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Wang Y, Shi J, Liu T, Zhang Y, Zhang L, Zhang X. Actinokineospora xionganensis sp. nov., a filamentous actinomycete isolated from the lakeside soil of Baiyangdian. Antonie van Leeuwenhoek 2021; 114:487-496. [PMID: 33674994 DOI: 10.1007/s10482-021-01532-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
A novel actinomycete, strain HBU206404T, belonging to the genus Actinokineospora, was isolated from the lakeside soil of Baiyangdian, in China. Cells grew at 9-37 °C (optimum temperature, 28 °C) and pH 6-9 (optimum, pH 7). Meso-diaminopimelic acid was the diagnostic diamino acid of the cell-wall peptidoglycan, and sugars present in whole-cell hydrolysates were arabinose, mannose, glucose and galactose. The predominant menaquinone was MK-9(H4). The predominant cellular fatty acids (> 5%) of the strain HBU206404T were iso-C16:0 (21.5%), iso-C15:0 (20.3%), C16:1ω7c/C16:1ω6c and/or C16:1ω6c/C16:1ω7c (15.0%), iso-C17:0 (8.6%), C16:0 (7.0%) and C17:1ω8c (6.9%). The major polar lipids of the strain HBU206404T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, six unknown aminolipids, two unknown aminolipids and an unidentified lipid. The 16S rRNA gene sequence analysis indicated that the strain HBU206404T was most closely related to Actinokineospora alba KCTC 19294T (99.58%), but whole-genome comparisons, using average nucleotide identity (ANI) value (91.77%) and digital DNA-DNA hybridization (dDDH) value (60%), confirmed low genome relatedness. Nitrogen metabolism pathway was found in the genome of strain HBU206404T which haboured nitrate reductase and nitrite reductase. Other phenotypic characteristics, such as ability to hydrolyze substances, enzyme activity, acid production from carbon source, etc., could also distinguish strain HBU206404T from Actinokineospora alba KCTC 19294T. On the basis of genetic and phenotypic evidence, strain HBU206404T represents a novel species of the genus Actinokineospora, for which the name Actinokineospora xionganensis sp. nov. is proposed. The type strain is HBU206404T (= MCCC 1K04412T = KCTC 49404T).
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Affiliation(s)
- Yuhui Wang
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Jiangli Shi
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Tongtong Liu
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Yufan Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Liping Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Xiumin Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China.
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Khan RSA, Ali Z, Niazi AK, Carolan JC, Wilkinson TL. In silico Characterization of a Candidate Protein from Aphid Gelling Saliva with Potential for Aphid Control in Plants. Protein Pept Lett 2020; 27:158-167. [DOI: 10.2174/0929866526666191014145839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 05/13/2019] [Accepted: 08/02/2019] [Indexed: 11/22/2022]
Abstract
Background:
Sheath or gelling saliva, secreted during feeding by aphids, is a hard material that
supports the piercing mouthparts and remains in the plant after feeding. Solidification or gelling of the saliva
might be due to the composition of amino acids in the constituent proteins, many of which probably interact
with plant defenses.
Objective :
The complete complement of proteins in the gelling saliva are still unknown, although one sheath
protein (SHP) has previously been identified as a potential candidate protein to control aphid feeding, but its
structure and its physiochemical role remains obscure. The current study provides structural information and
biochemical properties of the aphid sheath protein.
Methods:
The Sheath protein encoding gene was amplified from cDNA of the pea aphid (Acyrthosiphon pisum)
through PCR using specific gene primers. Sequence was in silico characterized by using EXPASY, Berkeley
Drosophila Genome Project (BDGP) Neural Network Promoter Prediction, BioEdit, Mega7, ProtParam, Phyre
server, 3D LigandSite SMART, MEME and GSDS programs, available online.
Results:
BLASTp analysis revealed that the sequenced gene was identical (100%) to the sequence from
Acyrthosiphon pisum, with 87% identity to Metpolophium dirhodum and 84% identity to Sitobion avenae.
Phylogenetically monocot feeders such as M. dirhodum and S. avenae are in a sister taxa to dicot feeders. In
silico analysis of the sequence revealed that sheath protein has a molecular weight of 144 kDa and 50% of the
protein is composed of only six amino acids, i.e., threonine, serine, aspartic acid, glutamic acid, isoleucine and
tyrosine. The computed IP value revealed that sheath protein is acidic in nature. Ligand binding sites for sheath
protein were predicted on residues 1123 and 1125 (isoleucine and glutamine, respectively). Metallic heterogens
are also present in sheath protein that are iron, zinc and magnesium, respectively.
Conclusion :
It is conceivable that variation in the salivary gene sequences may reveal important biological
information of relevance to the insect-plant interaction. Further exploration of insect salivary proteins, their
composition and structure will provide powerful information, especially when these proteins are interacting with
plant proteins, and specific information about the sheath protein, which is interacting with plants at a
molecular/cellular level, will be important to progress strategies aimed specifically against sucking pests such as
aphids.
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Affiliation(s)
- Rao Sohail Ahmad Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Zainab Ali
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Adnan Khan Niazi
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | | | - Thomas L. Wilkinson
- School of Biology and Environmental Sciences, University College Dublin, Dublin, Ireland
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Zhang X, Song S, Tang L, Wang Y, Zhang X, Li X, Yu X, Zhang J, Kwon SW, Zhang L. Gynurincola endophyticus gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae. Int J Syst Evol Microbiol 2019; 69:816-820. [PMID: 30694172 DOI: 10.1099/ijsem.0.003246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped (0.2-0.4 µm×1.2-1.7 µm), endophytic bacterium, designated HBUM179779T, was isolated from the stem of a medicinal plant,Gynura bicolor, collected from Pixian county in Sichuan province, China. The strain did not produce endospores and its cells could secrete mucus. The predominant menaquinone was MK-7. The polar lipids were phosphatidylethanolamine, phosphatidylinositolmannosides, two unknown aminolipids, two unknown glycolipids and an unknown phospholipid. Branched fatty acids (iso-) and hydroxy fatty acids were the main fatty acids, which mainly included iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HBUM179779T fell within the family Chitinophagaceae, and its closest neighbour was Pseudoflavitalea rhizosphaerae T16R-265T (94.46 %). However, strain HBUM179779T did not make a coherent clade with members of the recognized organisms. The average nucleotide identity value between strain HBUM179779T and Pseudoflavitalea rhizosphaerae T16R-265T was 67.1 %. On the basis of the phylogenetic and phenotypic characteristics of this bacterium, a novel genus and species, Gynurincola endophyticus gen. nov., sp. nov., is proposed. The type strain is HBUM179779T (=CGMCC 1.15525T=NBRC 112424T).
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Affiliation(s)
- Xiumin Zhang
- 1College of Life Sciences, Hebei University; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Baoding 071002, PR China
| | - Shuo Song
- 1College of Life Sciences, Hebei University; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Baoding 071002, PR China
| | - Lingjie Tang
- 1College of Life Sciences, Hebei University; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Baoding 071002, PR China
| | - Yuhui Wang
- 1College of Life Sciences, Hebei University; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Baoding 071002, PR China
| | - Xiaoxia Zhang
- 2Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiaojin Li
- 1College of Life Sciences, Hebei University; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Baoding 071002, PR China
| | - Xinrui Yu
- 1College of Life Sciences, Hebei University; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Baoding 071002, PR China
| | - Jinhua Zhang
- 1College of Life Sciences, Hebei University; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Baoding 071002, PR China
| | - Soon-Wo Kwon
- 3Korean Agricultural Culture Collection(KACC), Agricultural Microbiology Division, National Institute of Agricultural Sciences, Jeollabuk-do 55365, Republic of Korea
| | - Liping Zhang
- 1College of Life Sciences, Hebei University; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Baoding 071002, PR China
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Xia X. Imputing missing distances in molecular phylogenetics. PeerJ 2018; 6:e5321. [PMID: 30065887 PMCID: PMC6063210 DOI: 10.7717/peerj.5321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/05/2018] [Indexed: 12/27/2022] Open
Abstract
Missing data are frequently encountered in molecular phylogenetics, but there has been no accurate distance imputation method available for distance-based phylogenetic reconstruction. The general framework for distance imputation is to explore tree space and distance values to find an optimal combination of output tree and imputed distances. Here I develop a least-square method coupled with multivariate optimization to impute multiple missing distance in a distance matrix or from a set of aligned sequences with missing genes so that some sequences share no homologous sites (whose distances therefore need to be imputed). I show that phylogenetic trees can be inferred from distance matrices with about 10% of distances missing, and the accuracy of the resulting phylogenetic tree is almost as good as the tree from full information. The new method has the advantage over a recently published one in that it does not assume a molecular clock and is more accurate (comparable to maximum likelihood method based on simulated sequences). I have implemented the function in DAMBE software, which is freely available at http://dambe.bio.uottawa.ca.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
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Plaisier CL, Lo FY, Ashworth J, Brooks AN, Beer KD, Kaur A, Pan M, Reiss DJ, Facciotti MT, Baliga NS. Evolution of context dependent regulation by expansion of feast/famine regulatory proteins. BMC SYSTEMS BIOLOGY 2014; 8:122. [PMID: 25394904 PMCID: PMC4236453 DOI: 10.1186/s12918-014-0122-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/16/2014] [Indexed: 11/25/2022]
Abstract
Background Expansion of transcription factors is believed to have played a crucial role in evolution of all organisms by enabling them to deal with dynamic environments and colonize new environments. We investigated how the expansion of the Feast/Famine Regulatory Protein (FFRP) or Lrp-like proteins into an eight-member family in Halobacterium salinarum NRC-1 has aided in niche-adaptation of this archaeon to a complex and dynamically changing hypersaline environment. Results We mapped genome-wide binding locations for all eight FFRPs, investigated their preference for binding different effector molecules, and identified the contexts in which they act by analyzing transcriptional responses across 35 growth conditions that mimic different environmental and nutritional conditions this organism is likely to encounter in the wild. Integrative analysis of these data constructed an FFRP regulatory network with conditionally active states that reveal how interrelated variations in DNA-binding domains, effector-molecule preferences, and binding sites in target gene promoters have tuned the functions of each FFRP to the environments in which they act. We demonstrate how conditional regulation of similar genes by two FFRPs, AsnC (an activator) and VNG1237C (a repressor), have striking environment-specific fitness consequences for oxidative stress management and growth, respectively. Conclusions This study provides a systems perspective into the evolutionary process by which gene duplication within a transcription factor family contributes to environment-specific adaptation of an organism. Electronic supplementary material The online version of this article (doi:10.1186/s12918-014-0122-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Fang-Yin Lo
- Institute for Systems Biology, Seattle, WA, USA. .,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
| | | | - Aaron N Brooks
- Institute for Systems Biology, Seattle, WA, USA. .,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
| | - Karlyn D Beer
- Institute for Systems Biology, Seattle, WA, USA. .,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
| | | | - Min Pan
- Institute for Systems Biology, Seattle, WA, USA.
| | | | - Marc T Facciotti
- Department of Biomedical Engineering, University of California, Davis, CA, USA. .,Genome Center, University of California, Davis, CA, USA.
| | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, USA. .,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA. .,Department of Microbiology, University of Washington, Seattle, WA, USA. .,Department of Biology, University of Washington, Seattle, WA, USA.
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6
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Dennis MY, Nuttle X, Sudmant PH, Antonacci F, Graves TA, Nefedov M, Rosenfeld JA, Sajjadian S, Malig M, Kotkiewicz H, Curry CJ, Shafer S, Shaffer LG, de Jong PJ, Wilson RK, Eichler EE. Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell 2012; 149:912-22. [PMID: 22559943 DOI: 10.1016/j.cell.2012.03.033] [Citation(s) in RCA: 252] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/17/2012] [Accepted: 03/01/2012] [Indexed: 10/28/2022]
Abstract
Gene duplication is an important source of phenotypic change and adaptive evolution. We leverage a haploid hydatidiform mole to identify highly identical sequences missing from the reference genome, confirming that the cortical development gene Slit-Robo Rho GTPase-activating protein 2 (SRGAP2) duplicated three times exclusively in humans. We show that the promoter and first nine exons of SRGAP2 duplicated from 1q32.1 (SRGAP2A) to 1q21.1 (SRGAP2B) ∼3.4 million years ago (mya). Two larger duplications later copied SRGAP2B to chromosome 1p12 (SRGAP2C) and to proximal 1q21.1 (SRGAP2D) ∼2.4 and ∼1 mya, respectively. Sequence and expression analyses show that SRGAP2C is the most likely duplicate to encode a functional protein and is among the most fixed human-specific duplicate genes. Our data suggest a mechanism where incomplete duplication created a novel gene function-antagonizing parental SRGAP2 function-immediately "at birth" 2-3 mya, which is a time corresponding to the transition from Australopithecus to Homo and the beginning of neocortex expansion.
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Affiliation(s)
- Megan Y Dennis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, 98195, USA
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7
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Syrjänen L, Tolvanen M, Hilvo M, Olatubosun A, Innocenti A, Scozzafava A, Leppiniemi J, Niederhauser B, Hytönen VP, Gorr TA, Parkkila S, Supuran CT. Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates. BMC BIOCHEMISTRY 2010; 11:28. [PMID: 20659325 PMCID: PMC2918522 DOI: 10.1186/1471-2091-11-28] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Accepted: 07/26/2010] [Indexed: 11/10/2022]
Abstract
Background The β-carbonic anhydrase (CA, EC 4.2.1.1) enzymes have been reported in a variety of organisms, but their existence in animals has been unclear. The purpose of the present study was to perform extensive sequence analysis to show that the β-CAs are present in invertebrates and to clone and characterize a member of this enzyme family from a representative model organism of the animal kingdom, e.g., Drosophila melanogaster. Results The novel β-CA gene, here named DmBCA, was identified from FlyBase, and its orthologs were searched and reconstructed from sequence databases, confirming the presence of β-CA sequences in 55 metazoan species. The corresponding recombinant enzyme was produced in Sf9 insect cells, purified, kinetically characterized, and its inhibition was investigated with a series of simple, inorganic anions. Holoenzyme molecular mass was defined by dynamic light scattering analysis and gel filtration, and the results suggested that the holoenzyme is a dimer. Double immunostaining confirmed predictions based on sequence analysis and localized DmBCA protein to mitochondria. The enzyme showed high CO2 hydratase activity, with a kcat of 9.5 × 105 s-1 and a kcat/KM of 1.1 × 108 M-1s-1. DmBCA was appreciably inhibited by the clinically-used sulfonamide acetazolamide, with an inhibition constant of 49 nM. It was moderately inhibited by halides, pseudohalides, hydrogen sulfide, bisulfite and sulfate (KI values of 0.67 - 1.36 mM) and more potently by sulfamide (KI of 0.15 mM). Bicarbonate, nitrate, nitrite and phenylarsonic/boronic acids were much weaker inhibitors (KIs of 26.9 - 43.7 mM). Conclusions The Drosophila β-CA represents a highly active mitochondrial enzyme that is a potential model enzyme for anti-parasitic drug development.
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Affiliation(s)
- Leo Syrjänen
- Institute of Medical Technology, University of Tampere and Tampere University Hospital, Finland.
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Kanakaratne N, Wahala WMPB, Messer WB, Tissera HA, Shahani A, Abeysinghe N, de-Silva AM, Gunasekera M. Severe dengue epidemics in Sri Lanka, 2003-2006. Emerg Infect Dis 2009; 15:192-9. [PMID: 19193262 PMCID: PMC2662655 DOI: 10.3201/eid1502.080926] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
One-sentence summary for table of contents: Changes in transmission dynamics and virus genes are likely increasing emergence of severe epidemics in this country. Recent emergence of dengue hemorrhagic fever in the Indian subcontinent has been well documented in Sri Lanka. We compare recent (2003–2006) and past (1980–1997) dengue surveillance data for Sri Lanka. The 4 dengue virus (DENV) serotypes have been cocirculating in Sri Lanka for >30 years. Over this period, a new genotype of DENV-1 has replaced an old genotype. Moreover, new clades of DENV-3 genotype III viruses have replaced older clades. Emergence of new clades of DENV-3 in 1989 and 2000 coincided with abrupt increases in the number of reported dengue cases, implicating this serotype in severe epidemics. In 1980–1997, most reported dengue cases were in children. Recent epidemics have been characterized by many cases in children and adults. Changes in local transmission dynamics and genetic changes in DENV-3 are likely increasing emergence of severe dengue epidemics in Sri Lanka.
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Philpott S, Burger H, Tsoukas C, Foley B, Anastos K, Kitchen C, Weiser B. Human immunodeficiency virus type 1 genomic RNA sequences in the female genital tract and blood: compartmentalization and intrapatient recombination. J Virol 2005; 79:353-63. [PMID: 15596829 PMCID: PMC538688 DOI: 10.1128/jvi.79.1.353-363.2005] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Investigation of human immunodeficiency virus type 1 (HIV-1) in the genital tract of women is crucial to the development of vaccines and therapies. Previous analyses of HIV-1 in various anatomic sites have documented compartmentalization, with viral sequences from each location that were distinct yet phylogenetically related. Full-length RNA genomes derived from different compartments in the same individual, however, have not yet been studied. Furthermore, although there is evidence that intrapatient recombination may occur frequently, recombinants comprising viruses from different sites within one individual have rarely been documented. We compared full-length HIV-1 RNA sequences in the plasma and female genital tract, focusing on a woman with high HIV-1 RNA loads in each compartment who had been infected heterosexually and then transmitted HIV-1 by the same route. We cloned and sequenced 10 full-length HIV-1 RNA genomes from her genital tract and 10 from her plasma. We also compared viral genomes from the genital tract and plasma of four additional heterosexually infected women, sequencing 164 env and gag clones obtained from the two sites. Four of five women, including the one whose complete viral sequences were determined, displayed compartmentalized HIV-1 genomes. Analyses of full-length, compartmentalized sequences made it possible to document complex intrapatient HIV-1 recombinants that were composed of alternating viral sequences characteristic of each site. These findings demonstrate that the genital tract and blood harbor genetically distinct populations of replicating HIV-1 and provide evidence that recombination between strains from the two compartments contributes to rapid evolution of viral sequence variation in infected individuals.
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Affiliation(s)
- Sean Philpott
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
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10
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Gavrilin GV, Cherkasova EA, Lipskaya GY, Kew OM, Agol VI. Evolution of circulating wild poliovirus and of vaccine-derived poliovirus in an immunodeficient patient: a unifying model. J Virol 2000; 74:7381-90. [PMID: 10906191 PMCID: PMC112258 DOI: 10.1128/jvi.74.16.7381-7390.2000] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We determined nucleotide sequences of the VP1 and 2AB genes and portions of the 2C and 3D genes of two evolving poliovirus lineages: circulating wild viruses of T geotype and Sabin vaccine-derived isolates from an immunodeficient patient. Different regions of the viral RNA were found to evolve nonsynchronously, and the rate of evolution of the 2AB region in the vaccine-derived population was not constant throughout its history. Synonymous replacements occurred not completely randomly, suggesting the need for conservation of certain rare codons (possibly to control translation elongation) and the existence of unidentified constraints in the viral RNA structure. Nevertheless the major contribution to the evolution of the two lineages came from linear accumulation of synonymous substitutions. Therefore, in agreement with current theories of viral evolution, we suggest that the majority of the mutations in both lineages were fixed as a result of successive sampling, from the heterogeneous populations, of random portions containing predominantly neutral and possibly adverse mutations. As a result of such a mode of evolution, the virus fitness may be maintained at a more or less constant level or may decrease unless more-fit variants are stochastically generated. The proposed unifying model of natural poliovirus evolution has important implications for the epidemiology of poliomyelitis.
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Affiliation(s)
- G V Gavrilin
- A. N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Moscow 119899, Russia
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11
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Levin S, Almo SC, Satir BH. Functional diversity of the phosphoglucomutase superfamily: structural implications. PROTEIN ENGINEERING 1999; 12:737-46. [PMID: 10506283 DOI: 10.1093/protein/12.9.737] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Three-dimensional structural models of three members of the phosphoglucomutase (PGM) superfamily, parafusin, phosphoglucomutase-related protein and sarcoplasmic reticulum phosphoglucomutase, were constructed by homology modeling based on the known crystal structure of rabbit muscle phosphoglucomutase. Parafusin, phosphoglucomutase-related protein and sarcoplasmic reticulum phosphoglucomutase each have 50% or more identity with rabbit muscle phosphoglucomutase at the amino acid level and all are reported to exhibit no or minor phosphoglucomutase activity. There are four major insertions and two deletions in the parafusin sequence relative to PGM, all of which are located in surface-exposed loops connecting secondary structural elements. The remaining amino acid substitutions are distributed throughout the sequence and are not predicted to alter the polypeptide fold. Parafusin contains a putative protein kinase C site located on a surface loop in domain II that is not present in the homologs. Although the general domain structure and the active site of rabbit muscle phosphoglucomutase are preserved in the model of phosphoglucomutase-related protein, a major structural difference is likely to occur in domain 1 due to the absence of 55 amino acid residues in PGM-RP. This deletion predicts the loss of three alpha-helices and one beta-strand from an anti-parallel beta-sheet in this domain as compared with the rabbit muscle phosphoglucomutase.
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Affiliation(s)
- S Levin
- Departments of Anatomy and Structural Biology and Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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12
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Abstract
The evolutionary relationships of four eukaryotic kingdoms--Animalia, Plantae, Fungi, and Protista--remain unclear. In particular, statistical support for the closeness of animals to fungi rather than to plants is lacking, and a preferred branching order of these and other eukaryotic lineages is still controversial even though molecular sequences from diverse eukaryotic taxa have been analyzed. We report a statistical analysis of 214 sequences of nuclear small-subunit ribosomal RNA (srRNA) gene undertaken to clarify these evolutionary relationships. We have considered the variability of substitution rates and the nonindependence of nucleotide substitution across sites in the srRNA gene in testing alternative hypotheses regarding the branching patterns of eukaryote phylogeny. We find that the rates of evolution among sites in the srRNA sequences vary substantially and are approximately gamma distributed with size and shape parameter equal to 0.76. Our results suggest that (1) the animals and true fungi are indeed closer to each other than to any other "crown" group in the eukaryote tree, (2) red algae are the closest relatives of animals, true fungi, and green plants, and (3) the heterokonts and alveolates probably evolved prior to the divergence of red algae and animal-fungus-green-plant lineages. Furthermore, our analyses indicate that the branching order of the eukaryotic lineages that diverged prior to the evolution of alveolates may be generally difficult to resolve with the srRNA sequence data.
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Affiliation(s)
- S Kumar
- Department of Biology, Pennsylvania State University, University Park 16802, USA
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van Ham RC, Hart H, Mes TH, Sandbrink JM. Molecular evolution of noncoding regions of the chloroplast genome in the Crassulaceae and related species. Curr Genet 1994; 25:558-66. [PMID: 8082209 DOI: 10.1007/bf00351678] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Universal primers were used for PCR amplification of three noncoding regions of chloroplast DNA (cpDNA) in order to study sequence-length variation in the Crassulaceae and in related species. Several length mutations were observed that are of diagnostic value for evolutionary relationships in the Crassulaceae and the Saxifragaceae. Length variation and sequence divergence in the intergenic spacer between the trnL (UAA) 3' exon and the trnF (GAA) gene among 15 species were studied in detail by nucleotide-sequence analysis. A total of 50 insertion/deletion mutations were observed, accounting for a spacer-length variation in the range of 228-360 bp. Eighteen short direct repeat motifs (4-11 bp) and two inverted repeat motifs (7-11 bp) were found to be associated with length variation. Phylogenetic analysis of the sequence data indicated a pattern of relationships that was largely consistent with a previous analysis of cpDNA restriction-site variation. Evaluation of the level of homoplasy in insertion/deletion mutations within a phylogenetic framework revealed that only 1 out of 34 length mutations longer than 2 bp must have had multiple origins. The feasibility of the noncoding chloroplast DNA regions for molecular evolutionary studies is discussed.
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Affiliation(s)
- R C van Ham
- Department of Plant Ecology and Evolutionary Biology, University of Utrecht, The Netherlands
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