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Journal articles on the topic 'Ultrafast PCR'

Author: Grafiati

Published: 6 September 2023

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1

Son, Jun Ho, Byungrae Cho, SoonGweon Hong, Sang Hun Lee, Ori Hoxha, Amanda J. Haack, and Luke P. Lee. "Ultrafast photonic PCR." Light: Science & Applications 4, no. 7 (July 2015): e280-e280. http://dx.doi.org/10.1038/lsa.2015.53.

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2

You, Minli, Lei Cao, and Feng Xu. "Plasmon-Driven Ultrafast Photonic PCR." Trends in Biochemical Sciences 45, no. 2 (February 2020): 174–75. http://dx.doi.org/10.1016/j.tibs.2019.11.007.

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3

SUL, SUYEON, MI-JU KIM, JUNG-MIN LEE, SUNG-YEON KIM, and HAE-YEONG KIM. "Development of a Rapid On-Site Method for the Detection of Chicken Meat in Processed Ground Meat Products by Using a Direct Ultrafast PCR System." Journal of Food Protection 83, no. 6 (February 7, 2020): 984–90. http://dx.doi.org/10.4315/jfp-19-583.

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ABSTRACT In this study, we developed a rapid on-site detection method by using direct ultrafast PCR coupled with a microfluidic chip to identify the presence of chicken meat in processed ground meat products. Chicken-specific PCR primer targeting mitochondrial 16S rRNA gene was newly designed, and its specificity was confirmed against 17 other animal species and 4 different chicken meat samples from different countries of origin. The sensitivity of the chicken-specific ultrafast PCR was 0.1 pg of chicken DNA. To evaluate the limit of detection of the direct ultrafast PCR method, different percentages of chicken meat mixed with pork or beef were prepared. The limit of detection of the direct ultrafast PCR method for the chicken meat–pork and chicken meat–beef mixtures was 0.1% for both raw meat and autoclaved meat. This method was used for 15 commercialized processed ground meat products. In this method, the target sequence was successfully amplified, and the presence of chicken meat in processed ground meat products was identified within approximately 25 min, including the time for sample preparation. Thus, our study shows that this developed direct ultrafast PCR method is a rapid and accurate method for on-site detection of chicken DNA in commercial food products. HIGHLIGHTS

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4

You, Minli, Zedong Li, Shangsheng Feng, Bin Gao, Chunyan Yao, Jie Hu, and Feng Xu. "Ultrafast Photonic PCR Based on Photothermal Nanomaterials." Trends in Biotechnology 38, no. 6 (June 2020): 637–49. http://dx.doi.org/10.1016/j.tibtech.2019.12.006.

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5

Bang, Doyeon, Jonghwan Lee, SoonGweon Hong, Min Sun Song, and Luke P. Lee. "Nanocrescent Optical Antennas for Ultrafast Photonic PCR." Biophysical Journal 114, no. 3 (February 2018): 693a. http://dx.doi.org/10.1016/j.bpj.2017.11.3736.

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6

Lin, Yen-Heng, Xiang-Jun Liao, Wei Chang, and Chiuan-Chian Chiou. "Ultrafast DNA Amplification Using Microchannel Flow-Through PCR Device." Biosensors 12, no. 5 (May 6, 2022): 303. http://dx.doi.org/10.3390/bios12050303.

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Polymerase chain reaction (PCR) is limited by the long reaction time for point-of-care. Currently, commercial benchtop rapid PCR requires 30–40 min, and this time is limited by the absence of rapid and stable heating and cooling platforms rather than the biochemical reaction kinetics. This study develops an ultrafast PCR (<3 min) platform using flow-through microchannel chips. An actin gene amplicon with a length of 151 base-pairs in the whole genome was used to verify the ultrafast PCR microfluidic chip. The results demonstrated that the channel of 56 μm height can provide fast heat conduction and the channel length should not be short. Under certain denaturation and annealing/extension times, a short channel design will cause the sample to drive slowly in the microchannel with insufficient pressure in the channel, causing the fluid to generate bubbles in the high-temperature zone and subsequently destabilizing the flow. The chips used in the experiment can complete 40 thermal cycles within 160 s through a design with the 56 µm channel height and with each thermal circle measuring 4 cm long. The calculation shows that the DNA extension speed is ~60 base-pairs/s, which is consistent with the theoretical speed of the Klen Taq extension used, and the detection limit can reach 67 copies. The heat transfer time of the reagent on this platform is very short. The simple chip design and fabrication are suitable for the development of commercial ultrafast PCR chips.

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7

An, Yi-Quan, Shao-Lei Huang, Bang-Chao Xi, Xiang-Lian Gong, Jun-Hao Ji, You Hu, Yi-Jie Ding, et al. "Ultrafast Microfluidic PCR Thermocycler for Nucleic Acid Amplification." Micromachines 14, no. 3 (March 15, 2023): 658. http://dx.doi.org/10.3390/mi14030658.

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The polymerase chain reaction (PCR) is essential in nucleic acid amplification tests and is widely used in many applications such as infectious disease detection, tumor screening, and food safety testing; however, most PCR devices have inefficient heating and cooling ramp rates for the solution, which significantly limit their application in special scenarios such as hospital emergencies, airports, and customs. Here, we propose a temperature control strategy to significantly increase the ramp rates for the solution temperature by switching microfluidic chips between multiple temperature zones and excessively increasing the temperature difference between temperature zones and the solution; accordingly, we have designed an ultrafast thermocycler. The results showed that the ramp rates of the solution temperature are a linear function of temperature differences within a range, and a larger temperature difference would result in faster ramp rates. The maximum heating and cooling ramp rates of the 25 μL solution reached 24.12 °C/s and 25.28 °C/s, respectively, and the average ramp rate was 13.33 °C/s, 6–8 times higher than that of conventional commercial PCR devices. The thermocycler achieved 9 min (1 min pre-denaturation + 45 PCR cycles) ultrafast nucleic acid amplification, shortening the time by 92% compared to the conventional 120 min nucleic acid amplification, and has the potential to be used for rapid nucleic acid detection.

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8

Donia, Domenica Tommasa. "qRT-PCR for enterovirus detection: Conversion to ultrafast protocols." Journal of King Saud University - Science 30, no. 2 (April 2018): 180–84. http://dx.doi.org/10.1016/j.jksus.2017.04.003.

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9

Lee, Jonghwan, SoonGweon Hong, and Luke P. Lee. "Ultrafast Photonic PCR-based Precision Molecular Diagnostics for Dengue." Biophysical Journal 114, no. 3 (February 2018): 175a—176a. http://dx.doi.org/10.1016/j.bpj.2017.11.980.

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10

Chen, Xiaojing, Yiteng Liu, Xuan Zhan, Yibo Gao, Zhongyi Sun, Weijia Wen, and Weidong Zheng. "Ultrafast PCR Detection of COVID-19 by Using a Microfluidic Chip-Based System." Bioengineering 9, no. 10 (October 13, 2022): 548. http://dx.doi.org/10.3390/bioengineering9100548.

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With the evolution of the pandemic caused by the Coronavirus disease of 2019 (COVID-19), reverse transcriptase-polymerase chain reactions (RT-PCR) have invariably been a golden standard in clinical diagnosis. Nevertheless, the traditional polymerase chain reaction (PCR) is not feasible for field application due to its drawbacks, such as time-consuming and laboratory-based dependence. To overcome these challenges, a microchip-based ultrafast PCR system called SWM-02 was proposed to make PCR assay in a rapid, portable, and low-cost strategy. This novel platform can perform 6-sample detection per run using multiple fluorescent channels and complete an ultrafast COVID-19 RT-PCR test within 40 min. Here, we evaluated the performance of the microdevice using the gradient-diluted COVID-19 reference samples and commercial PCR kit and determined its limit-of-detection (LoD) as 500 copies/mL, whose variation coefficients for the nucleocapsid (N) gene and open reading frame 1 ab region (ORF1ab) gene are 1.427% and 0.7872%, respectively. The system also revealed an excellent linear correlation between cycle threshold (Ct) values and dilution factors (R2 > 0.99). Additionally, we successfully detected the target RNAs and internal gene in the clinical samples by fast PCR, which shows strong consistency with conventional PCR protocol. Hence, with compact dimension, user-friendly design, and fast processing time, SWM-02 has the capability of offering timely and sensitive on-site molecular diagnosis for prevention and control of pathogen transmission.

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11

Jung, Jae Hwan, Seok Jin Choi, Byung Hyun Park, Young Ki Choi, and Tae Seok Seo. "Ultrafast Rotary PCR system for multiple influenza viral RNA detection." Lab on a Chip 12, no. 9 (2012): 1598. http://dx.doi.org/10.1039/c2lc21269b.

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12

Zhang, Jiali, Zhuo Yang, Liying Liu, Tinglu Zhang, Lilei Hu, Chunrui Hu, Hu Chen, Ruihua Ding, Bo Liu, and Chang Chen. "Ultrafast Nucleic Acid Detection Equipment with Silicon-Based Microfluidic Chip." Biosensors 13, no. 2 (February 7, 2023): 234. http://dx.doi.org/10.3390/bios13020234.

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Recently, infectious diseases, such as COVID-19, monkeypox, and Ebola, are plaguing human beings. Rapid and accurate diagnosis methods are required to preclude the spread of diseases. In this paper, an ultrafast polymerase chain reaction (PCR) equipment is designed to detect virus. The equipment consists of a silicon-based PCR chip, a thermocycling module, an optical detection module, and a control module. Silicon-based chip, with its thermal and fluid design, is used to improve detection efficiency. A thermoelectric cooler (TEC), together with a computer-controlled proportional–integral–derivative (PID) controller, is applied to accelerate the thermal cycle. A maximum of four samples can be tested simultaneously on the chip. Two kinds of fluorescent molecules can be detected by optical detection module. The equipment can detect viruses with 40 PCR amplification cycles in 5 min. The equipment is portable, easily operated, and low equipment cost, which shows great potential in epidemic prevention.

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13

Kim, Seok Hwan, Yu-Si Lee, In-Sun Joo, Hyo Sun Kwak, Gyung Tae Chung, and Soon Han Kim. "Rapid Detection for Salmonella spp. by Ultrafast Real-time PCR Assay." Journal of Food Hygiene and Safety 33, no. 1 (February 28, 2018): 50–57. http://dx.doi.org/10.13103/jfhs.2018.33.1.50.

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14

Jabasini, M., A. A. Ewis, F. Xu, M. R. Mohamadi, G. Ping, T. Shinka, Y. Nakahori, and Y. Baba. "Multiplex PCR with Multichannel Microchip Electrophoresis: An Ultrafast Analysis for Genetic Diseases." Journal of Chromatographic Science 43, no. 5 (May 1, 2005): 221–25. http://dx.doi.org/10.1093/chromsci/43.5.221.

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15

Murphy, K., T. Raj, R. S. Winters, and P. S. White. "me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements." Bioinformatics 20, no. 4 (January 22, 2004): 588–90. http://dx.doi.org/10.1093/bioinformatics/btg466.

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16

Agrawal, Megha. "On-Chip PCR Based Plasmonic Microfluidic Platform: Ultrafast Point-of-Care Diagnostics of SARS-CoV-2." Biotechnology Kiosk 3, no. 1 (January 7, 2021): 5–11. http://dx.doi.org/10.37756/bk.21.3.1.1.

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It is critically important to have rapid screening and identification of contagious viral diseases such as the current COVID-19 pandemic that is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rapid and accurate diagnostic is essential for preventing worldwide spread of virus and ensuring in-time care for patients during the fast spread of pandemic diseases. Nanobiotechnology enabled tools have allowed to develop advanced polymerase chain reaction (PCR) based diagnostics of contagious viral diseases. To this end, microfluidic on-chip PCR platforms have shown huge promise for highly efficient, rapid and small-volume bioassay for point-of-care (POC) diagnostic applications in mitigating the challenges of SARS-CoV-2. Here, we discuss latest advances in ultrafast, real-time, and on-chip nanoplasmonic PCR for rapid and quantitative molecular diagnostics at POC level.

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17

Steijns, Linda S. W., and Jan Van Der Weide. "Ultrarapid drug metabolism: PCR-based detection of CYP2D6 gene duplication." Clinical Chemistry 44, no. 5 (May 1, 1998): 914–17. http://dx.doi.org/10.1093/clinchem/44.5.914.

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Abstract The enzyme debrisoquine 4-hydroxylase (CYP2D6), which metabolizes many widely used drugs, is highly polymorphic. The activity of the enzyme ranges between subjects from ultrafast to a complete absence. Therefore, metabolic capacity varies, producing intersubject differences in therapeutic efficacy and side effects at standard recommended doses. Up to 7% of Caucasians may demonstrate ultrarapid drug metabolism (UM) because of inherited alleles with multiplicate functional CYP2D6 genes, causing an increased amount of enzyme to be expressed. Identification of UM subjects is of potential clinical importance for adjustment of doses in drug therapy, as well as to avoid misidentification of noncompliance. In our study, we tested recently designed PCR assays for the detection of the UM genotype. We found a 3.5% prevalence of UMs carrying duplicate active CYP2D6 genes in a population consisting of 202 psychiatric patients.

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18

Lee, Ga-Young, Eiseul Kim, Seung-Min Yang, and Hae-Yeong Kim. "Rapid On-Site Identification for Three Arcidae Species (Anadara kagoshimensis, Tegillarca granosa, and Anadara broughtonii) Using Ultrafast PCR Combined with Direct DNA Extraction." Foods 11, no. 16 (August 14, 2022): 2449. http://dx.doi.org/10.3390/foods11162449.

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Granular ark (Tegillarca granosa), broughton’s ribbed ark (Anadara broughtonii), and half-crenate ark (Anadara kagoshimensis) are important fishery resources throughout Asia; granular ark exhibiting a higher economic value due to its rarity. However, due to the similar morphological characteristics of the three species, the less valuable species could be exploited for food fraud. In this study, we developed a rapid on-site identification method based on a microfluidic chip for the detection of the three ark shell species. We designed new species-specific primers, targeting the genes encoding mitochondrial cytochrome b or cytochrome c oxidase I, for the identification of the three ark shells and estimated their specificity against 17 species, which amplified only the target species. The sensitivity of each primer was 0.001 ng. In addition, this method was further improved to develop a direct ultrafast polymerase chain reaction (PCR) for on-site food monitoring, which would allow for completing the entire procedure (from sampling to obtaining the results) within 25 min without DNA extraction. Our direct, ultrafast PCR was successfully applied to differentiate the three species from 29 commercial products. Therefore, this assay could be used as a rapid and cost-effective approach for the on-site identification of ark shells in commercial food products.

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19

Fillerova, Regina, Jiri Gallo, Martin Radvansky, Veronika Kraiczova, Milos Kudelka, and Eva Kriegova. "Excellent Diagnostic Characteristics for Ultrafast Gene Profiling ofDEFA1-IL1B-LTFin Detection of Prosthetic Joint Infections." Journal of Clinical Microbiology 55, no. 9 (June 21, 2017): 2686–97. http://dx.doi.org/10.1128/jcm.00558-17.

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ABSTRACTThe timely and exact diagnosis of prosthetic joint infection (PJI) is crucial for surgical decision-making. Intraoperatively, delivery of the result within an hour is required. Alpha-defensin lateral immunoassay of joint fluid (JF) is precise for the intraoperative exclusion of PJI; however, for patients with a limited amount of JF and/or in cases where the JF is bloody, this test is unhelpful. Important information is hidden in periprosthetic tissues that may much better reflect the current status of implant pathology. We therefore investigated the utility of the gene expression patterns of 12 candidate genes (TLR1, -2, -4, -6, and10,DEFA1,LTF,IL1B,BPI,CRP,IFNG, andDEFB4A) previously associated with infection for detection of PJI in periprosthetic tissues of patients with total joint arthroplasty (TJA) (n= 76) reoperated for PJI (n= 38) or aseptic failure (n= 38), using the ultrafast quantitative reverse transcription-PCR (RT-PCR) Xxpress system (BJS Biotechnologies Ltd.). Advanced data-mining algorithms were applied for data analysis. For PJI, we detected elevated mRNA expression levels ofDEFA1(P< 0.0001),IL1B(P< 0.0001),LTF(P< 0.0001),TLR1(P= 0.02), andBPI(P= 0.01) in comparison to those in tissues from aseptic cases. A feature selection algorithm revealed that theDEFA1-IL1B-LTFpattern was the most appropriate for detection/exclusion of PJI, achieving 94.5% sensitivity and 95.7% specificity, with likelihood ratios (LRs) for positive and negative results of 16.3 and 0.06, respectively. Taken together, the results show thatDEFA1-IL1B-LTFgene expression detection by use of ultrafast qRT-PCR linked to an electronic calculator allows detection of patients with a high probability of PJI within 45 min after sampling. Further testing on a larger cohort of patients is needed.

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20

Wang, Rui, Rui Chen, Cheng Qian, Yanan Pang, Jian Wu, and Fuyou Li. "Ultrafast visual nucleic acid detection with CRISPR/Cas12a and rapid PCR in single capillary." Sensors and Actuators B: Chemical 326 (January 2021): 128618. http://dx.doi.org/10.1016/j.snb.2020.128618.

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21

Kim, Mi-Ju, Hee-In Kim, Jae-Hwan Kim, Seung-Man Suh, and Hae-Yeong Kim. "Rapid on-site detection of shrimp allergen tropomyosin using a novel ultrafast PCR system." Food Science and Biotechnology 28, no. 2 (September 27, 2018): 591–97. http://dx.doi.org/10.1007/s10068-018-0479-x.

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22

Kim, Mi-Ju, Sung-Yeon Kim, Seul-Ki Jung, Myo-Young Kim, and Hae-Yeong Kim. "Development and validation of ultrafast PCR assays to detect six species of edible insects." Food Control 103 (September 2019): 21–26. http://dx.doi.org/10.1016/j.foodcont.2019.03.039.

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23

Yin, Hao, Zhenhua Wu, Nan Shi, Yong Qi, Xiaoyu Jian, Lin Zhou, Yigang Tong, Zule Cheng, Jianlong Zhao, and Hongju Mao. "Ultrafast multiplexed detection of SARS-CoV-2 RNA using a rapid droplet digital PCR system." Biosensors and Bioelectronics 188 (September 2021): 113282. http://dx.doi.org/10.1016/j.bios.2021.113282.

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24

Houssin, Timothée, Jérémy Cramer, Rébecca Grojsman, Lyes Bellahsene, Guillaume Colas, Hélène Moulet, Walter Minnella, et al. "Ultrafast, sensitive and large-volume on-chip real-time PCR for the molecular diagnosis of bacterial and viral infections." Lab on a Chip 16, no. 8 (2016): 1401–11. http://dx.doi.org/10.1039/c5lc01459j.

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25

Jiang, Kunlun, Jung-Hoon Lee, To Sing Fung, Jingrui Wu, Congnuan Liu, Hua Mi, R. P. V. Jayanthe Rajapakse, Udeni B. R. Balasuriya, Yung-Kang Peng, and Yun Young Go. "Next-generation diagnostic test for dengue virus detection using an ultrafast plasmonic colorimetric RT-PCR strategy." Analytica Chimica Acta 1274 (September 2023): 341565. http://dx.doi.org/10.1016/j.aca.2023.341565.

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26

Hersberger, Martin, Jacqueline Marti-Jaun, Katharina Rentsch, and Edgar Hänseler. "Rapid Detection of the CYP2D6*3, CYP2D6*4, and CYP2D6*6 Alleles by Tetra-Primer PCR and of the CYP2D6*5 Allele by Multiplex Long PCR." Clinical Chemistry 46, no. 8 (August 1, 2000): 1072–77. http://dx.doi.org/10.1093/clinchem/46.8.1072.

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Abstract Background: Interindividual differences in CYP2D6 activity range from total absence of metabolism of certain drugs to ultrafast metabolism and can produce adverse effects or lack of therapeutic effect under standard therapy. Several mutations have been described in the CYP2D6 gene that abolish CYP2D6 activity. However, four mutations explain the majority of the poor metabolizers. We describe four single-tube assays to detect these mutations. Methods: Three tetra-primer PCR assays were developed to detect the mutations in the CYP2D6*3, *4, and *6 alleles. In these single-tube assays, the CYP2D6 locus is amplified directly, followed by the allele-specific amplification on this new template. In addition, a multiplex long PCR was developed to genotype the CYP2D6*5 allele. Two long PCR amplifications for detection of the deletion of CYP2D6 (*5) and for detection of the CYP2D6 gene region were combined in one tube. Results: Analysis of 114 alleles showed no CYP2D6*3 allele, and allele frequencies of 28.1% for CYP2D6*4, 2.6% for CYP2D6*5, and 0.9% for CYP2D6*6. Re-analysis of the DNA samples by restriction fragment length polymorphism and sequencing analysis confirmed these results. Furthermore, re-analysis of sequenced genomic DNA by tetra-primer PCR analysis (7–11 times) always showed identical results. Conclusions: Our set of single-tube assays allows rapid and reproducible genotyping of the majority of CYP2D6 poor metabolizers.

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27

Pérez-Lago, Laura, Marta Herranz, Iñaki Comas, María Jesús Ruiz-Serrano, Paula López Roa, Emilio Bouza, and Darío García-de-Viedma. "Ultrafast Assessment of the Presence of a High-Risk Mycobacterium tuberculosis Strain in a Population." Journal of Clinical Microbiology 54, no. 3 (December 30, 2015): 779–81. http://dx.doi.org/10.1128/jcm.02851-15.

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A persistent 8-year infection by a BeijingMycobacterium tuberculosisstrain from a previous outbreak after importation from West Africa obliged us to investigate secondary cases. We developed a multiplex PCR method based on whole-genome sequencing to target strain-specific single nucleotide polymorphisms (SNPs). In 1 week, we analyzed 868 isolates stored over 6 years. Only 2 cases (immigrants from Guinea Conakry) harbored the strain, which ruled out transmission—despite opportunities—and challenged some of the advantages associated with Beijing strains.

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Kim, Mi-Ju, Saet-Byul Park, Hyeon-Bee Kang, Kyung-Mi Lee, and Hae-Yeong Kim. "Development of ultrafast PCR for rapid detection of buckwheat allergen DNA (fag e 1) in processed foods." Food Control 130 (December 2021): 108334. http://dx.doi.org/10.1016/j.foodcont.2021.108334.

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29

JABASINI, Mohammad, Ashraf A. EWIS, Feng XU, Guichen PING, Maged FOUAD, Toshikatsu SHINKA, Yutaka NAKAHORI, Mitsuru ISHIKAWA, and Yoshinobu BABA. "Ultrafast Diagnosis of the Genetic-related Disorders Using the Combined Technologies of Multiplex PCR and Multichannel Microchip Electrophoresis." Analytical Sciences 21, no. 12 (2005): 1537–39. http://dx.doi.org/10.2116/analsci.21.1537.

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Li, Jiale, Jie Li, Shenghao Lin, Longjiao Zhu, Xiangyang Li, and Wentao Xu. "Advanced Technologies in On-Site Detection of Genetically Modified Products." Agriculture 12, no. 6 (June 20, 2022): 888. http://dx.doi.org/10.3390/agriculture12060888.

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Transgenic technology is significantly impacting life today. However, with the advancement of genetically modified technologies and the success of genetically modified product commercialization, new challenges have arisen for associated detecting technologies. The need for fast, precise, and portable systems for the on-site detection of genetically modified products has increased dramatically in recent years. This perspective examined the currently available technological support for portable immune biosensing, discussed a portable detection device for ultrafast PCR, and an on-site detection biosensor based on functional nucleic acid and superior detection devices in the field. Moreover, the on-site sequencing of genetically modified organisms was mentioned briefly. Lastly, the future outlook of genetically modified products detection was concluded and discussed in order to provide a comprehensive reference for future research and development in related fields.

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31

Tsai, Hsin-Yi, Liang-Chieh Chao, Chun-Han Chou, Yu-Hsuan Lin, Kuo-Cheng Huang, Min-Chi Hsieh, Yen-Ting Liao, Pei-Wen Wang, and Dar-Bin Shieh. "Enhanced fluorescence signal using stray light shutter in a quantitative PCR chip." Journal of Optics 24, no. 2 (December 31, 2021): 024003. http://dx.doi.org/10.1088/2040-8986/ac388f.

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Abstract Quantitative polymerase chain reaction (qPCR) is the most important quantitative sensing technique for pathogens, especially for emerging pandemics such as the coronavirus outbreak this year. The qPCR chip and device were investigated to meet the unmet needs of ultrafast inspection time, high accuracy, and small system volume. Therein, the fluorescence intensity was the most important signal in qPCR quantification of DNA amplifications, which is essential not only in the confirmative diagnosis of positive or negative infection, but also in the assessment of viral load for therapeutic and quarantine decision making. As the target DNAs got amplified, the interaction of fluorescence dye and double strand DNA will generate fluorescence signal proportional to amplified DNA in the intensity when excited by certain wavelength. A miniature spectro-detector was employed to receive the fluorescence scattering for digital output of the intensity in the qPCR chip in this study, and the optical simulation and actual experimental design and results according to the optical simulation results were performed to study the effect of the stray light shutter (SLS) in the improvement of the signal in fluorescence detection. The analysis results showed that the signal-to-noise ratio (SNR) of the fluorescence can be enhanced significantly for five times of the control using the SLS with a shape of extended component aperture, where the protruding structure was positioned away from the center. The experimental results showed that fluorescence intensity can be enhanced by 15.50% and 9.86% when adding the above shape of SLS in resin- and in glass-based chip, respectively. The results also demonstrated that the optical setup had good stability and repeatability in fluorescence detection, and variation was less than 1.00%. Our results can provide important reference to the development of qPCR chip to obtain the high SNR fluorescence signal in DNA quantification process.

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Tan, J., C. Zhou, X. Gao, M. Long, and H. Cao. "A NOVEL ULTRAFAST REAL-TIME PCR INSTRUMENT FOR RAPID DETECTION OF SARS-COV-2 NUCLEIC ACIDS IN 30 MINUTES." International Journal of Infectious Diseases 130 (May 2023): S100—S101. http://dx.doi.org/10.1016/j.ijid.2023.04.250.

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33

Ma, Jun-Yuan, Xiao-Fu Wang, Cheng Peng, Xiao-Yun Chen, Xiao-Li Xu, Wei Wei, Lei Yang, Jian Cai, and Jun-Feng Xu. "SMART: On-Site Rapid Detection of Nucleic Acid from Plants, Animals, and Microorganisms in under 25 Minutes." Biosensors 13, no. 1 (January 3, 2023): 82. http://dx.doi.org/10.3390/bios13010082.

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The rapid on-site nucleic acid detection method is urgently required in many fields. In this study, we report a portable and highly integrated device for DNA detection that combines ultrafast DNA adsorption and rapid DNA amplification. The device, known as silicon film mediated recombinase polymerase amplification (RPA) for nucleic acid detection (SMART), can detect target DNA in less than 25 min from plants, animals, and microbes. Utilizing SMART, transgenic maize was rapidly detected with high selectivity and sensitivity. The sensitivity threshold of the SMART for transgenic maize genomic DNA was 50 copies. The detection results of genuine samples containing plants, animals, and microbes by SMART were consistent with the conventional polymerase chain reaction (PCR) method, demonstrating the high robustness of SMART. Additionally, SMART does not require expensive equipment and is fast, affordable, and user-friendly, making it suited for the broad-scale on-site detection of nucleic acids.

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Park, Ji-Eun, Do-Geun Lee, Hong-Rae Kim, Mi-Ju Kim, Hae-Yeong Kim, and Hyun-Joong Kim. "Development of ultrafast PCR assays for the event-specific detection of eleven approved genetically modified canola events in South Korea." Food Chemistry 373 (March 2022): 131419. http://dx.doi.org/10.1016/j.foodchem.2021.131419.

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35

Gao, Wei, Jingjing Tian, Kunlun Huang, Zhansen Yang, Wentao Xu, and Yunbo Luo. "Ultrafast, universal and visual screening of dual genetically modified elements based on dual super PCR and a lateral flow biosensor." Food Chemistry 279 (May 2019): 246–51. http://dx.doi.org/10.1016/j.foodchem.2018.12.013.

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Kassem, Mahmoud, Daniel Goldstein, Patrick Schnell, Michael Grimm, Dionisia Marie Quiroga, Abdul Miah, Craig Vargo, et al. "Association of pathological complete response rates and TILs in triple-negative breast cancer patients." Journal of Clinical Oncology 39, no. 15_suppl (May 20, 2021): e12596-e12596. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.e12596.

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e12596 Background: Triple negative breast cancers (TNBC), characterized by the lack of expression of estrogen receptors and progesterone receptors as well as human epidermal growth factor receptor 2, are associated with high distant recurrence rate and death. As a result, the majority of patients with TNBC are treated with perioperative chemotherapy with the goal of eradicating micrometastases and preventing distrant relapse. The preoperative systemic therapy offers the advantages of permitting an assessment of chemo-sensitivity, increased rates of breast conserving surgery and the ability to adapt postoperative therapies depending on the response. Recently, neoadjuvant chemotherapy has been used at an increasing frequency. The response to neoadjuvant chemotherapy, as measured by the residual cancer burden index, for example, is correlated with the long-term prognosis of TNBC and HER2 expressing breast cancers. Previous studies suggest that tumor-infiltrating lymphocytes (TILs) may correlate with pathological complete response (pCR) rates in TNBC patients treated with neoadjuvant chemotherapy. The pathologic evaluation of TILs in TNBC has been recommended by the International TILs working group since 2014. In this study we sought to analyze the association of TILs with pCR in a cohort of TNBC patients treated with neoadjuvant chemotherapy. Methods: An IRB-approved single-institution retrospective analysis was performed on 127 patients diagnosed with TNBC who received neoadjuvant anthracycline and taxane based chemotherapy at the Ohio State University Comprehensive Cancer Center between January 1st, 2012 and November 31st, 2018. We analyzed TILs as a continuous variable as a part of a secondary analysis of this data. Whole tissue sections from archived H&E stained glass slides were scanned using Philips UltraFast Scanner at ×40 magnification with a single-focus layer. TIL scoring was performed according to guideline recommendations from the International TILs Working Group (2014). Results: A total of 127 female patients with TNBC were identified. The median age at diagnosis was 52.0 years (range 32.0, 74.0) and patients were predominately white (103, 81%), post-menopausal (68, 53.5%) and presented with invasive ductal cancer (113, 89%), stage II (88, 69%), and high grade (108, 85%). Of those patients, 56 had TILs measurement available. pCR was associated with statistically higher level of TILs in core biopsies taken prior to chemotherapy had (Wilcoxon rank-sum test, p = 0.04). Conclusions: The long-term prognosis of patients with TNBC is predicted by the response to neoadjuvant chemotherapy. Consistent with other studies, our study revealed that TILs are associated with a higher probability of pCR. Our future goals are to identify which TIL subsets correlate best with pCR and to identify the mechanism for the increased chemotherapy responsiveness of lymphocyte-infiltrated tumors.

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Maalouf, Mathieu, Alain Abou Khalil, Yoan Di Maio, Steve Papa, Xxx Sedao, Elisa Dalix, Sylvie Peyroche, Alain Guignandon, and Virginie Dumas. "Polarization of Femtosecond Laser for Titanium Alloy Nanopatterning Influences Osteoblastic Differentiation." Nanomaterials 12, no. 10 (May 10, 2022): 1619. http://dx.doi.org/10.3390/nano12101619.

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Ultrashort pulse lasers have significant advantages over conventional continuous wave and long pulse lasers for the texturing of metallic surfaces, especially for nanoscale surface structure patterning. Furthermore, ultrafast laser beam polarization allows for the precise control of the spatial alignment of nanotextures imprinted on titanium-based implant surfaces. In this article, we report the biological effect of beam polarization on human mesenchymal stem cell differentiation. We created, on polished titanium-6aluminum-4vanadium (Ti-6Al-4V) plates, a laser-induced periodic surface structure (LIPSS) using linear or azimuthal polarization of infrared beams to generate linear or radial LIPSS, respectively. The main difference between the two surfaces was the microstructural anisotropy of the linear LIPSS and the isotropy of the radial LIPSS. At 7 d post seeding, cells on the radial LIPSS surface showed the highest extracellular fibronectin production. At 14 days, qRT-PCR showed on the same surface an increase in osteogenesis-related genes, such as alkaline phosphatase and osterix. At 21 d, mineralization clusters indicative of final osteoinduction were more abundant on the radial LIPSS. Taken together, we identified that creating more isotropic than linear surfaces enhances cell differentiation, resulting in an improved osseointegration. Thus, the fine tuning of ultrashort pulse lasers may be a promising new route for the functionalization of medical implants.

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Ragazzo, Michele, Stefano Melchiorri, Laura Manzo, Valeria Errichiello, Giulio Puleri, Fabio Nicastro, and Emiliano Giardina. "Comparative Analysis of ANDE 6C Rapid DNA Analysis System and Traditional Methods." Genes 11, no. 5 (May 22, 2020): 582. http://dx.doi.org/10.3390/genes11050582.

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Rapid DNA analysis is an ultrafast and fully automated DNA-typing system, which can produce interpretable genetic profiles from biological samples within 90 minutes. This “swab in—profile out” method comprises DNA extraction, amplification by PCR multiplex, separation and detection of DNA fragments by capillary electrophoresis. The aim of study was the validation of the Accelerated Nuclear DNA Equipment (ANDE) 6C system as a typing method for reference samples according to the ISO/IEC 17025 standard. Here, we report the evaluation of the validity and reproducibility of results by the comparison of the genetic profiles generated by the ANDE 6C System with those generated by standard technologies. A quantity of 104 buccal swabs were analyzed both through the ANDE 6C technology and the traditional method (DNA extraction and quantification, amplification and separation by capillary electrophoresis). Positive typing was observed in 97% of cases for ANDE 6C technology with only three buccal swabs failing to reveal interpretable signals. Concordance was determined by comparing the allele calls generated by ANDE 6C and conventional technology. Comparison of 2800 genotypes revealed a concordance rate of 99.96%. These results met the ISO/IEC 17025 requirements, enabling us to receive the accreditation for this method. Finally, rapid technology has certainly reached a level of reliability which has made its use in laboratories of forensic genetics a reality.

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Kim, Hyun Gi, and Jang Hoon Lee. "Feasibility of Ultrafast Doppler technique for cranial ultrasound in neonates." Medical Ultrasonography 21, no. 3 (August 31, 2019): 288. http://dx.doi.org/10.11152/mu-1901.

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Aims: The aim of this study was to compare the performances of Ultrafast Doppler ultrasound (US) with classic Doppler US, for cranial ultrasound in neonates.Materials and methods: We measured the peak systolic velocity (PSV), end-diastolic velocity (EDV) and resistive index (RI) of the anterior cerebral artery (ACA), middle cerebral artery (MCA) and posterior cerebral artery (PCA) in neonates using both conventional and Ultrafast Doppler US and acquisition times were compared. Distal ACA branches were assessed with Ultrafast Doppler US.Results: A total of 138 neonates were included. The PSV and EDV of the cranial arteries were comparable between the two Doppler methods (PSV, 64.6-85.5 cm/s vs. 63.4-84.1 cm/s, p=0.100-0.510; EDV, 19.1-26.5 cm/s vs. 17.8-24.2 cm/s, p=0.100-0.981). The RIs of the ACA and PCA were not significantly different (0.69-0.73 vs 0.68-0.74, p=0.174-0.810). Ultrafast Doppler US required shorter acquisition times than conventional Doppler US (6.7 s vs. 11.0 s, p=0.003). The PSV and EDV of the distal ACA were higher than the proximal ACA (20.1-63.3 cm/s vs. 9.4-36.7, p<0.001) although the RI was similar (0.69 vs. 0.68, p=0.251).Conclusions: Ultrafast Doppler US provides comparable values to conventional Doppler US with shorter acquisition times. This novel imaging technique provides quantitative information and is suitable for distal cranial artery evaluation.

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Alkeskjold, Thomas T., Marko Laurila, Johannes Weirich, Mette M. Johansen, Christina B. Olausson, Ole Lumholt, Danny Noordegraaf, Martin D. Maack, and Christian Jakobsen. "Photonic crystal fiber amplifiers for high power ultrafast fiber lasers." Nanophotonics 2, no. 5-6 (December 16, 2013): 369–81. http://dx.doi.org/10.1515/nanoph-2013-0050.

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AbstractIn recent years, ultrafast laser systems using large-mode-area fiber amplifiers delivering several hundreds of watts of average power has attracted significant academic and industrial interest. These amplifiers can generate hundreds of kilowatts to megawatts of peak power using direct amplification and multi-gigawatts of peak power using pulse stretching techniques. These amplifiers are enabled by advancements in Photonic Crystal Fiber (PCF) design and manufacturing technology. In this paper, we will give a short overview of state-of-the-art PCF amplifiers and describe the performance in ultrafast ps laser systems.

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Gong, Jia-Min, and Zhan-Qiang Hui. "Experimental demonstration of all optical 100 Gbit/s wavelength conversion with 1-to-2 wavelength multicasting based on cross-phase modulation in dispersion flattened highly nonlinear photonic crystal fiber." Journal of Nonlinear Optical Physics & Materials 23, no. 03 (September 2014): 1450038. http://dx.doi.org/10.1142/s0218863514500386.

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This paper proposed and experimentally demonstrated the effective design of a single-to-dual channel 100 Gbit/s wavelength converter with a simple configuration consisting of a single dispersion flattened highly nonlinear photonic crystal fiber (DS-HNL-PCF) and two optical bandpass filters (OBPFs). The polarity-preserved, ultrafast wavelength conversion with single-to-dual channel multicasting is achieved by simultaneously filtering the red- and blue-chirped spectral component of a probe light. Moreover, the wavelength tunability and dynamic characteristics of designed wavelength converter are investigated. The results show that the designed ultrafast wavelength converter has a wide wavelength conversion range of 29 nm, and high tolerance to input power fluctuations. It is very attractive for engineering application in modern microwave and ultrafast photonic networks.

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Sharma, Sneha, and Jitendra Kumar. "Numerical analysis of optical logic gate based on nonlinear optical loop mirror with a photonic crystal fiber." Journal of Nonlinear Optical Physics & Materials 24, no. 02 (June 2015): 1550019. http://dx.doi.org/10.1142/s0218863515500198.

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Ultrafast all-optical XOR and XNOR logic gates have been analyzed based on photonic crystal fiber (PCF) nonlinear optical loop mirror (NOLM). The performance of the logic operation is evaluated numerically using the coupled nonlinear Schrödinger equation and split step Fourier method. The wavelength allocation, peak power and the pulse width of signal with respect to the group velocity dispersion (GVD) and the nonlinearity of PCF affect the performance of logic gate. A highly nonlinear PCF with flattened dispersion is proposed to obtain 1 Tb/s operation.

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Kaprou, Georgia D., Vasileios Papadopoulos, Dimitris P. Papageorgiou, Ioanna Kefala, George Papadakis, Electra Gizeli, Stavros Chatzandroulis, George Kokkoris, and Angeliki Tserepi. "Ultrafast, low-power, PCB manufacturable, continuous-flow microdevice for DNA amplification." Analytical and Bioanalytical Chemistry 411, no. 20 (June 3, 2019): 5297–307. http://dx.doi.org/10.1007/s00216-019-01911-1.

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Li, Dong Juan, Guang Hua Cheng, Zhi Yang, and Yi Shan Wang. "Ultrafast Laser Machine Based on All-Fiber Femtosecond Laser System." Advanced Materials Research 652-654 (January 2013): 2374–77. http://dx.doi.org/10.4028/www.scientific.net/amr.652-654.2374.

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A femtosecond laser machine consisting of femtosecond fiber laser, trepanning head, linear motor stages system and Siemens 840D system has been integrated for industry application. The femtosecond laser source is all fiber system which contains a fiber mode-lock laser at 1053 nm with a repetition rate of 3.9 MHz, a double-cladding gain fiber amplifiers and a PCF amplifier. An acoustical modulator has employed to tune repetition rate from 3.9 MHz to 100 KHz. An in-line fiber chirped grating is used to stretch the pulse duration to 700 ps. After the PCF amplifier pulse is compressed to sub-ps with 50% efficiency based two grating compressor. The system outputs an average power of 15 W at 100 KHz and 800 fs. Using four wedges trepanning head, cylinder hole is drilled in 1mm thickness SiC ceramics in 30 s.

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Tachibana, Sean R., Longteng Tang, Liangdong Zhu, Yuka Takeda, Keiji Fushimi, Yoshibumi Ueda, Takahiro Nakajima, et al. "An Engineered Biliverdin-Compatible Cyanobacteriochrome Enables a Unique Ultrafast Reversible Photoswitching Pathway." International Journal of Molecular Sciences 22, no. 10 (May 16, 2021): 5252. http://dx.doi.org/10.3390/ijms22105252.

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Cyanobacteriochromes (CBCRs) are promising optogenetic tools for their diverse absorption properties with a single compact cofactor-binding domain. We previously uncovered the ultrafast reversible photoswitching dynamics of a red/green photoreceptor AnPixJg2, which binds phycocyanobilin (PCB) that is unavailable in mammalian cells. Biliverdin (BV) is a mammalian cofactor with a similar structure to PCB but exhibits redder absorption. To improve the AnPixJg2 feasibility in mammalian applications, AnPixJg2_BV4 with only four mutations has been engineered to incorporate BV. Herein, we implemented femtosecond transient absorption (fs-TA) and ground state femtosecond stimulated Raman spectroscopy (GS-FSRS) to uncover transient electronic dynamics on molecular time scales and key structural motions responsible for the photoconversion of AnPixJg2_BV4 with PCB (Bpcb) and BV (Bbv) cofactors in comparison with the parent AnPixJg2 (Apcb). Bpcb adopts the same photoconversion scheme as Apcb, while BV4 mutations create a less bulky environment around the cofactor D ring that promotes a faster twist. The engineered Bbv employs a reversible clockwise/counterclockwise photoswitching that requires a two-step twist on ~5 and 35 picosecond (ps) time scales. The primary forward Pfr → Po transition displays equal amplitude weights between the two processes before reaching a conical intersection. In contrast, the primary reverse Po → Pfr transition shows a 2:1 weight ratio of the ~35 ps over 5 ps component, implying notable changes to the D-ring-twisting pathway. Moreover, we performed pre-resonance GS-FSRS and quantum calculations to identify the Bbv vibrational marker bands at ~659,797, and 1225 cm−1. These modes reveal a stronger H-bonding network around the BV cofactor A ring with BV4 mutations, corroborating the D-ring-dominant reversible photoswitching pathway in the excited state. Implementation of BV4 mutations in other PCB-binding GAF domains like AnPixJg4, AM1_1870g3, and NpF2164g5 could promote similar efficient reversible photoswitching for more directional bioimaging and optogenetic applications, and inspire other bioengineering advances.

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Alhefeiti, Maryam, Falguni Chandra, Ravindra Kumar Gupta, and Na’il Saleh. "Dyeing Non-Recyclable Polyethylene Plastic with Photoacid Phycocyanobilin from Spirulina Algae: Ultrafast Photoluminescence Studies." Polymers 14, no. 22 (November 9, 2022): 4811. http://dx.doi.org/10.3390/polym14224811.

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Despite the enormous environmental damage caused by plastic waste, it makes up over one-third of globally produced plastics. Polyethylene (PE) wastes have low recycling but high production rates. Towards the construction of ionic solar cells from PE, the present work describes the loading of a bioactive photoacid phycocyanobilin (PCB) dye from the pigment of Spirulina blue–green algae (as a natural resource) on low-density polyethylene (LDPE) plastic film. Dyeing was confirmed by X-ray photoelectron spectroscopy (XPS). Upon excitation of the Soret-band (400 nm), the photoluminescence (PL) spectra of PCB in neat solvents revealed two prominent emission peaks at 450–550 and 600–700 nm. The first band assigned to bilirubin-like (PCBBR) species predominated the spectral profile in the highly rigid solvent glycerol and upon loading 0.45 % (w/w) of the dye on plastic. The photoluminescence excitation (PLE) spectra of PCB for the second region (Q-band) at 672 nm in the same solvents confirmed the ground state heterogenicity previously associated with the presence of PCBA (neutral), PCBB (cationic), and PCBC (anionic) conformers. Time-resolved photoluminescence (TRPL) measurements induced via excitation of all PCB species at 510 nm in methanol revealed three-lifetime components with τ1 = ~0.1 ns and τ2 = ~2 ns associated with PCBBR species and τ3 = ~5 ns pertinent to the long-living photoproduct X*. Decay-associated spectra (DAS) analysis of the photoluminescence transient spectra of the final dyed films in the solid-state confirmed the improved generation of the long-living photoproduct as manifested in a significant increase in the PL intensity (~100-fold) and lifetime value (~90 ns) in the Q-region upon loading 6.92 % (w/w) of the dye on plastic. The photoproduct species were presumably assigned to the deprotonated PCB species, suggesting improved ionic mobility. The potential implementation of the PCB-sensitized PE solid wastes for the fabrication of ionic solar cells is discussed.

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Kim, Kwang-Ryul, Jae-Hee Cho, Na-Young Lee, Hyun-Jin Kim, Sung-Hak Cho, Hong-Jin Park, and Byoungdeog Choi. "High-precision and ultrafast UV laser system for next-generation flexible PCB drilling." Journal of Manufacturing Systems 38 (January 2016): 107–13. http://dx.doi.org/10.1016/j.jmsy.2015.12.001.

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Savikhin, Sergei, Wu Xu, Victor Soukoulis, Parag R. Chitnis, and Walter S. Struve. "Ultrafast Primary Processes in Photosystem I of the Cyanobacterium Synechocystis sp. PCC 6803." Biophysical Journal 76, no. 6 (June 1999): 3278–88. http://dx.doi.org/10.1016/s0006-3495(99)77480-1.

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Mak, Ka Fai, John C. Travers, Philipp Hölzer, Nicolas Y. Joly, and Philip St J. Russell. "Tunable vacuum-UV to visible ultrafast pulse source based on gas-filled Kagome-PCF." Optics Express 21, no. 9 (April 26, 2013): 10942. http://dx.doi.org/10.1364/oe.21.010942.

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Rifai, Kheireddine, Lütfü-Çelebi Özcan, François R. Doucet, Kyle Rhoderick, and François Vidal. "Ultrafast Elemental Mapping of Platinum Group Elements and Mineral Identification in Platinum-Palladium Ore Using Laser Induced Breakdown Spectroscopy." Minerals 10, no. 3 (February 25, 2020): 207. http://dx.doi.org/10.3390/min10030207.

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This paper demonstrates the capability of performing an ultrafast chemical mapping of drill cores collected from a platinum/palladium mine using laser-induced breakdown spectroscopy (LIBS). A scan of 40 mm × 30 mm was performed, using a commercial LIBS analyzer, onto the flat surface of a drill core with a scanning speed of 1000 Hz, and a spatial resolution of 50 µm, in about 8 min. Maps of the scanned areas for seven chemical elements (platinum, palladium, nickel, copper, iron, silicon, and magnesium), as well as a single map including the seven elements altogether, were then generated using the proprietary software integrated into the LIBS analyzer. Based on the latter image, seven minerals were identified using the principal component analysis (PCA) and correlations with the elemental maps.

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