scholarly journals DNA barcode-guided lentiviral CRISPRa tool to trace and isolate individual clonal lineages in heterogeneous cancer cell populations

2019 ◽  
Author(s):  
Y Akimov ◽  
D Bulanova ◽  
M Abyzova ◽  
K Wennerberg ◽  
T Aittokallio
Keyword(s):  
Dna Barcoding ◽  
Cancer Cell ◽  
Experimental Evaluation ◽  
System Performance ◽  
Dna Barcode ◽  
Lineage Tracing ◽  
Cell Populations ◽  
Functional Heterogeneity ◽  
High Complexity ◽  
Cell Lineages

AbstractThe genetic and functional heterogeneity of tumors imposes the challenge of understanding how a cancer progresses, evolves and adapts to treatment at the subclonal level. Therefore, there is a critical need for methods that enable profiling of individual cancer cell lineages. Here, we report a novel system that couples an established DNA barcoding technique for lineage tracing with a controlled DNA barcode-guided lineage isolation (B-GLI). B-GLI allows both high-complexity of lineage tracing and effective isolation of individual clones by CRISPRa-mediated induction of puromycin resistance, making it possible to unbiasedly trace, isolate, and study individual cancer cell lineages. We present experimental evaluation of the system performance in isolation of lineages and outline a comprehensive workflow for B-GLI applications. We believe the system has broad applications aimed at molecular and phenotypic profiling of individual lineages in heterogeneous cell populations.

scholarly journals Discrete and continuum phenotype-structured models for the evolution of cancer cell populations under chemotherapy

2020 ◽  
Vol 15 ◽  
pp. 14 ◽  
Author(s):  
Rebecca E.A. Stace ◽  
Thomas Stiehl ◽  
Mark A.J. Chaplain ◽  
Anna Marciniak-Czochra ◽  
Tommaso Lorenzi
Keyword(s):  
Cancer Cell ◽  
Cell Population ◽  
Evolutionary Dynamics ◽  
Analytical Description ◽  
Chemotherapeutic Agents ◽  
Cell Populations ◽  
Theoretical Ground ◽  
Individual Based Model ◽  
Nonlocal Parabolic Equation ◽  
Epigenetic Drug

We present a stochastic individual-based model for the phenotypic evolution of cancer cell populations under chemotherapy. In particular, we consider the case of combination cancer therapy whereby a chemotherapeutic agent is administered as the primary treatment and an epigenetic drug is used as an adjuvant treatment. The cell population is structured by the expression level of a gene that controls cell proliferation and chemoresistance. In order to obtain an analytical description of evolutionary dynamics, we formally derive a deterministic continuum counterpart of this discrete model, which is given by a nonlocal parabolic equation for the cell population density function. Integrating computational simulations of the individual-based model with analysis of the corresponding continuum model, we perform a complete exploration of the model parameter space. We show that harsher environmental conditions and higher probabilities of spontaneous epimutation can lead to more effective chemotherapy, and we demonstrate the existence of an inverse relationship between the efficacy of the epigenetic drug and the probability of spontaneous epimutation. Taken together, the outcomes of the model provide theoretical ground for the development of anticancer protocols that use lower concentrations of chemotherapeutic agents in combination with epigenetic drugs capable of promoting the re-expression of epigenetically regulated genes.

scholarly journals Differentiation of Mitragyna speciosa, a narcotic plant, from allied Mitragyna species using DNA barcoding-high-resolution melting (Bar-HRM) analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chayapol Tungphatthong ◽  
Santhosh Kumar J. Urumarudappa ◽  
Supita Awachai ◽  
Thongchai Sooksawate ◽  
Suchada Sukrong
Keyword(s):  
High Resolution ◽  
Dna Barcoding ◽  
High Resolution Melting ◽  
Dna Barcode ◽  
Herbal Medicines ◽  
Efficient Tool ◽  
Hrm Analysis ◽  
Mitragyna Speciosa ◽  
Leaf Powder

AbstractMitragyna speciosa (Korth.) Havil. [MS], or “kratom” in Thai, is the only narcotic species among the four species of Mitragyna in Thailand, which also include Mitragyna diversifolia (Wall. ex G. Don) Havil. [MD], Mitragyna hirsuta Havil. [MH], and Mitragyna rotundifolia (Roxb.) O. Kuntze [MR]. M. speciosa is a tropical tree belonging to the Rubiaceae family and has been prohibited by law in Thailand. However, it has been extensively covered in national and international news, as its abuse has become more popular. M. speciosa is a narcotic plant and has been used as an opium substitute and traditionally used for the treatment of chronic pain and various illnesses. Due to morphological disparities in the genus, the identification of plants in various forms, including fresh leaves, dried leaf powder, and finished products, is difficult. In this study, DNA barcoding combined with high-resolution melting (Bar-HRM) analysis was performed to differentiate M. speciosa from allied Mitragyna and to assess the capability of Bar-HRM assays to identify M. speciosa in suspected kratom or M. speciosa-containing samples. Bar-HRM analysis of PCR amplicons was based on the ITS2, rbcL, trnH-psbA, and matK DNA barcode regions. The melting profiles of ITS2 amplicons were clearly distinct, which enabled the authentication and differentiation of Mitragyna species from allied species. This study reveals that DNA barcoding coupled with HRM is an efficient tool with which to identify M. speciosa and M. speciosa-containing samples and ensure the safety and quality of traditional Thai herbal medicines.

scholarly journals Cancer stem cells and cisplatin‐resistant cells isolated from non‐small‐lung cancer cell lines constitute related cell populations

2014 ◽  
Vol 3 (5) ◽  
pp. 1099-1111 ◽  
Author(s):  
Blanca D. Lopez‐Ayllon ◽  
Veronica Moncho‐Amor ◽  
Ander Abarrategi ◽  
Inmaculada Ibañez Cáceres ◽  
Javier Castro‐Carpeño ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Stem Cells ◽  
Cancer Stem Cells ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Lines ◽  
Cell Populations ◽  
Lung Cancer Cell ◽  
Related Cell ◽  
Resistant Cells

Experimental evaluation of system performance

1973 ◽  
Vol 12 (3) ◽  
pp. 302-314 ◽  
Author(s):  
Y. Bard
Keyword(s):  
Experimental Evaluation ◽  
System Performance ◽  
Evaluation Of System Performance

Research Paper DNA barcode identification of fish products from Guiyang markets in southwest China

2022 ◽  
Author(s):  
Qian Tang ◽  
Qi Luo ◽  
Qian Duan ◽  
Lei Deng ◽  
Renyi Zhang
Keyword(s):  
Dna Barcoding ◽  
Molecular Identification ◽  
Fish Consumption ◽  
Southwest China ◽  
Dna Barcode ◽  
Guizhou Province ◽  
Accurate Identification ◽  
Continuous Growth ◽  
Fish Products ◽  
Fresh Frozen

Nowadays, the global fish consumption continues to rise along with the continuous growth of the population, which has led to the dilemma of overfishing of fishery resources. Especially high-value fish that are overfished are often replaced by other fish. Therefore, the accurate identification of fish products in the market is a problem worthy of attention. In this study, full-DNA barcoding (FDB) and mini-DNA barcoding (MDB) used to detect the fraud of fish products in Guiyang, Guizhou province in China. The molecular identification results showed that 39 of the 191 samples were not consistent with the labels. The mislabelling of fish products for fresh, frozen, cooked and canned were 11.70%, 20.00%, 34.09% and 50.00%, respectively. The average kimura 2 parameter distances of MDB within species and genera were 0.27% and 5.41%, respectively; while average distances of FDB were 0.17% within species and 6.17% within genera. In this study, commercial fraud is noticeable, most of the high-priced fish were replaced of low-priced fish with a similar feature. Our study indicated that DNA barcoding is a valid tool for the identification of fish products and that it allows an idea of conservation and monitoring efforts, while confirming the MDB as a reliable tool for fish products.

Phylogenetic Analysis of Black Peper (Piper Spp.) Population Collected in Different Locations of Vietnam Based on the ITSU1-4 Gene Region

2021 ◽  
Author(s):  
Sonexay Rasphone ◽  
Long Thanh Dang ◽  
Hoan Nguyen ◽  
Ngoc Quang Nguyen ◽  
Oanh Thi Duong ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Ribosomal Dna ◽  
Maximum Likelihood Method ◽  
Dna Barcode ◽  
Population Expansion ◽  
Nuclear Ribosomal Dna ◽  
Likelihood Method ◽  
Gene Region ◽  
Universal Primers ◽  
Intraspecific Distance

Abstract Background: The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. To compare and find out the analysis genetic diversity difference some pepper individuals collected in different localities in Vietnam when using the ITS of nuclear ribosomal DNA. The ITS gene region from the nuclear genomes were tested for their suitability as DNA barcoding regions of thirty-nine pepper individuals. Universal primers were used, and sequenced products were analyzed using the Maximum Likelihood method and Tamura-Nei model in the MEGA X program.Results: We did not observe high variability in intraspecific distance within the ITSu1-4 gene region between individuals, ranged from 0.000 to 0.155 (mean = 0.033). The size of the gene region has fluctuated from 667 to 685 bp between different individuals with the percentage (G + C) contained in the ITSu1-4 gene region was ranged from 54.776% to 60.805%, mean = 60.174%. The values of Fu’s Fs, D, Fu and Li’s D* and F* were negative as well (Fs = -0.209, D = -1.824; P < 0.05, D* = -1.205; not significant, P > 0.10 and F* = -1.699; not significant, 0.10 > P > 0.05), indicating an excess of recently derived haplotypes and suggesting that either population expansion or background selection has occurred. The value Strobeck’s S the obtained between individuals in a population is high (S = 0.684). The results of evolutionary relationships of taxa obtained 3 groups with the highest value of Fst is shown in the pairs of groups II and III (Fst = 0.151), and the lowest is in groups II and I (Fst = 0.015). All of the new sequences have been deposited in GeneBank under the following accession numbers MZ636718 to MZ636756.Conclusions: This database is an important resource for researchers working on Species of pepper in Vietnam and also provides a tool to create ITSu1-4 databases for any given taxonomy.

Capturing quantitative features of protein expression from in situ fluorescence microscopic images of cancer cell populations

2017 ◽  
pp. 279-297
Author(s):  
Joana Figueiredo ◽  
Ana Sofia Ribeiro ◽  
Tânia Mestre ◽  
Sofia Esménio ◽  
Martina Fonseca ◽  
...  
Keyword(s):  
Protein Expression ◽  
Cancer Cell ◽  
Cell Populations ◽  
Microscopic Images

scholarly journals Specification and DNA Barcoding of Thai Traditional Remedy for Chronic Kidney Disease: Pikad Tri-phol-sa-mut-than

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2023
Author(s):  
Suwimol Thariwong ◽  
Aekkhaluck Intharuksa ◽  
Panee Sirisa-ard ◽  
Wannaree Charoensup ◽  
Sunee Chansakaow
Keyword(s):  
Dna Barcoding ◽  
Herbal Remedy ◽  
Raw Materials ◽  
Dna Barcode ◽  
Raw Material ◽  
Morinda Citrifolia ◽  
Herbal Remedies ◽  
Scientific Database ◽  
Kidney Deficiency ◽  
Fruit Species

The Pikad Tri-phol-sa-mut-than (TS) remedy, a Thai traditional medicine, is officially recorded in Tamra Paetsart Sonkrau Chabub Anurak for its capabilities in treating kidney deficiency. TS remedy is composed of three fruit species—Aegle marmelos (L.) Corrêa., Coriandrum sativum L., and Morinda citrifolia L.—in an equal part by weight. The quality of the raw material is one of the essential factors that can affect the effectiveness and safety of treatment by herbal remedy. The pharmacognostic evaluation and DNA barcode of the three fruit species and TS remedy were performed in this study to authenticate them from contamination, and to provide the scientific database for further uses. Macroscopic and microscopic examination, chemical profile by TLC, and DNA barcoding were employed to positively identify the raw materials bought from the herbal market, especially the powder form. Consequently, the outcomes of this investigation can be used to develop an essential and effective tool for the authentication of crude drugs and herbal remedies.

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