151
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Selection, Identification and Functional Performance of Ammonia-Degrading Microbial Communities from an Activated Sludge for Landfill Leachate Treatment. Microorganisms 2023; 11:microorganisms11020311. [PMID: 36838276 PMCID: PMC9961800 DOI: 10.3390/microorganisms11020311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
The increasing amounts of municipal solid waste and their management in landfills caused an increase in the production of leachate, a liquid formed by the percolation of rainwater through the waste. Leachate creates serious problems to municipal wastewater treatment plants; indeed, its high levels of ammonia are toxic for bacterial cells and drastically reduce the biological removal of nitrogen by activated sludge. In the present work, we studied, using a metagenomic approach based on next-generation sequencing (NGS), the microbial composition of sludge in the municipal wastewater treatment plant of Porto Sant'Elpidio (Italy). Through activated sludge enrichment experiments based on the Repetitive Re-Inoculum Assay, we were able to select and identify a minimal bacterial community capable of degrading high concentrations of ammonium (NH4+-N ≅ 350 mg/L) present in a leachate-based medium. The analysis of NGS data suggests that seven families of bacteria (Alcaligenaceae, Nitrosomonadaceae, Caulobacteraceae, Xanthomonadaceae, Rhodanobacteraceae, Comamonadaceae and Chitinophagaceae) are mainly responsible for ammonia oxidation. Furthermore, we isolated from the enriched sludge three genera (Klebsiella sp., Castellaniella sp. and Acinetobacter sp.) capable of heterotrophic nitrification coupled with aerobic denitrification. These bacteria released a trace amount of both nitrite and nitrate possibly transforming ammonia into gaseous nitrogen. Our findings represent the starting point to produce an optimized microorganisms's mixture for the biological removal of ammonia contained in leachate.
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152
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Mittal S, Pathak B. A Step toward Amino Acid-Labeled DNA Sequencing: Boosting Transmission Sensitivity of Graphene Nanogap. ACS APPLIED BIO MATERIALS 2023; 6:218-227. [PMID: 36524773 DOI: 10.1021/acsabm.2c00851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Existing obstacles in next-generation DNA sequencing techniques, for instance, high noise, high translocation speed, and configurational fluctuations, call for approaches capable of reaching the goal and accelerating the process of personalized medicine development. The labeling nucleotide approach has the potential to overcome these barriers and boost the recognition sensitivity of a solid-state nanodevice. In this theoretical report, the first-principles density functional theory calculations have been employed to study the role of three different labels, tyrosine (Tyr), aspartic acid (Asp), and arginine (Arg), for labeling DNA nucleotides and study their effect in rapid and controlled DNA sequencing at atomic resolution. Remarkable differences in interaction energy values are noticed in all three cases of differently labeled nucleotides. The zero-bias transmission spectra confirm that proposed labels have the ability to detect the individual nucleotide, amplifying the tunneling current sensitivity by several orders of magnitude. The current-voltage characteristics of Arg-labeled nucleotides are found to be promising for single nucleotide recognition even at a very low bias voltage of 0.1 V.
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Affiliation(s)
- Sneha Mittal
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh453552, India
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh453552, India
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153
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Sato K, Seki T, Mizutani A, Muranaka Y, Hirota S, Nishi K, Yamazaki K, Nishii R, Nakanishi T, Tamai I, Kawai K, Kobayashi M. A single high-dose irradiation changes accumulation of methotrexate and gene expression levels of SLC and ABC transporters in cancer cells. Front Pharmacol 2023; 13:1069321. [PMID: 36712667 PMCID: PMC9874220 DOI: 10.3389/fphar.2022.1069321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/29/2022] [Indexed: 01/12/2023] Open
Abstract
Chemoradiotherapy is frequently used to treat cancer. Stereotactic body radiotherapy (SBRT) is a single high-dose radiotherapy used to treat a variety of cancers. The anticancer drug methotrexate (MTX) shows affinity for solute carrier (SLC) and ATP-binding cassette (ABC) transporters. This study investigated relationships between accumulation of methotrexate and gene expression levels of solute carrier and ATP-binding cassette transporters in cancer cells after a single and high-dose X-ray irradiation. Cancer cell lines were selected from lung and cervical cancer cell line that are commonly used for stereotactic body radiotherapy and effective with methotrexate. We examined expression levels of organic anion-transporting polypeptide (OATP)1B1, OATP1B3, OATP1B7, and organic anion transporter (OAT)1 as solute carrier transporters and multidrug resistance-associated protein (MRP)1 and MRP2 as ATP-binding cassette transporters, using real-time polymerase chain reaction and accumulation of 3H-MTX in cancer cells after 10-Gy irradiation, assuming stereotactic body radiotherapy. Cells were divided into three groups: Control without irradiation; 4 h after irradiation; and 24 h after irradiation. In control, gene expression levels of OAT1 in all cells was below the limit of measurement. After irradiation, gene expression levels of OATP1B1/1B3/1B7 showed changes in each cell line. Gene expression levels of MRP1/2 tended to increase after irradiation. Gene expression levels of OATP1B1/1B3/1B7 were much lower than those of MRP1/2. Accumulation of 3H-MTX tended to decrease over time after irradiation. Irradiation of cancer cells thus alters gene expression levels of both solute carrier transporters (OATP1B1/1B3/1B7) and ABC transporters (MRP1/2) and decreases accumulation of 3H-MTX in cancer cells over time due to elevated expression of MRP1/2.
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Affiliation(s)
- Kakeru Sato
- Division of Health Sciences, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Tatsuya Seki
- Division of Health Sciences, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Asuka Mizutani
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Yuka Muranaka
- Division of Health Sciences, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Shiho Hirota
- Division of Health Sciences, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kodai Nishi
- Department of Molecular Imaging and Theranostics, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Kana Yamazaki
- Department of Molecular Imaging and Theranostics, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Ryuichi Nishii
- Department of Molecular Imaging and Theranostics, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Takeo Nakanishi
- Faculty of Pharmacy, Takasaki University of Health and Welfare, Takasaki, Gunma, Japan
| | - Ikumi Tamai
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Keiichi Kawai
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan,Biomedical Imaging Research Center, University of Fukui, Fukui, Japan
| | - Masato Kobayashi
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan,*Correspondence: Masato Kobayashi,
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154
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Chen J, Šprem N, Wu Y, Xia S. Editorial: Application in evolutionary novelties and diversities: Medicine, agriculture, and conservation. Front Genet 2023; 13:1104836. [PMID: 36704349 PMCID: PMC9871380 DOI: 10.3389/fgene.2022.1104836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/07/2022] [Indexed: 01/12/2023] Open
Affiliation(s)
- Jianhai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China,*Correspondence: Jianhai Chen,
| | - Nikica Šprem
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Yongjie Wu
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
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155
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Mugnai F, Costantini F, Chenuil A, Leduc M, Gutiérrez Ortega JM, Meglécz E. Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies. PeerJ 2023; 11:e14616. [PMID: 36643652 PMCID: PMC9835706 DOI: 10.7717/peerj.14616] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/01/2022] [Indexed: 01/11/2023] Open
Abstract
Background In metabarcoding analyses, the taxonomic assignment is crucial to place sequencing data in biological and ecological contexts. This fundamental step depends on a reference database, which should have a good taxonomic coverage to avoid unassigned sequences. However, this goal is rarely achieved in many geographic regions and for several taxonomic groups. On the other hand, more is not necessarily better, as sequences in reference databases belonging to taxonomic groups out of the studied region/environment context might lead to false assignments. Methods We investigated the effect of using several subsets of a cytochrome c oxidase subunit I (COI) reference database on taxonomic assignment. Published metabarcoding sequences from the Mediterranean Sea were assigned to taxa using COInr, which is a comprehensive, non-redundant and recent database of COI sequences obtained both from BOLD and NCBI, and two of its subsets: (i) all sequences except insects (COInr-WO-Insecta), which represent the overwhelming majority of COInr database, but are irrelevant for marine samples, and (ii) all sequences from taxonomic families present in the Mediterranean Sea (COInr-Med). Four different algorithms for taxonomic assignment were employed in parallel to evaluate differences in their output and data consistency. Results The reduction of the database to more specific custom subsets increased the number of unassigned sequences. Nevertheless, since most of them were incorrectly assigned by the less specific databases, this is a positive outcome. Moreover, the taxonomic resolution (the lowest taxonomic level to which a sequence is attributed) of several sequences tended to increase when using customized databases. These findings clearly indicated the need for customized databases adapted to each study. However, the very high proportion of unassigned sequences points to the need to enrich the local database with new barcodes specifically obtained from the studied region and/or taxonomic group. Including novel local barcodes to the COI database proved to be very profitable: by adding only 116 new barcodes sequenced in our laboratory, thus increasing the reference database by only 0.04%, we were able to improve the resolution for ca. 0.6-1% of the Amplicon Sequence Variants (ASVs).
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Affiliation(s)
- Francesco Mugnai
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Ravenna, Italy
| | - Federica Costantini
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Ravenna, Italy,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma, Italy
| | - Anne Chenuil
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | | | | | - Emese Meglécz
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
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156
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Tripathy A, John V, Wadden J, Kong S, Sharba S, Koschmann C. Liquid biopsy in pediatric brain tumors. Front Genet 2023; 13:1114762. [PMID: 36685825 PMCID: PMC9853427 DOI: 10.3389/fgene.2022.1114762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/23/2022] [Indexed: 01/09/2023] Open
Abstract
Malignant primary brain tumors are the most common cancer in children aged 0-14 years, and are the most common cause of death among pediatric cancer patients. Compared to other cancers, pediatric brain tumors have been difficult to diagnose and study given the high risk of intracranial biopsy penetrating through vital midline structures, where the majority of pediatric brain tumors originate (Ostrom et al., 2015). Furthermore, the vast majority of these tumors recur. With limitations in the ability to monitor using clinical and radiographic methods alone, minimally invasive methods such as liquid biopsy will be crucial to our understanding and treatment. Liquid biopsy of blood, urine, and cerebrospinal fluid (CSF) can be used to sample cfDNA, ctDNA, RNA, extracellular vesicles, and tumor-associated proteins. In the past year, four seminal papers have made significant advances in the use of liquid biopsy in pediatric brain tumor patients (Liu et al., 2021; Cantor et al., 2022; Miller et al., 2022; Pagès et al., 2022). In this review, we integrate the results of these studies and others to discuss how the newest technologies in liquid biopsy are being developed for molecular diagnosis and treatment response in pediatric brain tumors.
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Affiliation(s)
- Arushi Tripathy
- Department of Neurosurgery, Michigan Medicine, Ann Arbor, MI, United States
| | - Vishal John
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, United States
| | - Jack Wadden
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, United States
| | - Seongbae Kong
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, United States
| | - Sana Sharba
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, United States
| | - Carl Koschmann
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, United States
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157
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Mittal S, Pathak B. Towards a graphene semi/hybrid-nanogap: a new architecture for ultrafast DNA sequencing. NANOSCALE 2023; 15:757-767. [PMID: 36525055 DOI: 10.1039/d2nr05200h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The tremendous upsurge in the research of next-generation sequencing (NGS) methods has broadly been driven by the rise of the wonder material graphene and continues to dominate the futuristic approaches for fast and accurate DNA sequencing. The success of graphene has also triggered the search for many new potential NGS methods capable of ultrafast, reliable, and controlled DNA sequencing. The present study delves into the potential of a new NGS architecture utilizing graphene, namely, a 'semi/hybrid-nanogap' for the identification of DNA nucleobases with single-base resolution. In the framework of first-principles density functional theory methods, we have calculated the transmission function and current-voltage (I-V) characteristics which are of particular significance for DNA sequencing applications. It is noted that the interaction energy values are significantly reduced compared to the previously reported graphene nanodevices, which can lead to a controlled translocation during experimental measurements. Based on the transmission function, each nucleobase can be identified with pertinent sensitivity. It is noticed that the use of highly conductive nucleobase analogs can facilitate improved single nucleobase sensing by increasing the transmission sensitivity. Therefore, we believe that the present study opens up promising frontiers for sequencing applications.
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Affiliation(s)
- Sneha Mittal
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
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158
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Zhang N, Ma L, Ding W. The Diagnostic Value of Blood Next-Generation Sequencing in Early Surgical Site Infection After Spine Surgery. Int J Gen Med 2023; 16:37-45. [PMID: 36636713 PMCID: PMC9830415 DOI: 10.2147/ijgm.s394255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Objective To determine the diagnostic value of blood next-generation sequencing (NGS) in early surgical site infection after spine surgery. Because the blood is sterile in healthy individuals, it is expected that blood NGS is both sensitive and specific for the detection of infection. Methods A total of 28 patients with definitive spinal surgical site infections and controls (n=30) were retrospectively included. The postoperative results of NGS and culture on different samples, such as blood and drainage fluid, were obtained and compared to evaluate the diagnostic value of blood NGS. The diagnostic value parameters (sensitivity, specificity, etc.) were calculated. Results Among the four bacteriological exam methods, blood NGS was both sensitive and specific for the determination of infection after spine surgery. The sensitivities of blood and drainage fluid NGS were similar (0.82 vs 0.89, P=0.617). However, the specificities of the two assessments differed, which were 0.97 for blood NGS and 0.40 for drainage fluid NGS (P<0.001). The sensitivities of bacterial culture were lower than those of NGS (blood: 0.82 vs 0.25, P<0.001; drainage fluid: 0.89 vs 0.61, P<0.001), regardless of the sample type. However, the specificities of bacterial culture were equal to or higher than those of NGS (blood: 0.97 vs 0.97, P=1.000; drainage fluid: 0.40 vs 0.80, P=0.002). Conclusion This article emphasizes the superiority of blood NGS in infection detection and bacterial determination in patients undergoing spine surgery. Compared with traditional drainage fluid bacterial culture and NGS, blood NGS was more sensitive and specific, and its extensive application could be expected.
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Affiliation(s)
- Nan Zhang
- Department of Spine Surgery, 3rd Hospital of Hebei Medical University, Shijiazhuang, People’s Republic of China
| | - Lei Ma
- Department of Spine Surgery, 3rd Hospital of Hebei Medical University, Shijiazhuang, People’s Republic of China
| | - Wenyuan Ding
- Department of Spine Surgery, 3rd Hospital of Hebei Medical University, Shijiazhuang, People’s Republic of China,Correspondence: Wenyuan Ding, Department of Spine Surgery, 3rd Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, 050051, People’s Republic of China, Email
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159
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Identification of Fish Species and Targeted Genetic Modifications Based on DNA Analysis: State of the Art. Foods 2023; 12:foods12010228. [PMID: 36613444 PMCID: PMC9818732 DOI: 10.3390/foods12010228] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Food adulteration is one of the most serious problems regarding food safety and quality worldwide. Besides misleading consumers, it poses a considerable health risk associated with the potential non-labeled allergen content. Fish and fish products are one of the most expensive and widely traded commodities, which predisposes them to being adulterated. Among all fraud types, replacing high-quality or rare fish with a less valuable species predominates. Because fish differ in their allergen content, specifically the main one, parvalbumin, their replacement can endanger consumers. This underlines the need for reliable, robust control systems for fish species identification. Various methods may be used for the aforementioned purpose. DNA-based methods are favored due to the characteristics of the target molecule, DNA, which is heat resistant, and the fact that through its sequencing, several other traits, including the recognition of genetic modifications, can be determined. Thus, they are considered to be powerful tools for identifying cases of food fraud. In this review, the major DNA-based methods applicable for fish meat and product authentication and their commercial applications are discussed, the possibilities of detecting genetic modifications in fish are evaluated, and future trends are highlighted, emphasizing the need for comprehensive and regularly updated online database resources.
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160
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Dong M, Zhang G, Meng J, Liu B, Jiang D, Liu F. MMP9-Associated Tumor Stem Cells, CCL1-Silenced Dendritic Cells, and Cytokine-Induced Killer Cells Have a Remarkable Therapeutic Efficacy for Acute Myeloid Leukemia by Activating T Cells. Stem Cells Int 2023; 2023:2490943. [PMID: 37200633 PMCID: PMC10188259 DOI: 10.1155/2023/2490943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/15/2023] [Accepted: 04/06/2023] [Indexed: 05/20/2023] Open
Abstract
Purpose Dendritic cells (DC) are specialized antigen-presenting cells, and cytokine-induced killer (CIK) cells have a specific killing activity to a variety of tumors. However, the underlining mechanism and function of DC-CIK cells in acute myeloid leukemia (AML) remain largely elusive. Methods Gene expression profiles of leukemia patients were obtained from TCGA, DC cell components were evaluated using the quanTIseq method, and cancer stem cell scores were estimated using machine learning methods. The transcriptomes were obtained in DC-CIK cells from normal and AML patients by high-throughput sequencing. Large differentially expressed mRNAs were verified by RT-qPCR assay, and MMP9 and CCL1 were selected for subsequent studies in vivo and in vitro experiments. Results Significant positive correlations were found with DC versus cancer stem cells (p = 0.008) and the expression of MMP9 versus cancer stem cells (p = 0.018). MMP9 and CCL1 were found to be highly expressed in DC-CIK cells from AML patients. DC-CIK cells with MMP9 and CCL1 knockout alone had little effect on leukemia cells, while knockdown of MMP9 and CCL1 in DC-CIK cells increased cytotoxicity, suppressed proliferation, and induced apoptosis of leukemia cells. In addition, we proved that MMP9- and CCL1-silenced DC-CIK cells significantly elevated the CD3+CD4+ and CD3+CD8+ cells and lowered the CD4+PD-1+ and CD8+PD-1+ T cells. Meanwhile, blockage of MMP9 and CCL1 in DC-CIK cells dramatically increased IL-2 and IFN-γ, increased CD107aþ (LAMP-1) and granzyme B (GZMB), and downregulated PD-1, CTLA4, TIM3, and LAG3 T cells from AML patients and AML model mice. Furthermore, activated T cells in DC-CIK cells knocking down MMP9 and CCL1 also prevented proliferation and accelerated apoptosis of AML cells. Conclusion Our findings demonstrated that blockage of MMP9 and CCL1 in DC-CIK cells could markedly enhance the therapeutic efficiency in AML via activating T cells.
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Affiliation(s)
- Min Dong
- Department of Hematology, The Second Affiliated Hospital of Hainan Medical University, Haikou 570000, China
| | - Guozhen Zhang
- Department of Hematology, The Second Affiliated Hospital of Hainan Medical University, Haikou 570000, China
| | - Jie Meng
- Department of Hematology, The Second Affiliated Hospital of Hainan Medical University, Haikou 570000, China
| | - Biou Liu
- Department of Hematology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Duanfeng Jiang
- Department of Hematology, The Second Affiliated Hospital of Hainan Medical University, Haikou 570000, China
| | - Feng Liu
- Department of Hematology, The Affiliated Hospital of Guilin Medical University, Guilin 541001, China
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161
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Davies M, Jurynec MJ, Gomez-Alvarado F, Hu D, Feeley SE, Allen-Brady K, Tashjian RZ, Feeley BT. Current cellular and molecular biology techniques for the orthopedic surgeon-scientist. J Shoulder Elbow Surg 2023; 32:e11-e22. [PMID: 35988889 DOI: 10.1016/j.jse.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/27/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023]
Affiliation(s)
- Michael Davies
- Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Michael J Jurynec
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA
| | - Francisco Gomez-Alvarado
- Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Hu
- Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Sonali E Feeley
- Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Kristina Allen-Brady
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Robert Z Tashjian
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA.
| | - Brian T Feeley
- Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA, USA
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162
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Tamura T, Yamamoto Shimojima K, Okamoto N, Yagasaki H, Morioka I, Kanno H, Minakuchi Y, Toyoda A, Yamamoto T. Long-read sequence analysis for clustered genomic copy number aberrations revealed architectures of intricately intertwined rearrangements. Am J Med Genet A 2023; 191:112-119. [PMID: 36282026 DOI: 10.1002/ajmg.a.62997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/13/2022] [Accepted: 08/24/2022] [Indexed: 12/14/2022]
Abstract
Most chromosomal aberrations revealed by chromosomal microarray testing (CMA) are simple; however, very complex chromosomal structural rearrangements can also be found. Although the mechanism of structural rearrangements has been gradually revealed, not all mechanisms have been elucidated. We analyzed the breakpoint-junctions (BJs) of two or more clustered copy number variations (CNVs) in the same chromosome arms to understand their conformation and the mechanism of complex structural rearrangements. Combining CMA with long-read whole-genome sequencing (WGS) analysis, we successfully determined all BJs for the clustered CNVs identified in four patients. Multiple CNVs were intricately intertwined with each other, and clustered CNVs in four patients were involved in global complex chromosomal rearrangements. The BJs of two clustered deletions identified in two patients showed microhomologies, and their characteristics were explained by chromothripsis. In contrast, the BJs in the other two patients, who showed clustered deletions and duplications, consisted of blunt-end and nontemplated insertions. These findings could be explained only by alternative nonhomologous end-joining, a mechanism related to polymerase theta. All the patients had at least one inverted segment. Three patients showed cryptic aberrations involving a disruption and a deletion/duplication, which were not detected by CMA but were first identified by WGS. This result suggested that complex rearrangements should be considered if clustered CNVs are observed in the same chromosome arms. Because CMA has potential limitations in genotype-phenotype correlation analysis, a more detailed analysis by whole genome examination is recommended in cases of suspected complex structural aberrations.
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Affiliation(s)
- Takeaki Tamura
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan.,Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Keiko Yamamoto Shimojima
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Hiroshi Yagasaki
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Yohei Minakuchi
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
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163
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Yu C, Qi X, Yan W, Wu W, Shen B. Next-Generation Sequencing Markup Language (NGSML): A Medium for the Representation and Exchange of NGS Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:576-585. [PMID: 35085089 DOI: 10.1109/tcbb.2022.3144170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
With the increasing demand for low-cost high-throughput sequencing of large genomes, next-generation sequencing (NGS) technology has developed rapidly. NGS can not only be used in basic scientific research but also in clinical diagnostics and healthcare. Numerous software systems and tools have been developed to analyze NGS data, and various data formats have been produced to accommodate different sequencing equipment providers or analytical software. However, the data interoperability between these tools brings great challenges to researchers. A generic format that could be shared by most of the software and tools in the NGS field would make data interoperability and sharing easier. In this paper, we defined a general XML-based NGS markup language (NGSML) format for the representation and exchange of NGS data. We also developed a user-friendly GUI tool, NGSMLEditor, for presenting, creating, editing, and converting NGSML files. By using NGSML, various types of NGS data can be saved in one unified format. Compared with the unstructured plain text file, a structured data format based on XML technology solves the incompatibility of various NGS data formats. The NGSML specifications are freely available from http://www.sysbio.org.cn/NGSML. NGSMLEditor is open source under GNU GPL and can be downloaded from the website.
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164
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Nourieh M, Vibert R, Saint-Ghislain M, Cyrta J, Vincent-Salomon A. Next-generation sequencing in breast pathology: real impact on routine practice over a decade since its introduction. Histopathology 2023; 82:162-169. [PMID: 36482269 PMCID: PMC10108312 DOI: 10.1111/his.14794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 12/13/2022]
Abstract
The diagnosis, histomolecular classes of breast cancers (luminal A, luminal B, HER2-enriched, and basal-like), and accurate prediction of prognosis are commonly determined using morphological and phenotypical analyses in clinical practice worldwide. Therapeutic strategies are mostly based on the disease stage and molecular subclasses of breast cancer. Targeted therapies, such as anti-HER2s, poly-ADP ribose polymerase inhibitors or, to a lesser extent, phosphatidylinositol 3 kinase inhibitors, have substantially improved breast cancer patient prognosis over the past decades. Human epidermal growth factor receptor 2 (HER2) overexpression is widely determined based on immunohistochemistry, while next-generation sequencing (NGS) is currently employed to assess the presence of molecular alterations, including breast cancer gene 1 (BRCA1) and 2 or phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) mutations, which are targets of these new approved therapies. In addition, next-generation sequencing (NGS) can aid the pathologist in challenging situations, such as a diagnostic workup for a metastatic carcinoma in lymph nodes of unknown origin, differential diagnosis of spindle cell tumourtumor in the breast between metaplastic carcinoma, malignant PT and sarcoma, o, as well as determining relatedness between primary breast cancers and recurrences. NGS offers a powerful tool that enables the pathologist to combine morphological analyses together with molecular alterations in challenging diagnostic situations.
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Affiliation(s)
- Maya Nourieh
- Department of Diagnostic and Theranostic Medicine, Versailles Saint Quentin University UVSQ, Institut CURIE, Saint-Cloud, France
| | - Roseline Vibert
- Department of Diagnostic and Theranostic Medicine, Paris Sciences Lettres University PSL, Institut CURIE, Paris, France
| | - Mathilde Saint-Ghislain
- Department of Medical Oncology, Paris Sciences Lettres University PSL, Institut CURIE, Paris, France
| | - Joanna Cyrta
- Department of Diagnostic and Theranostic Medicine, Paris Sciences Lettres University PSL, Institut CURIE, Paris, France
| | - Anne Vincent-Salomon
- Department of Diagnostic and Theranostic Medicine, Paris Sciences Lettres University PSL, Institut CURIE, Paris, France
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165
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Abeyrama DK, Boyle B, Burg TM. Comparison of genotyping by sequencing procedures to determine population genetic structure. Funct Integr Genomics 2022; 23:9. [PMID: 36538186 DOI: 10.1007/s10142-022-00929-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/07/2022] [Accepted: 11/16/2022] [Indexed: 03/21/2023]
Abstract
Advancements in technology over the past few decades have resulted in the development of genome sequencing at lower costs. Protocols, costs, and the amount of data produced by different sequencing technologies are highly variable. Ion Torrent and Illumina sequencing instruments are two sequencing technologies which use very similar library preparation procedures. Enzymatic combinations can be changed in genotyping by sequencing (GbS) library protocols without significant adjustments. To compare the outputs from two different GbS procedures, we sequenced samples of two sister species of yellow-nosed albatross collected at multiple geographic locations. The data sets involving different sequencing instruments and enzymatic combinations were analysed using the Stacks pipeline and aligned to the same reference genome. Both procedures identified the same genetic clusters separating Atlantic and Indian yellow-nosed albatross and substructure within Indian yellow-nosed albatross.
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166
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Jiang H, Li Y, Luan M, Huang S, Zhao L, Yang G, Pan G. Single-Molecule Real-Time Sequencing of Full-Length Transcriptome and Identification of Genes Related to Male Development in Cannabis sativa. PLANTS (BASEL, SWITZERLAND) 2022; 11:3559. [PMID: 36559671 PMCID: PMC9782162 DOI: 10.3390/plants11243559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/25/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Female Cannabis sativa plants have important therapeutic properties. The sex ratio of the dioecious cannabis is approximately 1:1. Cultivating homozygous female plants by inducing female plants to produce male flowers is of great practical significance. However, the mechanism underlying cannabis male development remains unclear. In this study, single-molecule real-time (SMRT) sequencing was performed using a mixed sample of female and induced male flowers from the ZYZM1 cannabis variety. A total of 15,241 consensus reads were identified, and 13,657 transcripts were annotated across seven public databases. A total of 48 lncRNAs with an average length of 986.54 bp were identified. In total, 8202 transcripts were annotated as transcription factors, the most common of which were bHLH transcription factors. Moreover, tissue-specific expression pattern analysis showed that 13 MADS transcription factors were highly expressed in male flowers. Furthermore, 232 reads of novel genes were predicted and enriched in lipid metabolism, and qRT-PCR results showed that CER1 may be involved in the development of cannabis male flowers. In addition, 1170 AS events were detected, and two AS events were further validated. Taken together, these results may improve our understanding of the complexity of full-length cannabis transcripts and provide a basis for understanding the molecular mechanism of cannabis male development.
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Affiliation(s)
- Hui Jiang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, Changsha 410205, China
| | - Ying Li
- State Key Laboratory Breeding Base of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, Changsha 410205, China
| | - Siqi Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, Changsha 410205, China
| | - Lining Zhao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, Changsha 410205, China
| | - Guang Yang
- State Key Laboratory Breeding Base of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Gen Pan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, Changsha 410205, China
- State Key Laboratory Breeding Base of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijing 100700, China
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167
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A narrative review of cancer molecular diagnostics: past, present, and future. JOURNAL OF BIO-X RESEARCH 2022. [DOI: 10.1097/jbr.0000000000000136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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168
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Steg A, Oczkowicz M, Smołucha G. Omics as a Tool to Help Determine the Effectiveness of Supplements. Nutrients 2022; 14:nu14245305. [PMID: 36558464 PMCID: PMC9784029 DOI: 10.3390/nu14245305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
There has been considerable interest in dietary supplements in the last two decades. Companies are releasing new specifics at an alarming pace, while dietary supplements are one of the less-studied substances released for public consumption. However, access to state-of-the-art and high-throughput techniques, such as the ones used in omics, make it possible to check the impact of a substance on human transcriptome or proteome and provide answers to whether its use is reasonable and beneficial. In this review, the main domains of omics are briefly introduced. The review focuses on the three most widely used omics techniques: NGS, LC-MS, NMR, and their usefulness in studying dietary supplements. Examples of studies are described for some of the most commonly supplemented substances, such as vitamins: D, E, A, and plant extracts: resveratrol, green tea, ginseng, and curcumin extract. Techniques used in omics have proven to be useful in studying dietary supplements. NGS techniques are helpful in identifying pathways that change upon supplementation and determining polymorphisms or conditions that qualify for the necessity of a given supplementation. LC-MS techniques are used to establish the serum content of supplemented a compound and its effects on metabolites. Both LC-MS and NMR help establish the actual composition of a compound, its primary and secondary metabolites, and its potential toxicity. Moreover, NMR techniques determine what conditions affect the effectiveness of supplementation.
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169
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Polymorphic Microsatellite Development, Genetic Diversity, Population Differentiation and Sexual State of Phytophthora capsici on Commercial Peppers in Three Provinces of Southwest China. Appl Environ Microbiol 2022; 88:e0161122. [PMID: 36354348 PMCID: PMC9746301 DOI: 10.1128/aem.01611-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pepper blight, caused by the oomycete pathogen Phytophthora capsici (P. capsici), is one of the most destructive soilborne diseases worldwide. Between 2019 and 2020, 235 single spore isolates of P. capsici were collected from 36 commercial pepper planting areas in Sichuan, Chongqing, and Guizhou provinces in China. A novel full set of 323 high-quality polymorphic microsatellites was obtained by resequencing 10 isolates. In total, 163 isolates with two alleles per microsatellite locus were used for population analysis and resulted in 156 genotypes on 10 microsatellite loci. The genetic diversity, population differentiation, principal component, genetic structure, and genetic relationships analyses showed an extensive variety of the P. capsici in Sichuan and Guizhou with clonal lineages, two shared genotypes, and no geographic differentiation. The population from Chongqing was differentiated from that of Sichuan and Guizhou and had the highest genetic diversity. There was no significant distinction between the populations of the two sampling years, but there was a small differentiation between the populations from bell peppers and hot peppers. The isolates from Southwest China were largely distant from the two reference isolates from the USA. The analysis of molecular variance showed that the major variance of the populations was within populations. The linkage equilibrium test, mating type composition, and oospore detection indicated that only P. capsici from the Jiulongpo district of Chongqing had appeared in sexual recombination. Overall, this study revealed that the high and complex genetic diversity population of P. capsici in Sichuan, Chongqing, and Guizhou with uneven geographic variation and limited sexual reproductive behavior in Chongqing, potentially driven by differences in the geographical environment, reproductive patterns, different cultivars, and artificial long-distance transfers. IMPORTANCE Phytophthora capsici, a notorious soilborne and rapidly evolving pathogen with a wide range of hosts, is a huge threat to pepper production worldwide. However, the detailed genetic structure and dynamics of P. capsici in most Chinese provinces are still unclear, even though China is the world's largest producer and consumer of peppers. Here, a novel full set of high-quality polymorphic microsatellites, obtained by genome resequencing data of 10 isolates from Southwest China, was provided for future population analyses. In this study, we further investigated and established the genetic structure, sexual recombination, geographic subdivisions, interannual stability, differentiation in different types of host peppers, and member relationships of P. capsici from three provinces in Southwest China. These results reveal the genetic structure and dynamics of P. capsici in three provinces of Southwest China and help us to execute more effective management strategies in the future.
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170
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Lam SY, Lau HL, Kwok CK. Capture-SELEX: Selection Strategy, Aptamer Identification, and Biosensing Application. BIOSENSORS 2022; 12:bios12121142. [PMID: 36551109 PMCID: PMC9776347 DOI: 10.3390/bios12121142] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 06/01/2023]
Abstract
Small-molecule contaminants, such as antibiotics, pesticides, and plasticizers, have emerged as one of the substances most detrimental to human health and the environment. Therefore, it is crucial to develop low-cost, user-friendly, and portable biosensors capable of rapidly detecting these contaminants. Antibodies have traditionally been used as biorecognition elements. However, aptamers have recently been applied as biorecognition elements in aptamer-based biosensors, also known as aptasensors. The systematic evolution of ligands by exponential enrichment (SELEX) is an in vitro technique used to generate aptamers that bind their targets with high affinity and specificity. Over the past decade, a modified SELEX method known as Capture-SELEX has been widely used to generate DNA or RNA aptamers that bind small molecules. In this review, we summarize the recent strategies used for Capture-SELEX, describe the methods commonly used for detecting and characterizing small-molecule-aptamer interactions, and discuss the development of aptamer-based biosensors for various applications. We also discuss the challenges of the Capture-SELEX platform and biosensor development and the possibilities for their future application.
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Affiliation(s)
- Sin Yu Lam
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China
| | - Hill Lam Lau
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China
| | - Chun Kit Kwok
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
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171
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Andrews PW, Barbaric I, Benvenisty N, Draper JS, Ludwig T, Merkle FT, Sato Y, Spits C, Stacey GN, Wang H, Pera MF. The consequences of recurrent genetic and epigenetic variants in human pluripotent stem cells. Cell Stem Cell 2022; 29:1624-1636. [PMID: 36459966 DOI: 10.1016/j.stem.2022.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022]
Abstract
It is well established that human pluripotent stem cells (hPSCs) can acquire genetic and epigenetic changes during culture in vitro. Given the increasing use of hPSCs in research and therapy and the vast expansion in the number of hPSC lines available for researchers, the International Society for Stem Cell Research has recognized the need to reassess quality control standards for ensuring the genetic integrity of hPSCs. Here, we summarize current knowledge of the nature of recurrent genetic and epigenetic variants in hPSC culture, the methods for their detection, and what is known concerning their effects on cell behavior in vitro or in vivo. We argue that the potential consequences of low-level contamination of cell therapy products with cells bearing oncogenic variants are essentially unknown at present. We highlight the key challenges facing the field with particular reference to safety assessment of hPSC-derived cellular therapeutics.
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Affiliation(s)
- Peter W Andrews
- Centre for Stem Cell Biology, School of Biological Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK; Steering Committee, International Stem Cell Initiative
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biological Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK; Steering Committee, International Stem Cell Initiative
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel; Steering Committee, International Stem Cell Initiative
| | - Jonathan S Draper
- Stem Cell Network, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada; Steering Committee, International Stem Cell Initiative
| | - Tenneille Ludwig
- WiCell Research Institute, Madison, WI, USA; University of Wisconsin-Madison, Madison, WI 53719, USA; Steering Committee, International Stem Cell Initiative
| | - Florian T Merkle
- Wellcome Trust-Medical Research Council Institute of Metabolic Science, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0QQ, UK; Steering Committee, International Stem Cell Initiative
| | - Yoji Sato
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki Ward, Kawasaki City, Kanagawa 210-9501, Japan; Steering Committee, International Stem Cell Initiative
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; Steering Committee, International Stem Cell Initiative
| | - Glyn N Stacey
- International Stem Cell Banking Initiative, 2 High Street, Barley, UK; National Stem Cell Resource Centre, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100190, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China; Steering Committee, International Stem Cell Initiative
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China; Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China; Steering Committee, International Stem Cell Initiative
| | - Martin F Pera
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; Steering Committee, International Stem Cell Initiative.
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172
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Senaratne TN, Saitta SC. Evaluating Genetic Disorders in the Neonate: The Role of Exome Sequencing in the NICU. Neoreviews 2022; 23:e829-e840. [PMID: 36450644 DOI: 10.1542/neo.23-12-e829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
With recent advances in the technologies used for genetic diagnosis as well as our understanding of the genetic basis of disease, a growing list of options is available for providers when caring for a newborn with features suggesting an underlying genetic etiology. The choice of the most appropriate genetic test for a specific situation includes clinical considerations such as the phenotypic features and type of genetic abnormality suspected, as well as practical considerations such as cost and turnaround time. In this review, we discuss clinical exome sequencing in the context of genetic evaluation of newborns, including technical considerations, variant interpretation, and incidental/secondary findings. Strengths and limitations of exome sequencing are discussed and compared with those of other commonly known tests such as karyotype analysis, fluorescence in situ hybridization, chromosomal microarray, and sequencing panels, along with integration of results from prenatal testing if available. We also review future directions including genome sequencing and other emerging technologies that are starting to be used in clinical settings.
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Affiliation(s)
- T Niroshi Senaratne
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Sulagna C Saitta
- Division of Clinical Genetics, Department of Pediatrics, Division of Reproductive Genetics, Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA
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173
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Savage SA, Jones K, Teshome K, Lori A, McReynolds LJ, Niewisch MR. Next-generation sequencing errors due to genetic variation in WRAP53 encoding TCAB1 on chromosome 17. Hum Mutat 2022; 43:1856-1859. [PMID: 36116037 PMCID: PMC9771914 DOI: 10.1002/humu.24469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/17/2022] [Accepted: 09/12/2022] [Indexed: 01/24/2023]
Abstract
Next-generation sequencing (NGS) is a valuable tool, but has limitations in sequencing through repetitive runs of single nucleotides (homopolymers). Pathogenic germline variants in WRAP53 encoding telomere Cajal body protein 1 (TCAB1) are a known cause of dyskeratosis congenita. We identified a significant NGS error in WRAP53, c.1562dup, p.Ala522Glyfs*8 (rs755116516 G>-/GG/GGG) that did not validate by Sanger sequencing. This error occurs because rs755116516 G>-/GG/GGG (Chr17:7,606,714) is polymorphic, and variants at this site challenge the ability of NGS to accurately call the correct number of nucleotides in a homopolymer run. This was further complicated by the fact that chr17:7,606,721 (rs769202794) is multiallelic G>A, C, T, and that chr17:7,606,722 is also multiallelic (rs7640C>A/G/T and rs373064567C>delC). In addition to the expert interpretation of potentially clinically actionable variants, it recommended that all variants in regions of the genome with homopolymers be validated by Sanger sequencing before clinical action.
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Affiliation(s)
- Sharon A. Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kedest Teshome
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Lisa J. McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Marena R. Niewisch
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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174
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Eren K, Taktakoğlu N, Pirim I. DNA Sequencing Methods: From Past to Present. Eurasian J Med 2022; 54:47-56. [PMID: 36655445 PMCID: PMC11163357 DOI: 10.5152/eurasianjmed.2022.22280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/18/2022] [Indexed: 01/19/2023] Open
Abstract
Next-generation sequencing (NGS) is a highly effective genetic diagnostic test used in disease diagnosis. Although the Sanger method is used as the traditional method in genome studies, the use of NGS methods has been increasing with the development of technology. The foundation of next-generation sequencing was laid with the methods developed by Allan Maxam-Walter Gilbert and 2 Nobel laureates, Frederick Sanger. Initially, first-generation sequencing methods completed a certain part of the DNA with great efforts in a few days, while in today's technology, the entire DNA of even the most complex organisms is sequenced in 1 day. Second- and third-generation sequencing methods have been developed with improvements in cost, time, and accuracy of sequencing. The data obtained from these methods are interpreted with bioinformatics and contributed to the development of next-generation sequencing technology. These developments have increased the interest in studies on the relationship between next-generation sequencing and DNA or RNA depending on diseases. In this review, past and present methods of next-generation sequencing technologies are mentioned in detail and the difficulties and conveniences of these methods are reviewed.
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Affiliation(s)
- Kübra Eren
- Faculty of Medicine, Department of Medical Biology and Genetic, Izmir Katip Celebi University, Izmir, Turkey
| | - Nursema Taktakoğlu
- Faculty of Medicine, Department of Medical Biology and Genetic, Izmir Katip Celebi University, Izmir, Turkey
| | - Ibrahim Pirim
- Faculty of Medicine, Department of Medical Biology and Genetic, Izmir Katip Celebi University, Izmir, Turkey
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175
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Wang X, Budowle B, Ge J. USAT: a bioinformatic toolkit to facilitate interpretation and comparative visualization of tandem repeat sequences. BMC Bioinformatics 2022; 23:497. [PMID: 36402991 PMCID: PMC9675219 DOI: 10.1186/s12859-022-05021-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/29/2022] [Indexed: 11/21/2022] Open
Abstract
Background Tandem repeats (TR), highly variable genomic variants, are widely used in individual identification, disease diagnostics, and evolutionary studies. The recent advances in sequencing technologies and bioinformatic tools facilitate calling TR haplotypes genome widely. Both length-based and sequence-based TR alleles are used in different applications. However, sequence-based TR alleles could provide the highest precision in characterizing TR haplotypes. The need to identify the differences at the single nucleotide level between or among TR haplotypes with an easy-use bioinformatic tool is essential. Results In this study, we developed a Universal STR Allele Toolkit (USAT) for TR haplotype analysis, which takes TR haplotype output from existing tools to perform allele size conversion, sequence comparison of haplotypes, figure plotting, comparison for allele distribution, and interactive visualization. An exemplary application of USAT for analysis of the CODIS core STR loci for DNA forensics with benchmarking human individuals demonstrated the capabilities of USAT. USAT has user-friendly graphic interfaces and runs fast in major computing operating systems with parallel computing enabled. Conclusion USAT is a user-friendly bioinformatics software for interpretation, visualization, and comparisons of TRs. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-05021-1.
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Affiliation(s)
- Xuewen Wang
- grid.266869.50000 0001 1008 957XCenter for Human Identification, Health Science Center, University of North Texas, Fort Worth, TX USA
| | - Bruce Budowle
- grid.266869.50000 0001 1008 957XCenter for Human Identification, Health Science Center, University of North Texas, Fort Worth, TX USA ,grid.266871.c0000 0000 9765 6057Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX USA
| | - Jianye Ge
- grid.266869.50000 0001 1008 957XCenter for Human Identification, Health Science Center, University of North Texas, Fort Worth, TX USA ,grid.266871.c0000 0000 9765 6057Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX USA
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176
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Usage of DNA Fingerprinting Technology to Check Sample Error and Contamination in Molecular Laboratories. Curr Issues Mol Biol 2022; 44:5543-5549. [DOI: 10.3390/cimb44110375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/25/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Sample identification error is a severe medical error in clinical molecular diagnostic laboratories, which can lead to reporting the wrong results for the patient involved. Sample contamination can also lead to incorrect test reports. Avoiding sample identification error and sample contamination could be life-saving. Sample switch and sample contamination could happen on laboratory bench works, especially when pipetting into multi-well plates. It is difficult to realize such errors during laboratory bench work. Laboratory staff may not be aware of such an error when it happens. DNA fingerprinting technology can be used to determine sample identity and subsequently identify sample switch and sample contamination in the laboratory. Our laboratory has explored the usage of this technology in our quality control process and successfully established that DNA fingerprinting can be used to monitor sample switch and sample contamination in next-generation sequencing and BCR/ABL1 real-time PCR bench work.
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177
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Luecke SM, Webb EM, Dahlen CR, Reynolds LP, Amat S. Seminal and vagino-uterine microbiome and their individual and interactive effects on cattle fertility. Front Microbiol 2022; 13:1029128. [PMID: 36425035 PMCID: PMC9679222 DOI: 10.3389/fmicb.2022.1029128] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/19/2022] [Indexed: 09/13/2023] Open
Abstract
Reproductive failure is a major economical drain on cow-calf operations across the globe. It can occur in both males and females and stem from prenatal and postnatal influences. Therefore, the cattle industry has been making efforts to improve fertility and the pregnancy rate in cattle herds as an attempt to maintain sustainability and profitability of cattle production. Despite the advancements made in genetic selection, nutrition, and the implementation of various reproductive technologies, fertility rates have not significantly improved in the past 50 years. This signifies a missing factor or factors in current reproductive management practices that influence successful fertilization and pregnancy. Emerging lines of evidence derived from human and other animals including cattle suggest that the microbial continuum along the male and female reproductive tracts are associated with male and female fertility-that is, fertilization, implantation, and pregnancy success-highlighting the potential for harnessing the male and female reproductive microbiome to improve fertility in cattle. The objective of this narrative review is to provide an overview of the recent studies on the bovine seminal and vagino-uterine microbiome and discuss individual and interactive roles of these microbial communities in defining cattle fertility.
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Affiliation(s)
- Sarah M. Luecke
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
| | - Emily M. Webb
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
| | - Carl R. Dahlen
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, United States
| | - Lawrence P. Reynolds
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, United States
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
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178
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Li W, Shao C, Zhou H, Du H, Chen H, Wan H, He Y. Multi-omics research strategies in ischemic stroke: A multidimensional perspective. Ageing Res Rev 2022; 81:101730. [PMID: 36087702 DOI: 10.1016/j.arr.2022.101730] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/23/2022] [Accepted: 09/03/2022] [Indexed: 01/31/2023]
Abstract
Ischemic stroke (IS) is a multifactorial and heterogeneous neurological disorder with high rate of death and long-term impairment. Despite years of studies, there are still no stroke biomarkers for clinical practice, and the molecular mechanisms of stroke remain largely unclear. The high-throughput omics approach provides new avenues for discovering biomarkers of IS and explaining its pathological mechanisms. However, single-omics approaches only provide a limited understanding of the biological pathways of diseases. The integration of multiple omics data means the simultaneous analysis of thousands of genes, RNAs, proteins and metabolites, revealing networks of interactions between multiple molecular levels. Integrated analysis of multi-omics approaches will provide helpful insights into stroke pathogenesis, therapeutic target identification and biomarker discovery. Here, we consider advances in genomics, transcriptomics, proteomics and metabolomics and outline their use in discovering the biomarkers and pathological mechanisms of IS. We then delineate strategies for achieving integration at the multi-omics level and discuss how integrative omics and systems biology can contribute to our understanding and management of IS.
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Affiliation(s)
- Wentao Li
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Chongyu Shao
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Huifen Zhou
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Haixia Du
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Haiyang Chen
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Haitong Wan
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Yu He
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
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179
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Valiant WG, Cai K, Vallone PM. A history of adventitious agent contamination and the current methods to detect and remove them from pharmaceutical products. Biologicals 2022; 80:6-17. [DOI: 10.1016/j.biologicals.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/26/2022] [Accepted: 10/25/2022] [Indexed: 11/08/2022] Open
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180
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Begik O, Mattick JS, Novoa EM. Exploring the epitranscriptome by native RNA sequencing. RNA (NEW YORK, N.Y.) 2022; 28:1430-1439. [PMID: 36104106 PMCID: PMC9745831 DOI: 10.1261/rna.079404.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Chemical RNA modifications, collectively referred to as the "epitranscriptome," are essential players in fine-tuning gene expression. Our ability to analyze RNA modifications has improved rapidly in recent years, largely due to the advent of high-throughput sequencing methodologies, which typically consist of coupling modification-specific reagents, such as antibodies or enzymes, to next-generation sequencing. Recently, it also became possible to map RNA modifications directly by sequencing native RNAs using nanopore technologies, which has been applied for the detection of a number of RNA modifications, such as N6-methyladenosine (m6A), pseudouridine (Ψ), and inosine (I). However, the signal modulations caused by most RNA modifications are yet to be determined. A global effort is needed to determine the signatures of the full range of RNA modifications to avoid the technical biases that have so far limited our understanding of the epitranscriptome.
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Affiliation(s)
- Oguzhan Begik
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra, Barcelona 08002, Spain
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181
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Li Z, Li Z, Yang Z, Li L, Gao L, Xie J, Liao D, Gao X, Hu Z, Niu B, Yao P, Zeng W, Li H, Yang H. Isolation and characterization of two novel serotypes of Tibet orbivirus from Culicoides and sentinel cattle in Yunnan Province of China. Transbound Emerg Dis 2022; 69:3371-3387. [PMID: 36047657 DOI: 10.1111/tbed.14691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/21/2022] [Accepted: 08/26/2022] [Indexed: 02/04/2023]
Abstract
Tibet orbivirus (TIBOV), a new candidate of Orbivirus genus, was initially isolated from mosquitoes in Tibet in 2009 and subsequently from both Culicoides and mosquitoes in several provinces of China and Japan. Little is known about the origin, genetic diversity, dissemination and pathogenicity of TIBOV, although its potential threat to animal health has been acknowledged. In this study, two viruses, V290/YNSZ and V298/YNJH, were isolated from the Culicoides and sentinel cattle in Yunnan Province. Their genome sequences, cell tropism in mammalian and insect cell lines along with pathogenicity in suckling mice were determined. Genome phylogenetic analyses confirmed their classification as TIBOV species; however, OC1 proteins of the V290/YNSZ and V298/YNJH shared maximum sequence identities of 31.5% and 33.9% with other recognized TIBOV serotypes (TIBOV-1 to TIBOV-4) and formed two monophyletic branches in phylogenetic tree, indicating they represented two novel TIBOV serotypes which were tentatively designated as TIBOV-5 and TIBOV-6. The viruses replicated robustly in BHK, Vero and C6/36 cells and triggered overt clinical symptoms in suckling mice after intracerebral inoculation, causing mortality of 100% and 25%. Cross-sectional epidemiology analysis revealed silent circulation of TIBOV in Yunnan Province with overall prevalence of 16.4% (18/110) in cattle, 10.8% (13/120) in goats and 5.5% (6/110) in swine. The prevalence patterns of four investigated TIBOV serotypes (TIBOV-1, -2, -5 and 6) differed from each one another, with their positive rates ranging from 8.2% (9/110) for TIBOV-2 in cattle to 0.9% (1/110) for TIBOV-1 and TIBOV-5 in cattle and swine. Our findings provided new insights for diversity, pathogenicity and epidemiology of TIBOV and formed a basis for future studies addressing the geographical distribution and the zoonotic potential of TIBOV.
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Affiliation(s)
- Zhanhong Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Zhuoran Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Zhenxing Yang
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Le Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Lin Gao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Jiarui Xie
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Defang Liao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Xiang Gao
- Animal Disease Control and Prevention Center of Jinghong County, Jinghong, China
| | - Zhongyan Hu
- Animal Disease Control and Prevention Center of Jinghong County, Jinghong, China
| | - Baosheng Niu
- Animal Disease Control and Prevention Center of Shizong County, Qujing, China
| | - Pingfen Yao
- Animal Disease Control and Prevention Center of Shizong County, Qujing, China
| | - Weikun Zeng
- School of Medicine, Kunming University, Kunming, China
| | - Huachun Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Heng Yang
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China.,College of Agriculture and Life Sciences, Kunming University, Kunming, China
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182
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Mukherjee P, Park SH, Pathak N, Patino CA, Bao G, Espinosa HD. Integrating Micro and Nano Technologies for Cell Engineering and Analysis: Toward the Next Generation of Cell Therapy Workflows. ACS NANO 2022; 16:15653-15680. [PMID: 36154011 DOI: 10.1021/acsnano.2c05494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The emerging field of cell therapy offers the potential to treat and even cure a diverse array of diseases for which existing interventions are inadequate. Recent advances in micro and nanotechnology have added a multitude of single cell analysis methods to our research repertoire. At the same time, techniques have been developed for the precise engineering and manipulation of cells. Together, these methods have aided the understanding of disease pathophysiology, helped formulate corrective interventions at the cellular level, and expanded the spectrum of available cell therapeutic options. This review discusses how micro and nanotechnology have catalyzed the development of cell sorting, cellular engineering, and single cell analysis technologies, which have become essential workflow components in developing cell-based therapeutics. The review focuses on the technologies adopted in research studies and explores the opportunities and challenges in combining the various elements of cell engineering and single cell analysis into the next generation of integrated and automated platforms that can accelerate preclinical studies and translational research.
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Affiliation(s)
- Prithvijit Mukherjee
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
| | - So Hyun Park
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, Texas 77030, United States
| | - Nibir Pathak
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Cesar A Patino
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Gang Bao
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, Texas 77030, United States
| | - Horacio D Espinosa
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
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183
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Schmitz JE, Stratton CW, Persing DH, Tang YW. Forty Years of Molecular Diagnostics for Infectious Diseases. J Clin Microbiol 2022; 60:e0244621. [PMID: 35852340 PMCID: PMC9580468 DOI: 10.1128/jcm.02446-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nearly 40 years have elapsed since the invention of the PCR, with its extremely sensitive and specific ability to detect nucleic acids via in vitro enzyme-mediated amplification. In turn, more than 2 years have passed since the onset of the coronavirus disease 2019 (COVID-19) pandemic, during which time molecular diagnostics for infectious diseases have assumed a larger global role than ever before. In this context, we review broadly the progression of molecular techniques in clinical microbiology, to their current prominence. Notably, these methods now entail both the detection and quantification of microbial nucleic acids, along with their sequence-based characterization. Overall, we seek to provide a combined perspective on the techniques themselves, as well as how they have come to shape health care at the intersection of technologic innovation, pathophysiologic knowledge, clinical/laboratory logistics, and even financial/regulatory factors.
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Affiliation(s)
- Jonathan E. Schmitz
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - David H. Persing
- Medical and Scientific Affairs, Cepheid, Sunnyvale, California, USA
| | - Yi-Wei Tang
- Medical Affairs, Danaher Diagnostic Platform/Cepheid, Shanghai, China
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184
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Lee H, Min JW, Mun S, Han K. Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101583. [PMID: 36295018 PMCID: PMC9605557 DOI: 10.3390/life12101583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022]
Abstract
Transposable elements (TEs) are classified into two classes according to their mobilization mechanism. Compared to DNA transposons that move by the "cut and paste" mechanism, retrotransposons mobilize via the "copy and paste" method. They have been an essential research topic because some of the active elements, such as Long interspersed element 1 (LINE-1), Alu, and SVA elements, have contributed to the genetic diversity of primates beyond humans. In addition, they can cause genetic disorders by altering gene expression and generating structural variations (SVs). The development and rapid technological advances in next-generation sequencing (NGS) have led to new perspectives on detecting retrotransposon-mediated SVs, especially insertions. Moreover, various computational methods have been developed based on NGS data to precisely detect the insertions and deletions in the human genome. Therefore, this review discusses details about the recently studied and utilized NGS technologies and the effective computational approaches for discovering retrotransposons through it. The final part covers a diverse range of computational methods for detecting retrotransposon insertions with human NGS data. This review will give researchers insights into understanding the TEs and how to investigate them and find connections with research interests.
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Affiliation(s)
- Haeun Lee
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea
| | - Jun Won Min
- Department of Surgery, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Seyoung Mun
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
- Correspondence: (S.M.); (K.H.)
| | - Kyudong Han
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
- HuNbiome Co., Ltd., R&D Center, Seoul 08507, Korea
- Correspondence: (S.M.); (K.H.)
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185
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Wang M, Tu Q. Effective data filtering is prerequisite for robust microbial association network construction. Front Microbiol 2022; 13:1016947. [PMID: 36267180 PMCID: PMC9577025 DOI: 10.3389/fmicb.2022.1016947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
Microorganisms do not exist as individual population in the environment. Rather, they form complex assemblages that perform essential ecosystem functions and maintain ecosystem stability. Besides the diversity and composition of microbial communities, deciphering their potential interactions in the form of association networks has attracted many microbiologists and ecologists. Much effort has been made toward the methodological development for constructing microbial association networks. However, microbial profiles suffer dramatically from zero values, which hamper accurate association network construction. In this study, we investigated the effects of zero-value issues associated with microbial association network construction. Using the TARA Oceans microbial profile as an example, different zero-value-treatment approaches were comparatively investigated using different correlation methods. The results suggested dramatic variations of correlation coefficient values for differently treated microbial profiles. Most specifically, correlation coefficients among less frequent microbial taxa were more affected, whichever method was used. Negative correlation coefficients were more problematic and sensitive to network construction, as many of them were inferred from low-overlapped microbial taxa. Consequently, microbial association networks were greatly differed. Among various approaches, we recommend sequential calculation of correlation coefficients for microbial taxa pairs by excluding paired zero values. Filling missing values with pseudo-values is not recommended. As microbial association network analyses have become a widely used technique in the field of microbial ecology and environmental science, we urge cautions be made to critically consider the zero-value issues in microbial data.
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Affiliation(s)
- Mengqi Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Xiamen University, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China
- *Correspondence: Qichao Tu,
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186
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Sharma R, Patil C, Majeed J, Kumar S, Aggarwal G. Next-generation sequencing in the biodiversity conservation of endangered medicinal plants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:73795-73808. [PMID: 36098925 DOI: 10.1007/s11356-022-22842-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Medicinal plants have been used as traditional herbal medicines in the treatment of various types of diseases. However, the increased demand for these plants highlights the importance of conservation specifically for endangered species. Significant advancements in next-generation sequencing (NGS) technologies have accelerated medicinal plant research while reducing costs and time demands. NGS systems enable high-throughput whole genome sequencing as well as direct RNA sequencing and transcriptome analysis. The sequence data sets created can be used in a variety of areas of study, including biodiversity conservation, comparative genomics, transcriptomic analysis, single cell mining, metagenomics, epigenetics, molecular marker discovery, multi genome sequencing, and so on. Commercial sequencing service providers are constantly working to improve technologies to address bioinformatics problems in NGS data analysis. Several genome sequencing projects on medicinal plants have been completed recently and a few more are in the works. In some medicinal plants, massive NGS-based data has been developed. In the present review, we have attempted to briefly discuss advancements in NGS technology on medicinally essential plants in India. The review will also provide ideas for applying NGS technologies for exploring genomes of various endangered medicinal plants whose genome sequences are not normally available and thus provides valuable insights for the conservation of these vulnerable species.
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Affiliation(s)
- Ruchika Sharma
- Centre for Precision Medicine and Pharmacy, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, 110017, India
| | - Chandragouda Patil
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, 110017, India
| | - Jaseela Majeed
- Department of Pharmaceutical Management, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, 110017, India
| | - Subodh Kumar
- Centre for Precision Medicine and Pharmacy, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, 110017, India
| | - Geeta Aggarwal
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, 110017, India.
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187
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Lee IK, Chang JP, Huang WC, Tai CH, Wu HT, Chi CH. Comparative of clinical performance between next-generation sequencing and standard blood culture diagnostic method in patients suffering from sepsis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:845-852. [PMID: 35995673 DOI: 10.1016/j.jmii.2022.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/08/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Next-generation sequencing (NGS) is a massively unbiased sequencing technology. The objective of this study was to evaluate the performance of NGS-based approach in the detection of microorganisms from septic patients and compare with results of blood culture (BC). METHODS The observational and non-interventional study was conducted from April 2019 to August 2019. RESULTS A total of 96 sets of BC and 48 NGS results obtained from 48 septic patients were analyzed in this study. Thirty-two microorganisms (27 bacteria, 3 fungi and 2 viral) were detected by NGS in 23 (47.9%) patients; and 18 bacteria in 18 (37.5%) patients by BC. Exclusion of skin commensals, the positivity of NGS and BC was 62.5% and 14.5%, respectively (P < 0.001). Microorganisms identified by NGS demonstrated positive agreement with BC in 12 (25%) patients, including concordant results in 11 (22.9%) cases, and discrepancy results in 1 (2%). Of 11 patients with concordant results, 4 had additional microorganisms detected by NGS. NGS-positive but BC-negative was found in 9 (18.7%) patients. Using NGS, difficult-to-culture micro-organisms such as Pneumocystic jirovecii was identified in 2 patients, and Leptospira interrogans in one. Six (12.5%) patients with BC-positive but NGS-negative, whereas skin commensals were isolated in 4 (66.6%) cases. The number of patients that were positive by BC only increase from 29% to 47.9% when combining NGS and BC analyses (P = 0.033). CONCLUSIONS Our study support the advantage of NGS for the diagnosis of infecting microorganisms in sepsis, especially for microorganisms that are currently difficult or impossible to culture.
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Affiliation(s)
- Ing-Kit Lee
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Jen-Ping Chang
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Division of Thoracic and Cardiovascular Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Wen-Chi Huang
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Chien-Hsiang Tai
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Huang-Tu Wu
- Joint Commission of Precision Medicine, Taipei, Taiwan
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188
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Schaflinger E, Enko D. Die Bedeutung der Hochdurchsatz-Sequenzierung in der medizinisch genetischen Diagnostik und Beratung. Dtsch Med Wochenschr 2022; 147:1336-1341. [DOI: 10.1055/a-1924-6646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
ZusammenfassungNext-Generation-Sequencing ist ein modernes diagnostisches Hochdurchsatz-Verfahren (Multi-Gen-Analysen), durch dessen Einsatz sowohl hereditäre Krebserkrankungen (Tumordispositionssyndrome, Keimbahndiagnostik) als auch somatische Alterationen in Tumoren besser abgeklärt werden können. Der breitere Einsatz dieser Technologie im medizinischen Alltag zeigt das tatsächliche Ausmaß der interindividuellen genetischen Variabilität. Wichtige Bedeutung hat dieses Verfahren für die Untersuchung von heterogenen genetischen Erkrankungen (z. B. Tumorerkrankungen, neurodegenerativen und -muskulären Erkrankungen) erlangt. Weitere Indikationsgebiete stellen die Pharmakogenetik sowie die nicht invasive Pränataldiagnostik dar. Es ist zu erwarten, dass dieses diagnostische Mittel eine breite klinische Anwendung finden wird. Mit der rasanten Zunahme und Komplexität genetischer Dateninformationen nimmt die richtige Interpretation und Übermittlung der Befunde in der humangenetischen Beratung (Keimbahndiagnostik) einen hohen Stellenwert ein. Die genetische Beratung muss entsprechend neu ausgerichtet und adaptiert werden.
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Affiliation(s)
| | - Dietmar Enko
- Klinisches Institut für Medizinische und Chemische Labordiagnostik, Medizinische Universität Graz
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189
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Geraldes I, Fernandes M, Fraga AG, Osório NS. The impact of single-cell genomics on the field of mycobacterial infection. Front Microbiol 2022; 13:989464. [PMID: 36246265 PMCID: PMC9562642 DOI: 10.3389/fmicb.2022.989464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Genome sequencing projects of humans and other organisms reinforced that the complexity of biological systems is largely attributed to the tight regulation of gene expression at the epigenome and RNA levels. As a consequence, plenty of technological developments arose to increase the sequencing resolution to the cell dimension creating the single-cell genomics research field. Single-cell RNA sequencing (scRNA-seq) is leading the advances in this topic and comprises a vast array of different methodologies. scRNA-seq and its variants are more and more used in life science and biomedical research since they provide unbiased transcriptomic sequencing of large populations of individual cells. These methods go beyond the previous “bulk” methodologies and sculpt the biological understanding of cellular heterogeneity and dynamic transcriptomic states of cellular populations in immunology, oncology, and developmental biology fields. Despite the large burden caused by mycobacterial infections, advances in this field obtained via single-cell genomics had been comparatively modest. Nonetheless, seminal research publications using single-cell transcriptomics to study host cells infected by mycobacteria have become recently available. Here, we review these works summarizing the most impactful findings and emphasizing the different and recent single-cell methodologies used, potential issues, and problems. In addition, we aim at providing insights into current research gaps and potential future developments related to the use of single-cell genomics to study mycobacterial infection.
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Affiliation(s)
- Inês Geraldes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
| | - Mónica Fernandes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
| | - Alexandra G. Fraga
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
- *Correspondence: Nuno S. Osório
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Jeckel AM, Beran F, Züst T, Younkin G, Petschenka G, Pokharel P, Dreisbach D, Ganal-Vonarburg SC, Robert CAM. Metabolization and sequestration of plant specialized metabolites in insect herbivores: Current and emerging approaches. Front Physiol 2022; 13:1001032. [PMID: 36237530 PMCID: PMC9552321 DOI: 10.3389/fphys.2022.1001032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Herbivorous insects encounter diverse plant specialized metabolites (PSMs) in their diet, that have deterrent, anti-nutritional, or toxic properties. Understanding how they cope with PSMs is crucial to understand their biology, population dynamics, and evolution. This review summarizes current and emerging cutting-edge methods that can be used to characterize the metabolic fate of PSMs, from ingestion to excretion or sequestration. It further emphasizes a workflow that enables not only to study PSM metabolism at different scales, but also to tackle and validate the genetic and biochemical mechanisms involved in PSM resistance by herbivores. This review thus aims at facilitating research on PSM-mediated plant-herbivore interactions.
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Affiliation(s)
- Adriana Moriguchi Jeckel
- Laboratory of Chemical Ecology, Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Franziska Beran
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Tobias Züst
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
| | - Gordon Younkin
- Boyce Thompson Institute, Ithaca, NY, United States
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Georg Petschenka
- Department of Applied Entomology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Prayan Pokharel
- Department of Applied Entomology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Domenic Dreisbach
- Institute for Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Stephanie Christine Ganal-Vonarburg
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
| | - Christelle Aurélie Maud Robert
- Laboratory of Chemical Ecology, Institute of Plant Sciences, University of Bern, Bern, Switzerland
- *Correspondence: Christelle Aurélie Maud Robert,
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191
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Alhamid G, Tombuloglu H, Rabaan AA, Al-Suhaimi E. SARS-CoV-2 detection methods: A comprehensive review. Saudi J Biol Sci 2022; 29:103465. [PMID: 36186678 PMCID: PMC9512523 DOI: 10.1016/j.sjbs.2022.103465] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 08/28/2022] [Accepted: 09/21/2022] [Indexed: 11/26/2022] Open
Abstract
The ongoing novel COVID-19 has remained the center of attention, since its declaration as a pandemic in March 2020, due to its rapid and uncontrollable worldwide spread. Diagnostic tests are the first line of defense against the transmission of this infectious disease among individuals, with reverse-transcription quantitative polymerase chain reaction (RT-qPCR) being the approved gold standard for showing high sensitivity and specificity in detecting SARS-CoV-2. However, alternative tests are being invested due to the global demand for facilities, reagents, and healthcare workers needed for rapid population-based testing. Also, the rapid evolution of the viral genome and the emergence of new variants necessitates updating the existing methods. Scientists are aiming to improve tests to be affordable, simple, fast, and at the same time accurate, and efficient, as well as friendly user testing. The current diagnostic methods are either molecular-based that detect nucleic acids abundance, like RT-qPCR and reverse-transcription loop-mediated isothermal amplification (RT-LAMP); or immunologically based that detect the presence of antigens or antibodies in patients’ specimens, like enzyme-linked immunosorbent assay (ELISA), lateral flow assay (LFA), chemiluminescent immunoassay (CLIA), and neutralization assay. In addition to these strategies, sensor-based or CRISPR applications are promising tools for the rapid detection of SARS-CoV-2. This review summarizes the most recent updates on the SARS-CoV-2 detection methods with their limitations. It will guide researchers, epidemiologists, and clinicians in identifying a more rapid, reliable, and sensitive method of diagnosing SARS-CoV-2 including the most recent variant of concern Omicron.
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Affiliation(s)
- Galyah Alhamid
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia.,Biotechnology Master Program, Imam Abdulrahman bin Faisal University, Saudi Arabia
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Ebtesam Al-Suhaimi
- Department of Biology, College of Science and Institute of Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
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192
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Martina M, Acquadro A, Gulino D, Brusco F, Rabaglio M, Portis E, Lanteri S. First genetic maps development and QTL mining in Ranunculus asiaticus L. through ddRADseq. FRONTIERS IN PLANT SCIENCE 2022; 13:1009206. [PMID: 36212343 PMCID: PMC9539318 DOI: 10.3389/fpls.2022.1009206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Persian Buttercup (Ranunculus asiaticus L.; 2x=2n=16; estimated genome size: 7.6Gb) is an ornamental and perennial crop native of Asia Minor and Mediterranean basin, marketed both as cut flower or potted plant. Currently new varieties are developed by selecting plants carrying desirable traits in segregating progenies obtained by controlled mating, which are propagated through rhizomes or micro-propagated in vitro. In order to escalate selection efficiency and respond to market requests, more knowledge of buttercup genetics would facilitate the identification of markers associated with loci and genes controlling key ornamental traits, opening the way for molecular assisted breeding programs. Reduced-representation sequencing (RRS) represents a powerful tool for plant genotyping, especially in case of large genomes such as the one of buttercup, and have been applied for the development of high-density genetic maps in several species. We report on the development of the first molecular-genetic maps in R. asiaticus based on of a two-way pseudo-testcross strategy. A double digest restriction-site associated DNA (ddRAD) approach was applied for genotyping two F1 mapping populations, whose female parents were a genotype of a so called 'ponpon' and of a 'double flower' varieties, while the common male parental ('Cipro') was a genotype producing a simple flower. The ddRAD generated a total of ~2Gb demultiplexed reads, resulting in an average of 8,3M reads per line. The sstacks pipeline was applied for the construction of a mock reference genome based on sequencing data, and SNP markers segregating in only one of the parents were retained for map construction by treating the F1 population as a backcross. The four parental maps (two of the female parents and two of the common male parent) were aligned with 106 common markers and 8 linkage groups were identified, corresponding to the haploid chromosome number of the species. An average of 586 markers were associated with each parental map, with a marker density ranging from 1 marker/cM to 4.4 markers/cM. The developed maps were used for QTL analysis for flower color, leading to the identification of major QTLs for purple pigmentation. These results contribute to dissect on the genetics of Persian buttercup, enabling the development of new approaches for future varietal development.
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Affiliation(s)
- Matteo Martina
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Davide Gulino
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | | | | | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
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193
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Carotenoids in Drug Discovery and Medicine: Pathways and Molecular Targets Implicated in Human Diseases. Molecules 2022; 27:molecules27186005. [PMID: 36144741 PMCID: PMC9503763 DOI: 10.3390/molecules27186005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/01/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022] Open
Abstract
Carotenoids are isoprenoid-derived natural products produced in plants, algae, fungi, and photosynthetic bacteria. Most animals cannot synthesize carotenoids because the biosynthetic machinery to create carotenoids de novo is absent in animals, except arthropods. Carotenoids are biosynthesized from two C20 geranylgeranyl pyrophosphate (GGPP) molecules made from isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) via the methylerythritol 4-phosphate (MEP) route. Carotenoids can be extracted by a variety of methods, including maceration, Soxhlet extraction, supercritical fluid extraction (SFE), microwave-assisted extraction (MAE), accelerated solvent extraction (ASE), ultrasound-assisted extraction (UAE), pulsed electric field (PEF)-assisted extraction, and enzyme-assisted extraction (EAE). Carotenoids have been reported to exert various biochemical actions, including the inhibition of the Akt/mTOR, Bcl-2, SAPK/JNK, JAK/STAT, MAPK, Nrf2/Keap1, and NF-κB signaling pathways and the ability to increase cholesterol efflux to HDL. Carotenoids are absorbed in the intestine. A handful of carotenoids and carotenoid-based compounds are in clinical trials, while some are currently used as medicines. The application of metabolic engineering techniques for carotenoid production, whole-genome sequencing, and the use of plants as cell factories to produce specialty carotenoids presents a promising future for carotenoid research. In this review, we discussed the biosynthesis and extraction of carotenoids, the roles of carotenoids in human health, the metabolism of carotenoids, and carotenoids as a source of drugs and supplements.
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194
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Misra P, Jadhav AR, Bapat SA. Single-cell sequencing: A cutting edge tool in molecular medical research. Med J Armed Forces India 2022; 78:S7-S13. [PMID: 36147383 PMCID: PMC9485843 DOI: 10.1016/j.mjafi.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/18/2022] [Indexed: 10/15/2022] Open
Abstract
The rapid development of advanced high throughput technologies and introduction of high resolution "omics" data through analysis of biological molecules has revamped medical research. Single-cell sequencing in recent years, is in fact revolutionising the field by providing a deeper, spatio-temporal analyses of individual cells within tissues and their relevance to disease. Like conventional sequencing, the single-cell approach deciphers the sequence of nucleotides in a given Deoxyribose Nucleic Acid (DNA), Ribose Nucleic Acid (RNA), Micro Ribose Nucleic Acid (miRNA), epigenetically modified DNA or chromatin DNA; however, the unit of analyses is changed to single cells rather than the entire tissue. Further, a large number of single cells analysed from a single tissue generate a unique holistic perception capturing all kinds of perturbations across different cells in the tissue that increases the precision of data. Inherently, execution of the technique generates a large amount of data, which is required to be processed in a specific manner followed by customised bioinformatic analysis to produce meaningful results. The most crucial role of single-cell sequencing technique is in elucidating the inter-cell genetic, epigenetic, transcriptomic and proteomic heterogeneity in health and disease. The current review presents a brief overview of this cutting-edge technology and its applications in medical research.
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Affiliation(s)
- Pratibha Misra
- Senior Advisor (Pathology & Biochemistry), 151 Base Hospital, Guwahati, India
| | - Amruta R. Jadhav
- Senior Research Fellow, National Centre for Cell Science (NCCS), Pune, India
| | - Sharmila A. Bapat
- Professor & Head, Ovarian Cancer Program, National Centre for Cell Science, (NCCS), Pune, India
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195
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Guilmatre A, Davous D, Sigy ADHD, Asselain B, Chevret S, Petit A. Quelles sont les pratiques en génétique des pédiatres onco-hématologues de la SFCE ? Une enquête du groupe socle éthique CONECT-AML. Bull Cancer 2022; 109:1162-1176. [DOI: 10.1016/j.bulcan.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/09/2022] [Indexed: 10/14/2022]
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196
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Biomolecular Mechanisms of Autoimmune Diseases and Their Relationship with the Resident Microbiota: Friend or Foe? PATHOPHYSIOLOGY 2022; 29:507-536. [PMID: 36136068 PMCID: PMC9505211 DOI: 10.3390/pathophysiology29030041] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 12/02/2022] Open
Abstract
The use of innovative approaches to elucidate the pathophysiological mechanisms of autoimmune diseases, as well as to further study of the factors which can have either a positive or negative effect on the course of the disease, is essential. In this line, the development of new molecular techniques and the creation of the Human Genome Program have allowed access to many more solutions to the difficulties that exist in the identification and characterization of the microbiome, as well as changes due to various factors. Such innovative technologies can rekindle older hypotheses, such as molecular mimicry, allowing us to move from hypothesis to theory and from correlation to causality, particularly regarding autoimmune diseases and dysbiosis of the microbiota. For example, Prevotella copri appears to have a strong association with rheumatoid arthritis; it is expected that this will be confirmed by several scientists, which, in turn, will make it possible to identify other mechanisms that may contribute to the pathophysiology of the disease. This article seeks to identify new clues regarding similar correlations between autoimmune activity and the human microbiota, particularly in relation to qualitative and quantitative microbial variations therein.
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197
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Osek J, Lachtara B, Wieczorek K. Listeria monocytogenes in foods-From culture identification to whole-genome characteristics. Food Sci Nutr 2022; 10:2825-2854. [PMID: 36171778 PMCID: PMC9469866 DOI: 10.1002/fsn3.2910] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen, which is able to persist in the food production environments. The presence of these bacteria in different niches makes them a potential threat for public health. In the present review, the current information on the classical and alternative methods used for isolation and identification of L. monocytogenes in food have been described. Although these techniques are usually simple, standardized, inexpensive, and are routinely used in many food testing laboratories, several alternative molecular-based approaches for the bacteria detection in food and food production environments have been developed. They are characterized by the high sample throughput, a short time of analysis, and cost-effectiveness. However, these methods are important for the routine testing toward the presence and number of L. monocytogenes, but are not suitable for characteristics and typing of the bacterial isolates, which are crucial in the study of listeriosis infections. For these purposes, novel approaches, with a high discriminatory power to genetically distinguish the strains during epidemiological studies, have been developed, e.g., whole-genome sequence-based techniques such as NGS which provide an opportunity to perform comparison between strains of the same species. In the present review, we have shown a short description of the principles of microbiological, alternative, and modern methods of detection of L. monocytogenes in foods and characterization of the isolates for epidemiological purposes. According to our knowledge, similar comprehensive papers on such subject have not been recently published, and we hope that the current review may be interesting for research communities.
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Affiliation(s)
- Jacek Osek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Beata Lachtara
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Kinga Wieczorek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
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198
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Wang L, Li H, Li J, Li G, Zahid MS, Li D, Ma C, Xu W, Song S, Li X, Wang S. Transcriptome analysis revealed the expression levels of genes related to abscisic acid and auxin biosynthesis in grapevine ( Vitis vinifera L.) under root restriction. FRONTIERS IN PLANT SCIENCE 2022; 13:959693. [PMID: 36092429 PMCID: PMC9449541 DOI: 10.3389/fpls.2022.959693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The root system is essential for the stable growth of plants. Roots help anchor plants in the soil and play a crucial role in water uptake, mineral nutrient absorption and endogenous phytohormone formation. Root-restriction (RR) cultivation, a powerful technique, confines plant roots to a specific soil space. In the present study, roots of one-year-old "Muscat Hamburg" grapevine under RR and control (nR) treatments harvested at 70 and 125 days after planting were used for transcriptome sequencing, and in total, 2031 (nR7 vs. nR12), 1445 (RR7 vs. RR12), 1532 (nR7 vs. RR7), and 2799 (nR12 vs. RR12) differentially expressed genes (DEGs) were identified. Gene Ontology (GO) enrichment analysis demonstrated that there were several genes involved in the response to different phytohormones, including abscisic acid (ABA), auxin (IAA), ethylene (ETH), gibberellins (GAs), and cytokinins (CTKs). Among them, multiple genes, such as PIN2 and ERF113, are involved in regulating vital plant movements by various phytohormone pathways. Moreover, following RR cultivation, DEGs were enriched in the biological processes of plant-type secondary cell wall biosynthesis, the defense response, programmed cell death involved in cell development, and the oxalate metabolic process. Furthermore, through a combined analysis of the transcriptome and previously published microRNA (miRNA) sequencing results, we found that multiple differentially expressed miRNAs (DEMs) and DEG combinations in different comparison groups exhibited opposite trends, indicating that the expression levels of miRNAs and their target genes were negatively correlated. Furthermore, RR treatment indeed significantly increased the ABA content at 125 days after planting and significantly decreased the IAA content at 70 days after planting. Under RR cultivation, most ABA biosynthesis-related genes were upregulated, while most IAA biosynthesis-related genes were downregulated. These findings lay a solid foundation for further establishing the network through which miRNAs regulate grapevine root development through target genes and for further exploring the molecular mechanism through which endogenous ABA and IAA regulate root architecture development in grapevine.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Xiangyi Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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199
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Dotolo S, Esposito Abate R, Roma C, Guido D, Preziosi A, Tropea B, Palluzzi F, Giacò L, Normanno N. Bioinformatics: From NGS Data to Biological Complexity in Variant Detection and Oncological Clinical Practice. Biomedicines 2022; 10:biomedicines10092074. [PMID: 36140175 PMCID: PMC9495893 DOI: 10.3390/biomedicines10092074] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/22/2022] Open
Abstract
The use of next-generation sequencing (NGS) techniques for variant detection has become increasingly important in clinical research and in clinical practice in oncology. Many cancer patients are currently being treated in clinical practice or in clinical trials with drugs directed against specific genomic alterations. In this scenario, the development of reliable and reproducible bioinformatics tools is essential to derive information on the molecular characteristics of each patient’s tumor from the NGS data. The development of bioinformatics pipelines based on the use of machine learning and statistical methods is even more relevant for the determination of complex biomarkers. In this review, we describe some important technologies, computational algorithms and models that can be applied to NGS data from Whole Genome to Targeted Sequencing, to address the problem of finding complex cancer-associated biomarkers. In addition, we explore the future perspectives and challenges faced by bioinformatics for precision medicine both at a molecular and clinical level, with a focus on an emerging complex biomarker such as homologous recombination deficiency (HRD).
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Affiliation(s)
- Serena Dotolo
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Cristin Roma
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Davide Guido
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Alessia Preziosi
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Beatrice Tropea
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Fernando Palluzzi
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Luciano Giacò
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
- Correspondence:
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200
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Xu Z, Tu S, Pass C, Zhang Y, Liu H, Diers J, Fu Y, He DZZ, Zuo J. Profiling mouse cochlear cell maturation using 10× Genomics single-cell transcriptomics. Front Cell Neurosci 2022; 16:962106. [PMID: 36060279 PMCID: PMC9434313 DOI: 10.3389/fncel.2022.962106] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Juvenile and mature mouse cochleae contain various low-abundant, vulnerable sensory epithelial cells embedded in the calcified temporal bone, making it challenging to profile the dynamic transcriptome changes of these cells during maturation at the single-cell level. Here we performed the 10x Genomics single-cell RNA sequencing (scRNA-seq) of mouse cochleae at postnatal days 14 (P14) and 28. We attained the transcriptomes of multiple cell types, including hair cells, supporting cells, spiral ganglia, stria fibrocytes, and immune cells. Our hair cell scRNA-seq datasets are consistent with published transcripts from bulk RNA-seq. We also mapped known deafness genes to corresponding cochlear cell types. Importantly, pseudotime trajectory analysis revealed that inner hair cell maturation peaks at P14 while outer hair cells continue development until P28. We further identified and confirmed a long non-coding RNA gene Miat to be expressed during maturation in cochlear hair cells and spiral ganglia neurons, and Pcp4 to be expressed during maturation in cochlear hair cells. Our transcriptomes of juvenile and mature mouse cochlear cells provide the sequel to those previously published at late embryonic and early postnatal ages and will be valuable resources to investigate cochlear maturation at the single-cell resolution.
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Affiliation(s)
- Zhenhang Xu
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States
| | - Shu Tu
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States
| | - Caroline Pass
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States
| | - Yan Zhang
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States
| | - Huizhan Liu
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States
| | - Jack Diers
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States
| | - Yusi Fu
- Lynch Comprehensive Cancer Research Center, Creighton University School of Medicine, Omaha, NE, United States
| | - David Z. Z. He
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States
| | - Jian Zuo
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States
- *Correspondence: Jian Zuo,
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