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Zhang Z, Li M, Zhang S, Qin Y, Zhao J, Li Y, Stephenson SL, Qiu J, Liu P. Diversity of Cellular Slime Molds (Dictyostelids) in the Fanjing Mountain Nature Reserve and Geographical Distribution Comparisons with Other Representative Nature Reserves in Different Climate Zones of China. Microorganisms 2024; 12:1061. [PMID: 38930443 PMCID: PMC11206006 DOI: 10.3390/microorganisms12061061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Protected areas are widely considered an essential strategy for biodiversity conservation. Dictyostelids are unique protists known to have important ecological functions in promoting soil and plant health through their top-down regulation of ecosystem processes, such as decomposition, that involve bacterial populations. But the relationship between dictyostelid diversity within protected areas remains poorly understood, especially on a large scale. Herein, we report data on the distribution of dictyostelids, identified with ITS + SSU rRNA molecular and morphology-based taxonomy, from soil samples collected in the Fanjing Mountain protected area of Guizhou Province, Southwest China. We compared the biodiversity data of dictyostelids in Fanjing Mountain with similar data from previously sampled sites in four other protected areas, including Changbai Mountain (CB), Gushan Mountain (GS), Baiyun Mountain (BY), and Qinghai-Tibet Plateau (QT) in China. We identified four species of dictyostelids belonging to three genera (Dictyostelium, Heterostelium, and Polysphondylium) and herein provide information on the taxonomy of these species. Two species (Heterostelium pallidum and Dictyostelium purpureum) are common and widely distributed throughout the world, but one species (Polysphondylium fuscans) was new to China. Our data indicate that there is no distinguishable significant correlation between the dictyostelid species studied and environmental factors. Overall, the similarity index between Baiyun Mountain in Henan Province and Fanjing Mountain in Guizhou Province, located at approximately the same longitude, is the highest, and the Jaccard similarity coefficients (Jaccard index) of family, genus, and species are 100%, 100%, and 12.5%, respectively. From a species perspective, species in the same climate zone are not closely related, but obvious geographical distributions are evident in different climate zones. This preliminary study provided evidence of the ecological adaptation of dictyostelids to different biological niches.
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Affiliation(s)
- Zhaojuan Zhang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (Z.Z.); (M.L.); (S.Z.); (Y.Q.); (J.Z.); (Y.L.)
| | - Meng Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (Z.Z.); (M.L.); (S.Z.); (Y.Q.); (J.Z.); (Y.L.)
| | - Shufei Zhang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (Z.Z.); (M.L.); (S.Z.); (Y.Q.); (J.Z.); (Y.L.)
| | - Yue Qin
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (Z.Z.); (M.L.); (S.Z.); (Y.Q.); (J.Z.); (Y.L.)
| | - Jing Zhao
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (Z.Z.); (M.L.); (S.Z.); (Y.Q.); (J.Z.); (Y.L.)
| | - Yu Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (Z.Z.); (M.L.); (S.Z.); (Y.Q.); (J.Z.); (Y.L.)
| | - Steven L. Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Junzhi Qiu
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Pu Liu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (Z.Z.); (M.L.); (S.Z.); (Y.Q.); (J.Z.); (Y.L.)
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Mukherjee S, Mukherjee A, Bytesnikova Z, Ashrafi AM, Richtera L, Adam V. 2D graphene-based advanced nanoarchitectonics for electrochemical biosensors: Applications in cancer biomarker detection. Biosens Bioelectron 2024; 250:116050. [PMID: 38301543 DOI: 10.1016/j.bios.2024.116050] [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: 09/15/2023] [Revised: 01/01/2024] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
Low-cost, rapid, and easy-to-use biosensors for various cancer biomarkers are of utmost importance in detecting cancer biomarkers for early-stage metastasis control and efficient diagnosis. The molecular complexity of cancer biomarkers is overwhelming, thus, the repeatability and reproducibility of measurements by biosensors are critical factors. Electrochemical biosensors are attractive alternatives in cancer diagnosis due to their low cost, simple operation, and promising analytical figures of merit. Recently graphene-derived nanostructures have been used extensively for the fabrication of electrochemical biosensors because of their unique physicochemical properties, including the high electrical conductivity, adsorption capacity, low cost and ease of mass production, presence of oxygen-containing functional groups that facilitate the bioreceptor immobilization, increased flexibility and mechanical strength, low cellular toxicity. Indeed, these properties make them advantageous compared to other alternatives. However, some drawbacks must be overcome to extend their use, such as poor and uncontrollable deposition on the substrate due to the low dispersity of some graphene materials and irreproducibility of the results because of the differences in various batches of the produced graphene materials. This review has documented the most recently developed strategies for electrochemical sensor fabrication. It differs in the categorization method compared to published works to draw greater attention to the wide opportunities of graphene nanomaterials for biological applications. Limitations and future scopes are discussed to advance the integration of novel technologies such as artificial intelligence, the internet of medical things, and triboelectric nanogenerators to eventually increase efficacy and efficiency.
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Affiliation(s)
- Soumajit Mukherjee
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
| | - Atripan Mukherjee
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnici 835, 252 41, Dolni Breznany, Czech Republic
| | - Zuzana Bytesnikova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
| | - Amir M Ashrafi
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
| | - Lukas Richtera
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic.
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Munan S, Chang YT, Samanta A. Chronological development of functional fluorophores for bio-imaging. Chem Commun (Camb) 2024; 60:501-521. [PMID: 38095135 DOI: 10.1039/d3cc04895k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Functional fluorophores represent an emerging research field, distinguished by their diverse applications, especially in sensing and cellular imaging. After the discovery of quinine sulfate and subsequent elucidation of the fluorescence mechanism by Sir George Stokes, research in the field of fluorescence gained momentum. Over the past few decades, advancements in sophisticated instruments, including super-resolution microscopy, have further promoted cellular imaging using traditional fluorophores. These advancements include deciphering sensing mechanisms via photochemical reactions and scrutinizing the applications of fluorescent probes that specifically target organelles. This approach elucidates molecular interactions with biomolecules. Despite the abundance of literature illustrating different classes of probe development, a concise summary of newly developed fluorophores remains inadequate. In this review, we systematically summarize the chronological discovery of traditional fluorophores along with new fluorophores. We briefly discuss traditional fluorophores ranging from visible to near-infrared (NIR) in the context of cellular imaging and in vivo imaging. Furthermore, we explore ten new core fluorophores developed between 2007 and 2022, which exhibit advanced optical properties, providing new insights into bioimaging. We illustrate the utilization of new fluorophores in cellular imaging of biomolecules, such as reactive oxygen species (ROS), reactive nitrogen species (RNS), and proteins and microenvironments, especially pH and viscosity. Few of the fluorescent probes provided new insights into disease progression. Furthermore, we speculate on the potential prospects and significant challenges of existing fluorophores and their potential biomedical research applications. By addressing these aspects, we intend to illuminate the compelling advancements in fluorescent probe development and their potential influence across various fields.
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Affiliation(s)
- Subrata Munan
- Molecular Sensors and Therapeutics (MST) Research Laboratory, Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi NCR, NH 91, Tehsil Dadri 201314, Uttar Pradesh, India.
| | - Young-Tae Chang
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
| | - Animesh Samanta
- Molecular Sensors and Therapeutics (MST) Research Laboratory, Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi NCR, NH 91, Tehsil Dadri 201314, Uttar Pradesh, India.
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Zhang Z, Yang Y, Zhao J, Li Y, Stephenson SL, Qiu J, Liu P. Environmental factors influencing the diversity and distribution of dictyostelid cellular slime molds in forest and farmland soils of western China. Microbiol Spectr 2023; 11:e0173223. [PMID: 37962389 PMCID: PMC10715086 DOI: 10.1128/spectrum.01732-23] [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: 04/25/2023] [Accepted: 10/04/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE Soil protists are an essential yet seriously understudied component of the soil microbiome. In this study, 11 new records of dictyostelids belonging to 2 orders, 3 families, and 4 genera were identified from 99 soil samples collected from different elevations and habitats in central Gansu and the southeastern and southcentral portions of Guizhou Province, China. We found that dictyostelid communities were significantly different between Gansu and Guizhou Provinces, apparently in response to different environmental factors. Moreover, dictyostelids were found to have the highest species diversity in mixed forests. Soil pH, temperature, and elevation were determined to be the primary factors that affect the distribution and occurrence of dictyostelids in Guizhou and Gansu Provinces. This work supplements the survey data available for dictyostelids elsewhere in China. These new findings have significant implications for our understanding of the diversity of soil microorganisms.
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Affiliation(s)
- Zhaojuan Zhang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yingkun Yang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jing Zhao
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yu Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Steven L. Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Junzhi Qiu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Pu Liu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
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Diversity of Dictyostelid Cellular Slime Molds, Including Two Species New to Science, in Forest Soils of Changbai Mountain, China. Microbiol Spectr 2022; 10:e0240222. [PMID: 36190423 PMCID: PMC9620775 DOI: 10.1128/spectrum.02402-22] [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] [Indexed: 01/04/2023] Open
Abstract
Dictyostelid cellular slime molds (dictyostelids) are protists that are common inhabitants of most soils, where they feed upon bacteria. Changbai Mountain is the highest mountain in northeast China. Soil samples collected on Changbai Mountain yielded 11 isolates representing six species of dictyostelid samples. Two of these species (Dictyostelium robusticaule and Heterostelium recretum) were found to be new to science, based on morphology, SSU rDNA sequences, and an ATPase subunit 1 gene (atp1) phylogeny. The present study also demonstrated that the increased accuracy and lower costs associated with the use of atp1 sequences make them a complement of SSU rDNA sequences for identifying dictyostelids. Changbai Mountain is characterized by a higher diversity of dictyostelids than indicated by the few previous reports. Moreover, the data for Changbai Mountain, compared with comparable data for Taiwan, suggest that differences in diversity at the family level are possibly related to latitude. Mixed broadleaf-conifer forests produced more isolates and species than broadleaf forests at the same elevation and also had the highest species richness, which indicates an effect of vegetation on dictyostelids. However, the pattern of slightly decreasing diversity with increasing elevation in dictyostelids was also apparent. IMPORTANCE Dictyostelium robusticaule and Heterostelium recretum are two new species of dictyostelids reported in this study. The potential use of atp1 sequences is a complement of SSU rDNA sequences for the identifying dictyostelids. A pattern of slightly decreasing diversity with increasing elevation in dictyostelids was observed, with the conditions that exist at lower elevations apparently more suitable for dictyostelids, whereas differences of diversity observed at the family level are possibly related to latitude.
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Luo L, Chen Q, Luo Q, Qin S, Liu Z, Li Q, Huang X, Xiao H, Xu N. Establishment and performance evaluation of multiplex PCR-dipstick DNA chromatography assay for simultaneous diagnosis of four sexually transmitted pathogens. J Microbiol Methods 2021; 186:106250. [PMID: 34029611 DOI: 10.1016/j.mimet.2021.106250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/01/2022]
Abstract
INTRODUCTION Rapid, sensitive, and specific diagnostic methods are indispensable for sexually transmitted infections (STIs). In this study, a multiplex PCR-dipstick DNA chromatography assay for diagnosis of four STI pathogens, namely Neisseria gonorrhoeae (N. gonorrhoeae), Mycoplasma hominis (M. hominis), Ureaplasma (U. urealyticum and U. parvum), and Chlamydia trachomatis (C. trachomatis), was established and evaluated. METHODS Based on the hybridization of probes and interaction between streptavidin and biotin, PCR products were visualized through hybridization of specific probes and enzymatic color generation. The sensitivity and specificity of all four pathogens were evaluated. Clinical performance of the test was evaluated using 295 specimens, and comparisons among results were determined via culture or colloidal gold assay. RESULTS No cross-reactions were observed, confirming the high specificity of this method. The limit of detection (LOD) of the four STI pathogens was 100 copies/μL. The sensitivity between PCR-dipstick DNA chromatography and culture or colloidal gold assay ranged from 84.6% to 100%. The specificity was between 93.5% and 96.6%, positive predictive value ranged from 53.6% to 86.7%, negative predictive value was over 98.3%, kappa value ranged from 0.676 to 0.864 (Cohen's kappa coefficient test), and the agreement rate was over 93.5%. CONCLUSION In conclusion, PCR-dipstick DNA chromatography serves as a rapid, sensitive, and specific method for simultaneous diagnosis of four STI pathogens.
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Affiliation(s)
- Li Luo
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Qianming Chen
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Qiang Luo
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Sheng Qin
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Zhenjie Liu
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Qiong Li
- Research and Development Department, Guangzhou Biotron Technology Co. Ltd, Room 204, Zone C, Science and Technology Innovation Base, No. 80, Lanyue Road, Science City, Guangzhou 510000, China
| | - Xianzhang Huang
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China.
| | - Hui Xiao
- Research and Development Department, Guangzhou Biotron Technology Co. Ltd, Room 204, Zone C, Science and Technology Innovation Base, No. 80, Lanyue Road, Science City, Guangzhou 510000, China.
| | - Ning Xu
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China.
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Analysis about impact of morphological and nanoparticle volume fraction aspects of TiO2–Cu in enhancement of thermo-physical features of newtonian fluid flowing in a rotating porous channel. APPLIED NANOSCIENCE 2021. [DOI: 10.1007/s13204-021-01770-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Liu P, Zhang S, Zou Y, Li Z, Stephenson SL, Li Y. Distribution and ecology of dictyostelids in China. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2020.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Dictyostelid Cellular Slime Molds from the Russian Far East. Protist 2020; 171:125756. [PMID: 33126017 DOI: 10.1016/j.protis.2020.125756] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 08/05/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022]
Abstract
Dictyostelid cellular slime molds (dictyostelids) are important soil microorganisms that feed mostly on bacteria in the soil and leaf litter layer. The Russian Far East is the easternmost part of Russia and thus is located in the Middle East of Siberia. In September 2018, 14 samples of mixed soil/humus were collected from the most southeastern portion of the Russian Far East, including Sakhalin Island, Ussuriysk and Vladivostok, and then processed for dictyostelids. Seven species in four genera were recovered. Four of these species (Cavenderia fasciculata, Heterostelium tenuissimum, Dictyostelium longosporum and Polysphondylium patagonicum) were recorded for the first time from Russia, and one species (H. multibrachiatum sp. nov.) in described herein as new to science.
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