h turnaround time from the collection of a Salmonella-contaminated lettuce sample to the phylogenetic identification of the pathogen. An improved efficiency such as this is important for further expanding the use of whole-genome and metagenomics sequencing in the microbial analysis of food. Our results suggest the potential of the quasimetagenomics approach in areas where rapid detection and subtyping of foodborne pathogens are important, such as for foodborne outbreak response and the precision tracking and monitoring of foodborne pathogens in production environments and supply chains.

Successful preimplantation genetic diagnosis by targeted next-generation sequencing on an ion torrent personal genome machine platform.

Hearing loss may place a heavy burden on the patient and patient's family. Given the high incidence of hearing loss among newborns and the huge cost of treatment and care (including cochlear implantation), prenatal diagnosis is strongly recommended. Termination of the fetus may be considered as an extreme outcome to the discovery of a potential deaf fetus, and therefore preimplantation genetic diagnosis has become an important option for avoiding the birth of affected children without facing the risk of abortion following prenatal diagnosis. In one case, a couple had a 7-year-old daughter affected by non-syndromic sensorineural hearing loss. The affected fetus carried a causative compound heterozygous mutation c.919-2 A>G (IVS7-2 A>G) and c.1707+5 G>A (IVS15+5 G>A) of the solute carrier family 26 member 4 gene inherited from maternal and paternal sides, respectively. The present study applied multiple displacement amplification for whole genome amplification of biopsied trophectoderm cells and next-generation sequencing (NGS)-based single nucleotide polymorphism haplotyping on an Ion Torrent Personal Genome Machine. One unaffected embryo was transferred in a frozen-thawed embryo transfer cycle and the patient was impregnated. To conclude, to the best of our knowledge, this may be the first report of NGS-based preimplantation genetic diagnosis (PGD) for non-syndromic hearing loss caused by a compound heterozygous mutation using an Ion Torrent Personal Genome Machine. NGS provides unprecedented high-throughput, highly parallel and base-pair resolution data for genetic analysis. The method meets the requirements of medium-sized diagnostics laboratories. With decreased costs compared with previous techniques (such as Sanger sequencing), this technique may have potential widespread clinical application in PGD of other types of monogenic disease.

Fine Registration for VHR Images Based on Superpixel Registration-Noise Estimation

Local nonlinear geometric distortion is problematic in the registration of very high-resolution (VHR) images. In the standard registration approach, the precision of control points generated from salient feature matching cannot be guaranteed. This letter introduces a novel superpixel registration-noise (RN) estimation method based on a two-step fine registration technique that can be estimate and mitigate the local residual misalignments in VHR images. The first step employs superpixel sparse representation and multiple displacement analysis to estimate RN information of the preregistered image. The second step optimizes the control points obtained in preregistration by combining the RN information and gross error information, and finally fine registers the input image by employing local rectification. The experiments using two data sets generated from Chinese GF2, GF1, and ZY3 satellites are discussed in this letter, and the promising results verify the effectiveness of the proposed new method.

Accurate and sensitive single-cell-level detection of copy number variations by micro-channel multiple displacement amplification (μcMDA).

Whole genome amplification (WGA) has laid the foundation for investigating complex genomic alteration with single-cell or even single-molecule resolution. Coupled with sequencing-based copy number variation (CNV) analysis, it promotes understanding of the nature of commonly existing genetic heterogeneity by constructing the sequencing profiles for every single cell. However, prevailing methods only provide insights into limited aspects due to their intrinsic technical challenges. Their output data, as a result, fails to render comprehensive information (which is) concerned. Here, we describe the CNV detection analysis based on micro-channel multiple displacement amplification (μcMDA), a protocol able to provide optimized amplification uniformity while inheriting the advantages of MDA chemistry. We demonstrate the analysis of both the normal diploid YH-1 cell line and the aneuploid K562 cancer cell line. In the detection of simulated CNVs ranging from 300 kb to 2 Mb, μcMDA can respectively increase the detection rates of copy number loss and gain by 28.8% and 40.2% on average, using only 0.2× sequencing data. When detecting the inherent CNVs in tumor cells, the resolution of CNV recognition can be improved to 250 kb. Starting from either superabundant template copies or minute single-cell-level input, this easily accessible approach is capable of providing quantitatively reliable coverage as well as more robust GC-content regression for CNV detection.

Derivation and application of an analytical rock displacement solution on rectangular cavern wall using the inverse mapping method.

Rectangular caverns are increasingly used in underground engineering projects, the failure mechanism of rectangular cavern wall rock is significantly different as a result of the cross-sectional shape and variations in wall stress distributions. However, the conventional computational method always results in a long-winded computational process and multiple displacement solutions of internal rectangular wall rock. This paper uses a Laurent series complex method to obtain a mapping function expression based on complex variable function theory and conformal transformation. This method is combined with the Schwarz-Christoffel method to calculate the mapping function coefficient and to determine the rectangular cavern wall rock deformation. With regard to the inverse mapping concept, the mapping relation between the polar coordinate system within plane ς and a corresponding unique plane coordinate point inside the cavern wall rock is discussed. The disadvantage of multiple solutions when mapping from the plane to the polar coordinate system is addressed. This theoretical formula is used to calculate wall rock boundary deformation and displacement field nephograms inside the wall rock for a given cavern height and width. A comparison with ANSYS numerical software results suggests that the theoretical solution and numerical solution exhibit identical trends, thereby demonstrating the method’s validity. This method greatly improves the computing accuracy and reduces the difficulty in solving for cavern boundary and internal wall rock displacements. The proposed method provides a theoretical guide for controlling cavern wall rock deformation failure.

Nanoparticle-based lateral flow biosensor combined with multiple cross displacement amplification for rapid, visual and sensitive detection of Vibrio cholerae.

Vibrio cholerae is an important human pathogen that is responsible for cholera, a severe acute watery diarrhea. In the current study, a multiple cross displacement amplification (MCDA) coupled with amplicon detection by chromatographic lateral flow biosensor (LFB) method (MCDA-LFB) was successfully established and evaluated for the identification of V. cholerae. A set of 10 primers was designed specifically to recognize 10 different regions of the V. cholerae-specific gene ompW. The optimized time and temperature conditions for the MCDA were 30 min and 63°C, respectively. The MCDA-LFB assay correctly identified 31 strains of V. cholerae but did not detect 13 non-cholerae Vibrio strains and 30 non-Vibrio strains. The sensitivity of MCDA-LFB for target pathogen detection in pure culture was 10 fg per reaction. In the case of spiked shrimp samples without enrichment, the limit of detection was 4.1 CFUs per reaction or equivalent to 4.1×102 CFU g-1. The whole process, including shrimp homogenates processing (30 min), MCDA reaction (30 min) and results reporting (2 min), could be finished within 65 min. These results show that this assay is suitable for the rapid, sensitive and specific detection of V. cholerae in food, environmental and clinical samples.

A novel isothermal amplification-based method to detect Mycobacterium tuberculosis complex

Mycobacterium tuberculosis (MTB) is the causative agent of pulmonary tuberculosis. Rapid and accurate diagnosis is crucial to tuberculosis control and prevention. A series of diagnostic methods has been available for MTB detection; however, new rapid, simple and affordable methods are needed. In this study, a multiple cross displacement amplification (MCDA)-based assay was developed to detect the IS6110 gene of the M. tuberculosis complex. Hydroxy naphthol blue (HNB), a colorimetric indicator, was used to detect amplification products. Amplification was carried out at a constant temperature (68°C) for only 40min, followed by direct determination of amplification products through observation of color variations. The entire detection procedure, from processing of specimens to reading of results, required only 85min. Moreover, this assay, hereafter designated MTB-MCDA-HNB, was able to detect as little as 1pg of DNA extracted from the Bacille Calmette-Guerin (BCG) strain of Mycobacterium bovis. No cross-reaction with nontuberculous mycobacteria (NTM) species was observed. Moreover, during testing of clinical samples, the sensitivity and specificity of MCDA results were 94.7% and 92.9%, respectively, when compared to results obtained using the Xpert MTB/RIF method. Therefore, the MTB-MCDA-HNB method developed in this study holds promise for application as an effective point-of-care test to detect M. tuberculosis.

First report on an X-linked hypohidrotic ectodermal dysplasia family with X chromosome inversion: Breakpoint mapping reveals the pathogenic mechanism and preimplantation genetics diagnosis achieves an unaffected birth

BackgroundTo investigate the etiology of X-linked hypohidrotic ectodermal dysplasia (XLHED) in a family with an inversion of the X chromosome [inv(X)(p21q13)] and to achieve a healthy birth following preimplantation genetic diagnosis (PGD). MethodsNext generation sequencing (NGS) and Sanger sequencing analysis were carried out to define the inversion breakpoint. Multiple displacement amplification, amplification of breakpoint junction fragments, Sanger sequencing of exon 1 of ED1, haplotyping of informative short tandem repeat markers and gender determination were performed for PGD. ResultsNGS data of the proband sample revealed that the size of the possible inverted fragment was over 42Mb, spanning from position 26, 814, 206 to position 69, 231, 915 on the X chromosome. The breakpoints were confirmed by Sanger sequencing. A total of 5 blastocyst embryos underwent trophectoderm biopsy. Two embryos were diagnosed as carriers and three were unaffected. Two unaffected blastocysts were transferred and a singleton pregnancy was achieved. Following confirmation by prenatal diagnosis, a healthy baby was delivered. ConclusionsThis is the first report of an XLHED family with inv(X). ED1 is disrupted by the X chromosome inversion in this XLHED family and embryos with the X chromosomal abnormality can be accurately identified by means of PGD.

Nanoparticles-based lateral flow biosensor coupled with multiple cross displacement amplification Plus for simultaneous detection of nucleic acid and prevention of carryover contamination

Abstract Isothermal amplification techniques, which avoid thermal cycling, are often confounded by non-specific amplification arising from off-target hybrids, interactions between (hetero-dimer) or within (self-dimerization) primers and carryover contaminants. Here, we developed a new method, termed multiple cross displacement amplification Plus (MCDA Plus), which uses self-avoiding molecular recognition system (SAMRS) components and antarctic thermal sensitive uracil-DNA-glycosylase (AUDG) enzyme to improve the specificity of MCDA and prevent carryover contamination, respectively. In the presence of SAMRS components, the false positive results arising from off-target hybrids and undesired interactions between or within primers are completely eliminated, which increase the reproducibility of the assay. In the presence of AUDG, the false positive results generating from carryover contaminants are removed, thus the genuine positive results are obtained from the amplification of target sequences. Moreover, we also devised a new analysis strategy, which was intended for the detection of amplified products using lateral flow biosensor (LFB). The analysis system only required a single labeled primer, thus eliminated the false positive result yielding from hybridization (the labeled primer and probe, or between two labeled primers). Therefore, the SAMRS components, AUDG and LFB convert standard MCDA from an assay suited only for the research laboratory into one that has applicable value at points-of-care testing, in the field environments and in poor-resource settings. For demonstration purpose, Mycobacterium tuberculosis complex (MTC), which is the causes of human Tuberculosis (TB), are detected by the novel MCDA Plus technique to demonstrate the capability of target analysis. The performance of MCDA Plus assay in identifying MTC from pure culture and clinical samples is successfully evaluated. The proof-of-concept technique can be reconfigured to detect various nucleic acid sequences by redesigning the specific MCDA Plus primers.

1D-Reactor Decentralized MDA for Uniform and Accurate Whole Genome Amplification.

Multiple displacement amplification (MDA), a most popular isothermal whole genome amplification (WGA) method, suffers the major hurdle of highly uneven amplification, thus, leading to many problems in approaching biological applications related to copy-number assessment. In addition to the optimization of reagents and conditions, complete physical separation of the entire reaction system into numerous tiny chambers or droplets using microfluidic devices, has been proven efficient to mitigate this amplifying bias in recent works. Here, we present another MDA advance, microchannel MDA (μcMDA), which decentralizes MDA reagents throughout a one-dimensional slender tube. Due to the double effect from soft partition of high molecular-weight DNA molecules and less-limited diffusion of small particles, μcMDA is shown to be significantly effective at improving the amplification uniformity, which enables us to accurately detect single nucleotide variants (SNVs) with higher efficiency and sensitivity. More importantly, this straightforward method requires neither customized instruments nor complicated operations, making it a ready-to-use technique in almost all biological laboratories.

Detection and Subtyping of Salmonella from Raw Chicken through Targeted Salmonella Capture, Genome Amplification and Whole Genome Sequencing

The often low abundance and uneven distribution of bacterial foodborne pathogens in food samples makes rapid, sensitive and specific detection of these pathogens an enduring challenge. Selective concentration of a target organism is often required to bring pathogen cells to a detectable level for subsequent analyses. For example, culture enrichment is still the most widely used method in spite of its lengthy process (i.e., more than 12 hours) that is intrinsically restricted in speed by the length of cell cycle. Alternative concentration approaches to culture enrichment have been developed. For instance, immunomagnetic separation (IMS) has been applied to certain food matrices. In addition to enriching bacterial cells, amplification of bacterial genomes, for instance, through multiple displacement amplification (MDA), has been shown to facilitate molecular detection of difficult-to-culture pathogens from clinical samples. We have recently shown that by concatenating IMS, MDA and real-time PCR, we could detect low levels of Salmonella enterica (~10 CFU/g) in raw chicken breast without culture enrichment (Hyeon and Deng, Food Microbiology, 2017) In this study, we aimed to develop a workflow that consists of 1) specific concentration of Salmonella cells, 2) high-efficiency amplification of bacterial genomes, and 3) molecular detection of Salmonella. The modular design of this workflow allows customized combination of different sample processing and detection methods to meet specific detection need for speed, sensitivity or specificity. In particular, we will demonstrate that the use of a novel magnetoelastic biosensor (Chai et al., Journal of Food Protection, 2012) and whole genome sequencing (WGS) can allow strain-level identification of Salmonella from raw chicken with no or shortened culture enrichment.

Volume Adjustable Topology Optimization with Multiple Displacement Constraints

AbstractMost topology optimization methods seek optimal topologies that satisfy a minimum compliance with a pre-specified volume constraint in the design domain. However, practical designs often include various functional constraints and the optimal solid volume ratios are unknown a priori, which implies a gap between topology optimization methods and practical designs in industries. This paper studies the performance-based topology optimization (PTO) problem that searches for the optimal topology with minimum compliance to satisfy the pre-specified functional constraints without a pre-specified volume constraint. A novel element-based evolutionary switching method (ESM), which can automatically adjust solid volume ratio and material distribution, is developed and implemented using the commercial finite element software ABAQUS. The effects of displacement constraints on the optimal topologies are investigated, and the differences between PTO problems and the topology optimization problem which has a volume constraint are discussed. Numerical examples demonstrate that the optimal topologies are mainly determined by the load pattern and locally changed with respect to the location of the active displacement constraints. In addition, the displacement constraints to a large extent control the solid volume ratio of optimal topologies according to the allowable displacements in PTO problems. Finally, the proposed ESM could provide conservative solutions to the topology optimization with multiple displacement constraints problems.