Barcode System Research Articles

Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling

Multiomic profiling of single cells by sequencing is a powerful technique for investigating cellular diversity. Existing droplet-based microfluidic methods produce many cell-free droplets, underutilizing bead barcodes and reagents. Combinatorial indexing on microplates is more efficient for barcoding but labor-intensive. Here we present Overloading And unpacKing (OAK), which uses a droplet-based barcoding system for initial compartmentalization followed by a second aliquoting round to achieve combinatorial indexing. We demonstrate OAK’s versatility with single-cell RNA sequencing as well as paired single-nucleus RNA sequencing and accessible chromatin profiling. We further showcase OAK’s performance on complex samples, including differentiated bronchial epithelial cells and primary retinal tissue. Finally, we examine transcriptomic responses of over 400,000 melanoma cells to a RAF inhibitor, belvarafenib, discovering a rare resistant cell population (0.12%). OAK’s ultra-high throughput, broad compatibility, high sensitivity, and simplified procedures make it a powerful tool for large-scale molecular analysis, even for rare cells.

Chromosome-specific barcode system with centromeric repeat in cultivated soybean and wild progenitor.

Wild soybean Glycine soja is the progenitor of cultivated soybean Glycine max Information on soybean functional centromeres is limited despite extensive genome analysis. These species are an ideal model for studying centromere dynamics for domestication and breeding. We performed a detailed chromatin immunoprecipitation analysis using centromere-specific histone H3 protein to delineate two distinct centromeric DNA sequences with unusual repeating units with monomer sizes of 90-92 bp (CentGm-1) and 413-bp (CentGm-4) shorter and longer than standard nucleosomes. These two unrelated DNA sequences with no sequence similarity are part of functional centromeres in both species. Our results provide a comparison of centromere properties between a cultivated and a wild species under the effect of the same kinetochore protein. Possible sequence homogenization specific to each chromosome could highlight the mechanism for evolutionary conservation of centromeric properties independent of domestication and breeding. Moreover, a unique barcode system to track each chromosome is developed using CentGm-4 units. Our results with a unifying centromere composition model using CentGm-1 and CentGm-4 superfamilies could have far-reaching implications for comparative and evolutionary genome research.

Pembuatan Barcode Kemasan Produk Pada CV. Kuliner Makmur Sejahtera Kota Padang

Rendang, a traditional Minangkabau dish from West Sumatra, Indonesia, has gained international recognition and has inspired many entrepreneurs to promote this cuisine globally. One such entrepreneur is CV. Kuliner Makmur Sejahtera (KMS), which produces rendang under the brand Katuju. To enhance operational efficiency and support global market expansion, KMS requires an improved inventory management system. The primary challenge is the difficulty in monitoring inventory and tracking products without a barcode system. This community service program aims to address this issue by implementing barcode technology on Katuju's product packaging. The activities include designing, creating, and printing barcodes, as well as training KMS staff on how to use them. The process starts with observation and interviews to identify needs, followed by barcode design and production using an online barcode generator, and testing the barcode functionality with a scanning system. The results indicate that the community service team successfully trained KMS in barcode creation and printing, and integrated barcodes into product packaging. Evaluation through questionnaires showed participant satisfaction with the program and readiness to apply the barcode system to their products. This program is expected to improve inventory management, data accuracy, and support CV. KMS's global market expansion by providing tools necessary for efficient product tracking and valuable consumer data collection.

Fuzzy logic-based barcode scanning system for food products halal identification

Halal status in food products is fundamental for Muslims and may be crucial for those who are allergic to non-halal ingredients when choosing suitable foods for consumption. However, with the rising demand for food products and the advancement of science and technology, contamination with non-halal substances is likely to occur in food production. Furthermore, some irresponsible food industry players tend to replace halal with non-halal ingredients to reduce costs. Therefore, it is crucial to identify the contents of halal food products to ensure compliance with the guidelines outlined by the Department of Islamic Development Malaysia (JAKIM). In this study, an integrated fuzzy logic barcode scanning system was developed to determine non-halal ingredients and traces in packaged food products. Although the information on food products can be easily accessed from the open-source web data bank, using the proposed fuzzy logic based-barcode scanning system to identify the authenticity of halal food products is an alternative option for providing accurate, reliable, and fast detection. The inputs for the fuzzy logic framework are halal logo, alcohol, animal fats, gelatin, ham, bacon, L-cysteine, lipase, mono-and diglycerides, pepsin, rennet, sodium stearoyl lactylate, vanilla extract, whey, and E-code of E120, E422, E441, E470, E542, and E904. On the other hand, the outputs are halal, uncertain, and non-halal. The fuzzy logic-based barcode system was able to identify the halal status for three different categories: samples with a halal logo, uncertain halal status samples, and non-halal samples.

Development of Cost-Effective SNP Markers for Genetic Variation Analysis and Variety Identification in Cultivated Pears (Pyrus spp.).

Pear (Pyrus spp.) is a major fruit crop in the Rosaceae family, and extensive efforts have been undertaken to develop elite varieties. With advances in genome sequencing technologies, single-nucleotide polymorphisms (SNPs) are commonly used as DNA markers in crop species. In this study, a large-scale discovery of SNPs was conducted using genotyping by sequencing in a collection of 48 cultivated pear accessions. A total of 256,538 confident SNPs were found on 17 chromosomes, and 288 SNPs were filtered based on polymorphic information content, heterozygosity rate, and genome distribution. This subset of SNPs was used to genotype an additional 144 accessions, consisting of P. pyrifolia (53), P. ussuriensis (27), P. bretschneideri (19), P. communis (26), interspecific hybrids (14), and others (5). The 232 SNPs with reliable polymorphisms revealed genetic variations between and within species in the 192 pear accessions. The Asian species (P. pyrifolia, P. ussuriensis, and P. bretschneideri) and interspecific hybrids were genetically differentiated from the European species (P. communis). Furthermore, the P. pyrifolia population showed higher genetic diversity relative to the other populations. The 232 SNPs and four subsets (192, 96, 48, and 24 SNPs) were assessed for variety identification. The 192 SNP subset identified 173 (90.1%) of 192 accessions, which was comparable to 175 (91.1%) from the 232 SNPs. The other three subsets showed 81.8% (24 SNPs) to 87.5% (96 SNPs) identification rates. The resulting SNPs will be a useful resource to investigate genetic variations and develop an efficient DNA barcoding system for variety identification in cultivated pears.

Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure.

Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonization, disease, antimicrobial resistance and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enhances the development of robust genome-wide typing schemes to define the overall bacterial population structure and lineages within it. Using the previously published data, we developed the Pneumococcal Genome Library (PGL), a curated dataset of 30 976 genomes and contextual data for carriage and disease pneumococci recovered between 1916 and 2018 in 82 countries. We leveraged the size and diversity of the PGL to develop a core genome multilocus sequence typing (cgMLST) scheme comprised of 1222 loci. Finally, using multilevel single-linkage clustering, we stratified pneumococci into hierarchical clusters based on allelic similarity thresholds and defined these with a taxonomic life identification number (LIN) barcoding system. The PGL, cgMLST scheme and LIN barcodes represent a high-quality genomic resource and fine-scale clustering approaches for the analysis of pneumococcal populations, which support the genomic epidemiology and surveillance of this leading global pathogen.

Development of mitochondrial DNA cytochrome c oxidase subunit I primer sets to construct DNA barcoding library using next-generation sequencing.

Insects are one of the most diverse eukaryotic groups on the planet, with one million or more species present, including those yet undescribed. The DNA barcoding system has been developed, which has aided in the identification of cryptic species and undescribed species. The mitochondrial cytochrome c oxidase I region (mtDNA COI) has been utilised for the barcoding analysis of insect taxa. Thereafter, next-generation sequencing (NGS) technology has been developed, allowing for rapid acquisition of massive amounts of sequence data for genetic analyses. Although NGS-based PCR primers designed to amplify the mtDNA COI region have been developed, their target regions were only a part of COI region and/or there were taxonomic bias for PCR amplification. As the mtDNA COI region is a traditional DNA marker for the DNA barcoding system, modified primers for this region would greatly contribute to taxonomic studies. In this study, we redesigned previously developed PCR primer sets that targetted the mtDNA COI barcoding region to improve amplification efficiency and to enable us to conduct sequencing analysis on NGS. As a result, the redesigned primer sets achieved a high success rate (> 85%) for species examined in this study, covering four insect orders (Coleoptera, Lepidoptera, Orthoptera and Odonata). Thus, by combining the primers with developed primer sets for 12S or 16S rRNA regions, we can conduct more detailed taxonomic, phylogeographic and conservation genetic studies using NGS.

Offline Entry and Exit Gate Management System: A Barcode-Based Registration System at Jigme Namgyel Engineering College

The barcode system is used to automate data collection and is valuable to eliminate the possibility of human error, and the data obtained through the barcode is generated rapidly. Further, barcode scanning automatically enters a large amount of data into a system, making it efficient for recordkeeping and streamlining the records. Previously, Jigme Namgyel Engineering College (JNEC), had a paper-based registration system. It generated a great deal of paper, and time was consumed in long queues while students entered and exited the campus. Therefore, a QR system was developed whereby users scan outgoing/incoming QR through Google scanners and fill an online form. The system was also found to be time-consuming as the user had to punch in details manually and there was also a need for an internet connection. Although the system did help curb paper wastage. Therefore, to overcome the limitations of both systems, a Barcode System has been developed, wherein the barcode present in the user ID card is scanned and the user details will be auto-generated in the system. This system was developed and designed using Microsoft Access (MS Access). Problem-Based Learning (PBL) methodology was also implemented along with the System Development Life Cycle (SDLC). The system allows users to view and print the user record based on department. Generate users’ entry and exit reports, and also sort the report by date. The Barcode system is found to be the quickest and easiest way for the user to get registered. It is essential because it fulfills the primary role of keeping the record of outgoing or incoming users faster and easier. The Barcode system also fulfills the aim of going green by reducing paper wastage.

Teaching information flow in supply chains: A role‐playing game using TagScan

AbstractInformation flow is one of the three main flows of supply chains. It is an abstract concept that can be challenging for students to grasp in its entirety. This article describes a role‐playing game for teaching the topic of information flow in an undergraduate supply chain management course. The game allows students to simulate receiving and fulfilling customer orders by playing five roles within a manufacturing company. Students use TagScan, an augmented reality barcoding and logistics system launched by a technology company in western Canada, to track information throughout the game. Pre‐ and postsurvey results demonstrate the effectiveness of the proposed game in helping students visualize abstract course concepts and understand the types of information being tracked, the available information transmission technology, and the dynamics of information flow in a supply chain. Students were actively engaged in this in‐class activity and responded positively to the learning‐by‐gaming experience.

Capillary-Electrophoresis-Based Species Barcoding of Big Cats: CR-mtDNA-Length Polymorphism.

This study aimed to provide an overview of the methodological approach used for the species determination of big cats. The molecular system described herein employs mitochondrial DNA control region (CR-mtDNA)-length polymorphism in combination with highly sensitive and precise capillary electrophoresis. We demonstrated that the described CR-mtDNA barcoding system can be utilized for species determination where the presence of biological material from big cats is expected or used as a confirmatory test alongside Sanger or massive parallel sequencing (MPS). We have also addressed the fact that species barcoding, when based on the analysis of mtDNA targets, can be biased by nuclear inserts of the mitochondrial genome (NUMTs). The CR-mtDNA barcoding system is suitable even for problematic and challenging samples, such as hair. CR-mtDNA-length polymorphisms can also distinguish hybrids from pure breeds.

Abstract NG08: Dissecting and quantifying pancreatic cancer plasticity using single-cell multiomics, lineage tracing and functional genomics reveals novel mediators of therapy resistance

Abstract NG08: Dissecting and quantifying pancreatic cancer plasticity using single-cell multiomics, lineage tracing and functional genomics reveals novel mediators of therapy resistance

Optimizing Nucleic Acid Delivery Systems through Barcode Technology.

Conventional biological experiments often focus on in vitro assays because of the inherent limitations when handling multiple variables in vivo, including labor-intensive and time-consuming procedures. Often only a subset of samples demonstrating significant efficacy in the in vitro assays can be evaluated in vivo. Nonetheless, because of the low correlation between the in vitro and in vivo tests, evaluation of the variables under examination in vivo and not solely in vitro is critical. An emerging approach to achieve high-throughput in vivo tests involves using a barcode system consisting of various nucleotide combinations. Unique barcodes for each variant enable the simultaneous testing of multiple entities, eliminating the need for separate individual tests. Subsequently, to identify crucial parameters, samples were collected and analyzed using barcode sequencing. This review explores the development of barcode design and its applications, including the evaluation of nucleic acid delivery systems and the optimization of gene expression in vivo.

Abstract 3110: An enhanced and cost-efficient method for neoantigen immunogenicity screening method: Double Barcode Neoepitope ScanTM

Abstract Neoantigens, HLA bound peptides generated by tumor-specific mutations, have emerged as promising targets for cancer immunotherapeutic. However, the significant challenge in neoantigen-based therapies is that the neoantigens are rare and difficult to predict. Therefore, in addition to prediction algorithms, the optimization of validation methods is essential for the reliable selection of highly immunogenic neoepitopes. In this study, we have developed a cost-effective screening method to validate large scale of neoantigen candidates. The DNA library-based methods have been employed for antigen selection and T cell receptor identification. We improved the DNA library-based neoantigen screening method by adding two barcodes to each minigene transcribing multiple neoantigen candidates and pooled synthesis of minigenes. We initially designed the barcodes to allow analysis in a 10 by 10 format for screening of hundreds of neoantigens so that PCR with each barcode result in amplification of ten candidates. The second barcode allowed the deconvolution of immunogenicity results without the need for synthesis of individual peptides. In this method B cell was used as antigen-presenting cell, which were co-transfected with mRNA for a minigene pool, 41BBL, and OX40L after expansion with CD40L/IL4/IL21. The resulting B cells were co-cultured with T cells and T cell responses were evaluated using ELISpot. To validate the method the TESLA consortium reported tetramer positive neoantigens were included in minigene. In results, the neoantigens including each barcode were amplified to form a pool of ten neoantigens as a minigene and confirmed that the neoantigens were equally amplified by nested PCR. The neoantigen pools synthesized as mRNA were transfected for presentation in B cells. The result of the targeting a neoantigen pool containing tetramer-positive neoantigens of the TESLA consortium showed a positive for ELISpot. In conclusion, our optimized screening method, employing the double barcode system, offers a time- and cost-efficient approach for the selection of immunogenic neoantigens without the need for individual peptides. This method will facilitate large-scale screening to identify actual neoantigens with immunogenic potential, contributing to the development of neoantigen-targeted vaccines. Citation Format: Seong Gwang Kim, Min-Ho Jung, Hyun-Ji Hwang, Sejin Oh, Seong-Eui Hong, Soonmyung Paik, Hae-Suk Kim. An enhanced and cost-efficient method for neoantigen immunogenicity screening method: Double Barcode Neoepitope ScanTM [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 3110.

Rethinking about Tangible Cultural Heritage Like Architect Sinan in The Digital Age: A Synthesis between The Ages

The study is to endeavor to design proposals that will enrich the visiting experience of the architectural sites built by Sinan in line with the desires, needs, and expectations of modern-day visitors, assuming that Architect Sinan lived in today's digital age. Based on the steps of multimedia development method, technology-based recommendations have been developed for three architectural sites: the Süleymaniye Mosque, its cemetery area, and the tomb, all of which were constructed by Sinan. The on-site observation method and observation forms were utilized. Additionally, written sources (such as autobiographies, books, articles, inventories, etc.) and visual sources (documentaries) were consulted to explore Sinan's exceptional personality and construction techniques. Based on the findings from on-site observations, the following stages, enriched with visuals, are proposed as recommendations: designing a large-sized digital book, measuring 1.5x1 meters, where visitors can turn the pages by moving their hands in the air inside the mosque. Developing a matrix barcode system within the cemetery area, containing information about the individuals buried there, including important details about their lives. Creating a virtual reality application and simulation that starts with an audio narration of Sinan's own life story and then guides visitors to his tomb by describing its location.

Oligo-barcode illuminates holocentric karyotype evolution in Rhynchospora (Cyperaceae).

Holocentric karyotypes are assumed to rapidly evolve through chromosome fusions and fissions due to the diffuse nature of their centromeres. Here, we took advantage of the recent availability of a chromosome-scale reference genome for Rhynchospora breviuscula, a model species of this holocentric genus, and developed the first set of oligo-based barcode probes for a holocentric plant. These probes were applied to 13 additional species of the genus, aiming to investigate the evolutionary dynamics driving the karyotype evolution in Rhynchospora. The two sets of probes were composed of 27,392 (green) and 23,968 (magenta) oligonucleotides (45-nt long), and generated 15 distinct FISH signals as a unique barcode pattern for the identification of all five chromosome pairs of the R. breviuscula karyotype. Oligo-FISH comparative analyzes revealed different types of rearrangements, such as fusions, fissions, putative inversions and translocations, as well as genomic duplications among the analyzed species. Two rounds of whole genome duplication (WGD) were demonstrated in R. pubera, but both analyzed accessions differed in the complex chain of events that gave rise to its large, structurally diploidized karyotypes with 2n = 10 or 12. Considering the phylogenetic relationships and divergence time of the species, the specificity and synteny of the probes were maintained up to species with a divergence time of ~25 My. However, karyotype divergence in more distant species hindered chromosome mapping and the inference of specific events. This barcoding system is a powerful tool to study chromosomal variations and genomic evolution in holocentric chromosomes of Rhynchospora species.

Abstract B037: ClonMapper Duo: An scRNAseq compatible lineage tracing method to track cell-cell fusion at single-cell resolution

Abstract Spontaneous cell-cell fusion in cancer can generate genetic heterogeneity and often leads to more pathological phenotypes. While the consequences of cell-cell fusion in cancer continue to be revealed, few tools exist to determine the mechanisms and cell states which promote cell-cell fusion. To meet this need, we engineered ClonMapper Duo, a two-color, two-index expressed barcoding system which allows tracking of cell-cell fusion using live-cell imaging and lineage tracing of fusion cells in scRNAseq. The ClonMapper Duo system was created by modifying the ClonMapper DNA barcoding system to express indexed barcodes on either H2B-GFP or H2B-mCherry. Briefly, 8 unique 5-nucleotide sequences were designed by maximizing Hamming distance and 4 sequences were assigned to GFP and mCherry each. The index sequences were placed adjacent to a 15N random nucleotide in the expressed barcode region of the construct. Low-diversity GFP and mCherry barcoded cell libraries were created through lentiviral transduction of HCC1806, MDA-MB-231, and MCF-7 cells. Diversity and evenness of each library was confirmed via targeted barcode sequencing. For each cell line, homotypic GFP and mCherry barcoded cells were cocultured together for 1 week. A parallel culture was monitored using live-cell imaging to measure the rate of spontaneous cell-cell fusion and the probability of different fates (e.g. death, hybrid formation, senescence) for each cell line. Spontaneously fused cells identified by expression of both GFP and mCherry were enriched by FACS. Enriched fusion cells were expanded in parallel with the parental cocultures until ~1e5 fusion cells or 1 week was reached. Fusion and parental populations for each cell line were multiplexed for scRNAseq using the 10X Genomics 3’ CellPlex Kit. FACS enriched multibarcoded fusion cells were further bioinformatically distinguished from cell multiplets and the barcodes of spontaneously fused cells were traced to their single-barcoded cell lineage of origin. From this data set we ask: 1. Are certain cell lineages more primed for fusion than others, i.e. does a more fusogenic cell phenotype exist or is fusion random? 2. Is there a convergent state of post-fusion cells or does fusion tend to diversify phenotypes? Here, we will present the first results from this two-color, two-index live-cell imaging and scRNAseq lineage tracing system toward understanding cancer cell-cell fusion at a single cell resolution. Combining lineage traced transcriptomic data from scRNAseq with fusion rates and outcomes from live-cell imaging using ClonMapper Duo provides an unprecedented look into the causes and consequences of spontaneous cell-cell fusion in cancer. Citation Format: Andrea L. Gardner, Lan Zheng, Daylin Morgan, Kennedy Howland, Amy Brock. ClonMapper Duo: An scRNAseq compatible lineage tracing method to track cell-cell fusion at single-cell resolution [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr B037.

Abstract A019: The role of tumor transcriptional variability in evading acute CD8+ T cell exposure in melanoma

Abstract Throughout melanoma progression and immunotherapy treatment, melanoma cells often develop an ability to evade the immune system. Thus, there is a pressing need to identify and target the melanoma cell-intrinsic mechanisms underlying immune evasion. Our laboratory has pioneered the identification of transcriptional pathways that underlie melanoma progression. We have found that within even clonal melanoma cell populations, subclones of cells demonstrate tremendous heterogeneity in their transcriptional state. We previously demonstrated that these varying transcriptional states correspond to varying sensitivities of melanoma cells to stressors such as targeted therapies, and that these states can be stable across multiple cell divisions. We hypothesize that varying transcriptional states also correspond to cells that have differing abilities to evade CD8+ T cells, which are major effector cells against melanoma. To study the interactions between melanoma cells and CD8+ T cells, we engineered an ovalbumin antigen and OT-I T cell receptor system using mouse melanoma cell lines. We combined this system with DNA barcoding, which enables us to track subclones of cells undergoing immune selection. When cocultured together in vitro, ovalbumin-expressing melanoma cells are effectively killed by OT-I cells. However, we find that subclones of melanoma cells consistently possess different sensitivity to OT-I cells, and these differences are not due to their genetic background nor their ability to express and present ovalbumin. We then leveraged our DNA barcoding system with single cell RNA sequencing (scRNA-seq) to link the lineage and transcriptional state of single melanoma cells that persist through OT-I coculture. By expanding on these preliminary results, we aim to identify novel melanoma cell targets to decrease immune evasion. Citation Format: Raymond W.S. Ng, Sydney M Shaffer. The role of tumor transcriptional variability in evading acute CD8+ T cell exposure in melanoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr A019.

Digitalization of Student Administration Services at Politeknik Negeri Ujung Pandang

The process of handling student correspondence submitted to the Study Program / Department, then processed by academics and signed by Deputy Director 1 has experienced obstacles in terms of the time to complete the various kinds of letters needed by students. Sometimes it takes up to one week to complete the process. If a student sends a Professional Work Practice (PKP) application letter to the Industry and the letter is rejected, the student must repeat the process of proposing the application letter with a long time. This is because the correspondence process still uses conventional methods. This research aims to develop a web application that is integrated with various related units in handling student correspondence at Ujung Pandang State Polytechnic. The waterfall method is used in its development, including needs analysis, design, development, testing, and implementation. The result is an application that facilitates the management of student letter administration with a barcode system for verification and signing, ensuring efficiency and effectiveness in the process. The results of this research are as follows: 1) Assist the storage of data management of academic administration services; 2) The process of inputting statement letter data becomes easier and faster; 3) Make it easier for department / study program / related unit admins to manage statement letters; 4) searching for administrative service data and statement letters is easier and faster; 5) integrated student data and statement letters can improve the quality of administrative services at Politeknik Negeri Ujung Pandang.

Exploring DNA barcode for accurate identification of threatened Aconitum L. species from Western Himalaya.

Aconitum species, belonging to Ranunculaceae, have high medicinal importance but due to their overexploitation come under IUCN (International Union for Conservation of Nature) red list. The precise identification of the Aconitum species is equally important because they are used in herbal formulations. The present study aimed to develop an efficient DNA barcode system for the authentic identification of Aconitum species. A set of 92 barcode gene sequences (including 12 developed during the present study and 80 retrieved from NCBI) of 5 Aconitum species (A. heterophyllum, A. vialoceum, A. japonicum, A. napellus, and A. stapfianum) were analyzed using three methods (tree-based, distance-based, and similarity-based) for species discrimination. The PWG-distance method was found most effective for species discrimination. The discrimination rate of PWG- distance ranged from 33.3% (rbcL + trnH-psbA) to 100% (ITS, rbcL + ITS, ITS + trnH-psbA and rbcL + ITS + trnH-psbA). Among DNA barcodes and their combinations, the ITS marker had the highest degree of species discrimination (NJ-40%, PWG-100% and BLAST-40%), followed by trnH-psbA (NJ-20%, PWG-60% and BLAST-20%). ITS also had higher barcoding gap as compared to other individual barcodes and their combinations. Further, we also analyzed six Aconitum species (A. balfourii, A. ferox, A. heterophyllum, A. rotundifolium, A. soongaricum and A. violaceum) existing in Western Himalaya. These species were distinguished clearly through tree-based method using the ITS barcode gene with 100% species resolution. ITS showed the best species discrimination power and was used to develop species-specific barcodes for Aconitum species. DNA barcodes developed during the present study can be used to identify Aconitum species.

Improving laboratory turnaround times in clinical settings: A systematic review of the impact of lean methodology application.

Lean methodology, originally developed in the manufacturing sector, is a process management philosophy focused on maximizing value by eliminating waste. Its application in laboratory settings, particularly concerning laboratory turnaround times (TAT), involves a systematic approach to identifying inefficiencies and optimizing processes to enhance value for end customers. This systematic review was registered in PROSPERO with identification number (CRD42024552350) and reported based on the 2020 PRISMA checklist. An extensive search strategy was performed using PubMed, Scopus, and Embase databases and gray literatures. Advanced searching was used using Boolean operators (AND & OR). After articles were exported to endnote x8, duplications were removed and articles were selected based on titles, abstracts, and full texts. The illegibility of the articles was independently assessed by the three authors (NC, DMB, and BBT), and the disagreements were settled through scientific consensus. Methodological quality was assessed using JBI critical appraisal checklist. In this review, electronic databases search yielded 1261 articles, of which 7 met the inclusion criteria. The review demonstrated, implementation of lean principle into the routine laboratory testing had an overall impact 76.1% on reducing laboratory TAT. Transportation, manual data processing, inefficient workflow, and the heavy workload were identified as the main wasteful procedures. To eliminate these non-value-added steps, several intervention techniques were implemented, including the use of a barcoding system, process redesign, workflow optimization, hiring additional staff, and relocating the sample collection room closer to the result distribution center. Lean implementation is crucial in the medical laboratory industry for optimizing processes, reducing TAT, and ultimately enhancing customer satisfaction. As a result, all clinical laboratories should adopt and implement lean principles in their routine testing processes. The medical laboratory industry should also proactively look for and apply lean tools, provide ongoing training, and foster awareness among laboratory staffs.