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Wojczulanis-Jakubas K, Hoover B, Jakubas D, Fort J, Grémillet D, Gavrilo M, Zielińska S, Zagalska-Neubauer M. Diversity of major histocompatibility complex of II B gene and mate choice in a monogamous and long-lived seabird, the Little Auk (Alle alle). PLoS One 2024; 19:e0304275. [PMID: 38865310 PMCID: PMC11168636 DOI: 10.1371/journal.pone.0304275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 05/09/2024] [Indexed: 06/14/2024] Open
Abstract
The major histocompatibility complex (MHC) plays a key role in the adaptive immune system of vertebrates, and is known to influence mate choice in many species. In birds, the MHC has been extensively examined but mainly in galliforms and passerines while other taxa that represent specific ecological and evolutionary life-histories, like seabirds, are underexamined. Here, we characterized diversity of MHC Class II B exon 2 in a colonial pelagic seabird, the Little Auk (or Dovekie Alle alle). We further examined whether MHC variation could be maintained through balancing selection and disassortative mating. We found high polymorphism at the genotyped MHC fragment, characterizing 99 distinct alleles across 140 individuals from three populations. The alleles frequencies exhibited a similar skewed distribution in both sexes, with the four most commonly occurring alleles representing approximately 35% of allelic variation. The results of a Bayesian site-by-site selection analysis suggest evidence of balancing selection and no direct evidence for MHC-dependent disassortative mating preferences in the Little Auk. The latter result might be attributed to the high overall polymorphism of the examined fragment, which itself may be maintained by the large population size of the species.
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Affiliation(s)
| | - Brian Hoover
- Farallon Institute, Petaluma, California, United States of America
| | - Dariusz Jakubas
- Department of Vertebrate Ecology and Zoology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Jérôme Fort
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266 CNRS – La Rochelle University, 17000 La Rochelle, France
| | - David Grémillet
- Excellence Chair Nouvelle Aquitaine - CEBC UMR 7372 CNRS, La Rochelle Université, Villiers-en-Bois, France & FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch, South Africa
| | | | - Sylwia Zielińska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
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Milani M, Naddaf SR, Ziapour SP, Sepahi AA, Rohani M. Borrelia theileri infections in Rhipicephalus annulatus ticks from the north of Iran. EXPERIMENTAL & APPLIED ACAROLOGY 2024; 93:81-95. [PMID: 38869723 DOI: 10.1007/s10493-024-00924-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/08/2024] [Indexed: 06/14/2024]
Abstract
Ticks serve as vectors and reservoirs of various Borrelia species, potentially causing diseases in humans and animals. Mazandaran, a fertile green land in northern Iran, provides ample grazing grounds for livestock and harbors at least 26 hard tick species. This study investigated Borrelia infection in hard ticks from forest areas in this region and compared their genetic identity with the species data in the GenBank database. A total of 2,049 ticks were collected manually from mammalian hosts or using dragging and flagging methods. These ticks were then grouped into 190 pools and 41 individuals based on host, species, developmental stage, and gender. A real-time PCR (qPCR) detected Borrelia DNA in 26 pools from female, male, and nymph of Rhipicephalus annulatus (n = 17) and Ixodes ricinus (n = 9) ticks and one individual female Haemaphysalis punctata tick. The generated partial flaB and glpQ sequences from qPCR-positive Rh. annulatus ticks exhibited the highest identities of 98.1-100% and 98.2% with Borrelia theileri and closely related undefined isolates. Additionally, in phylogenetic analysis, these sequences clustered within well-supported clades with B. theileri and the closely related undefined isolates from various geographic regions, confirming the presence of B. theileri in the north of Iran. Divergence in B. theileri flaB and glpQ sequences across various geographical areas suggests potential subspeciation driven by adaptations to different tick species. This divergence in our flaB sequences implies the possible introduction of B. theileri-infected ticks from different geographical origins into Iran.
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Affiliation(s)
- Mahnaz Milani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Saied Reza Naddaf
- Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran.
| | - Seyyed Payman Ziapour
- Department of Parasitology, Zoonoses Research Center, Pasteur Institute of Iran, Amol, Mazandaran, Iran
| | - Abbas Akhavan Sepahi
- Department of Microbiology, Faculty of Biology, North Branch, Islamic Azad University, Tehran, Iran
| | - Mahdi Rohani
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran.
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Hossain MA, Al Amin M, Khan MA, Refat MRR, Sohel M, Rahman MH, Islam A, Hoque MN. Genome-Wide Investigation Reveals Potential Therapeutic Targets in Shigella spp. BIOMED RESEARCH INTERNATIONAL 2024; 2024:5554208. [PMID: 38595330 PMCID: PMC11003385 DOI: 10.1155/2024/5554208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 02/21/2024] [Accepted: 03/01/2024] [Indexed: 04/11/2024]
Abstract
Shigella stands as a major contributor to bacterial dysentery worldwide scale, particularly in developing countries with inadequate sanitation and hygiene. The emergence of multidrug-resistant strains exacerbates the challenge of treating Shigella infections, particularly in regions where access to healthcare and alternative antibiotics is limited. Therefore, investigations on how bacteria evade antibiotics and eventually develop resistance could open new avenues for research to develop novel therapeutics. The aim of this study was to analyze whole genome sequence (WGS) of human pathogenic Shigella spp. to elucidate the antibiotic resistance genes (ARGs) and their mechanism of resistance, gene-drug interactions, protein-protein interactions, and functional pathways to screen potential therapeutic candidate(s). We comprehensively analyzed 45 WGS of Shigella, including S. flexneri (n = 17), S. dysenteriae (n = 14), S. boydii (n = 11), and S. sonnei (n = 13), through different bioinformatics tools. Evolutionary phylogenetic analysis showed three distinct clades among the circulating strains of Shigella worldwide, with less genomic diversity. In this study, 2,146 ARGs were predicted in 45 genomes (average 47.69 ARGs/genome), of which only 91 ARGs were found to be shared across the genomes. Majority of these ARGs conferred their resistance through antibiotic efflux pump (51.0%) followed by antibiotic target alteration (23%) and antibiotic target replacement (18%). We identified 13 hub proteins, of which four proteins (e.g., tolC, acrR, mdtA, and gyrA) were detected as potential hub proteins to be associated with antibiotic efflux pump and target alteration mechanisms. These hub proteins were significantly (p < 0.05) enriched in biological process, molecular function, and cellular components. Therefore, the finding of this study suggests that human pathogenic Shigella strains harbored a wide range of ARGs that confer resistance through antibiotic efflux pumps and antibiotic target modification mechanisms, which must be taken into account to devise and formulate treatment strategy against this pathogen. Moreover, the identified hub proteins could be exploited to design and develop novel therapeutics against MDR pathogens like Shigella.
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Affiliation(s)
- Md. Arju Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
- Department of Microbiology, Primeasia University, Dhaka 1213, Bangladesh
| | - Md. Al Amin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Md. Arif Khan
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
- EcoHealth Alliance, New York, NY 10018, USA
| | - Md. Rashedur Rahman Refat
- Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Md Sohel
- Department of Biochemistry and Molecular Biology, Primeasia University, Banani, Dhaka 1213, Bangladesh
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia 7003, Bangladesh
| | - Ariful Islam
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
- EcoHealth Alliance, New York, NY 10018, USA
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
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Zhang J, Zhao R, Lin S, Yang D, Lu S, Liu Z, Gao Y, Zhang Y, Hou B, Xi C, Liu J, Bing J, Pang E, Lin K, Zeng S. Comparison of genes involved in brain development: insights into the organization and evolution of the telencephalic pallium. Sci Rep 2024; 14:6102. [PMID: 38480729 PMCID: PMC10937912 DOI: 10.1038/s41598-024-51964-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 01/11/2024] [Indexed: 03/17/2024] Open
Abstract
The mechanisms underlying the organization and evolution of the telencephalic pallium are not yet clear.. To address this issue, we first performed comparative analysis of genes critical for the development of the pallium (Emx1/2 and Pax6) and subpallium (Dlx2 and Nkx1/2) among 500 vertebrate species. We found that these genes have no obvious variations in chromosomal duplication/loss, gene locus synteny or Darwinian selection. However, there is an additional fragment of approximately 20 amino acids in mammalian Emx1 and a poly-(Ala)6-7 in Emx2. Lentiviruses expressing mouse or chick Emx2 (m-Emx2 or c-Emx2 Lv) were injected into the ventricle of the chick telencephalon at embryonic Day 3 (E3), and the embryos were allowed to develop to E12-14 or to posthatchling. After transfection with m-Emx2 Lv, the cells expressing Reelin, Vimentin or GABA increased, and neurogenesis of calbindin cells changed towards the mammalian inside-out pattern in the dorsal pallium and mesopallium. In addition, a behavior test for posthatched chicks indicated that the passive avoidance ratio increased significantly. The study suggests that the acquisition of an additional fragment in mammalian Emx2 is associated with the organization and evolution of the mammalian pallium.
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Affiliation(s)
- Jiangyan Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing, China
| | - Rui Zhao
- Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing, China
| | - Shiying Lin
- Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing, China
| | - Dong Yang
- Beijing Key Laboratory of Genetic Engineering Drugs and Biological Technology, Beijing Normal University, Beijing, China
| | - Shan Lu
- Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing, China
| | - Zenan Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing, China
| | - Yuanyuan Gao
- Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing, China
| | - Yiyun Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing, China
| | - Bing Hou
- Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing, China
| | - Chao Xi
- Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing, China
| | - Jin Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing, China
| | - Jie Bing
- Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing, China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China.
| | - Shaoju Zeng
- Beijing Key Laboratory of Gene Resource and Molecular Development, Beijing Normal University, Beijing, China.
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Tebit DM, Nickel G, Gibson R, Rodriguez M, Hathaway NJ, Bain K, Reyes-Rodriguez AL, Ondoa P, Heeney JL, Li Y, Bongorno J, Canaday D, McDonald D, Bailey JA, Arts EJ. Replicative fitness and pathogenicity of primate lentiviruses in lymphoid tissue, primary human and chimpanzee cells: relation to possible jumps to humans. EBioMedicine 2024; 100:104965. [PMID: 38215691 PMCID: PMC10827413 DOI: 10.1016/j.ebiom.2023.104965] [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: 08/15/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Simian immunodeficiency viruses (SIV) have been jumping between non-human primates in West/Central Africa for thousands of years and yet, the HIV-1 epidemic only originated from a primate lentivirus over 100 years ago. METHODS This study examined the replicative fitness, transmission, restriction, and cytopathogenicity of 22 primate lentiviruses in primary human lymphoid tissue and both primary human and chimpanzee peripheral blood mononuclear cells. FINDINGS Pairwise competitions revealed that SIV from chimpanzees (cpz) had the highest replicative fitness in human or chimpanzee peripheral blood mononuclear cells, even higher fitness than HIV-1 group M strains responsible for worldwide epidemic. The SIV strains belonging to the "HIV-2 lineage" (including SIVsmm, SIVmac, SIVagm) had the lowest replicative fitness. SIVcpz strains were less inhibited by human restriction factors than the "HIV-2 lineage" strains. SIVcpz efficiently replicated in human tonsillar tissue but did not deplete CD4+ T-cells, consistent with the slow or nonpathogenic disease observed in most chimpanzees. In contrast, HIV-1 isolates and SIV of the HIV-2 lineage were pathogenic to the human tonsillar tissue, almost independent of the level of virus replication. INTERPRETATION Of all primate lentiviruses, SIV from chimpanzees appears most capable of infecting and replicating in humans, establishing HIV-1. SIV from other Old World monkeys, e.g. the progenitor of HIV-2, replicate slowly in humans due in part to restriction factors. Nonetheless, many of these SIV strains were more pathogenic than SIVcpz. Either SIVcpz evolved into a more pathogenic virus while in humans or a rare SIVcpz, possibly extinct in chimpanzees, was pathogenic immediately following the jump into human. FUNDING Support for this study to E.J.A. was provided by the NIH/NIAID R01 AI49170 and CIHR project grant 385787. Infrastructure support was provided by the NIH CFAR AI36219 and Canadian CFI/Ontario ORF 36287. Efforts of J.A.B. and N.J.H. was provided by NIH AI099473 and for D.H.C., by VA and NIH AI AI080313.
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Affiliation(s)
- Denis M Tebit
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Global Biomed Scientific, LLC, P.O. Box 2368, Forest, VA, USA
| | - Gabrielle Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Richard Gibson
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Myriam Rodriguez
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Nicolas J Hathaway
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Katie Bain
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Angel L Reyes-Rodriguez
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Pascal Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia; Department of Global Health, Institute of Global Health and Development, University of Amsterdam, Amsterdam, the Netherlands
| | - Jonathan L Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Yue Li
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Jennifer Bongorno
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - David Canaday
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - David McDonald
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Eric J Arts
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Microbiology and Immunology, Western University, Ontario, Canada.
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Lee JS, Min JW, Gye SB, Kim YW, Kang HC, Choi YS, Seo WS, Lee BY. Suppression of UVB-Induced MMP-1 Expression in Human Skin Fibroblasts Using Lysate of Lactobacillus iners Derived from Korean Women's Skin in Their Twenties. Curr Issues Mol Biol 2024; 46:513-526. [PMID: 38248335 PMCID: PMC10814086 DOI: 10.3390/cimb46010033] [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: 12/18/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
The process of skin aging is intricate, involving intrinsic aging, influenced by internal factors, and extrinsic aging, mainly caused by exposure to UV radiation, resulting in photoaging. Photoaging manifests as skin issues such as wrinkles and discoloration. The skin microbiome, a diverse community of microorganisms on the skin's surface, plays a crucial role in skin protection and can be affected by factors like humidity and pH. Probiotics, beneficial microorganisms, have been investigated for their potential to enhance skin health by regulating the skin microbiome. This can be accomplished through oral probiotics, impacting the gut-skin axis, or topical applications introducing live bacteria to the skin. Probiotics mitigate oxidative stress, suppress inflammation, and maintain the skin's extracellular matrix, ultimately averting skin aging. However, research on probiotics derived from human skin is limited, and there is no established product for preventing photoaging. The mechanism by which probiotics shield the skin microbiome and skin layers from UV radiation remains unclear. Recently, researchers have discovered Lactobacillus in the skin, with reports indicating a decrease in this microorganism with age. In a recent study, scientists isolated Lactobacillus iners KOLBM20 from the skin of individuals in their twenties and confirmed its effectiveness. A comparative analysis of genetic sequences revealed that strain KOLBM20 belongs to the Lactobacillus genus and closely relates to L. iners DSM13335(T) with a 99.20% similarity. Importantly, Lactobacillus iners KOLBM20 displayed anti-wrinkle properties by inhibiting MMP-1. This investigation demonstrated the inhibitory effect of KOLBM20 strain lysate on MMP-1 expression. Moreover, the data suggest that KOLBM20 strain lysate may prevent UVB-induced MMP-1 expression by inhibiting the activation of the ERK, JNK, and p38 signaling pathways induced by UVB. Consequently, KOLBM20 strain lysate holds promise as a potential therapeutic agent for preventing and treating skin photoaging.
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Affiliation(s)
- Jin-Sung Lee
- Department of Applied Biotechnology, Ajou University, Suwon 16499, Republic of Korea;
- R&D Complex, Kolmar Korea, 61, 8-gil, Heolleung-ro, Seocho-gu, Seoul 06800, Republic of Korea; (S.-B.G.); (Y.-W.K.)
| | - Jin-Woo Min
- Green & Biome Customizing Laboratory, GFC Co., Ltd., Hwaseong 18471, Republic of Korea; (J.-W.M.); (H.-C.K.)
| | - Seong-Bong Gye
- R&D Complex, Kolmar Korea, 61, 8-gil, Heolleung-ro, Seocho-gu, Seoul 06800, Republic of Korea; (S.-B.G.); (Y.-W.K.)
| | - Yong-Woo Kim
- R&D Complex, Kolmar Korea, 61, 8-gil, Heolleung-ro, Seocho-gu, Seoul 06800, Republic of Korea; (S.-B.G.); (Y.-W.K.)
| | - Hee-Cheol Kang
- Green & Biome Customizing Laboratory, GFC Co., Ltd., Hwaseong 18471, Republic of Korea; (J.-W.M.); (H.-C.K.)
| | - Yoon-Seo Choi
- Graduate School-Interdisciplinary Program in Biocosmetics, Sungkyunkwan University, Suwon 16419, Republic of Korea;
| | - Won-Sang Seo
- Green & Biome Customizing Laboratory, GFC Co., Ltd., Hwaseong 18471, Republic of Korea; (J.-W.M.); (H.-C.K.)
| | - Bun-Yeoul Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
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Qiu L, Jiang S, Zhou F, Huang J, Guo Y. Molecular cloning and characterization of a cyclin B gene on the ovarian maturation stage of black tiger shrimp (Penaeus monodon). Mol Biol Rep 2023; 50:S1-S8. [PMID: 17245552 DOI: 10.1007/s11033-006-9052-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2006] [Accepted: 12/20/2006] [Indexed: 10/23/2022]
Abstract
The techniques of homology cloning and anchored PCR were used to clone the cyclin B gene from black tiger shrimp. The full length cDNA of black tiger shrimp cyclin B (btscyclin B) contained a 5' untranslated region (UTR) of 102 bp, an ORF of 1,206 bp encoding a polypeptide of 401 amino acids with an estimated molecular mass of 45 kDa and a 3' UTR of 396 bp. The searches for protein sequence similarities with BLAST analysis indicated that the deduced amino acid sequence of btscyclin B was homological to the cyclin B of other species and even the mammalians. Two conserved signature sequences of cyclin B gene family were found in the btscyclin B deduced amino acid sequence. The temporal expressions of cyclin B gene in the different tissues, including liver, ovary, muscle, brain stomach, heart and intestine, were measured by RT-PCR. mRNA expression of cyclin B could be detected in liver, ovary, muscle, brain, stomach, heart and strongest in the ovary, but almost not be detected in the intestine. In ovarian maturation stages, the expression of btscyclin B was different. The result indicated that btscyclin B was constitutive expressed and played an important role in the cell division stage.
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Affiliation(s)
- Lihua Qiu
- Biotechnology and aquiculture Laboratory, The South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingangxi Road, Guangzhou, 510300, P.R. China
| | - Shigui Jiang
- Biotechnology and aquiculture Laboratory, The South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingangxi Road, Guangzhou, 510300, P.R. China.
| | - Falin Zhou
- Biotechnology and aquiculture Laboratory, The South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingangxi Road, Guangzhou, 510300, P.R. China
| | - Jianhua Huang
- Biotechnology and aquiculture Laboratory, The South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingangxi Road, Guangzhou, 510300, P.R. China
| | - Yihui Guo
- Biotechnology and aquiculture Laboratory, The South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingangxi Road, Guangzhou, 510300, P.R. China
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8
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Salehi Z, Sharifynia S, Jamzivar F, Shams-Ghahfarokhi M, Poorabdollah M, Abtahian Z, Nasiri N, Marjani M, Moniri A, Salehi M, Tabarsi P, Razzaghi-Abyaneh M. Clinical epidemiology of pulmonary aspergillosis in hospitalized patients and contribution of Cyp51A, Yap1, and Cdr1B mutations to voriconazole resistance in etiologic Aspergillus species. Eur J Clin Microbiol Infect Dis 2023:10.1007/s10096-023-04608-7. [PMID: 37142789 DOI: 10.1007/s10096-023-04608-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 04/19/2023] [Indexed: 05/06/2023]
Abstract
Pulmonary aspergillosis is a life-threatening fungal infection with worldwide distribution. In the present study, clinical epidemiology of pulmonary aspergillosis and antifungal susceptibility of etiologic Aspergillus species were evaluated in one-hundred fifty patients with special focus on the frequency of voriconazole resistance. All the cases were confirmed by the clinical pictures, laboratory findings, and isolation of etiologic Aspergillus species which belonged to two major species, i.e., A. flavus and A. fumigatus. Seventeen isolates displayed voriconazole MIC greater than or equal to the epidemiological cutoff value. Expression of cyp51A, Cdr1B, and Yap1 genes was analyzed in voriconazole-intermediate/resistant isolates. In A. flavus, Cyp51A protein sequencing showed the substitutions T335A and D282E. In the Yap1 gene, A78C replacement led to Q26H amino acid substitution that was not reported previously in A. flavus resistant to voriconazole. No mutations associated with voriconazole resistance were found in the three genes of A. fumigatus. The expression of Yap1 was higher than that of two other genes in both A. flavus and A. fumigatus. Overall, voriconazole-resistant strains of both A. fumigatus and A. flavus demonstrated overexpression of Cdr1B, Cyp51A, and Yap1 genes compared to voriconazole-susceptible strains. Although there are still ambiguous points about the mechanisms of azole resistance, our results showed that mutations were not present in majority of resistant and intermediate isolates, while all of these isolates showed overexpression in all three genes studied. As a conclusion, it seems that the main reason of the emergence of mutation in voriconazole-resistant isolates of A. flavus and A. fumigatus is previous or prolonged exposure to azoles.
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Affiliation(s)
- Zahra Salehi
- Department of Mycology, Pasteur Institute of Iran, Tehran, 1316943551, Iran
| | - Somayeh Sharifynia
- Clinical Tuberculosis and Epidemiology Research Center, NRITLD, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | | | - Mihan Poorabdollah
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Abtahian
- Clinical Tuberculosis and Epidemiology Research Center, NRITLD, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Naser Nasiri
- HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Majid Marjani
- Clinical Tuberculosis and Epidemiology Research Center, NRITLD, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afshin Moniri
- Clinical Tuberculosis and Epidemiology Research Center, NRITLD, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Salehi
- Research Center for Antibiotic Stewardship & Antimicrobial Resistance, Department of Infectious Diseases, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Payam Tabarsi
- Clinical Tuberculosis and Epidemiology Research Center, NRITLD, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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9
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Zhang X, Purba ER, Sun J, Zhang QH, Dong SL, Zhang YN, He P, Mang D, Zhang L. Functional differentiation of two general-odorant binding proteins in Hyphantria cunea (Drury) (Lepidoptera: Erebidae). PEST MANAGEMENT SCIENCE 2023. [PMID: 37103977 DOI: 10.1002/ps.7515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/21/2023] [Accepted: 04/27/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND General odor-binding proteins (GOBPs) play critical roles in insect olfactory recognition of sex pheromones and plant volatiles. Therefore, the identification of GOBPs in Hyphantria cunea (Drury) based on their characterization to pheromone components and plant volatiles is remain unknown. RESULTS In this study, two H. cunea (HcunGOBPs) genes were cloned, and their expression profiles and odorant binding characteristics were systematically analyzed. Firstly, the tissue expression study showed that both HcunGOBP1 and HcunGOBP2 were highly expressed in the antennae of both sexes, indicating their potential involvement in the perception of sex pheromones. Secondly, these two HcunGOBPs genes were expressed in Escherichia coli and ligand binding assays were used to assess the binding affinities to its sex pheromone components including two aldehydes and two epoxides, and some plant volatiles. HcunGOBP2 showed high binding affinities to two aldehyde components (Z9, Z12, Z15-18Ald and Z9, Z12-18Ald), and showed low binding affinities to two epoxide components (1, Z3, Z6-9S, 10R-epoxy-21Hy and Z3, Z6-9S, 10R-epoxy-21Hy), whereas HcunGOBP1 showed weak but significant binding to all four sex pheromone components. Furthermore, both HcunGOBPs demonstrated variable binding affinities to the plant volatiles tested. Thirdly, in silico studies of HcunGOBPs utilized homology, structure modeling, and molecular docking revealed critical hydrophobic residues might be involved in the binding of HcunGOBPs to their sex pheromone components and plant volatiles. CONCLUSION Our study suggests that these two HcunGOBPs may serve as potential targets for future studies of HcunGOBPs ligand binding, providing insight in the mechanism of olfaction in H. cunea. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xiaoqing Zhang
- Anhui Provincial Key Laboratory of Microbial Control, Engineering Research Center of Fungal Biotechnology, Ministry of Education School of Forestry & Landscape Architecture, Anhui Agricultural University, Hefei, China
- Education Ministry, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Endang R Purba
- Structural Cellular Biology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jing Sun
- College of Life Science, Hebei University, Baoding, China
| | | | - Shuang-Lin Dong
- Education Ministry, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ya-Nan Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Peng He
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Dingze Mang
- College of Life Science, Hebei University, Baoding, China
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Longwa Zhang
- Anhui Provincial Key Laboratory of Microbial Control, Engineering Research Center of Fungal Biotechnology, Ministry of Education School of Forestry & Landscape Architecture, Anhui Agricultural University, Hefei, China
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10
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Sala A, Ardizzoni A, Spaggiari L, Vaidya N, van der Schaaf J, Rizzato C, Cermelli C, Mogavero S, Krüger T, Himmel M, Kniemeyer O, Brakhage AA, King BL, Lupetti A, Comar M, de Seta F, Tavanti A, Blasi E, Wheeler RT, Pericolini E. A New Phenotype in Candida-Epithelial Cell Interaction Distinguishes Colonization- versus Vulvovaginal Candidiasis-Associated Strains. mBio 2023; 14:e0010723. [PMID: 36856418 PMCID: PMC10128025 DOI: 10.1128/mbio.00107-23] [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: 01/18/2023] [Accepted: 02/09/2023] [Indexed: 03/02/2023] Open
Abstract
Vulvovaginal candidiasis (VVC) affects nearly 3/4 of women during their lifetime, and its symptoms seriously reduce quality of life. Although Candida albicans is a common commensal, it is unknown if VVC results from a switch from a commensal to pathogenic state, if only some strains can cause VVC, and/or if there is displacement of commensal strains with more pathogenic strains. We studied a set of VVC and colonizing C. albicans strains to identify consistent in vitro phenotypes associated with one group or the other. We find that the strains do not differ in overall genetic profile or behavior in culture media (i.e., multilocus sequence type [MLST] profile, rate of growth, and filamentation), but they show strikingly different behaviors during their interactions with vaginal epithelial cells. Epithelial infections with VVC-derived strains yielded stronger fungal proliferation and shedding of fungi and epithelial cells. Transcriptome sequencing (RNA-seq) analysis of representative epithelial cell infections with selected pathogenic or commensal isolates identified several differentially activated epithelial signaling pathways, including the integrin, ferroptosis, and type I interferon pathways; the latter has been implicated in damage protection. Strikingly, inhibition of type I interferon signaling selectively increases fungal shedding of strains in the colonizing cohort, suggesting that increased shedding correlates with lower interferon pathway activation. These data suggest that VVC strains may intrinsically have enhanced pathogenic potential via differential elicitation of epithelial responses, including the type I interferon pathway. Therefore, it may eventually be possible to evaluate pathogenic potential in vitro to refine VVC diagnosis. IMPORTANCE Despite a high incidence of VVC, we still have a poor understanding of this female-specific disease whose negative impact on women's quality of life has become a public health issue. It is not yet possible to determine by genotype or laboratory phenotype if a given Candida albicans strain is more or less likely to cause VVC. Here, we show that Candida strains causing VVC induce more fungal shedding from epithelial cells than strains from healthy women. This effect is also accompanied by increased epithelial cell detachment and differential activation of the type I interferon pathway. These distinguishing phenotypes suggest it may be possible to evaluate the VVC pathogenic potential of fungal isolates. This would permit more targeted antifungal treatments to spare commensals and could allow for displacement of pathogenic strains with nonpathogenic colonizers. We expect these new assays to provide a more targeted tool for identifying fungal virulence factors and epithelial responses that control fungal vaginitis.
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Affiliation(s)
- Arianna Sala
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea Ardizzoni
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Luca Spaggiari
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Modena, Italy
| | - Nikhil Vaidya
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Jane van der Schaaf
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Cosmeri Rizzato
- Department of Translational Research and of New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Claudio Cermelli
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Selene Mogavero
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Maximilian Himmel
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Benjamin L. King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
| | - Antonella Lupetti
- Department of Translational Research and of New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Manola Comar
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Trieste, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Francesco de Seta
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Trieste, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | | | - Elisabetta Blasi
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Robert T. Wheeler
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
| | - Eva Pericolini
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
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11
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Miles S, Mourglia-Ettlin G, Fernández V. Identification of Omega-class glutathione transferases in helminths of the Taeniidae family. Mol Biochem Parasitol 2023; 254:111559. [PMID: 37024059 DOI: 10.1016/j.molbiopara.2023.111559] [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: 08/05/2022] [Revised: 03/07/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023]
Abstract
Glutathione transferase enzymes (GSTs) are believed to be a major detoxification system in helminth parasites and have been associated with immunomodulation of the host response. Echinococcus granulosus sensu lato (s.l.) is a cestode parasite known to express at least five different GSTs, but no Omega-class enzymes have been reported in this parasite or in any other cestode. Herein we report the identification of a new member of the GST superfamily in E. granulosus s.l., which is phylogenetically related to the Omega-class: EgrGSTO. Through mass spectrometry, we showed that the 237 amino acids protein EgrGSTO is expressed by the parasite. Moreover, we identified homologues of EgrGSTO in other eight members of the Taeniidae family, including E. canadensis, E. multilocularis, E. oligarthrus, Hydatigera taeniaeformis, Taenia asiatica, T. multiceps, T. saginata and T. solium. A manual sequence inspection and rational modification yielded eight Taeniidae's GSTO sequences, each one encoding for a 237 aa polypeptide showing 80.2% overall identity. To the best of our knowledge, this is the first description of genes encoding for Omega-class GSTs in worms belonging to the Taeniidae family -that at least in E. granulosus s.l. is expressed as a protein- suggesting the gene encodes for a functional protein.
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Affiliation(s)
- Sebastián Miles
- Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Gustavo Mourglia-Ettlin
- Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Verónica Fernández
- Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay.
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12
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Mohamed HMA, Aljasir SF, Moftah RF, Younis W. Mycological evaluation of frozen meat with special reference to yeasts. Vet World 2023; 16:571-579. [PMID: 37041834 PMCID: PMC10082747 DOI: 10.14202/vetworld.2023.571-579] [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: 11/16/2022] [Accepted: 01/30/2023] [Indexed: 04/13/2023] Open
Abstract
Background and Aim Fungi can play beneficial and detrimental roles in meat products; however, the diversity and significance of fungi in meat products are poorly understood. This study aimed to isolate and characterize fungal species from frozen beef samples collected from retail stores in the Qena Governorate, Egypt. Materials and Methods A total of 70 frozen beef samples were collected from retail stores in Qena, Egypt. All samples were subjected to mycological examination. Fungal colonies were identified using conventional approaches, as well as the VITEK 2 system and DNA sequencing of the internal transcribed spacer region. Analyses of enzymatic activity, biofilm formation ability, and the antimicrobial resistance profiles of the isolated yeasts were also conducted. Results Molds and yeasts were isolated from 40% and 60% of meat samples, respectively. Mold isolates were dominated by Aspergillus, Penicillium, and Cladosporium spp., whereas yeast isolates were identified as Candida albicans, Candida parapsilosis, Yarrowia lipolytica, Saccharomyces cerevisiae, and Rhodotorula mucilaginosa. Compared to other yeast species, the highest production of lipase and protease was observed in Candida species. The strongest ability to form biofilms was observed in Candida spp., followed by S. cerevisiae, Y. lipolytica, and R. mucilaginosa. The results of antimicrobial susceptibility testing revealed that all yeast isolates showed notable resistance to fluconazole and itraconazole. Conclusion A significant correlation between antimicrobial resistance and biofilm formation was observed in several species. This study highlights the importance of the dangers of yeasts in food products and the extent of their impact on public health.
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Affiliation(s)
- Hams M. A. Mohamed
- Department of Microbiology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Sulaiman F. Aljasir
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Rofida F. Moftah
- Department of Food Science and Technology, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Waleed Younis
- Department of Microbiology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
- Corresponding author: Waleed Younis, e-mail: Co-authors: HMAM: , SFA: , RFM:
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13
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A Salt-Tolerant Strain of Trichoderma longibrachiatum HL167 Is Effective in Alleviating Salt Stress, Promoting Plant Growth, and Managing Fusarium Wilt Disease in Cowpea. J Fungi (Basel) 2023; 9:jof9030304. [PMID: 36983472 PMCID: PMC10052927 DOI: 10.3390/jof9030304] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Salt stress is a constraint factor in agricultural production and restricts crops yield and quality. In this study, a salt-tolerant strain of Trichoderma longibrachiatum HL167 was obtained from 64 isolates showing significant salt tolerance and antagonistic activity to Fusarium oxysporum. T. longibrachiatum HL167 inhibited F. oxysporum at a rate of 68.08% in 200 mM NaCl, penetrated F. oxysporum under 200 mM NaCl, and eventually induced F. oxysporum hyphae breaking, according to electron microscope observations. In the pot experiment, pretreatment of cowpea seedlings with T. longibrachiatum HL167 reduced the accumulation level of ROS in tissues and the damage caused by salt stress. Furthermore, in the field experiment, it was discovered that treating cowpea with T. longibrachiatum HL167 before root inoculation with F. oxysporum can successfully prevent and control the development of cowpea Fusarium wilt, with the best control effect reaching 61.54%. Moreover, the application of HL 167 also improved the K+/Na+ ratio of cowpea, alleviated the ion toxicity of salt stress on cowpea, and HL167 was found to effectively colonize the cowpea roots. T. longibrachiatum HL167, which normally survives in saline–alkali environments and has the functions of disease prevention and plant growth promotion capabilities, has important research implications for improving the saline–alkali soil environment and for the sustainable development of green agriculture.
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14
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Liu S, Liu X, Zhang T, Bai S, He K, Zhang Y, Francis F, Wang Z. Secondary symbionts affect aphid fitness and the titer of primary symbiont. FRONTIERS IN PLANT SCIENCE 2023; 14:1096750. [PMID: 36818877 PMCID: PMC9933779 DOI: 10.3389/fpls.2023.1096750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Bacterial symbionts associated with aphids are important for their ecological fitness. The corn leaf aphid, Rhopalosiphum maidis (Fitch), is one of the most damaging aphid pests on maize and has been reported to harbor Hamiltonella defensa and Regiella insecticola while the effects of the secondary symbionts (S-symbionts) on host ecology and primary symbiont Buchnera aphidicola remain unclear. Here, four aphid strains were established, two of which were collected from Langfang - Hebei Province, China, with similar symbiont pattern except for the presence of H. defensa. Two other aphid strains were collected from Nanning - Guangxi Province, China, with the same symbiont infection except for the presence of R. insecticola. Phylogenetic analysis and aphid genotyping indicated that the S-symbiont-infected and free aphid strains from the same location had identical genetic backgrounds. Aphid fitness measurement showed that aphid strain infected with H. defensa performed shortened developmental duration for 1st instar and total nymph stages, reduced aphid survival rate, offspring, and longevity. While the developmental duration of H-infected strains was accelerated, and the adult weight was significantly higher compared to the H-free strain. Infection with R. insecticola did not affect the aphid's entire nymph stage duration and survival rate. As the H-strain does, aphids infected with R. insecticola also underwent a drop in offspring, along with marginally lower longevity. Unlike the H-infected strain, the R-infected strain performed delayed developmental duration and lower adult weight. The B. aphidicola titers of the H-infected strains showed a steep drop during the aphid 1st to 3rd instar stages, while the augmentation of B. aphidicola titers was found in the R-infected strain during the aphid 1st to 3rd instar. Our study investigated for the first time the effect of the S-symbionts on the ecology fitness and primary symbiont in R. maidis, indicating that infection with secondary symbionts leads to the modulation of aphid primary symbiont abundance, together inducing significant fitness costs on aphids with further impact on environmental adaptation and trophic interactions.
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Affiliation(s)
- Shen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Xiaobei Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tiantao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuxiong Bai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kanglai He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongjun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Frédéric Francis
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Zhenying Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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15
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Udomsil N, Pongjanla S, Rodtong S, Tanasupawat S, Yongsawatdigul J. Extremely halophilic strains of
Halobacterium salinarum
as a potential starter culture for fish sauce fermentation. J Food Sci 2022; 87:5375-5389. [DOI: 10.1111/1750-3841.16368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/14/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022]
Affiliation(s)
- Natteewan Udomsil
- Food Technology Program School of Interdisciplinary Studies Mahidol University Kanchanaburi Campus Kanchanaburi Thailand
| | - Sirinya Pongjanla
- School of Food Technology, Institute of Agricultural Technology Suranaree University of Technology Nakhon Ratchasima Thailand
| | - Sureelak Rodtong
- School of Preclinical Sciences, Institute of ScienceSuranaree University of Technology Nakhon RatchasimaThailand
- Microbial Cultures Research Center for Food and Bioplastics Production Suranaree University of Technology Nakhon Ratchasima Thailand
| | - Somboon Tanasupawat
- Department of Microbiology, Faculty of Pharmaceutical Sciences Chulalongkorn University Bangkok Thailand
| | - Jirawat Yongsawatdigul
- School of Food Technology, Institute of Agricultural Technology Suranaree University of Technology Nakhon Ratchasima Thailand
- Microbial Cultures Research Center for Food and Bioplastics Production Suranaree University of Technology Nakhon Ratchasima Thailand
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Virological responses to tenofovir-alafenamide-containing antiretroviral therapy in people living with HIV co-infected with lamivudine-resistant or lamivudine-susceptible hepatitis B virus. Int J Antimicrob Agents 2022; 60:106682. [PMID: 36279976 DOI: 10.1016/j.ijantimicag.2022.106682] [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: 12/01/2021] [Revised: 08/11/2022] [Accepted: 10/17/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Data on the effectiveness of tenofovir alafenamide (TAF) against lamivudine-resistant (LAM-R) hepatitis B virus (HBV) among patients co-infected with human immunodeficiency virus (HIV) and HBV are limited. METHODS Between April and December 2018, HIV-positive patients co-infected with LAM-R or lamivudine-susceptible (LAM-S) HBV who switched from tenofovir-disoproxil-fumarate-containing antiretroviral therapy (ART) to TAF-containing ART were followed for 96 weeks. Plasma HBV and HIV loads, HBV serological markers, and liver function before and after the switch were analysed. RESULTS In total, 182 patients co-infected with HIV and HBV were included in this study: 45 with LAM-R HBV and 137 with LAM-S HBV. At baseline, 28.9% and 7.4% of patients in the LAM-R and LAM-S groups, respectively, tested positive for hepatitis B virus envelope antigen (HBeAg) (P<0.001), and the respective percentages of patients who had achieved plasma HBV DNA <20 IU/mL were 95.5% and 97.1%. At weeks 48 and 96, 100% and 94.9% of patients in the LAM-R group, respectively, and 97.1% and 95.6% of patients in the LAM-S group, respectively, maintained plasma HBV DNA <20 IU/mL. Lamivudine resistance of HBV and baseline hepatitis B virus surface antigen (HBsAg) level were associated with HBsAg decrement at week 96 at a degree of 0.25 log10 IU/mL [95% confidence interval (CI) 0.059-0.246] and 0.22 log10 IU/mL (per 1-log10IU/mL increase, 95% CI 0.018-0.101), respectively. At week 96, 2.2% (4/182) of patients had HBsAg loss; no patients in the LAM-R group and 25.0% (2/8) of patients in the LAM-S group had HBeAg seroconversion. CONCLUSIONS Switching to TAF-containing regimens maintained high rates of HBV viral suppression in patients co-infected with either LAM-R or LAM-S HBV. The decrease in HBsAg was minimal, and HBsAg seroconversion occurred infrequently.
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Yang Z, Tian S, Li X, Dai Z, Yan A, Chen Z, Chen J, Tang Q, Cheng C, Xu Y, Deng C, Liu C, Kang L, Xie D, Zhao J, Chen X, Zhang X, Wu Y, Li A, Su J. Multi-omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:812-829. [PMID: 36129373 DOI: 10.1111/tpj.15983] [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: 04/07/2022] [Revised: 08/31/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
Jute (Corchorus sp.) is the most important bast fiber crop worldwide; however, the mechanisms underlying domestication and improvement remain largely unknown. We performed multi-omics analysis by integrating de novo sequencing, resequencing, and transcriptomic and epigenetic sequencing to clarify the domestication and improvement of dark jute Corchorus olitorius. We demonstrated that dark jute underwent early domestication and a relatively moderate genetic bottleneck during improvement breeding. A genome-wide association study of 11 important agronomic traits identified abundant candidate loci. We characterized the selective sweeps in the two breeding stages of jute, prominently, soil salinity differences played an important role in environmental adaptation during domestication, and the strongly selected genes for improvement had an increased frequency of favorable haplotypes. Furthermore, we speculated that an encoding auxin/indole-3-acetic acid protein COS07g_00652 could enhance the flexibility and strength of the stem to improve fiber yield. Our study not only provides valuable genetic resources for future fiber breeding in jute, but also is of great significance for reviewing the genetic basis of early crop breeding.
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Affiliation(s)
- Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing, 100015, China
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiangkong Li
- Novogene Bioinformatics Institute, Beijing, 100015, China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - An Yan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 637616, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Zhong Chen
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 637616, Singapore
| | - Jiquan Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Canhui Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Ling Kang
- Novogene Bioinformatics Institute, Beijing, 100015, China
| | - Dongwei Xie
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Jian Zhao
- Novogene Bioinformatics Institute, Beijing, 100015, China
| | - Xiaojun Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Xiaoyu Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Yupeng Wu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Alei Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
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Fikri S, Lessard MH, Perreault V, Doyen A, Labrie S. Candida krusei is the major contaminant of ultrafiltration and reverse osmosis membranes used for cranberry juice production. Food Microbiol 2022; 109:104146. [DOI: 10.1016/j.fm.2022.104146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 10/14/2022]
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19
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Ghafari S, Lay EN, Garshasbi M. Development of a dimensionless and dynamic model of the three-phase trickle bed reactor in light naphtha isomerization process: effects of axial mass dispersion and liquid-solid mass transfer on isomers concentration. INTERNATIONAL JOURNAL OF CHEMICAL REACTOR ENGINEERING 2022. [DOI: 10.1515/ijcre-2021-0274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
This study develops a general dimensionless model for a three-phase trickle bed reactor in the light naphtha isomerization process. The simulations are accomplished to study its conduct. The model brings up a one-dimensional axial dispersed flow to characterize dispersity and liquid-solid mass transfer in the forms of dimensionless Peclet and mass Stanton numbers under adiabatic conditions. It considers the essential reactions extant in the isomerization process comprising isomerization, hydrogenation, and hydrocracking reactions applying a precise approach of dimensionless kinetic equations and rate constants. The Crank–Nicolson method and a nonstandard finite difference approach are utilized for large systems of time-spatial PDEs to resolve the dynamic reactor model with MATLAB software. The aim is to elucidate how these large systems of PDEs and nonlinear ODEs can be solved with a comprehensive computation in the form of physical dimensionless numbers. The isomers compositions estimated with the suggested model are in corroboration simulation results obtained by empirical information. The dynamics are evaluated to consider the system conduct with a variation in the hydrogen concentration of the feedstock.
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Affiliation(s)
- Sara Ghafari
- Department of Chemical Engineering , University of Kashan , Ravand Street, P.O. Box 87317-51167 , Kashan , Iran
| | - Ebrahim Nemati Lay
- Department of Chemical Engineering , University of Kashan , Ravand Street, P.O. Box 87317-51167 , Kashan , Iran
| | - Morteza Garshasbi
- Department of Applied Mathematics , School of Mathematics, Iran University of Science and Technology , P.O. Box 1684613114 , Tehran , Iran
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Lacticaseibacillus rhamnosus Fmb14 prevents purine induced hyperuricemia and alleviate renal fibrosis through gut-kidney axis. Pharmacol Res 2022; 182:106350. [PMID: 35843568 DOI: 10.1016/j.phrs.2022.106350] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 11/22/2022]
Abstract
Hyperuricemia is a critical threat to human health, and conventional medical treatment only aims to treat acute gouty arthritis. Purine diet-mediated chronic hyperuricemia and related syndromes are neglected in clinical therapeutics. In this study, the prevention ability of Lacticaseibacillus rhamnosus Fmb14, screened from Chinese yogurt, was evaluated in chronic purine-induced hyperuricemia (CPH) mice. After 12 weeks of Fmb14 administration, serum uric acid (SUA) in CPH mice decreased by 36.8 %, from 179.1 to 113.2 µmol/L, and the mortality rate decreased from 30 % to 10 %. The prevention role of Fmb14 in CPH was further investigated, and the reduction of uric acid by Fmb14 was attributed to the reduction of XOD (xanthine oxidase) in the liver and URAT1 in the kidney, as well the promotion of ABCG2 in the colon. Fmb14 administration Increased ZO-1 and Occludin expression in the colon and decreased fibrosis degree in the kidney indicated that Fmb14 administration had preventive effects through the gut-kidney axis in CPH. In specific, Fmb14 administration upregulated the diversity of gut microbiota, increased short-chain fatty acids (SCFA) by 35 % in colon materials and alleviated the inflammatory response by reducing biomarkers levels of IL-1β, IL-18 and TNF-α at 11.6 %, 21.7 % and 26.5 % in serum, compared to CPH group, respectively. Additionally, 16 S rRNA sequencing showed 31.5 % upregulation of Prevotella, 20.5 % and 21.6 % downregulation of Ruminococcus and Suterella at the genus level, which may be a new gut microbial marker in hyperuricemia. In conclusion, Fmb14 ameliorated CPH through the gut-kidney axis, suggesting a new strategy to prevent hyperuricemia.
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21
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Molecular epidemiology, antifungal susceptibility, and ERG11 gene mutation of candida species isolated from vulvovaginal candidiasis: Comparison between recurrent and non-recurrent infections. Microb Pathog 2022; 170:105696. [DOI: 10.1016/j.micpath.2022.105696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022]
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22
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Sponge–Microbial Symbiosis and Marine Extremozymes: Current Issues and Prospects. SUSTAINABILITY 2022. [DOI: 10.3390/su14126984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Marine microorganisms have great potential for producing extremozymes. They enter useful relationships like many other organisms in the marine habitat. Sponge–microbial symbiosis enables both sponges and microorganisms to mutually benefit each other while performing their activities within the ecosystem. Sponges, because of their nature as marine cosmopolitan benthic epifaunas and filter feeders, serve as a host for many extremophilic marine microorganisms. Potential extremozymes from microbial symbionts are largely dependent on their successful relationship. Extremozymes have found relevance in food processing, bioremediation, detergent, and drug production. Species diversity approach, industrial-scale bioremediation, integrative bioremediation software, government and industrial support are considered. The high cost of sampling, limited research outcomes, low species growth in synthetic media, laborious nature of metagenomics projects, difficulty in the development of synthetic medium, limited number of available experts, and technological knowhow are current challenges. The unique properties of marine extremozymes underpin their application in industry and biotechnological processes. There is therefore an urgent need for the development of cost-effective methods with government and industry support.
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Miles S, Mourglia-Ettlin G, Fernández V. Expanding the family of Mu-class glutathione transferases in the cestode parasite Echinococcus granulosus sensu lato. Gene 2022; 835:146659. [PMID: 35680021 DOI: 10.1016/j.gene.2022.146659] [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: 04/21/2022] [Accepted: 06/02/2022] [Indexed: 11/04/2022]
Abstract
Glutathione transferases (GSTs) perform catalytic and non-catalytic activities, mostly involved in stress-response and cell detoxification. Helminth parasites express several GSTs of multiple classes that are involved in the neutralization of potentially harmful oxidants, and in the inactivation or removal of xenobiotics. Additionally, GSTs participate in immunomodulatory processes that facilitate the parasite establishment and survival within its host. In Echinococcus granulosus sensu lato (s.l.) -the cestode parasite responsible for cystic echinococcosis- only one Mu-class GST has been reported. In the present work, by using bioinformatic and proteomic approaches we searched for novel Mu-class GSTs potentially involved in the parasite oxidative-stress metabolism. In the genome of E. granulosus s.l., 6 GST-related sequences were found to constitute a strongly conserved phylogenetical clade with Mu-class members. Among them, 5 displayed conserved gene structure (exon/intron), as well as specific residues and motifs characteristic of Mu-class enzymes. By proteomic analysis, 3 Mu-GSTs were identified to be expressed in the protoscolex parasite stage, 2 of them being firstly described as Mu-class GSTs here. The existence of more than one productive Mu-GST gene expands the parasite xenobiotic phase II metabolism, which might have beneficial roles on E. granulosus s.l. ability to successfully infect its host.
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Affiliation(s)
- Sebastian Miles
- Área Inmunología, Departamento de Biociencias, Facultad de Química - Instituto de Higiene, Universidad de la República, Montevideo, Uruguay; Graduate Program in Chemistry, Facultad de Química, Universidad de la República, Uruguay
| | - Gustavo Mourglia-Ettlin
- Área Inmunología, Departamento de Biociencias, Facultad de Química - Instituto de Higiene, Universidad de la República, Montevideo, Uruguay
| | - Verónica Fernández
- Área Inmunología, Departamento de Biociencias, Facultad de Química - Instituto de Higiene, Universidad de la República, Montevideo, Uruguay.
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24
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Stimulatory Effects of Extracellular Vesicles Derived from Leuconostoc holzapfelii That Exists in Human Scalp on Hair Growth in Human Follicle Dermal Papilla Cells. Curr Issues Mol Biol 2022; 44:845-866. [PMID: 35723343 PMCID: PMC8929027 DOI: 10.3390/cimb44020058] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/18/2022] [Accepted: 01/25/2022] [Indexed: 12/24/2022] Open
Abstract
Human hair follicle dermal papilla cells (HFDPCs) located in hair follicles (HFs) play a pivotal role in hair follicle morphogenesis, hair cycling, and hair growth. Over the past few decades, probiotic bacteria (PB) have been reported to have beneficial effects such as improved skin health, anti-obesity, and immuno-modulation for conditions including atopic dermatitis and inflammatory bowel disease (IBD). PB can secrete 50~150 nm sized extracellular vesicles (EVs) containing microbial DNA, miRNA, proteins, lipids, and cell wall components. These EVs can regulate communication between bacteria or between bacteria and their host. Although numerous biological effects of PB-EVs have been reported, the physiological roles of Leuconostoc holzapfelii (hs-Lh), which is isolated from human scalp tissue, and the extracellular vesicles derived from them (hs-LhEVs) are largely unknown. Herein, we investigated the effects of hs-LhEVs on hair growth in HFDPCs. We show that hs-LhEVs increase cell proliferation, migration, and regulate the cell cycle. Furthermore, hs-LhEVs were found to modulate the mRNA expression of hair-growth-related genes in vitro. These data demonstrate that hs-LhEVs can reduce apoptosis by modulating the cell cycle and promote hair growth by regulation via the Wnt/β-catenin signal transduction pathway.
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Effect of Different Initial Fermentation pH on Exopolysaccharides Produced by Pseudoalteromonas agarivorans Hao 2018 and Identification of Key Genes Involved in Exopolysaccharide Synthesis via Transcriptome Analysis. Mar Drugs 2022; 20:md20020089. [PMID: 35200619 PMCID: PMC8877158 DOI: 10.3390/md20020089] [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: 11/29/2021] [Revised: 12/15/2021] [Accepted: 01/17/2022] [Indexed: 01/07/2023] Open
Abstract
Exopolysaccharides (EPSs) are carbohydrate polymers produced and secreted by microorganisms. In a changing marine environment, EPS secretion can reduce damage from external environmental disturbances to microorganisms. Meanwhile, EPSs have promising application prospects in the fields of food, cosmetics, and pharmaceuticals. Changes in external environmental pH have been shown to affect the synthesis of EPSs in microorganisms. In this study, we analyzed the effects of different initial fermentation pHs on the production, monosaccharide composition, and antioxidant activity of the EPSs of Pseudoalteromonas agarivorans Hao 2018. In addition, the transcriptome sequence of P. agarivorans Hao 2018 under different initial fermentation pH levels was determined. GO and KEGG analyses showed that the differentially expressed genes were concentrated in the two-component regulatory system and bacterial chemotaxis pathways. We further identified the expression of key genes involved in EPS synthesis during pH changes. In particular, the expression of genes encoding the glucose/galactose MFS transporter, phosphomannomutase, and mannose-1-phosphate guanylyltransferase was upregulated when the environmental pH increased, thus promoting EPS synthesis. This study not only contributes to elucidating the environmental adaptation mechanisms of P. agarivorans, but also provides important theoretical guidance for the directed development of new products using biologically active polysaccharides.
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Abstract
Over the past three decades, computational capabilities have grown at such a rapid rate that they have given rise to many computationally heavy science fields such as phylogenomics. As increasingly more genomes are sequenced in the three domains of life, larger and more species-complete phylogenetic tree reconstructions are leading to a better understanding of the tree of life and the evolutionary histories in deep times. However, these large datasets pose unique challenges from a modeling and computational perspective: accurately describing the evolutionary process of thousands of species is still beyond the capability of current models, while the computational burden limits our ability to test multiple hypotheses. Thus, it is common practice to reduce the size of a dataset by selecting species to represent a clade (taxon sampling). Unfortunately, this process is subjective, and comparisons of large tree of life studies show that choice and number of species used in a dataset can alter the topology obtained. Thus, taxon sampling is, in itself, a process that needs to be fully investigated to determine its effect on phylogenetic stability. Here, we present the theory and practical application of an automated pipeline that can be easily implemented to explore the effect of taxon sampling on phylogenetic reconstructions. The application of this approach was recently discussed in a study of Terrabacteria and shows its power in investigating the accuracy of deep nodes of a phylogeny.
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Affiliation(s)
| | - Fabia Ursula Battistuzzi
- Department of Biological Sciences, Oakland University, Rochester, MI, USA.
- Center for Data Science and Big Data Analytics, Oakland University, Rochester, MI, USA.
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27
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Dziech A. Identification of Wolf-Dog Hybrids in Europe – An Overview of Genetic Studies. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.760160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Significant development of genetic tools during the last decades provided opportunities for more detailed analyses and deeper understanding of species hybridization. New genetic markers allowed for reliable identification of admixed individuals deriving from recent hybridization events (a few generations) and those originating from crossings up to 19 generations back. Implementation of microsatellites (STRs) together with Bayesian clustering provided abundant knowledge regarding presence of admixed individuals in numerous populations and helped understand the problematic nature of studying hybridization (i.a., defining a reliable thresholds for recognizing individuals as admixed or obtaining well-grounded results representing actual proportion of hybrids in a population). Nevertheless, their utilization is limited to recent crossbreeding events. Single Nucleotide Polymorphisms (SNPs) proved to be more sensible tools for admixture analyses furnishing more reliable knowledge, especially for older generation backcrosses. Small sets of Ancestry Informative Markers (AIMs) of both types of markers were effective enough to implement in monitoring programs, however, SNPs seem to be more appropriate because of their ability to identify admixed individuals up to 3rd generations. The main aim of this review is to summarize abundant knowledge regarding identification of wolf-dog hybrids in Europe and discuss the most relevant problems relating to the issue, together with advantages and disadvantages of implemented markers and approaches.
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Keita A, Rigaill J, Pillet S, Sereme Y, Coulibaly S, Diallo F, Verhoeven P, Pozzetto B, Thiero TA, Bourlet T. Evidence of HIV-1 Genital Shedding after One Year of Antiretroviral Therapy in Females Recently Diagnosed in Bamako, Mali. Microorganisms 2021; 9:microorganisms9102164. [PMID: 34683485 PMCID: PMC8538623 DOI: 10.3390/microorganisms9102164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 11/22/2022] Open
Abstract
Little is known about the dynamic of HIV-1 shedding and resistance profiles in the female genital reservoir after antiretroviral therapy (ART) initiation in resource-limited countries (RLCs), which is critical for evaluating the residual sexual HIV-1 transmission risk. The present study aimed to evaluate the efficacy of 1 year duration ART at blood and genital levels in females newly diagnosed for HIV-1 from three centers in Bamako, Mali. Seventy-eight consenting females were enrolled at the time of their HIV-1 infection diagnosis. HIV-1 RNA loads (Abbott Real-Time HIV-1 assay) were tested in blood and cervicovaginal fluids (CVF) before and 12 months after ART initiation. Primary and acquired resistances to ART were evaluated by ViroseqTM HIV-1 genotyping assay. The vaginal microbiota was analyzed using IonTorrentTM NGS technology (Thermo Fisher Scientific). Proportions of primary drug resistance mutations in blood and CVF were 13.4% and 25%, respectively. Discrepant profiles were observed in 25% of paired blood/CVF samples. The acquired resistance rate was 3.1% in blood. At month 12, undetectable HIV-1 RNA load was reached in 84.6% and 75% of blood and CVF samples, respectively. A vaginal dysbiosis was associated with HIV RNA shedding. Our findings emphasize the need of reinforcing education to improve retention in care system, as well as the necessity of regular virological monitoring before and during ART and of implementing vaginal dysbiosis diagnosis and treatment in RLCs.
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Affiliation(s)
- Abdelaye Keita
- Département Qualité Sécurité et Sûreté Biologique, Institut National de Recherche en Santé Publique (INRSP), Bamako BP 1771, Mali; (A.K.); (S.C.); (T.A.T.)
- GIMAP Team 15, Inserm, U1111, CNRS, UMR5308, Centre International de Recherche en Infectiologie, Faculty of Medicine, University of Lyon 1, 42000 Saint-Etienne, France; (J.R.); (S.P.); (Y.S.); (P.V.); (B.P.)
| | - Josselin Rigaill
- GIMAP Team 15, Inserm, U1111, CNRS, UMR5308, Centre International de Recherche en Infectiologie, Faculty of Medicine, University of Lyon 1, 42000 Saint-Etienne, France; (J.R.); (S.P.); (Y.S.); (P.V.); (B.P.)
- Laboratoire des Agents Infectieux et d’Hygiène, Biology Pathology Department, University Hospital of Saint-Etienne, 42000 Saint-Etienne, France
| | - Sylvie Pillet
- GIMAP Team 15, Inserm, U1111, CNRS, UMR5308, Centre International de Recherche en Infectiologie, Faculty of Medicine, University of Lyon 1, 42000 Saint-Etienne, France; (J.R.); (S.P.); (Y.S.); (P.V.); (B.P.)
- Laboratoire des Agents Infectieux et d’Hygiène, Biology Pathology Department, University Hospital of Saint-Etienne, 42000 Saint-Etienne, France
| | - Youssouf Sereme
- GIMAP Team 15, Inserm, U1111, CNRS, UMR5308, Centre International de Recherche en Infectiologie, Faculty of Medicine, University of Lyon 1, 42000 Saint-Etienne, France; (J.R.); (S.P.); (Y.S.); (P.V.); (B.P.)
| | - Souleymane Coulibaly
- Département Qualité Sécurité et Sûreté Biologique, Institut National de Recherche en Santé Publique (INRSP), Bamako BP 1771, Mali; (A.K.); (S.C.); (T.A.T.)
| | - Fodé Diallo
- Centre d’Ecoute de Soins et d’Accompagnement (CESAC), ARCAD/SIDA Clinic, Bamako BPE 2561, Mali;
| | - Paul Verhoeven
- GIMAP Team 15, Inserm, U1111, CNRS, UMR5308, Centre International de Recherche en Infectiologie, Faculty of Medicine, University of Lyon 1, 42000 Saint-Etienne, France; (J.R.); (S.P.); (Y.S.); (P.V.); (B.P.)
- Laboratoire des Agents Infectieux et d’Hygiène, Biology Pathology Department, University Hospital of Saint-Etienne, 42000 Saint-Etienne, France
| | - Bruno Pozzetto
- GIMAP Team 15, Inserm, U1111, CNRS, UMR5308, Centre International de Recherche en Infectiologie, Faculty of Medicine, University of Lyon 1, 42000 Saint-Etienne, France; (J.R.); (S.P.); (Y.S.); (P.V.); (B.P.)
- Laboratoire des Agents Infectieux et d’Hygiène, Biology Pathology Department, University Hospital of Saint-Etienne, 42000 Saint-Etienne, France
| | - Tenin Aoua Thiero
- Département Qualité Sécurité et Sûreté Biologique, Institut National de Recherche en Santé Publique (INRSP), Bamako BP 1771, Mali; (A.K.); (S.C.); (T.A.T.)
| | - Thomas Bourlet
- GIMAP Team 15, Inserm, U1111, CNRS, UMR5308, Centre International de Recherche en Infectiologie, Faculty of Medicine, University of Lyon 1, 42000 Saint-Etienne, France; (J.R.); (S.P.); (Y.S.); (P.V.); (B.P.)
- Laboratoire des Agents Infectieux et d’Hygiène, Biology Pathology Department, University Hospital of Saint-Etienne, 42000 Saint-Etienne, France
- Correspondence: ; Tel.: +33-4-7782-8106
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Kim DH, Lee J, Rhee J, Lee JY, Lim SH. Loss of the R2R3 MYB Transcription Factor RsMYB1 Shapes Anthocyanin Biosynthesis and Accumulation in Raphanus sativus. Int J Mol Sci 2021; 22:10927. [PMID: 34681588 PMCID: PMC8535906 DOI: 10.3390/ijms222010927] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/03/2021] [Accepted: 10/04/2021] [Indexed: 11/26/2022] Open
Abstract
The red or purple color of radish (Raphanus sativus L.) taproots is due to anthocyanins, which have nutritional and aesthetic value, as well as antioxidant properties. Moreover, the varied patterns and levels of anthocyanin accumulation in radish roots make them an interesting system for studying the transcriptional regulation of anthocyanin biosynthesis. The R2R3 MYB transcription factor RsMYB1 is a key positive regulator of anthocyanin biosynthesis in radish. Here, we isolated an allele of RsMYB1, named RsMYB1Short, in radish cultivars with white taproots. The RsMYB1Short allele carried a 4 bp insertion in the first exon causing a frame-shift mutation of RsMYB1, generating a truncated protein with only a partial R2 domain at the N-terminus. Unlike RsMYB1Full, RsMYB1Short was localized to the nucleus and the cytoplasm and failed to interact with their cognate partner RsTT8. Transient expression of genomic or cDNA sequences for RsMYB1Short in radish cotyledons failed to induce anthocyanin accumulation, but that for RsMYB1Full activated it. Additionally, RsMYB1Short showed the lost ability to induce pigment accumulation and to enhance the transcript level of anthocyanin biosynthetic genes, while RsMYB1Full promoted both processes when co-expressed with RsTT8 in tobacco leaves. As the result of the transient assay, co-expressing RsTT8 and RsMYB1Full, but not RsMYB1Short, also enhanced the promoter activity of RsCHS and RsDFR. We designed a molecular marker for RsMYB1 genotyping, and revealed that the RsMYB1Short allele is common in white radish cultivars, underscoring the importance of variation at the RsMYB1 locus in anthocyanin biosynthesis in the radish taproot. Together, these results indicate that the nonsense mutation of RsMYB1 generated the truncated protein, RsMYB1Short, that had the loss of ability to regulate anthocyanin biosynthesis. Our findings highlight that the frame shift mutation of RsMYB1 plays a key role in anthocyanin biosynthesis in the radish taproot.
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Affiliation(s)
- Da-Hye Kim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong 17579, Korea;
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea;
| | - Jundae Lee
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea;
| | - JuHee Rhee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea;
| | - Jong-Yeol Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea;
| | - Sun-Hyung Lim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong 17579, Korea;
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30
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Al-Rowaily SL, Alghamdi AO, Alghamdi SS, Assaeed AM, Hegazy A, Afzal M, Migdadi HM. Assessment of morphological and molecular variability of some Solanum melongena L. cultivars and wild Solanum incanum L. in Saudi Arabia. Biol Futur 2021; 72:187-199. [PMID: 34554472 DOI: 10.1007/s42977-020-00052-2] [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: 03/02/2020] [Accepted: 11/23/2020] [Indexed: 10/22/2022]
Abstract
The genus Solanum exhibits a wide range of variability in morphology, flavor, and tolerance to biotic and abiotic stresses. Phenotypic and genetic variability using ISSR and RAPD markers of Solanum incanum distributed in Al-Baha province of the Kingdom of Saudi Arabia is assessed. Thirty samples are representing three different locations: Baljershy, Aqeeq, and Tohama, besides twenty-five samples representing five different commercial cultivars tested. Growth type, the number of leaves per plant, fruit size (phenotypic traits), crude protein, carbohydrates, digestive organic matter, and Mg, Ca, P were the principal contributors in the PCA. Molecular analysis showed that 114 ISSR and 80 RAPD alleles with a 100% polymorphism were recorded. The polymorphism information content (PIC) values ranged from 0.84 to 0.91 for ISSR and from 0.59 to 0.89 for RAPD data. Similarity values ranged from 0.16 to 1.00, with an average of 0.47 for ISSR and from 0.01 to 0.97, with an average of 0.36 for RAPD. It resulted in a positive and significant correlation between morphological, molecular, nutritional, and chemical analysis of fruits using Mantel analysis. UPGMA and PCA for morphological traits and molecular data discriminated commercial cultivars and wild relatives. Solanum incanum was more diverse than commercial varieties. This study revealed a wide genetic diversity among and within collected eggplant accessions and may use in breeding programs of eggplants. There is a need to increase the present eggplant collection to widen the genetic diversity of cultivated eggplant varieties in Saudi Arabia.
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Affiliation(s)
- Saud L Al-Rowaily
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Abdullah O Alghamdi
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Salem S Alghamdi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Abdulaziz M Assaeed
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Ahmad Hegazy
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Muhammad Afzal
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Hussein M Migdadi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia. .,National Agricultural Research Centre, P. O Box: 639, Baq'a, 19381, Jordan.
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Dong W, Wu D, Yan C, Wu D. Mapping and Analysis of a Novel Genic Male Sterility Gene in Watermelon ( Citrullus lanatus). FRONTIERS IN PLANT SCIENCE 2021; 12:639431. [PMID: 34539684 PMCID: PMC8442748 DOI: 10.3389/fpls.2021.639431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/19/2021] [Indexed: 05/15/2023]
Abstract
Seed production is critical for watermelon production, which mostly involves first-generation hybrid varieties. However, watermelon hybrid seed production currently requires complex procedures, including artificial isolation and pollination. Therefore, the development and use of a male-sterile system to generate watermelon hybrids can simplify the process. The scarcity of male-sterile watermelon germplasm resources necessitates the use of molecular breeding methods. Unfortunately, the genes responsible for male sterility in watermelon have not been cloned. Thus, the genetic basis of the male sterility remains unknown. In this study, two DNA pools derived from male-sterile and normal plants in the F2 population were used for whole-genome resequencing. The Illumina high-throughput sequencing resulted in 62.99 Gbp clean reads, with a Q30 of 80% after filtering. On the basis of the SNP index association algorithm, eight candidate regions (0.32 Mb) related to specific traits were detected on chromosome 6. Expression pattern analyses and watermelon transformation studies generated preliminary evidence that Cla006625 encodes a pollen-specific leucine-rich repeat protein (ClaPEX1) influencing the male sterility of watermelon. The identification and use of genic male sterility genes will promote watermelon male sterility research and lay the foundation for the efficient application of seed production technology.
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Affiliation(s)
- Wei Dong
- School of Life Science, Henan University, Kaifeng, China
| | - Dewei Wu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, China
| | - Chen Yan
- School of Life Science, Henan University, Kaifeng, China
| | - Defeng Wu
- School of Life Science, Henan University, Kaifeng, China
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32
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Gracy Jenifer S, Marimuthu G, Raghuram H. Isolation and characterization of chitinolytic bacterium, Escherichia fergusonii AMC01 from insectivorous bat, Taphozous melanopogon. J Basic Microbiol 2021; 61:940-946. [PMID: 34398462 DOI: 10.1002/jobm.202100271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/17/2021] [Accepted: 08/07/2021] [Indexed: 11/12/2022]
Abstract
Chitinases are capable of hydrolyzing insoluble chitin into its oligo and monomeric parts and have received increased consideration because of their wide scope of biotechnological applications. The commercial application of microbial chitinase is appealing due to the relative ease of enormous production and to meet the current world demands. This study aimed at isolation and characterization of chitin degrading bacteria from the gut of Indian tropical insectivorous black-bearded tomb bat, Taphozous melanopogon. The isolated bacterial strains were characterized through biochemical analysis and nucleic acid-based approaches by 16S ribosomal RNA amplification and sequencing. The BLAST (Basic Local Alignment Search Tool) and phylogenetic analysis showed that the bacterial strain exhibited a close resemblance with Escherichia fergusonii. The chitinolytic activity of the E. fergusonii AMC01 was identified using supplemented colloidal chitin with agar medium. Compiling all, these findings would facilitate in constructing a database and presumably promote the use of E. fergusonii AMC01 as an efficient strain for the chitinase production.
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Affiliation(s)
| | - Ganapathy Marimuthu
- Department of Animal Behaviour and Physiology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Hanumanthan Raghuram
- PG and Research Department of Zoology, The American College, Madurai, Tamil Nadu, India
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Salehi Z, Shams-Ghahfarokhi M, Razzaghi-Abyaneh M. Molecular Epidemiology, Genetic Diversity, and Antifungal Susceptibility of Major Pathogenic Dermatophytes Isolated From Human Dermatophytosis. Front Microbiol 2021; 12:643509. [PMID: 34149634 PMCID: PMC8213211 DOI: 10.3389/fmicb.2021.643509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/19/2021] [Indexed: 12/16/2022] Open
Abstract
Background Dermatophytes are a homogeneous group of species with low genetic diversity, and there are still many uncertainties about the boundaries among species. Objectives Aiming at clarifying the relationships among species in the genus and introducing suitable genes for multilocus sequence typing (MLST), a new MLST scheme approach was developed to characterize the major pathogenic dermatophytes. Methods We performed maximum parsimony (MP), MrBayes, RAxML, and eBURST analyses, based on the MLST scheme to scrutinize the evolution within 95 clinical isolates and four reference strains belonging to the four major dermatophytes species. Then, the discriminatory power, pairwise genetic distances, ratio dN/dS, and sequence types (STs) of these isolates were determined. Also, to study taxonomy, sequences of the internal transcribed spacer (ITS), Beta-tubulin (BT2), and translation elongation factor 1-α (TEF-1α) genes of other dermatophytes species available in the GenBank were analyzed. Results Findings of the present study indicated that three genes: BT2, ITS, and TEF−1α, which showed the greatest diversity among dermatophyte species, were suitable for MLST. The most prevalent STs were seen among the species of Trichophyton interdigitale. Also, two new genotypes, i.e., XXVII and XXVIII, were introduced for T. interdigitale and Trichophyton mentagrophytes. The least informative sites were found in Epidermophyton floccosum, Trichophyton rubrum, and T. mentagrophytes, while the most informative sites were observed in T. interdigitale. Furthermore, the most informative locus was TEF-1α. The phylogenetic tree, constructed by the combination of the three genes, shows a new topological pattern that confirms the derivation of the anthropophilic and zoophilic genera from the geophilic genus. Also, the phylogenetic analyses and pairwise distances of the combination of the three loci showed that Trichophyton tonsurans and Trichophyton equinum were a species complex, where T. equinum is derived from T. tonsurans. Conclusions Results of this study showed that MLST is very effective in determining the boundaries between species and taxonomy. Considering that there is no database for MLST dermatophytes, further studies are needed to determine the suitable genes for MLST. Also, the determination of STs in epidemiological studies and raising epidemiological information are helpful. This study was a new starting point to determine the ST and a foundation for a dermatophyte MLST database.
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Affiliation(s)
- Zahra Salehi
- Department of Mycology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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SPATS1 (spermatogenesis-associated, serine-rich 1) is not essential for spermatogenesis and fertility in mouse. PLoS One 2021; 16:e0251028. [PMID: 33945571 PMCID: PMC8096103 DOI: 10.1371/journal.pone.0251028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/19/2021] [Indexed: 12/20/2022] Open
Abstract
SPATS1 (spermatogenesis-associated, serine-rich 1) is an evolutionarily conserved, testis-specific protein that is differentially expressed during rat male meiotic prophase. Some reports have suggested a link between SPATS1 underexpression/mutation and human pathologies such as male infertility and testicular cancer. Given the absence of functional studies, we generated a Spats1 loss-of-function mouse model using CRISPR/Cas9 technology. The phenotypic analysis showed no overt phenotype in Spats1-/- mice, with both males and females being fertile. Flow cytometry and histological analyses did not show differences in the testicular content and histology between WT and knockout mice. Moreover, no significant differences in sperm concentration, motility, and morphology, were observed between WT and KO mice. These results were obtained both for young adults and for aged animals. Besides, although an involvement of SPATS1 in the Wnt signaling pathway has been suggested, we did not detect changes in the expression levels of typical Wnt pathway-target genes in mutant individuals. Thus, albeit Spats1 alteration might be a risk factor for male testicular health, we hereby show that this gene is not individually essential for male fertility and spermatogenesis in mouse.
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Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol 2021; 38:3022-3027. [PMID: 33892491 PMCID: PMC8233496 DOI: 10.1093/molbev/msab120] [Citation(s) in RCA: 5925] [Impact Index Per Article: 1975.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/20/2021] [Indexed: 12/11/2022] Open
Abstract
The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. They are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. Also added is a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled graphical user interface and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.
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Affiliation(s)
- Koichiro Tamura
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan.,Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan
| | - Glen Stecher
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Department of Biology, Temple University, Philadelphia, PA, USA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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Adhiambo M, Makwaga O, Adungo F, Kimani H, Mulama DH, Korir JC, Mwau M. Human immunodeficiency virus (HIV) type 1 genetic diversity in HIV positive individuals on antiretroviral therapy in a cross-sectional study conducted in Teso, Western Kenya. Pan Afr Med J 2021; 38:335. [PMID: 34046145 PMCID: PMC8140725 DOI: 10.11604/pamj.2021.38.335.26357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 04/01/2021] [Indexed: 11/16/2022] Open
Abstract
Introduction high HIV-1 infection rates and genetic diversity especially in African population pose significant challenges in HIV-1 clinical management and drug design and development. HIV-1 is a major health challenge in Kenya and causes mortality and morbidity in the country as well as straining the healthcare system and the economy. This study sought to identify HIV-1 genetic subtypes circulating in Teso, Western Kenya which borders the Republic of Uganda. Methods a cross-sectional study was conducted in January 2019 to December 2019. Sequencing of the partial pol gene was carried out on 80 HIV positive individuals on antiretroviral therapy. Subtypes and recombinant forms were generated using the jumping profile hidden Markov model. Alignment of the sequences was done using ClustalW program and phylogenetic tree constructed using MEGA7 neighbor-joining method. Results sixty three samples were successful sequenced. In the analysis of these sequences, it was observed that HIV-1 subtype A1 was predominant 43 (68.3%) followed by D 8 (12.7%) and 1 (1.6%) each of C, G and B and inter-subtype recombinants A1-D 3 (4.8%), A1-B 2 (3.2%) and 1 (1.6%) each of A1-A2, A1-C, BC and BD. Phylogenetic analysis of these sequences showed close clustering of closely related and unrelated sequences with reference sequences. Conclusion there was observed increased genetic diversity of HIV-1 subtypes which not only pose a challenge in disease control and management but also drug design and development. Therefore, there is need for continued surveillance to enhance future understanding of the geographical distribution and transmission patterns of the HIV epidemic.
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Affiliation(s)
- Maureen Adhiambo
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya.,Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Olipher Makwaga
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya.,Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Ferdinard Adungo
- Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Humphrey Kimani
- Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - David Hughes Mulama
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Jackson Cheruiyot Korir
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Matilu Mwau
- Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
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Guo Y, Peng D, Han L, Liu T, Li G, Garber PA, Zhou J. Mitochondrial DNA control region sequencing of the critically endangered Hainan gibbon ( Nomascus hainanus) reveals two female origins and extremely low genetic diversity. Mitochondrial DNA B Resour 2021; 6:1355-1359. [PMID: 33889748 PMCID: PMC8032330 DOI: 10.1080/23802359.2021.1909432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/22/2021] [Indexed: 11/25/2022] Open
Abstract
The Hainan gibbon (Nomascus hainanus) is endemic to China and is the world's rarest ape. The remaining wild population totals only 33 individuals. In the current study, we sequenced the Mitochondrial DNA control region of 12 wild Hainan gibbons representing three social groups of the five remaining groups. By conducting population genetic analyses, we found that the proportion of four nucleotides (T, C, A and G) were 29.0%, 27.2%, 31.9% and 11.9%, respectively. Hypervariable segments of the mtDNA D-loop region (1005 bp in length), indicated five variable sites (a point mutation), with only two haplotypes present among the 12 samples. We observed that the genetic diversity of Hainan gibbons is lower than that reported in any other wild primate population, and that the two haplotypes detected, represent two ancestral lineages. These findings have important implications for proposing effective conservation strategies to protect this Critically Endangered ape species.
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Affiliation(s)
- Yanqing Guo
- College of Life Sciences, Northwest University, Xian, China
| | - Dong Peng
- School of Karst Science, Guizhou Normal University, Guiyang, China
| | - Ling Han
- School of Karst Science, Guizhou Normal University, Guiyang, China
| | - Tao Liu
- School of Karst Science, Guizhou Normal University, Guiyang, China
| | - Gang Li
- School of Karst Science, Guizhou Normal University, Guiyang, China
| | - Paul A. Garber
- Department of Anthropology, Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, USA
- International Centre of Biodiversity and Primate Conservation, Dali University, Dali, Yunnan, China
| | - Jiang Zhou
- College of Life Sciences, Northwest University, Xian, China
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Kim SJ, Kim C, Chung HC, Park YH, Park KT. Full-length ORF2 sequence-based genetic and phylogenetic characterization of Korean feline caliciviruses. J Vet Sci 2021; 22:e32. [PMID: 33908206 PMCID: PMC8170210 DOI: 10.4142/jvs.2021.22.e32] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/08/2021] [Accepted: 02/21/2021] [Indexed: 11/20/2022] Open
Abstract
Feline calicivirus (FCV) is a highly infectious pathogen in cats and widely distributed worldwide with high genetic variation. Full-length open reading frame 2 of 5 from recently isolated Korean FCV isolates were sequenced and compared with those of global isolates. The results of phylogenetic analysis supported dividing global FCV isolates into two genogroups (type I and II) and demonstrated the presence of genogroup II in Korea, indicating their geographic spread in East Asia. High sequence variations in region E of the FCV isolates emphasizes that a novel vaccine needs to be developed to induce protective immunity against various FCV strains.
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Affiliation(s)
- Sung Jae Kim
- Department of Veterinary Microbiology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Cheongung Kim
- Department of Veterinary Microbiology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Hee Chun Chung
- Department of Veterinary Microbiology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Yong Ho Park
- Department of Veterinary Microbiology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Kun Taek Park
- Department of Biotechnology, Inje University, Gimhae 50834, Korea.
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Lim SH, Kim DH, Jung JA, Lee JY. Alternative Splicing of the Basic Helix-Loop-Helix Transcription Factor Gene CmbHLH2 Affects Anthocyanin Biosynthesis in Ray Florets of Chrysanthemum ( Chrysanthemum morifolium). FRONTIERS IN PLANT SCIENCE 2021; 12:669315. [PMID: 34177983 PMCID: PMC8222801 DOI: 10.3389/fpls.2021.669315] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/17/2021] [Indexed: 05/19/2023]
Abstract
Chrysanthemum is an important ornamental crop worldwide. Some white-flowered chrysanthemum cultivars produce red ray florets under natural cultivation conditions, but little is known about how this occurs. We compared the expression of anthocyanin biosynthetic and transcription factor genes between white ray florets and those that turned red based on cultivation conditions to comprehend the underlying mechanism. Significant differences in the expression of CmbHLH2 were detected between the florets of different colors. CmbHLH2 generated two alternatively spliced transcripts, designated CmbHLH2Full and CmbHLH2Short . Compared with CmbHLH2Full , CmbHLH2Short encoded a truncated protein with only a partial MYB-interaction region and no other domains normally present in the full-length protein. Unlike the full-length form, the splicing variant protein CmbHLH2Short localized to the cytoplasm and the nucleus and could not interact with CmMYB6. Additionally, CmbHLH2Short failed to activate anthocyanin biosynthetic genes and induce pigment accumulation in transiently transfected tobacco leaves, whereas CmbHLH2Full promoted both processes when simultaneously expressed with CmMYB6. Co-expressing CmbHLH2Full and CmMYB6 also enhanced the promoter activities of CmCHS and CmDFR. Notably, the Arabidopsis tt8-1 mutant, which lacks red pigmentation in the leaves and seeds, could be complemented by the heterologous expression of CmbHLH2Full, which restored red pigmentation and resulted in red pigmentation in high anthocyanin and proanthocyanidin contents in the leaves and seeds, respectively, whereas expression of CmbHLH2Short did not. Together, these results indicate that CmbHLH2 and CmMYB6 interaction plays a key role in the anthocyanin pigmentation changes of ray florets in chrysanthemum. Our findings highlight alternative splicing as a potential approach to modulate anthocyanin biosynthesis in specific tissues.
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Affiliation(s)
- Sun-Hyung Lim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong, South Korea
- *Correspondence: Sun-Hyung Lim,
| | - Da-Hye Kim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong, South Korea
- National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Jae-A. Jung
- Floriculture Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju, South Korea
| | - Jong-Yeol Lee
- National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea
- Jong-Yeol Lee,
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Zhang D, Li W, Chen ZJ, Wei FG, Liu YL, Gao LZ. SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng. Sci Rep 2020; 10:15310. [PMID: 32943706 PMCID: PMC7499265 DOI: 10.1038/s41598-020-72291-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/19/2020] [Indexed: 02/08/2023] Open
Abstract
Panax notoginseng is one of the most widely used traditional Chinese herbs with particularly valued roots. Triterpenoid saponins are mainly specialized secondary metabolites, which medically act as bioactive components. Knowledge of the ginsenoside biosynthesis in P. notoginseng, which is of great importance in the industrial biosynthesis and genetic breeding program, remains largely undetermined. Here we combined single molecular real time (SMRT) and Second-Generation Sequencing (SGS) technologies to generate a widespread transcriptome atlas of P. notoginseng. We mapped 2,383 full-length non-chimeric (FLNC) reads to adjacently annotated genes, corrected 1,925 mis-annotated genes and merged into 927 new genes. We identified 8,111 novel transcript isoforms that have improved the annotation of the current genome assembly, of which we found 2,664 novel lncRNAs. We characterized more alternative splicing (AS) events from SMRT reads (20,015 AS in 6,324 genes) than Illumina reads (18,498 AS in 9,550 genes), which contained a number of AS events associated with the ginsenoside biosynthesis. The comprehensive transcriptome landscape reveals that the ginsenoside biosynthesis predominantly occurs in flowers compared to leaves and roots, substantiated by levels of gene expression, which is supported by tissue-specific abundance of isoforms in flowers compared to roots and rhizomes. Comparative metabolic analyses further show that a total of 17 characteristic ginsenosides increasingly accumulated, and roots contained the most ginsenosides with variable contents, which are extraordinarily abundant in roots of the three-year old plants. We observed that roots were rich in protopanaxatriol- and protopanaxadiol-type saponins, whereas protopanaxadiol-type saponins predominated in aerial parts (leaves, stems and flowers). The obtained results will greatly enhance our understanding about the ginsenoside biosynthetic machinery in the genus Panax.
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Affiliation(s)
- Dan Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - Zhong-Jian Chen
- Wenshan Sanqi Institute of Science and Technology, Wenshan University, Wenshan, 663000, China
| | - Fu-Gang Wei
- Wenshan Miaoxiang Notoginseng Industral Co., LTD, Wenshan, 663000, China
| | - Yun-Long Liu
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650204, China
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China. .,Plant Germplasm and Genomics Center, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650204, China.
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Mokhtarian K, Falak R, Heidari Z. Evaluation of Gelatinolytic and Collagenolytic Activity of Fasciola hepatica Recombinant Cathepsin-L1. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2357. [PMID: 32884958 PMCID: PMC7461709 DOI: 10.30498/ijb.2020.143160.2357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background: Cysteine proteases of the liver fluke, Fasciola hepatica, participate in catabolism of proteins, migration of the fluke through host tissues and combat host immune system Objectives: In this study, we evaluated proteolytic activity of F. hepatica recombinant cathepsin L1 (rCL1) against gelatin and collagen as common substrates Material and Methods: The coding sequences of F. hepatica CL1 were cloned and expressed in E. coli, in our previous study. The rCL1 was purified by nickel affinity chromatography
with a HisTrap Column. The protein concentrations of the purified fractions were determined by Bradford assay. Rat collagen type-1 was treated with distinct amounts of rCL1
at 37 °C, overnight, and the byproduct was analyzed by SDS-PAGE. Furthermore, we used bovine skin gelatin as zymography substrate to evaluate the gelatinolytic activity of the purified rCL1. Results: Recombinant CL1 was capable to digest intact type-1 collagen within 24 h and the gelatinlytic activity of rCL1 was visible at approximately 37 kDa region,
with optimal activity at acidified conditions (pH 4) Conclusion: Findings provide a possible mechanism by which a major secretory molecule of F. hepatica could be involved in parasite survival as well as its pathogenesis.
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Affiliation(s)
- Kobra Mokhtarian
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Reza Falak
- Immunology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Heidari
- Department of Medical Parasitology, School of Medicine, Ardabil University of Medical Sciences
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Molecular Characterization of Porcine Epidemic Diarrhea Virus and Its New Genetic Classification Based on the Nucleocapsid Gene. Viruses 2020; 12:v12080790. [PMID: 32717934 PMCID: PMC7472284 DOI: 10.3390/v12080790] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/19/2020] [Accepted: 07/21/2020] [Indexed: 11/17/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) causes continuous, significant damage to the swine industry worldwide. By RT-PCR-based methods, this study demonstrated the ongoing presence of PEDV in pigs of all ages in Korea at the average detection rate of 9.92%. By the application of Bayesian phylogenetic analysis, it was found that the nucleocapsid (N) gene of PEDV could evolve at similar rates to the spike (S) gene at the order of 10-4 substitutions/site/year. Based on branching patterns of PEDV strains, three main N gene-base genogroups (N1, N2, and N3) and two sub-genogroups (N3a, N3b) were proposed in this study. By analyzing the antigenic index, possible antigenic differences also emerged in both the spike and nucleocapsid proteins between the three genogroups. The antigenic indexes of genogroup N3 strains were significantly lower compared with those of genogroups N1 and N2 strains in the B-cell epitope of the nucleocapsid protein. Similarly, significantly lower antigenic indexes in some parts of the B-cell epitope sequences of the spike protein (COE, S1D, and 2C10) were also identified. PEDV mutants derived from genetic mutations of the S and N genes may cause severe damage to swine farms by evading established host immunities.
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Allam AM, Elbayoumy MK, Abdel-Rahman EH, Hegazi AG, Farag TK. Molecular characterization of the 2018 outbreak of lumpy skin disease in cattle in Upper Egypt. Vet World 2020; 13:1262-1268. [PMID: 32848299 PMCID: PMC7429391 DOI: 10.14202/vetworld.2020.1262-1268] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 05/13/2020] [Indexed: 11/16/2022] Open
Abstract
Background and Aim Lumpy skin disease (LSD), an infectious disease of cattle, is characterized by raised nodules on the skin. Although the morbidity rate of LSD is low, it has a considerable fatality rate. Despite the annual mass vaccination of livestock with sheep pox vaccine (Veterinary Serum and Vaccine Research Institute, Egypt) enforced by Egyptian authorities, the LSD virus (LSDV) continues to circulate almost every summer. The present study aimed to discover the cause of cows naturally infected with LSDV circulating in Upper Egypt during the summer of 2018 using polymerase chain reaction (PCR) assay and to analyze their phylogenetics against reference genome sequences. Materials and Methods We cultured LSDV in specific pathogen-free embryonated chicken eggs (SPF-ECE) and used conventional PCR to identify fusion and P32 genes, previously deposited in GenBank (MN694826, MN694827, and MN954664). Sequencing and phylogenetic analyses were performed on these two highly conserved viral genes. Results LSDV infection of SPF-ECE resulted in characteristic white pock lesions. PCR products were identified on 1.5% agarose gel after electrophoresis at the expected positions for the fusion and P32 genes at 472 and 587 bp, respectively. Conclusion The present study revealed that the two viral genes were identified from the Beni Suef and Sohag Governorates in all clinical cases and confirmed the circulation of LSDV in this outbreak. After sequencing, these genes were identical to those of the LSDV that had been identified and recorded in GenBank for the past 3 years.
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Affiliation(s)
- Ahmad M Allam
- Department of Parasitology and Animal Diseases, National Research Centre, EL Buhouth St., 12622 Giza, Egypt
| | - Mohamed Karam Elbayoumy
- Department of Parasitology and Animal Diseases, National Research Centre, EL Buhouth St., 12622 Giza, Egypt
| | - Eman H Abdel-Rahman
- Department of Parasitology and Animal Diseases, National Research Centre, EL Buhouth St., 12622 Giza, Egypt
| | - Ahmed G Hegazi
- Department of Zoonotic Disease, National Research Centre, EL Buhouth St., 12622 Giza, Egypt
| | - Tarek Korany Farag
- Department of Parasitology and Animal Diseases, National Research Centre, EL Buhouth St., 12622 Giza, Egypt
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Zhang JH, Lv HZ, Liu WJ, Ji AJ, Zhang X, Song JY, Luo HM, Chen SL. bHLH transcription factor SmbHLH92 negatively regulates biosynthesis of phenolic acids and tanshinones in Salvia miltiorrhiza. CHINESE HERBAL MEDICINES 2020; 12:237-246. [PMID: 36119017 PMCID: PMC9476745 DOI: 10.1016/j.chmed.2020.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/25/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022] Open
Abstract
Objective Salvia miltiorrhiza is a valuable herbal medicine with tanshinone and phenolic acid as the main biological active ingredients. The biosynthetic regulation of these bioactive compounds is controlled by a set of transcription factors (TFs). The basic helix-loop-helix (bHLH) transcription factor plays an important role in various physiological and biochemical processes in plants. However, research on bHLH TFs regulating phenolic acid or tanshinone biosynthesis in S. miltiorrhiza is limited. Methods qRT-PCR was used for gene expression analysis. The subcellular localization of SmbHLH92 was detected by SmbHLH92-GFP transient transformation into tobacco leaves, and its fluorescence was observed using a confocal laser scanning microscope. The transcriptional activity of SmbHLH92 was confirmed in the AH109 yeast strain. RNA interference hairy roots of SmbHLH92-RNAi transgenic lines were obtained through Agrobacterium-mediated genetic transformation. Ultra performance liquid chromatography (UPLC) was used to detect the changes of phenolic acids and tanshinones. Results SmbHLH92 is a bHLH transcription factor that is highly expressed in the root and phloem of S. miltiorrhiza. The subcellular localization and transcriptional activity of SmbHLH92 indicated that SmbHLH92 was located in the nucleus and may be a transcription factor. RNA interference (RNAi) of SmbHLH92 in hairy roots of S. miltiorrhiza significantly increased the accumulation of phenolic acid and tanshinone. Quantitative RT-PCR (RT-qPCR) analysis showed the transcription level of genes encoding the key enzymes involved in the phenolic acid and tanshinone biosynthetic pathways was increased in the hairy roots of the SmbHLH92-RNAi transgenic line, comparing with the control line. Conclusion These data indicate that SmbHLH92 is a negative regulator involved in the regulation of phenolic acid and tanshinone biosynthesis in S. miltiorrhiza.
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Bioprospecting of Bioactive Metabolites from Monochaetia karstenii. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.2.54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Mohamadnia A, Salehi Z, Namvar Z, Tabarsi P, Pourabdollah-Toutkaboni M, Rezaie S, Marjani M, Moniri A, Abtahian Z, Mahdaviani SA, Mortezaee V, Askari E, Sharifynia S. Molecular identification, phylogenetic analysis and antifungal susceptibility patterns of Aspergillusnidulans complex and Aspergillusterreus complex isolated from clinical specimens. J Mycol Med 2020; 30:101004. [PMID: 32534826 DOI: 10.1016/j.mycmed.2020.101004] [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: 12/28/2019] [Revised: 03/15/2020] [Accepted: 05/26/2020] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Aspergillus sections Terrei and Nidulantes are the less common causes of invasive aspergillosis and pulmonary aspergillosis (PA) in immunocompromised patients when compared to A. fumigatus and A. flavus. Identifying these fungi as the infectious agent is crucial because of the resistance to amphotericin B (AMB) and increased lethality. The aim of this study was to identify the molecular status, evaluate the genetic diversity and examine the antifungal susceptibility profile of the uncommon Aspergillus species. Forty-five uncommon Aspergillus species were identified based on the microscopic and macroscopic criteria. Then, the molecular identification was performed using the sequencing beta tubulin (benA) gene. In vitro antifungal susceptibility to amphotericin B (AMB), itraconazole (ITC), ravuconazole (RAV), voriconazole (VRC), caspofungin (CFG) isavuconazole (ISA) and posaconazole (POS) test was performed according to the CLSI M38-A2 guidelines. RESULTS A. terreus was the most species detected, followed by A. nidulans, A. latus, A.ochraceus, and A. citrinoterreus, respectively. The analysis of the benA gene showed the presence of 12 distinct genotypes among the A. terreus isolates. The other species did not show any intraspecies variation. CFG exhibited the lowest MEC50/MIC50 (0.007μg/mL), followed by POS (0.125μg/mL), VRC, ITC, ISA (0.25μg/mL), RAV (0.5μg/mL), and AMB (8μg/mL). Among all the isolates, only 15.5% (7/45) were susceptible to AMB. CONCLUSION Antifungal susceptibility pattern of the uncommon Aspergillus species is useful to improve patient management and increase knowledge concerning the local epidemiology. Moreover, this information is necessary when an outbreak dealing with drug-resistant infections occurs.
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Affiliation(s)
- A Mohamadnia
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Z Salehi
- Department of Mycology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14115-331, Iran
| | - Z Namvar
- Department of Biotechnology, Animal Breeding Center, Tehran, Iran
| | - P Tabarsi
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M Pourabdollah-Toutkaboni
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S Rezaie
- Division of Molecular Biology, Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - M Marjani
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - A Moniri
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Z Abtahian
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S A Mahdaviani
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - V Mortezaee
- Department of Medical mycology, Mazandaran University of Medical Sciences, Sari, Iran
| | - E Askari
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S Sharifynia
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Bai H, Song Z, Zhang Y, Li Z, Wang Y, Liu X, Ma J, Quan J, Wu X, Liu M, Zhou J, Dong Z, Li D. The bHLH transcription factor PPLS1 regulates the color of pulvinus and leaf sheath in foxtail millet (Setaria italica). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1911-1926. [PMID: 32157354 DOI: 10.1007/s00122-020-03566-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/15/2020] [Indexed: 05/20/2023]
Abstract
The bHLH transcription factor, PPLS1, interacts with SiMYB85 to control the color of pulvinus and leaf sheath by regulating anthocyanin biosynthesis in foxtail millet (Setaria italica). Foxtail millet (Setaria italica), a self-pollinated crop with numerous small florets, is difficult for cross-pollination. The color of pulvinus and leaf sheath with purple being dominant to green is an indicative character and often used for screening authentic hybrids in foxtail millet crossing. Deciphering molecular mechanism controlling this trait would greatly facilitate genetic improvement of cultivars in foxtail millet. Here, using the F2 bulk specific-locus amplified fragment sequencing approach, we mapped the putative causal gene for the purple color of pulvinus and leaf sheath (PPLS) trait to a 100 Kb region on chromosome 7. Expression analyses of the 15 genes in this region revealed that Seita.7G195400 (renamed here as PPLS1) was differentially expressed between purple and green cultivars. PPLS1 encodes a bHLH transcription factor and is localized in the nucleus with a transactivation activity. Furthermore, we observed that expression of a MYB transcription factor gene, SiMYB85 (Seita.4G086300) involved in anthocyanin biosynthesis, shows a totally positive association with that of PPLS1. Heterologous co-expression of both PPLS1 and SiMYB85 in tobacco leaves led to elevated anthocyanin accumulation and expression of some anthocyanin-related genes. Furthermore, PPLS1 physically interacts with SiMYB85. Taken together, our results suggest that PPLS1 interacts with SiMYB85 to control the color of pulvinus and leaf sheath by regulating anthocyanin biosynthesis in foxtail millet.
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Affiliation(s)
- Hui Bai
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, 050035, China
| | - Zhenjun Song
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, 050035, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yan Zhang
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Zhiyong Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, 050035, China
| | - Yongfang Wang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, 050035, China
| | - Xue Liu
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing Key Laboratory of Vegetable Germplasms Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Jifang Ma
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, 050035, China
| | - Jianzhang Quan
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, 050035, China
| | - Xianghong Wu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, China
| | - Min Liu
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Jun Zhou
- College of Life Sciences, Nankai University, Tianjin, 300071, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Zhiping Dong
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, 050035, China.
| | - Dayong Li
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing Key Laboratory of Vegetable Germplasms Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China.
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Di Cataldo S, Ulloa-Contreras C, Cevidanes A, Hernández C, Millán J. Babesia vogeli in dogs in Chile. Transbound Emerg Dis 2020; 67:2296-2299. [PMID: 32367669 DOI: 10.1111/tbed.13609] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/02/2020] [Accepted: 04/27/2020] [Indexed: 11/28/2022]
Abstract
We report the presence of Babesia vogeli in dogs in Chile. During two surveillance campaigns separated by a year, sixty-three blood samples from free-ranging rural dogs in Coquimbo, Chile, were analysed through conventional PCR screening of the 18S rRNA for Babesia species. Sequencing confirmed the presence of Babesia vogeli in 6.3% of the tested animals, with positive cases in both years. All the sequences showed 100% nucleotide sequence identity among them and 99.8% with other previously published sequences from dogs. No clinical signs or haematological abnormalities other than thrombocytopenia were found in the parasitized individuals. This is the first report of a canine piroplasmid in Chile.
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Affiliation(s)
- Sophia Di Cataldo
- Programa de Doctorado en Medicina de la Conservación, Universidad Andrés Bello, Santiago, Chile
| | | | - Aitor Cevidanes
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Claudia Hernández
- Laboratorio de Diagnóstico Veterinario, HCV, Escuela de Medicina Veterinaria, Universidad Andrés Bello, Lo Pinto, Chile
| | - Javier Millán
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Zaragoza, Spain.,Fundación ARAID, Zaragoza, Spain
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Nelapati AK, Das BK, Ponnan Ettiyappan JB, Chakraborty D. In-silico epitope identification and design of Uricase mutein with reduced immunogenicity. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.01.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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D1- but not D2-like dopamine receptor antagonist in the CA1 region of the hippocampus reduced stress-induced reinstatement in extinguished morphine-conditioning place preference in the food-deprived rats. Behav Pharmacol 2020; 31:196-206. [DOI: 10.1097/fbp.0000000000000546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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