Barcode Tags Research Articles

Abstract 6225: Tumor evolution through selection by ECM stiffness

Abstract In this study, we used experimental evolution to investigate the extent to which the mechanical stiffness of the tumor extracellular matrix (ECM) exerts selection pressure on a genetically diverse population of breast cancer cells. Polyacrylamide hydrogels were fabricated and conjugated with collagen type I to create the ECM with different stiffness. MDA-MB-231 cells were continuously cultured on the hydrogels of the same corresponding stiffness. Growth rate was determined at certain time points by harvesting and counting the cells. Abundance of clonal MDA-MB-231 cells labeled with heritable DNA barcodes underwent the same selection was identified with sequencing of DNA barcode tags. Cellular phenotypes were characterized through immunofluorescence staining and confocal microscopy. 3D migration of the cancer cells was examined using Boyden chamber assay. Cellular contractility was measured through traction force microscopy. Whole genome transcriptome sequencing (RNA-seq), assay for transposase-accessible chromatin with sequencing, and reduced representation bisulfite sequencing were performed for transcriptomic and epigenetic analysis. Sustained culture of MDA-MB-231 breast cancer cells overall three months on soft ECM resulted in an increased proliferation rate and beta1 integrin-dependent spreading area of the cells. Such changes did not occur in clonal cells with low genetic variation and did not occur in ancestral cells on stiff substrates. Barcode analysis revealed two distinct surviving populations post-genetic selection, with one demonstrating robust proliferation on both soft and stiff ECM, and the other exhibiting preferential adaptation to the soft matrix. The soft-selected populations exhibited nuclear localization of the transcriptional regulator yes-associated protein and less wrinkled nuclei compared with ancestral populations when both populations were grown on soft ECM. Aggressive migration was observed in the soft-selected populations, indicating a more malignant selected phenotype. The soft-selected cells showed increased RhoA activity and contractile tension on a soft substrate compared to the ancestral cells. RNA-seq analysis revealed systematic differences between ancestral, stiff-selected, and soft-selected populations corresponding to enriched biological processes related to cell adhesion and ECM organization. Significant differences in DNA methylation and chromatin accessibility were observed in soft selected populations which were correlated with changes in RNA expression. ECM stiffness exerts selection pressure on genetically variable cancer cell populations, selecting specific genetic variants in a cell population optimally adapted for that stiffness. Selected variants on soft ECM tend to be highly migratory, proliferative and generate high traction even on soft ECM. Our results highlight the importance of ECM stiffness-driven evolution in cancer development. Citation Format: Ting-Ching Wang, Suchitaa Sawhney, Daylin Morgan, Richa Rashmi, Marcos R. Estecio, Amy Brock, Irtisha Singh, Richard L. Bennett, Charles F. Baer, Jonathan D. Licht, Tanmay P. Lele. Tumor evolution through selection by ECM stiffness [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6225.

Genome Sequence Resource of Curvularia clavata Causing Leaf Spot Disease on Tobacco by Oxford Nanopore PromethION.

Genome Sequence Resource of Curvularia clavata Causing Leaf Spot Disease on Tobacco by Oxford Nanopore PromethION.

Strategies for activity analysis of single nucleotide polymorphisms associated with human diseases.

Genome-wide association studies (GWAS) have identified a large number of single nucleotide polymorphism (SNP) sites associated with human diseases. In the annotation of human diseases, especially cancers, SNPs, as an important component of genetic factors, have gained increasing attention. Given that most of the SNPs are located in non-coding regions, the functional verification of these SNPs is a great challenge. The key to functional annotation for risk SNPs is to screen SNPs with regulatory activity from thousands of disease associated-SNPs. In this review, we systematically recapitulate the characteristics and functional roles of SNP sites, discuss three parallel reporter screening strategies in detail based on barcode tag classification, and recommend the common in silico strategies to help supplement the annotation of SNP sites with epigenetic activity analysis, prediction of target genes and trans-acting factors. We hope that this review will contribute to this exuberant research field by providing robust activity analysis strategies that can facilitate the translation of GWAS results into personalized diagnosis and prevention measures for human diseases.

Performance of QR Code Detectors near Nyquist Limits.

For the interacting with real world, augmented reality devices need lightweight yet reliable methods for recognition and identification of physical objects. In that regard, promising possibilities are offered by supporting computer vision with 2D barcode tags. These tags, as high contrast and visually well-defined objects, can be used for finding fiducial points in the space or to identify physical items. Currently, QR code readers have certain demands towards the size and visibility of the codes. However, the increase of resolution of built-in cameras makes it possible to identify smaller QR codes in the scene. On the other hand, growing resolutions cause the increase to the computational effort of tag location. Therefore, resolution reduction in decoders is a common trade-off between processing time and recognition capabilities. In this article, we propose the simulation method of QR codes scanning near limits that stem from Shannon’s theorem. We analyze the efficiency of three publicly available decoders versus different size-to-sampling ratios (scales) and MTF characteristics of the image capture subsystem. The MTF we used is based on the characteristics of real devices, and it was modeled using Gaussian low-pass filtering. We tested two tasks—decoding and locating-and-decoding. The findings of the work are several-fold. Among others, we identified that, for practical decoding, the QR-code module should be no smaller than 3–3.5 pixels, regardless of MTF characteristics. We confirmed the superiority of Zbar in practical tasks and the worst recognition capabilities of OpenCV. On the other hand, we identified that, for borderline cases, or even below Nyquist limit where the other decoders fail, OpenCV is still capable of decoding some information.

Encoding Multiple Information into European Article Number (EAN)‐13 Codes with Various Chromic Sensing Materials to Construct Intelligent Barcodes

An intelligent encoding/decoding scheme for barcodes is studied that can realize transformation among different barcodes under external stimuli. The proposed scheme is compatible with the European Article Number (EAN)‐13 encoding/decoding system. First, the transformation mechanism among different barcodes is analyzed. Two different transformation strategies, the bar transformation and the background color transformation, are discussed. To demonstrate the possible applications, a temperature‐sensitive barcode tag (TSBT) and pH‐indicative barcode tag (PSBT) are developed by embedding the corresponding thermochromic and pH‐sensitive materials into the traditional EAN‐13 barcodes. Except for the conventional identification function, these tags can be used as environmental sensors to sense temperature and pH values. The maximum recognition rates of the TSBT and PSBT are 100% and 98%, respectively. The technology is universal and versatile because different kinds of sensitive tags can be constructed easily. This sensitive barcode technology can be expected to provide an efficient, accurate, and low‐cost solution to real‐time detection.

Smart Shopping with Smart Cart

Every day, huge numbers of consumers come to shop for numerous goods at mall round the world. lately, shoppers use a handcart or basket when buying the groceries at a mall . additionally, the procurement of products involves a classy process during which the purchasers must bring the items they have to urge to the check-out area, then stand and wait during an extended line so as that the products are often scanned, the whole amount calculated and thus the bill paid. As a results of this problem, this research study presents the event of a sensible cart for smart shopping. A barcode tag is found on every item during a mall , and therefore the smart cart will include a barcode reader on a cart also as cart has its own serial number in order that every cart can identified uniquely and cashier also can keep a track on the item inserted in cart . customer also can scan using his/her mobile devices through application the serial number given on smart cart and track the small print of things added in cart and parallely customer can ask queries also as can give feedback of products and item. While shopping, customers can scan the products then place them within the basket or cart, and therefore the mobile device will record and display the worth and name of every item. Also, the basket will have a weight sensor system which may confirm the accurate pricing of produce during the shopping process. Calculation of the whole cost of the customer's groceries are getting to be performed and stored within the memory of the smart basket's microcontroller. This data are getting to be sent from the basket to the foremost computer's server via a transmitter. Therefore, the proposed smart basket will allow shoppers to avoid waiting in line and having to constantly believe the number of money they go to need to spend.

Using Barcode to Track Student Attendance and Assets in Higher Education Institutions

Abstract Most instructors and staff in a university environment use manual methods of tracking student attendance and college assets. However, these methods have several disadvantages; the major drawbacks of taking attendance manually are errors in data collection and the loss of part of the lecture time. As for asset tracking, the common issues are human errors in data collection, wrong inventory estimation and time wastage during the process. Automated identification and data capturing technologies can help address these issues. This paper investigates the implementation of one such system, the barcode technology, to read and process student attendance data in classroom settings and to track periodic inventory of assets within the college facilities such as devices, equipment, office furniture, classrooms, and laboratories. The paper measures faculty members and staff response on usability, comfort level, and efficiency for the proposed barcode system. This work shows that barcode technology eliminates data entry errors and improves efficiency for entering data with a minimum cost of creating barcode tags and hardware.

Implementing a HBIM approach to manage the translocation of heritage buildings

PurposeThe purpose of the paper is to present a study which exploited synergies between the fields of Heritage BIM, conservation and building translocation to develop a new approach to support a digitally enabled translocation process. The translocation (or relocation) of buildings or structures is a niche area of the construction sector and much of the significant work in this field has focused on the relocation of heritage buildings. However, hitherto there was a paucity of work between translocation and the process and technology of BIM.Design/methodology/approachThe study employed a constructive research approach to analyse the phenomenon of heritage translocation. As part of this approach, semi-structured interviews were undertaken with professionals engaged in heritage translocation projects within the UK, and this was supported by a multi-faceted review of literature within the cross cutting themes of translocation and HBIM. Building on the results, a BIM-enabled process was implemented to support the translocation of a 19th-century timber framed building in the UK.FindingsFollowing analysis of results of semi-structured interviews and supported by findings from prevailing literature in the field of translocation and HBIM, a HBIM for Translocation Conceptual Framework (TransHBIM) was developed. Building on the key constructs of the framework, a HBIM-based workflow was implemented to develop a digitally enabled translocation process, which provided a new approach to managing and documenting heritage translocation where disassembly and reconstruction are utilised. The workflow provided a more effective way of documenting individual elements of the building within a digital environment opening up potential for new simulation of the entire process.Originality/valueCurrent approaches to translocation involve traditional/manual methods of recording the building and cataloguing the key heritage elements for all aspects of the process. This new approach implements BIM technologies and processes along with the use of barcode or RFID tags to create a digital bridge between the physical elements of the building and the BIM database. This provides more accurate recording of the heritage and also opens up opportunities to support the process with additional digital simulation techniques enhancing the efficiency of the entire process.

Internet of Things (IoT) Based Smart Shop (S-SHOP) System with RFID Technique

Billing system technology in the market nowadays is less efficient in parallel with revolution of technology. Conventional method widely uses a barcode scanner that has disadvantages as it is a manual system and requires man power. Besides that, the conventional method does not store the information such as warranty of the product and the information of a buyer. Using the smart shop billing system using Radio Frequency Identification (RFID) reader and RFID tag, the system will become more efficient and automated. The system consists of two main elements which are passive RFID tag (125 kHz) and RFID reader (ID-20LA) that has similar function with a barcode tag and a barcode scanner. For the hardware components, the Espresso Lite V2.0 acts as a microcontroller and UC00C acts as Universal Asynchronous Receiver/Transmitter (UART) converter and Arduino IDE is used as a platform to link between hardware and software. The system is completed with the Internet of Things (IoT) technique to make sure the system can be operated wirelessly. As a result, all the information from the reader will be sent to Google spreadsheet as a cloud to store the information about the item to generate GUI bill. In conclusion this proposed system also uses a real time tracking.

Does sociality drive diversity and composition of airway microbiota in cetaceans?

The number of social contacts of mammals is positively correlated with the diversity of their gut microbes. There is some evidence that sociality also affects microbes in the respiratory tract. We tested whether the airway microbiota of cetacean species differ depending on the whales' level of sociality. We sampled the blow of blue (Balaenoptera musculus), grey (Eschrichtius robustus), humpback (Megaptera novaeangliae) and long-finned pilot whales (PWs) (Globicephala melas) and analysed the blow microbiota by barcode tag sequencing targeting the V4 region of the bacterial 16S rRNA gene. Humpback whales (HWs) show higher levels of sociality than blue (BW) and grey (GW), while PWs are the most gregarious among the four species. The blow samples of the HWs showed the highest richness and diversity. HWs were also the only species with a species-specific clustering of their microbial community composition and a relatively large number of core taxa. Therefore, we conclude that it cannot be sociality alone shaping the diversity and composition of airway microbiota. We suggest the whale species' lung volume and size of the plume of exhaled air as an additional factor impacting the transmission potential of blow microbiota from one individual whale to another.

Single Cell DNA Sequencing Identifies Combinatorial Mutation Patterns and Clonal Architecture in Myeloid Malignancies

Genomic studies of myeloid malignancies (MM), including acute myeloid leukemia (AML), myeloproliferative neoplasms (MPN) and myelodysplasia (MDS), identified mutations with different allele frequencies. Recent studies of clonal hematopoiesis (CH) discovered a subset of MM disease alleles, while other alleles are only observed in overt MM. These observations suggest an important pathogenetic role for the chronology of mutational acquisition. Although bulk sequencing informs prognostication, it cannot distinguish which mutations occur in the same clone and cannot offer definitive evidence of mutational order. Delineation of clonal architecture at the single cell level is key to understanding how the sequential/parallel acquisition of somatic mutations contributes to myeloid transformation. In order to elucidate the clonal structure of MM, we designed a custom single cell 109 amplicon panel of the most frequently mutated amplicons in 50 MM genes using the Mission Bio Tapestri v2 platform. Viable cells were sorted from 90 samples from 78 patients with CH, AML, and MPN/post-MPN AML followed by single cell amplification/sequencing. Mutation calls were filtered based on read depth, quality, and alleles genotyped per cell. We reconstructed a random distribution of clones by permuting genotype calls across cells and generated empirical p values for each clone. To identify dominant clones, we used a Poisson test to determine clones were significantly enriched compared to the mean clone size. Clones with significant p-values (p <0.05) were used to generate plots of clonal architecture of each sample (Figure 1A). Despite significant clonal complexity, the majority of MM patients (80%;72/90) present with one (51/90; 56.7%) or two (21/90; 23.3%) dominant clones. These data show there are specific genotypic combinations which lead to clonal dominance with increased fitness relative to other clones and/or suppression of minor clones by dominant clone(s). We next investigated whether specific molecularly defined AML subtypes had increased clonal complexity. FLT3-ITD mutant AML samples had a significantly greater number of clones (p < 0.002) compared to AML samples with multiple epigenetic modifier mutations. Similar findings were not observed when comparing AML samples with epigenetic mutations to RAS pathway mutant samples. We next investigated whether specific mutations were likely to co-occur/be mutually exclusive at a single cell level. We observed evidence of oligoclonality in CH, including parallel acquisition of DNMT3A mutations and clones with multiple mutations in the absence of progression to MM. By contrast, in MM the dominant clone(s) almost always harbored multiple epigenetic modifier mutations, suggesting cooperative epigenetic remodeling in myeloid transformation. Mutations in signaling effectors (FLT3-ITD/TKD; RAS/RAS) were mutually exclusive. We observed distinct FLT3-mutant clones in FLT3-mutant AML patients and parallel acquisition of different RAS pathway mutations. We used this data to develop clonal architecture trees in each patient, giving us a definitive picture of mutational acquisition and transformation at a single cell level. We calculated a Shannon diversity score and observed an increase in clonal complexity with disease evolution; CH samples had the lowest clonal diversity and FLT3-ITD AML patients the highest clonal diversity (Figure 1B). We extended our findings by combining cell surface marker assessment and single cell mutational analysis. Patient samples were stained with an antibody cocktail of 6 oligo-conjugated antibodies with barcode tags prior to single cell sequencing, which allowed simultaneous acquisition of single cell immunophenotypic and genotypic data. This allows us to identify distinct populations of stem/progenitor cells with distinct clonal/mutational repertoires (Figure 1C). Additional data will be presented with this novel approach, which allows us to combine an assessment of stem/progenitor cell frequency with genetic data. This includes studies of CD34+ and CD34- AML, which show striking differences in mutational representation in different stem/progenitor compartments. In summary, our studies of clonal architecture at a single cell level provide us novel insights into the pathogenesis of myeloid transformation and give us new insights into how clonal complexity contributes to disease progression. Disclosures Ooi: Mission Bio: Employment, Equity Ownership. Mendez:Mission Bio: Employment, Equity Ownership. Carroll:Janssen Pharmaceuticals: Consultancy; Incyte: Research Funding; Astellas Pharmaceuticals: Research Funding. Papaemmanuil:Celgene: Research Funding. Viny:Mission Bio: Other: Sponsored travel; Hematology News: Membership on an entity's Board of Directors or advisory committees. Levine:Roche: Consultancy, Research Funding; Amgen: Honoraria; Imago Biosciences: Membership on an entity's Board of Directors or advisory committees; Isoplexis: Membership on an entity's Board of Directors or advisory committees; Qiagen: Membership on an entity's Board of Directors or advisory committees; C4 Therapeutics: Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy; Prelude Therapeutics: Research Funding; Loxo: Membership on an entity's Board of Directors or advisory committees; Lilly: Honoraria; Gilead: Consultancy; Celgene: Consultancy, Research Funding.

Optimization of a microarray for fission yeast.

Bar-code (tag) microarrays of yeast gene-deletion collections facilitate the systematic identification of genes required for growth in any condition of interest. Anti-sense strands of amplified bar-codes hybridize with ~10,000 (5,000 each for up- and down-tags) different kinds of sense-strand probes on an array. In this study, we optimized the hybridization processes of an array for fission yeast. Compared to the first version of the array (11 µm, 100K) consisting of three sectors with probe pairs (perfect match and mismatch), the second version (11 µm, 48K) could represent ~10,000 up-/down-tags in quadruplicate along with 1,508 negative controls in quadruplicate and a single set of 1,000 unique negative controls at random dispersed positions without mismatch pairs. For PCR, the optimal annealing temperature (maximizing yield and minimizing extra bands) was 58℃ for both tags. Intriguingly, up-tags required 3× higher amounts of blocking oligonucleotides than down-tags. A 1:1 mix ratio between up- and down-tags was satisfactory. A lower temperature (25℃) was optimal for cultivation instead of a normal temperature (30℃) because of extra temperature-sensitive mutants in a subset of the deletion library. Activation of frozen pooled cells for >1 day showed better resolution of intensity than no activation. A tag intensity analysis showed that tag(s) of 4,316 of the 4,526 strains tested were represented at least once; 3,706 strains were represented by both tags, 4,072 strains by up-tags only, and 3,950 strains by down-tags only. The results indicate that this microarray will be a powerful analytical platform for elucidating currently unknown gene functions.

Barcode identification for single cell genomics

BackgroundSingle-cell sequencing experiments use short DNA barcode ‘tags’ to identify reads that originate from the same cell. In order to recover single-cell information from such experiments, reads must be grouped based on their barcode tag, a crucial processing step that precedes other computations. However, this step can be difficult due to high rates of mismatch and deletion errors that can afflict barcodes.ResultsHere we present an approach to identify and error-correct barcodes by traversing the de Bruijn graph of circularized barcode k-mers. Our approach is based on the observation that circularizing a barcode sequence can yield error-free k-mers even when the size of k is large relative to the length of the barcode sequence, a regime which is typical single-cell barcoding applications. This allows for assignment of reads to consensus fingerprints constructed from k-mers.ConclusionWe show that for single-cell RNA-Seq circularization improves the recovery of accurate single-cell transcriptome estimates, especially when there are a high number of errors per read. This approach is robust to the type of error (mismatch, insertion, deletion), as well as to the relative abundances of the cells. Sircel, a software package that implements this approach is described and publically available.

Whole Genome Sequencing of Influenza A and B Viruses With the MinION Sequencer in the Clinical Setting: A Pilot Study.

Introduction: Whole genome sequencing (WGS) of influenza viruses is important for preparing vaccines and coping with newly emerging viruses. However, WGS is difficult to perform using conventional next-generation sequencers in developing countries, where facilities are often inadequate. In this study, we developed a high-throughput WGS method for influenza viruses in clinical specimens with the MinION portable sequencer.Methods: Whole genomes of influenza A and B viruses were amplified by multiplex RT-PCR from 13 clinical specimens collected in Tokyo, Japan. Barcode tags for multiplex MinION sequencing were added with each multiplex RT-PCR amplicon by nested PCR with custom barcoded primers. All barcoded amplicons were mixed and multiplex sequencing using the MinION sequencer with 1D2 sequencing kit. In addition, multiplex RT-PCR amplicons generated from each clinical specimen were sequenced using the Illumina MiSeq platform to validate the performance of MinION sequencer. The accuracy, recall, and precision rates of MinION sequencing were calculated by comparing the results of variant calling in the Illumina MiSeq platform and MinION sequencer.Results: Whole genomes of influenza A and B viruses were successfully amplified by multiplex RT-PCR from 13 clinical samples. We identified 6 samples as influenza type A virus H3N2 subtype and 7 as influenza B virus Yamagata lineage using the Illumina MiSeq platform. The overall accuracy, recall, and precision rates of the MinION sequencer were, respectively 99.95%, 89.41%, and 97.88% from 1D reads and 99.97%, 93.28%, and 99.86% from 1D2 reads.Conclusion: We developed a novel WGS method for influenza A and B viruses. It is necessary to improve read accuracy and analytical tools in order to better utilize the MinION sequencer for real-time monitoring of genetic rearrangements and for evaluation of newly emerging viruses.

Abstract 2347: High-throughput scRNA-seq analysis using Celsee Nano-prep 250K sequencing chip on Celsee C-PREP GENESIS

Abstract For effective targeted therapeutics, it is critical to identify cancer mutations in cells that are often regional and heterogenic. Recent advances in single-cell mRNA sequencing (scRNA-seq) have made it possible to study intratumor heterogeneity and its role in cancer progression, metastasis, and treatment resistance. Next-generation sequencing (NGS)-based studies have identified critical genetic alterations in a variety of malignancies. However, the current workflow of existing technologies leads to significant loss of cells and thus loss of critical information. In this study we present a technology that decreases cell loss and increases efficiency of scRNA-seq. C-PREP GENESIS is a fully automated, random-access, multiple-sample processor for single-cell sequencing preparation. C-PREP GENESIS allows automated fluid dispensing and controlled pumping through Nanochips. The instrument utilizes unitized reagent cartridge for dispensing reagents for wash, lysis, cDNA synthesis and oil (for partitioning). With its automated thermocycling (4oC- 100oC), it can achieve the single cell to cDNA synthesis on beads with unique cell barcode and UMI tags in under 2 hours with an efficiency of ~80% of the 50,000 single cells captured on the nano-PREP 250K sequencing chip. The cDNA can then be retrieved from the chip for downstream library preparation. Alternatively, users can perform a targeted library prep PCR on the same instrument. Here we present scRNA-seq analysis of single cells obtained from patient tumor biopsy samples and cancer tissue culture single cells to discuss the critical mutations observed in single cells of the heterogenic tumor populations. Citation Format: Vishal Premdev Sharma, William Chiro Chow, Brian Boniface, Kyle Gleason, Austin Payne, Priya Gogoi, Kalyan Handique. High-throughput scRNA-seq analysis using Celsee Nano-prep 250K sequencing chip on Celsee C-PREP GENESIS [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2347.

Candidate DNA Barcode Tags Combined With High Resolution Melting (Bar-HRM) Curve Analysis for Authentication of Senna alexandrina Mill. With Validation in Crude Drugs.

Senna alexandrina (Fabaceae) is a globally recognized medicinal plant for its laxative properties as well as the only source of sennosides, and is highly exported bulk herb from India. Its major procurement is exclusively from limited cultivation, which leads to risks of deliberate or unintended adulteration. The market raw materials are in powdered or finished product form, which lead to difficulties in authentication. Here, DNA barcode tags based on chloroplast genes (rbcL and matK) and intergenic spacers (psbA-trnH and ITS) were developed for S. alexandrina along with the allied species. The ability and performance of the ITS1 region to discriminate among the Senna species resulted in the present proposal of the ITS1 tags as successful barcode. Further, these tags were coupled with high-resolution melting (HRM) curve analysis in a real-time PCR genotyping method to derive Bar-HRM (Barcoding-HRM) assays. Suitable HRM primer sets were designed through SNP detection and mutation scanning in genomic signatures of Senna species. The melting profiles of S. alexandrina and S. italica subsp. micrantha were almost identical and the remaining five species were clearly separated so that they can be differentiated by HRM method. The sensitivity of the method was utilized to authenticate market samples [Herbal Sample Assays (HSAs)]. HSA01 (S. alexandrina crude drug sample from Bangalore) and HSA06 (S. alexandrina crude drug sample from Tuticorin, Tamil Nadu, India) were found to be highly contaminated with S. italica subsp. micrantha. Species admixture samples mixed in varying percentage was identified sensitively with detection of contamination as low as 1%. The melting profiles of PCR amplicons are clearly distinct, which enables the authentic differentiation of species by the HRM method. This study reveals that DNA barcoding coupled with HRM is an efficient molecular tool to authenticate Senna herbal products in the market for quality control in the drug supply chain.CIMAP Communication Number: CIMAP/PUB/2017/31

Vehicle autonomous localization in local area of coal mine tunnel based on vision sensors and ultrasonic sensors.

This paper presents a vehicle autonomous localization method in local area of coal mine tunnel based on vision sensors and ultrasonic sensors. Barcode tags are deployed in pairs on both sides of the tunnel walls at certain intervals as artificial landmarks. The barcode coding is designed based on UPC-A code. The global coordinates of the upper left inner corner point of the feature frame of each barcode tag deployed in the tunnel are uniquely represented by the barcode. Two on-board vision sensors are used to recognize each pair of barcode tags on both sides of the tunnel walls. The distance between the upper left inner corner point of the feature frame of each barcode tag and the vehicle center point can be determined by using a visual distance projection model. The on-board ultrasonic sensors are used to measure the distance from the vehicle center point to the left side of the tunnel walls. Once the spatial geometric relationship between the barcode tags and the vehicle center point is established, the 3D coordinates of the vehicle center point in the tunnel’s global coordinate system can be calculated. Experiments on a straight corridor and an underground tunnel have shown that the proposed vehicle autonomous localization method is not only able to quickly recognize the barcode tags affixed to the tunnel walls, but also has relatively small average localization errors in the vehicle center point’s plane and vertical coordinates to meet autonomous unmanned vehicle positioning requirements in local area of coal mine tunnel.

Using circular dot pattern code tag for medical information on the round type medical package

Administration of medicines is important issue for patient safety in medical applications. Especially, manufacture date and expiry date are very important. Medical applications have strong needs for embedded tags on medical bottles to facilitate medicine management. One-dimensional 1D barcode cannot represent the required information capacity. Two-dimensional 2D barcode and radio-frequency identification RFID systems can support information capacity. However, 2D barcode is hard to recognition, if 2D barcode tag is attached on curvature surface. RFID is 100 times more expensive than barcode systems and also it is difficult to embed RFID tags on curvature. In this paper, we propose circular dot pattern code CDPC tag for cylindrical and round type medical bottle identification and management. CDPC is based on topology of dot pattern code, and it is well suited to recognising tags in curvature environments. Experimental results show that CDPC outperformed 2D barcode in its recognition rate on curvature, including cylindrical and round shape.

DNA Barcoding: Current Status Application And Future Perspectives

Traditional morphology-based insect identification is time-consuming and require specialists whose numbers are insufficient and dwindling. DNA barcoding refers to the technique of sequencing a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene, the “DNA barcode, “ from a taxonomically unknown specimen and performing comparisons with a reference library of barcodes of known species origin to establish a specieslevel identification. The standardized sequence region is called a DNA barcode because it is like a barcode tag for each taxon. Since the proposition of this concept and the launch of a large project named the Barcode of Life, this simple technique has attracted attention from taxonomist. As an index of diversity, DNA barcoding is distinct from the science of circumscribing species and resolving their evolutionary relationships, but it can serve as a powerful scaffold both to motivate and guide these efforts. The extreme diversity of insects and their economical, epidemiological and agricultural importance have made this group a major target of DNA barcoding. However, there is some controversy about the utility of DNA barcoding. Consequently, in this review, we present an overview of DNA barcoding, current satatus, advances and application of insect DNA barcoding.

High-Throughput Sequencing of Complete Mitochondrial Genomes.

Next-generation sequencing has revolutionized mitogenomics, turning a cottage industry into a high throughput process. This chapter outlines methodologies used to sequence, assemble, and annotate mitogenomes of non-model organisms using Illumina sequencing technology, utilizing either long-range PCR amplicons or gDNA as starting template. Instructions are given on how to extract DNA, conduct long-range PCR amplifications, generate short Sanger barcode tag sequences, prepare equimolar sample pools, construct and assess quality library preparations, assemble Illumina reads using either seeded reference mapping or de novo assembly, and annotate mitogenomes in the absence of an automated pipeline. Notes and recommendations, derived from our own experience, are given throughout this chapter.