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Jaglan K, Dhaka SS, Magotra A, Patil CS, Ghanghas A. Exploring MicroRNA biogenesis, applications and bioinformatics analysis in livestock: A comprehensive review. Reprod Domest Anim 2024; 59:e14529. [PMID: 38268204 DOI: 10.1111/rda.14529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Small non-coding RNAs called microRNAs (miRNAs) control the expression of genes post-transcriptionally. Their correlation with commercial economic traits including milk, meat and egg production, as well as their effective role in animal productivity, fertility, embryo survival and disease resistance, make them significant in livestock research. The miRNAs exhibit distinct spatial and temporal expression patterns, offering insights into their functional roles within cells and tissues. Aberrant miRNA production can disrupt vital cellular processes and genetic networks, contributing to conditions like metabolic disorders and viral diseases. These short RNA molecules are present in extracellular fluids, displaying remarkable stability against RNA degradation enzymes and extreme environmental conditions. miRNAs preservation is facilitated through packaging in lipid vesicles or complex formation with RNA-binding proteins. Numerous studies have illuminated the roles of miRNAs in diverse physiological processes, including embryonic stem cell differentiation, haematopoietic stem cell proliferation and differentiation and the coordinated development of organ systems. The integration of miRNA profiling, next-generation sequencing and bioinformatics analysis paves the way for transformative advancements in livestock research and industry. The present review underscores the applications of miRNAs in livestock, showcasing their potential to improve breeding strategies, diagnose diseases and enhance our understanding of fundamental biological processes.
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Affiliation(s)
- Komal Jaglan
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - S S Dhaka
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Ankit Magotra
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - C S Patil
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Amandeep Ghanghas
- Department of Livestock Production Management, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
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Natonek-Wiśniewska M, Krzyścin P, Koseniuk A. Qualitative and Quantitative Detection of Mealworm DNA in Raw and Commercial Food Products Using Real-Time PCR. Genes (Basel) 2022; 13:genes13081400. [PMID: 36011310 PMCID: PMC9407359 DOI: 10.3390/genes13081400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/29/2022] [Accepted: 08/04/2022] [Indexed: 11/30/2022] Open
Abstract
Considering food safety and an increasing public awareness of the ingredients, production process and origin of foods, the application of insects as food requires the development of tests for the reliable identification of their presence. The aim of the study was (1) the determination of appropriate modifications of the selected method for isolating the DNA of two life stages of mealworm, i.e., larva and adult, from commercial food products; (2) the determination of the method parameters for the qualitative and quantitative analysis of mealworm contents based on the detection of a species-specific mitochondrial DNA fragment, using real-time PCR; (3) the application of a method to test the commercial food products of mealworm. A total of nine species of adult insect were investigated (field cricket, Dubia cockroach, Madagascar cockroach, banded cricket, migratory locust, yellow mealworm, superworm, house fly and lacewing), theirlarvaes (yellow mealworms and superworms) and thirteen commercial food products (dried whole insects, powder and granules) representing various insect species and origins which were purchased from the European market. The obtained results showed that the efficiency of the modification of the DNA extraction method is dependent on the life stage of the mealworm. We proved the high sensitivity of the test, with the range of the method being 0.1–100%; we also proved the biological specificity in this range, and the linearity. The linearity of the test was also statistically verified using the Fisher–Snedecor test. One-way variance analysis showed statistically significant differences between the cT values of the two mealworm life stages studied, and similarly, between the threshold cycle (cT) values of adult forms. In contrast, for the inside group of mealworm larvae, there was no significant difference observed between the results of the cT values. The test is effective for processed food products and may be used to monitor food. The research proved the suitability of the applied method for the analysis of samples that are commercially available as food for exotic animals. The hereby-developed method is based on widely used laboratory techniques, and does not require any additional investment in equipment. The availabilityof such a methodallows for the verification of the accuracy of the declared species component of the food products.
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3
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Borvinskaya EV, Kochneva AA, Drozdova PB, Balan OV, Zgoda VG. Temperature-induced reorganisation of Schistocephalus solidus (Cestoda) proteome during the transition to the warm-blooded host. Biol Open 2021; 10:bio058719. [PMID: 34787304 PMCID: PMC8609239 DOI: 10.1242/bio.058719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/10/2021] [Indexed: 11/30/2022] Open
Abstract
The protein composition of the cestode Schistocephalus solidus was measured in an experiment simulating the trophic transmission of the parasite from a cold-blooded to a warm-blooded host. The first hour of host colonisation was studied in a model experiment, in which sticklebacks Gasterosteus aculeatus infected with S. solidus were heated at 40°C for 1 h. As a result, a decrease in the content of one tegument protein was detected in the plerocercoids of S. solidus. Sexual maturation of the parasites was initiated in an experiment where S. solidus larvae were taken from fish and cultured in vitro at 40°C for 48 h. Temperature-independent changes in the parasite proteome were investigated by incubating plerocercoids at 22°C for 48 h in culture medium. Analysis of the proteome allowed us to distinguish the temperature-induced genes of S. solidus, as well as to specify the molecular markers of the plerocercoid and adult worms. The main conclusion of the study is that the key enzymes of long-term metabolic changes (glycogen consumption, protein production, etc.) in parasites during colonisation of a warm-blooded host are induced by temperature.
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Affiliation(s)
| | - Albina A. Kochneva
- Institute of Biology, Karelian Research Centre of the Russian Academy of Sciences, 11 Pushkinskaya Street, 185910 Petrozavodsk, Karelia, Russia
| | - Polina B. Drozdova
- Institute of Biology, Irkutsk State University, 3 Lenin St, 664025 Irkutsk, Russia
| | - Olga V. Balan
- Institute of Biology, Karelian Research Centre of the Russian Academy of Sciences, 11 Pushkinskaya Street, 185910 Petrozavodsk, Karelia, Russia
| | - Victor G. Zgoda
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya street, 119121 Moscow, Russia
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4
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Geraci F, Manzini G. EZcount: An all-in-one software for microRNA expression quantification from NGS sequencing data. Comput Biol Med 2021; 133:104352. [PMID: 33852974 DOI: 10.1016/j.compbiomed.2021.104352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 01/03/2023]
Abstract
MicroRNAs (miRNAs) are short endogenous molecules of RNA that influence cell regulation by suppressing genes. Their ubiquity throughout all branches of the tree of life has suggested their central role in many cellular functions. Nowadays, several personalized medicine applications rely on miRNAs as biomarkers for diagnoses, prognoses, and prediction of drug response. The increasing ease of sequencing miRNAs contrasts with the difficulty of accurately quantifying their concentration. The use of general purpose aligners is only a partial solution as they have limited possibilities to accurately solve ambiguous mapping due to the short length of these sequences. We developed EZcount, an all-in-one software that, with a single command, performs the entire quantification process: from raw fastq files to read counts. Experiments show that EZcount is more sensitive and accurate than methods based on sequence alignment, independently of the library preparation protocol and sequencing machine. The parallel architecture of EZcount makes it fast enough to process a sample in minutes using a standard workstation. EZcount runs on all of the most common operating systems (Linux, Windows and MacOS) and is freely available for download at https://gitlab.com/BioAlgo/miR-pipe. A detailed description of the datasets, the raw experimental results, and all the scripts used for testing are available as supplementary material.
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Affiliation(s)
- Filippo Geraci
- Institute for Informatics and Telematics, CNR, Pisa, 56124, Italy.
| | - Giovanni Manzini
- Institute for Informatics and Telematics, CNR, Pisa, 56124, Italy; Department of Computer Science, University of Pisa, Pisa, 56127, Italy.
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Vasconcelos AM, Carmo MB, Ferreira B, Viegas I, Gama-Carvalho M, Ferreira A, Amaral AJ. IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner. BMC Bioinformatics 2021; 22:37. [PMID: 33522913 PMCID: PMC7852101 DOI: 10.1186/s12859-021-03955-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/01/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND IsomiRs are miRNA variants that vary in length and/or sequence when compared to their canonical forms. These variants display differences in length and/or sequence, including additions or deletions of one or more nucleotides (nts) at the 5' and/or 3' end, internal editings or untemplated 3' end additions. Most available tools for small RNA-seq data analysis do not allow the identification of isomiRs and often require advanced knowledge of bioinformatics. To overcome this, we have developed IsomiR Window, a platform that supports the systematic identification, quantification and functional exploration of isomiR expression in small RNA-seq datasets, accessible to users with no computational skills. METHODS IsomiR Window enables the discovery of isomiRs and identification of all annotated non-coding RNAs in RNA-seq datasets from animals and plants. It comprises two main components: the IsomiR Window pipeline for data processing; and the IsomiR Window Browser interface. It integrates over ten third-party softwares for the analysis of small-RNA-seq data and holds a new algorithm that allows the detection of all possible types of isomiRs. These include 3' and 5'end isomiRs, 3' end tailings, isomiRs with single nucleotide polymorphisms (SNPs) or potential RNA editings, as well as all possible fuzzy combinations. IsomiR Window includes all required databases for analysis and annotation, and is freely distributed as a Linux virtual machine, including all required software. RESULTS IsomiR Window processes several datasets in an automated manner, without restrictions of input file size. It generates high quality interactive figures and tables which can be exported into different formats. The performance of isomiR detection and quantification was assessed using simulated small-RNA-seq data. For correctly mapped reads, it identified different types of isomiRs with high confidence and 100% accuracy. The analysis of a small RNA-seq data from Basal Cell Carcinomas (BCCs) using isomiR Window confirmed that miR-183-5p is up-regulated in Nodular BCCs, but revealed that this effect was predominantly due to a novel 5'end variant. This variant displays a different seed region motif and 1756 isoform-exclusive mRNA targets that are significantly associated with disease pathways, underscoring the biological relevance of isomiR-focused analysis. IsomiR Window is available at https://isomir.fc.ul.pt/ .
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Affiliation(s)
- Ana M Vasconcelos
- Lasige - Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | | | - Beatriz Ferreira
- BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Lisbon, Portugal
| | - Inês Viegas
- BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Lisbon, Portugal
| | - Margarida Gama-Carvalho
- BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Lisbon, Portugal
| | - António Ferreira
- Lasige - Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Andreia J Amaral
- CIISA - Centro de Investigação Interdisciplinar Em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisbon, Portugal.
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6
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Weke K, Singh A, Uwugiaren N, Alfaro JA, Wang T, Hupp TR, O'Neill JR, Vojtesek B, Goodlett DR, Williams SM, Zhou M, Kelly RT, Zhu Y, Dapic I. MicroPOTS Analysis of Barrett's Esophageal Cell Line Models Identifies Proteomic Changes after Physiologic and Radiation Stress. J Proteome Res 2021; 20:2195-2205. [PMID: 33491460 PMCID: PMC8155554 DOI: 10.1021/acs.jproteome.0c00629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Moving from macroscale
preparative systems in proteomics to micro-
and nanotechnologies offers researchers the ability to deeply profile
smaller numbers of cells that are more likely to be encountered in
clinical settings. Herein a recently developed microscale proteomic
method, microdroplet processing in one pot for trace samples (microPOTS),
was employed to identify proteomic changes in ∼200 Barrett’s
esophageal cells following physiologic and radiation stress exposure.
From this small population of cells, microPOTS confidently identified
>1500 protein groups, and achieved a high reproducibility with
a Pearson’s
correlation coefficient value of R > 0.9 and over
50% protein overlap from replicates. A Barrett’s cell line
model treated with either lithocholic acid (LCA) or X-ray had 21 (e.g.,
ASNS, RALY, FAM120A, UBE2M, IDH1, ESD) and 32 (e.g., GLUL, CALU, SH3BGRL3,
S100A9, FKBP3, AGR2) overexpressed proteins, respectively, compared
to the untreated set. These results demonstrate the ability of microPOTS
to routinely identify and quantify differentially expressed proteins
from limited numbers of cells.
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Affiliation(s)
- Kenneth Weke
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Ashita Singh
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K.,Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Naomi Uwugiaren
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Javier A Alfaro
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland.,Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K
| | - Tongjie Wang
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K
| | - Ted R Hupp
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland.,Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K
| | - J Robert O'Neill
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, U.K.,Cambridge Oesophagogastric Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, U.K
| | - Borek Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - David R Goodlett
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland.,University of Victoria - Genome British Columbia Proteomics Centre, Victoria, BC V8Z 7X8, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Irena Dapic
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland
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Sinha K, Sharma P, Som Chaudhury S, Das Mukhopadhyay C, Ruidas B. Species detection using probe technology. FOOD TOXICOLOGY AND FORENSICS 2021:313-346. [DOI: 10.1016/b978-0-12-822360-4.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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8
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Vivek AT, Kumar S. Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq. Brief Bioinform 2020; 22:6041165. [PMID: 33333550 DOI: 10.1093/bib/bbaa322] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.
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Affiliation(s)
- A T Vivek
- National Institute of Plant Genome Research in New Delhi, India
| | - Shailesh Kumar
- National Institute of Plant Genome Research in New Delhi
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Zhu Y, Wang J, Wang F, Yan Z, Liu G, Ma Y, Zhu W, Li Y, Xie L, Bazhin AV, Guo X. Differential MicroRNA Expression Profiles as Potential Biomarkers for Pancreatic Ductal Adenocarcinoma. BIOCHEMISTRY (MOSCOW) 2019; 84:575-582. [PMID: 31234772 DOI: 10.1134/s0006297919050122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains a clinical challenge due to its poor prognosis. Therefore, the early diagnosis of PDAC is extremely important for achieving a cure. MicroRNAs (miRNAs) could serve as a potential biomarker for the early detection and prognosis of PDAC. In this work we analyzed plasma samples from healthy persons and PDAC patients to assess differential miRNA expression profiles by next generation sequencing technology and bioinformatics analysis. In this way, 165 mature miRNAs were found to be significantly deregulated in the patient group, of which 75 and 90 mature miRNAs were up- and down-regulated compared with healthy individuals, respectively. Furthermore, 1029 novel miRNAs were identified. In conclusion, plasma miRNA expression profiles are different between healthy individuals and patients with PDAC. These data provide a possibility for use of miRNA as diagnostic and prognostic biomarkers of PDAC.
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Affiliation(s)
- Y Zhu
- Department of Oncology, International Joint Laboratory for Cell Medical Engineering of Henan Province, Henan University Huaihe Hospital, Kaifeng, Henan, 475000, P. R. China.
| | - J Wang
- Department of Oncology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450014, P. R. China.
| | - F Wang
- Department of Preventive Medicine, Cell Signal Transduction Laboratory, Joint National Laboratory for Antibody Drug Engineering, Institute of Biomedical Informatics, Medical School, Henan University, Kaifeng, Henan, 475004, P. R. China
| | - Z Yan
- Department of Preventive Medicine, Cell Signal Transduction Laboratory, Joint National Laboratory for Antibody Drug Engineering, Institute of Biomedical Informatics, Medical School, Henan University, Kaifeng, Henan, 475004, P. R. China
| | - G Liu
- Department of Oncology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450014, P. R. China
| | - Y Ma
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, Tianjin, 300353, P. R. China.
| | - W Zhu
- Department of Anesthesia, Stanford University, CA 94305, USA.
| | - Y Li
- Department of Preventive Medicine, Cell Signal Transduction Laboratory, Joint National Laboratory for Antibody Drug Engineering, Institute of Biomedical Informatics, Medical School, Henan University, Kaifeng, Henan, 475004, P. R. China
| | - L Xie
- Department of Preventive Medicine, Cell Signal Transduction Laboratory, Joint National Laboratory for Antibody Drug Engineering, Institute of Biomedical Informatics, Medical School, Henan University, Kaifeng, Henan, 475004, P. R. China
| | - A V Bazhin
- Department of General, Visceral, and Transplantation Surgery, Ludwig-Maximilians-University Munich, Munich, 81377, Germany.
| | - X Guo
- Department of Preventive Medicine, Cell Signal Transduction Laboratory, Joint National Laboratory for Antibody Drug Engineering, Institute of Biomedical Informatics, Medical School, Henan University, Kaifeng, Henan, 475004, P. R. China.
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10
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Horta MAC, Filho JAF, Murad NF, de Oliveira Santos E, Dos Santos CA, Mendes JS, Brandão MM, Azzoni SF, de Souza AP. Network of proteins, enzymes and genes linked to biomass degradation shared by Trichoderma species. Sci Rep 2018; 8:1341. [PMID: 29358662 PMCID: PMC5778038 DOI: 10.1038/s41598-018-19671-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/05/2018] [Indexed: 12/16/2022] Open
Abstract
Understanding relationships between genes responsible for enzymatic hydrolysis of cellulose and synergistic reactions is fundamental for improving biomass biodegradation technologies. To reveal synergistic reactions, the transcriptome, exoproteome, and enzymatic activities of extracts from Trichoderma harzianum, Trichoderma reesei and Trichoderma atroviride under biodegradation conditions were examined. This work revealed co-regulatory networks across carbohydrate-active enzyme (CAZy) genes and secreted proteins in extracts. A set of 80 proteins and respective genes that might correspond to a common system for biodegradation from the studied species were evaluated to elucidate new co-regulated genes. Differences such as one unique base pair between fungal genomes might influence enzyme-substrate binding sites and alter fungal gene expression responses, explaining the enzymatic activities specific to each species observed in the corresponding extracts. These differences are also responsible for the different architectures observed in the co-expression networks.
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Affiliation(s)
| | - Jaire Alves Ferreira Filho
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Natália Faraj Murad
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Clelton Aparecido Dos Santos
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Juliano Sales Mendes
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Marcelo Mendes Brandão
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Sindelia Freitas Azzoni
- Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil. .,Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, SP, Brazil.
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11
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Ali E, Sultana S, Hamid SBA, Hossain M, Yehya WA, Kader A, Bhargava SK. Gelatin controversies in food, pharmaceuticals, and personal care products: Authentication methods, current status, and future challenges. Crit Rev Food Sci Nutr 2017; 58:1495-1511. [PMID: 28033035 DOI: 10.1080/10408398.2016.1264361] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Gelatin is a highly purified animal protein of pig, cow, and fish origins and is extensively used in food, pharmaceuticals, and personal care products. However, the acceptability of gelatin products greatly depends on the animal sources of the gelatin. Porcine and bovine gelatins have attractive features but limited acceptance because of religious prohibitions and potential zoonotic threats, whereas fish gelatin is welcomed in all religions and cultures. Thus, source authentication is a must for gelatin products but it is greatly challenging due to the breakdown of both protein and DNA biomarkers in processed gelatins. Therefore, several methods have been proposed for gelatin identification, but a comprehensive and systematic document that includes all of the techniques does not exist. This up-to-date review addresses this research gap and presents, in an accessible format, the major gelatin source authentication techniques, which are primarily nucleic acid and protein based. Instead of presenting these methods in paragraph form which needs much attention in reading, the major methods are schematically depicted, and their comparative features are tabulated. Future technologies are forecasted, and challenges are outlined. Overall, this review paper has the merit to serve as a reference guide for the production and application of gelatin in academia and industry and will act as a platform for the development of improved methods for gelatin authentication.
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Affiliation(s)
- Eaqub Ali
- a Nanotechnology and Catalysis Research Centre (NANOCAT) , University of Malaya , Kuala Lumpur , Malaysia.,b Centre for Research in Biotechnology for Agriculture (CEBAR) , University of Malaya , Kuala Lumpur , Malaysia
| | - Sharmin Sultana
- a Nanotechnology and Catalysis Research Centre (NANOCAT) , University of Malaya , Kuala Lumpur , Malaysia
| | - Sharifah Bee Abd Hamid
- a Nanotechnology and Catalysis Research Centre (NANOCAT) , University of Malaya , Kuala Lumpur , Malaysia
| | - Motalib Hossain
- a Nanotechnology and Catalysis Research Centre (NANOCAT) , University of Malaya , Kuala Lumpur , Malaysia
| | - Wageeh A Yehya
- a Nanotechnology and Catalysis Research Centre (NANOCAT) , University of Malaya , Kuala Lumpur , Malaysia
| | - Abdul Kader
- c School of Aquaculture and Fisheries , University of Malaysia Terrenganu , Kuala Terrenganu , Terrenganu , Malaysia
| | - Suresh K Bhargava
- d College of Science, Engineering and Health , RMIT University , Melbourne , VIC , Australia
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12
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Aberrant expression of microRNA induced by high-fructose diet: implications in the pathogenesis of hyperlipidemia and hepatic insulin resistance. J Nutr Biochem 2017; 43:125-131. [PMID: 28284064 DOI: 10.1016/j.jnutbio.2017.02.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 01/16/2017] [Accepted: 02/08/2017] [Indexed: 01/22/2023]
Abstract
Fructose is a highly lipogenic sugar that can alter energy metabolism and trigger metabolic disorders. In the current study, microRNAs (miRNAs) altered by a high-fructose diet were comprehensively explored to elucidate their significance in the pathogenesis of chronic metabolic disorders. miRNA expression profiling using small noncoding RNA sequencing revealed that 19 miRNAs were significantly upregulated and 26 were downregulated in the livers of high-fructose-fed mice compared to chow-fed mice. Computational prediction and functional analysis identified 10 miRNAs, miR-19b-3p, miR-101a-3p, miR-30a-5p, miR-223-3p, miR-378a-3p, miR-33-5p, miR-145a-3p, miR-128-3p, miR-125b-5p and miR-582-3p, assembled as a regulatory network to potentially target key genes in lipid and lipoprotein metabolism and insulin signaling at multiple levels. qRT-PCR analysis of their potential target genes [IRS-1, FOXO1, SREBP-1c/2, ChREBP, insulin-induced gene-2 (Insig-2), microsomal triglyceride transfer protein (MTTP) and apolipoprotein B (apoB)] demonstrated that fructose-induced alterations of miRNAs were also reflected in mRNA expression profiles of their target genes. Moreover, the miRNA profile induced by high-fructose diet differed from that induced by high-fat diet, indicating that miRNAs mediate distinct pathogenic mechanisms in dietary-induced metabolic disorders. This study presents a comprehensive analysis of a new set of hepatic miRNAs, which were altered by high-fructose diet and provides novel insights into the interaction between miRNAs and their target genes in the development of metabolic syndrome.
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De Novo transcriptome characterization of Dracaena cambodiana and analysis of genes involved in flavonoid accumulation during formation of dragon's blood. Sci Rep 2016; 6:38315. [PMID: 27922066 PMCID: PMC5138819 DOI: 10.1038/srep38315] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/07/2016] [Indexed: 12/13/2022] Open
Abstract
Dragon’s blood is a red resin mainly extracted from Dracaena plants, and has been widely used as a traditional medicine in East and Southeast Asia. The major components of dragon’s blood are flavonoids. Owing to a lack of Dracaena plants genomic information, the flavonoids biosynthesis and regulation in Dracaena plants remain unknown. In this study, three cDNA libraries were constructed from the stems of D. cambodiana after injecting the inducer. Approximately 266.57 million raw sequencing reads were de novo assembled into 198,204 unigenes, of which 34,873 unique sequences were annotated in public protein databases. Many candidate genes involved in flavonoid accumulation were identified. Differential expression analysis identified 20 genes involved in flavonoid biosynthesis, 27 unigenes involved in flavonoid modification and 68 genes involved in flavonoid transport that were up-regulated in the stems of D. cambodiana after injecting the inducer, consistent with the accumulation of flavonoids. Furthermore, we have revealed the differential expression of transcripts encoding for transcription factors (MYB, bHLH and WD40) involved in flavonoid metabolism. These de novo transcriptome data sets provide insights on pathways and molecular regulation of flavonoid biosynthesis and transport, and improve our understanding of molecular mechanisms of dragon’s blood formation in D. cambodiana.
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Yan JF, Kim H, Jeong SK, Lee HJ, Sethi MK, Lee LY, Beavis RC, Im H, Snyder MP, Hofree M, Ideker T, Wu SL, Paik YK, Fanayan S, Hancock WS. Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. J Proteome Res 2015; 14:4995-5006. [PMID: 26435392 DOI: 10.1021/acs.jproteome.5b00827] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
V-erb-b2 erythroblastic leukemia viral oncogene homologue 2, known as ERBB2, is an important oncogene in the development of certain cancers. It can form a heterodimer with other epidermal growth factor receptor family members and activate kinase-mediated downstream signaling pathways. ERBB2 gene is located on chromosome 17 and is amplified in a subset of cancers, such as breast, gastric, and colon cancer. Of particular interest to the Chromosome-Centric Human Proteome Project (C-HPP) initiative is the amplification mechanism that typically results in overexpression of a set of genes adjacent to ERBB2, which provides evidence of a linkage between gene location and expression. In this report we studied patient samples from ERBB2-positive together with adjacent control nontumor tissues. In addition, non-ERBB2-expressing patient samples were selected as comparison to study the effect of expression of this oncogene. We detected 196 proteins in ERBB2-positive patient tumor samples that had minimal overlap (29 proteins) with the non-ERBB2 tumor samples. Interaction and pathway analysis identified extracellular signal regulated kinase (ERK) cascade and actin polymerization and actinmyosin assembly contraction as pathways of importance in ERBB2+ and ERBB2- gastric cancer samples, respectively. The raw data files are deposited at ProteomeXchange (identifier: PXD002674) as well as GPMDB.
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Affiliation(s)
- Julia Fangfei Yan
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Hoguen Kim
- Yonsei University College of Medicine, Yonsei University , 50-1 Yonsei-Ro, Seodaemun-gu, Seoul 120-752, Korea
| | - Seul-Ki Jeong
- Yonsei Proteome Research Center, Yonsei University , 262 Seongsanno, Seodaemun-gu, Seoul 120-749, Korea
| | - Hyoung-Joo Lee
- Yonsei Proteome Research Center, Yonsei University , 262 Seongsanno, Seodaemun-gu, Seoul 120-749, Korea
| | - Manveen K Sethi
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Ling Y Lee
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Ronald C Beavis
- Department of Biochemistry and Medical Genetics, Faculty of Health Sciences, University of Manitoba , 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - Hogune Im
- Department of Genetics, Stanford University , Stanford, California 94305, United States
| | - Michael P Snyder
- Department of Genetics, Stanford University , Stanford, California 94305, United States
| | - Matan Hofree
- Department of Computer Science and Engineering, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Trey Ideker
- Program in Bioinformatics, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Shiaw-Lin Wu
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Young-Ki Paik
- Yonsei University College of Medicine, Yonsei University , 50-1 Yonsei-Ro, Seodaemun-gu, Seoul 120-752, Korea.,Yonsei Proteome Research Center, Yonsei University , 262 Seongsanno, Seodaemun-gu, Seoul 120-749, Korea
| | - Susan Fanayan
- Department of Biomedical Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - William S Hancock
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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Schönbach C, Tan T, Ranganathan S. InCoB2014: mining biological data from genomics for transforming industry and health. BMC Genomics 2014; 15 Suppl 9:I1. [PMID: 25521539 PMCID: PMC4290585 DOI: 10.1186/1471-2164-15-s9-i1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The 13th International Conference on Bioinformatics (InCoB2014) was held for the first time in Australia, at Sydney, July 31-2 August, 2014. InCoB is the annual scientific gathering of the Asia-Pacific Bioinformatics Network (APBioNet), hosted since 2002 in the Asia-Pacific region. Of 106 full papers submitted to the BMC track of InCoB2014, 50 (47.2%) were accepted in BMC Bioinformatics, BMC Genomics and BMC Systems Biology supplements, with three papers in a new BMC Medical Genomics supplement. While the majority of presenters and authors were from Asia and Australia, the increasing number of US and European conference attendees augurs well for the international flavour of InCoB. Next year's InCoB will be held jointly with the Genome Informatics Workshop (GIW), September 9-11, 2015 in Tokyo, Japan, with a view to integrate bioinformatics communities in the region.
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