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Murtskhvaladze M, Tarkhnishvili D, Anderson CL, Kotorashvili A. Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection. PLoS One 2020; 15:e0233680. [PMID: 32511235 PMCID: PMC7279592 DOI: 10.1371/journal.pone.0233680] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 05/11/2020] [Indexed: 11/18/2022] Open
Abstract
We generated a phylogeny for Caucasian rock lizards (Darevskia), and included six other families of true lizards (Lacertini), based on complete mitochondrial genome analysis. Next-generation sequencing (NGS) of genomic DNA was used to obtain 16 new mitogenomes of Darevskia. These, along with 35 sequences downloaded from GenBank: genera Darevskia, Zootoca, Podarcis, Phoenicolacerta, Takydromus, Lacerta, and Eremias-were used in the analysis. All four analytical methods (Bayesian Inference, BI; Maximum Likelihood, ML; Maximum Parsimony, MP; and Neighbor-Joining, NJ) showed almost congruent intra-generic topologies for Darevskia and other lizard genera. However, ML and NJ methods on one side, and BI and MP methods on the other harvested conflicting phylogenies. The ML/NJ topology supports earlier published separation of Darevskia into three mitochondrial clades (Murphy, Fu, Macculloch, Darevsky, and Kupinova, 2000), but BI and MP topologies support that the basal branching occurred between D. parvula from the western Lesser Caucasus and the rest of Darevskia. All topologies altered the phylogenetic position of some individual species, including D. daghestanica, D. derjugini, and D. chlorogaster. Reanalysis after excluding four saturated genes from the data set, and excluding genus Eremias gives fully convergent topologies. The most basal branching for true lizards was between Far Eastern Takydromus and the Western Eurasian genera (BI). Comparing phylogenetic performance of individual genes relative to whole mitogenome data, concatenated 16S RNA (the least saturated gene in our analyses) and Cytochrome b genes generate a robust phylogeny that is fully congruent with that based on the complete mitogenome.
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Affiliation(s)
- Marine Murtskhvaladze
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
- L. Sakvarelidze National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - David Tarkhnishvili
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
| | - Cort L. Anderson
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
| | - Adam Kotorashvili
- L. Sakvarelidze National Center for Disease Control and Public Health, Tbilisi, Georgia
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Kunchulia M, Kotaria N, Pilz K, Kotorashvili A, Herzog MH. Associations between genetic variations and global motion perception. Exp Brain Res 2019; 237:2729-2734. [DOI: 10.1007/s00221-019-05627-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 08/13/2019] [Indexed: 02/04/2023]
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Farlow J, Donduashvili M, Kokhreidze M, Kotorashvili A, Vepkhvadze NG, Kotaria N, Gulbani A. Intra-epidemic genome variation in highly pathogenic African swine fever virus (ASFV) from the country of Georgia. Virol J 2018; 15:190. [PMID: 30547827 PMCID: PMC6295034 DOI: 10.1186/s12985-018-1099-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 11/21/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND African swine fever virus (ASFV) causes an acute hemorrhagic infection in suids with a mortality rate of up to 100%. No vaccine is available and the potential for catastrophic disease in Europe remains elevated due to the ongoing ASF epidemic in Russia and Baltic countries. To date, intra-epidemic whole-genome variation for ASFV has not been reported. To provide a more comprehensive baseline for genetic variation early in the ASF outbreak, we sequenced two Georgian ASFV samples, G-2008/1 and G-2008/2, derived from domestic porcine blood collected in 2008. METHODS Genomic DNA was extracted directly from low-volume ASFV PCR-positive porcine blood samples and subjected to next generation sequencing on the Illumina Miseq platform. De novo and mapped sequence assemblies were performed using CLCBio software. Genomic illustrations, sequence alignments and assembly figures were generated using Geneious v10.2.4. Sequence repeat architecture was analyzed using DNASTAR GeneQuest 14.1.0. RESULTS The G-2008/1 and G-2008/2 genomes were distinguished from each other by coding changes in seven genes, including MGF 110-1 L, X69R, MGF 505-10R, EP364R, H233R, E199L, and MGF 360-21R in addition to eight homopolymer tract variations. The 2008/2 genome possessed a novel allele state at a previously undescribed intergenic repeat locus between genes C315R and C147L. The C315R/C147L locus represents the earliest observed variable repeat sequence polymorphism reported among isolates from this epidemic. No sequence variation was observed in conventional ASFV subtyping markers. The two genomes exhibited complete collinearity and identical gene content with the Georgia 2007/1 reference genome. Approximately 56 unique homopolymer A/T-tract variations were identified that were unique to the Georgia 2007/1 genome. In both 2008 genomes, within-sample sequence read heterogeneity was evident at six homopolymeric G/C-tracts confined to the known hypervariable ~ 7 kb region in the left terminal region of the genome. CONCLUSIONS This is the first intra-epidemic comparative genomic analysis reported for ASFV and provides insight into the intra-epidemic microevolution of ASFV. The genomes reported here, in addition to the G-2007/1 genome, provide an early baseline for future genome-level comparisons and epidemiological tracing efforts.
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Affiliation(s)
- Jason Farlow
- Farlow Scientific Consulting Company, LLC, Lewiston, UT 84320 USA
| | | | | | - Adam Kotorashvili
- Richard G. Lugar Center for Public Health Research at the National Center for Disease Control (NCDC), Tbilisi, Georgia
| | | | - Nato Kotaria
- Richard G. Lugar Center for Public Health Research at the National Center for Disease Control (NCDC), Tbilisi, Georgia
| | - Ana Gulbani
- Laboratory of the Ministry of Agriculture, Tbilisi, Georgia
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Farlow J, Bolkvadze D, Leshkasheli L, Kusradze I, Kotorashvili A, Kotaria N, Balarjishvili N, Kvachadze L, Nikolich M, Kutateladze M. Correction to: Genomic characterization of three novel Basilisk-like phages infecting Bacillus anthracis. BMC Genomics 2018; 19:713. [PMID: 30261838 PMCID: PMC6158857 DOI: 10.1186/s12864-018-5105-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 11/10/2022] Open
Abstract
Following the publication of this article [1], the authors noted two typographical errors: one in Table 1 with regard to the location of the Basilisk Phage, which was incorrectly captured as "Kutaisis, country of Georgia Utah, USA" but should be "Utah, USA".
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Affiliation(s)
- J Farlow
- Farlow Scientific Consulting Company, LLC, Lewiston, UT, USA.
- Department of Bacteriophage Therapeutics, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Silver Spring, MD, USA.
| | - D Bolkvadze
- George Eliava Institute for Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
| | - L Leshkasheli
- George Eliava Institute for Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
| | - I Kusradze
- George Eliava Institute for Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
| | - A Kotorashvili
- Lugar Center for Public Health Research at National Center for Disease Contro, Tbilisi, Georgia
| | - N Kotaria
- Lugar Center for Public Health Research at National Center for Disease Contro, Tbilisi, Georgia
| | - N Balarjishvili
- George Eliava Institute for Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
| | - L Kvachadze
- George Eliava Institute for Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
| | - M Nikolich
- Department of Bacteriophage Therapeutics, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Silver Spring, MD, USA
| | - M Kutateladze
- George Eliava Institute for Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
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Sahin M, Buyuk F, Baillie L, Wölfel R, Kotorashvili A, Rehn A, Antwerpen M, Grass G. The identification of novel single nucleotide polymorphisms to assist in mapping the spread of Bacillus anthracis across the Southern Caucasus. Sci Rep 2018; 8:11254. [PMID: 30050151 PMCID: PMC6062627 DOI: 10.1038/s41598-018-29738-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/17/2018] [Indexed: 11/08/2022] Open
Abstract
Anthrax is common as a zoonotic disease in the southern Caucasus area including parts of Turkey and Georgia. In this region, population genetics of the etiological agent Bacillus anthracis comprises, where known, the major canonical single nucleotide polymorphism (canSNP) groups A.Br.Aust94 and A.Br.008/009 of the pathogen's global phylogeny, respectively. Previously, isolates of B. anthracis from Turkey have been genotyped predominantly by multi locus variable number of tandem repeat analysis (MLVA) or canSNP typing. While whole genome sequencing is the future gold standard, it is currently still costly. For that reason we were interested in identifying novel SNPs which could assist in further distinguishing closely related isolates using low cost assay platforms. In this study we sequenced the genomes of seven B. anthracis strains collected from the Kars province of Eastern Anatolia in Turkey and discovered new SNPs which allowed us to assign these and other geographically related strains to three novel branches of the major A-branch canSNP-group (A.Br.) Aust94. These new branches were named Kafkas-Geo 1-3 and comprised isolates from the Kars region and the neighboring republic of Georgia suggesting a common ancestry. The novel SNPs identified in this study connect the population genetics of B. anthracis in the South Caucasus and Turkey and will likely assist efforts to map the spread of the pathogen across this region.
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Affiliation(s)
| | | | | | - Roman Wölfel
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Adam Kotorashvili
- Lugar Center for Public Health Research at the National Center for Disease Control, Tbilisi, Georgia
| | | | | | - Gregor Grass
- Bundeswehr Institute of Microbiology, Munich, Germany.
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Karchava M, Chkhartishvili N, Sharvadze L, Abutidze A, Dvali N, Gatserelia L, Dzigua L, Bolokadze N, Dolmazashvili E, Kotorashvili A, Imnadze P, Gamkrelidze A, Tsertsvadze T. Impact of hepatitis C virus recombinant form RF1_2k/1b on treatment outcomes within the Georgian national hepatitis C elimination program. Hepatol Res 2018; 48:36-44. [PMID: 28258606 DOI: 10.1111/hepr.12890] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/02/2017] [Accepted: 03/02/2017] [Indexed: 02/08/2023]
Abstract
AIM Hepatitis C virus (HCV) recombinant form RF1_2k/1b is common in ethnic Georgians. This chimera virus contains genomic fragments of genotype 2 and genotype 1 and is misclassified as genotype 2 by standard genotyping. We aimed to identify RF1_2k/1b strains among genotype 2 patients and assess its impact on treatment outcomes. METHODS The study included 148 patients with HCV genotype 2 as determined by 5-untranslated region/core genotyping assay. RF1_2k/1b was identified by sequencing the non-structural protein 5B region. Patients were treated within the national hepatitis C elimination program with sofosbuvir/ribavirin (SOF/RBV), interferon (IFN)/SOF/RBV, or ledipasvir (LDV)/SOF/RBV. RESULTS Of 148 patients, 103 (69.5%) had RF1_ 2k/1b. Sustained virologic response (SVR) data was available for 136 patients (RF1_ 2k/1b, n = 103; genotype 2, n = 33). Sustained virologic response was achieved in more genotype 2 patient than in RF1_2k/1b patients (97.0% vs. 76.7%, P = 0.009). Twelve weeks of LDV/SOF/RBV treatment was highly effective (100% SVR) in both genotypes. Among RF1_2k/1b patients, LDV/SOF/RBV for 12 weeks was superior (100% SVR) to SOF/RBV for 12 weeks (56.4%, P < 0.0001) or 20 weeks (79.2%, P = 0.05). Twelve weeks of IFN/SOF/RBV also showed better response than SOF/RBV for 12 weeks (88.9% vs. 56.4%, P = 0.02) in these patients. CONCLUSIONS High prevalence of the RF1_2k/1b strain can significantly affect treatment outcomes. Treatment with IFN/SOF/RBV and especially LDV/SOF/RBV ensured significantly higher SVR in patients infected with RF1_2k/1b strain compared to standard HCV genotype 2 treatment with SOF/RBV. There is a need to reassess existing methods for the management of HCV genotype 2 infections, especially in areas with high prevalence of the RF1_2k/1b strain.
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Affiliation(s)
- Marine Karchava
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia.,Hepatology Clinic- Hepa, Tbilisi, Georgia
| | | | - Lali Sharvadze
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia.,Hepatology Clinic- Hepa, Tbilisi, Georgia.,Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Akaki Abutidze
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia.,Hepatology Clinic- Hepa, Tbilisi, Georgia
| | - Natia Dvali
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia
| | - Lana Gatserelia
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia.,Hepatology Clinic- Hepa, Tbilisi, Georgia
| | - Lela Dzigua
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia
| | - Natalia Bolokadze
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia.,Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Ekaterine Dolmazashvili
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia.,Hepatology Clinic- Hepa, Tbilisi, Georgia.,Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Adam Kotorashvili
- National Center for Diseases Control and Public Health, Tbilisi, Georgia
| | - Paata Imnadze
- National Center for Diseases Control and Public Health, Tbilisi, Georgia
| | - Amiran Gamkrelidze
- National Center for Diseases Control and Public Health, Tbilisi, Georgia
| | - Tengiz Tsertsvadze
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia.,Hepatology Clinic- Hepa, Tbilisi, Georgia.,Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
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Gogniashvili M, Jinjikhadze T, Maisaia I, Akhalkatsi M, Kotorashvili A, Kotaria N, Beridze T, Dudnikov AJ. Complete chloroplast genomes of Aegilops tauschii Coss. and Ae. cylindrica Host sheds light on plasmon D evolution. Curr Genet 2016; 62:791-798. [PMID: 26923563 DOI: 10.1007/s00294-016-0583-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 02/11/2016] [Accepted: 02/13/2016] [Indexed: 10/22/2022]
Abstract
Hexaploid wheat (Triticum aestivum L., genomes AABBDD) originated in South Caucasus by allopolyploidization of the cultivated Emmer wheat T. dicoccum (genomes AABB) with the Caucasian Ae. tauschii ssp strangulata (genomes DD). Genetic variation of Ae. tauschii is an important natural resource, that is why it is of particular importance to investigate how this variation was formed during Ae. tauschii evolutionary history and how it is presented through the species area. The D genome is also found in tetraploid Ae. cylindrica Host (2n = 28, CCDD). The plasmon diversity that exists in Triticum and Aegilops species is of great significance for understanding the evolution of these genera. In the present investigation the complete nucleotide sequence of plasmon D (chloroplast DNA) of nine accessions of Ae. tauschii and two accessions of Ae. cylindrica are presented. Twenty-eight SNPs are characteristic for both TauL1 and TauL2 accessions of Ae. tauschii using TauL3 as a reference. Four SNPs are additionally observed for TauL2 lineage. The longest (27 bp) indel is located in the intergenic spacer Rps15-ndhF of SSC. This indel can be used for simple determination of TauL3 lineage among Ae. tauschii accessions. In the case of Ae. cylindrica additionally 7 SNPs were observed. The phylogeny tree shows that chloroplast DNA of TauL1 and TauL2 diverged from the TauL3 lineage. TauL1 lineage is relatively older then TauL2. The position of Ae. cylindrica accessions on Ae. tauschii phylogeny tree constructed on chloroplast DNA variation data is intermediate between TauL1 and TauL2. The complete nucleotide sequence of chloroplast DNA of Ae. tauschii and Ae. cylindrica allows to refine the origin and evolution of D plasmon of genus Aegilops.
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Affiliation(s)
- Mari Gogniashvili
- Institute of Molecular Genetics, Agricultural University of Georgia, #240 D. Agmashenebeli Alley, 0159, Tbilisi, Georgia.
| | | | - Inesa Maisaia
- Institute of Botany, Ilia State University, Tbilisi, Georgia
| | - Maia Akhalkatsi
- Institute of Botany, Ilia State University, Tbilisi, Georgia
| | - Adam Kotorashvili
- National Centre for Disease Control and Public Health, Tbilisi, Georgia
| | - Nato Kotaria
- National Centre for Disease Control and Public Health, Tbilisi, Georgia
| | - Tengiz Beridze
- Institute of Molecular Genetics, Agricultural University of Georgia, #240 D. Agmashenebeli Alley, 0159, Tbilisi, Georgia
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Tevdoradze E, Farlow J, Kotorashvili A, Skhirtladze N, Antadze I, Gunia S, Balarjishvili N, Kvachadze L, Kutateladze M. Whole genome sequence comparison of ten diagnostic brucellaphages propagated on two Brucella abortus hosts. Virol J 2015; 12:66. [PMID: 25896365 PMCID: PMC4422536 DOI: 10.1186/s12985-015-0287-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 03/24/2015] [Indexed: 11/24/2022] Open
Abstract
Background Recently the genome sequences of two brucellaphages, isolated in Georgia (Tb) and Mexico (Pr) were reported revealing pronounced sequence homogeneity and the presence of two major indels discriminating the two phages. Subsequent genome sequencing of six diagnostic brucellaphages: Tbilisi (Tb), Firenze (Fz), Weybridge (Wb), S708, Berkeley (Bk) and R/C phages identified three major genetic groups. However, the propensity for fine-scale genetic variability of diverse brucellaphages grown on multiple hosts within a single Brucella species remains unknown. Methods We sequenced the complete genomes of ten brucellaphages following initial propagation on B. abortus strain 141 and after subsequent propagation on B. abortus strain S19. All brucellaphages were isolated and propagated at the Eliava Institute including the original Tb phage. Genomic libraries were quantified using the Qbit and sheared on the Covaris M220. QC for fragmentation was performed on the BioAnalyzer 2100. DNA libraries were prepared using an Illumina Paired-End protocol and sequenced on the Illumina MiSeq. Sequence analysis was performed using Geneious and MEGA software. Results Comparative whole genome sequence analysis revealed genetic homogeneity consistent with previously published data as well as multiple nucleotide variations. Genomic changes as a result of passages were observed in similar genes and predominantly occurred at identical sites in separate phages. Multiple instances of within-sample genetic heterogeneity were observed often at shared genomics positions across phages. Positive selection was detected in the tail collar protein gene. We also identified a Staphylothermus marinus F1-like CRISPR spacer and sequences orthologous to both prophage antirepressors of Brucella spp. and intergenic sequences encoded by Ochrobactrum anthropi. Conclusion We surveyed whole genome level diversity in phage lytic for B. abortus as they are propagated on alternate vaccine strains within the species. Our data extend previous results indicating select variable hotspots and broad genomic homogeneity as well as multiple common polymorphisms and within-sample variation. These data also provide additional genomes for future reference in comparative studies involving the molecular evolution and host specificity of brucellaphages.
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Affiliation(s)
- Ekaterine Tevdoradze
- George Eliava Institute for Bacteriophages, Microbiology and Virology, Tbilisi, Georgia.
| | - Jason Farlow
- Academic Engagement Program (AEP) Pennsylvania State University, University Park, State College, USA. .,Farlow Scientific Consulting Company, LLC, Lewiston, Utah, USA.
| | - Adam Kotorashvili
- Lugar Center for Public Health Research at National Center for Disease Control, Tbilisi, Georgia.
| | - Natia Skhirtladze
- George Eliava Institute for Bacteriophages, Microbiology and Virology, Tbilisi, Georgia.
| | - Irina Antadze
- George Eliava Institute for Bacteriophages, Microbiology and Virology, Tbilisi, Georgia.
| | - Sophio Gunia
- George Eliava Institute for Bacteriophages, Microbiology and Virology, Tbilisi, Georgia.
| | - Nana Balarjishvili
- George Eliava Institute for Bacteriophages, Microbiology and Virology, Tbilisi, Georgia.
| | - Leila Kvachadze
- George Eliava Institute for Bacteriophages, Microbiology and Virology, Tbilisi, Georgia.
| | - Mzia Kutateladze
- George Eliava Institute for Bacteriophages, Microbiology and Virology, Tbilisi, Georgia.
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Farlow J, Filippov AA, Sergueev KV, Hang J, Kotorashvili A, Nikolich MP. Comparative whole genome analysis of six diagnostic brucellaphages. Gene 2014; 541:115-22. [PMID: 24530704 DOI: 10.1016/j.gene.2014.01.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 11/04/2013] [Accepted: 01/07/2014] [Indexed: 11/24/2022]
Abstract
Whole genome sequencing of six diagnostic brucellaphages, Tbilisi (Tb), Firenze (Fz), Weybridge (Wb), S708, Berkeley (Bk) and R/C, was followed with genomic comparisons including recently described genomes of the Tb phage from Mexico (TbM) and Pr phage to elucidate genomic diversity and candidate host range determinants. Comparative whole genome analysis revealed high sequence homogeneity among these brucellaphage genomes and resolved three genetic groups consistent with defined host range phenotypes. Group I was composed of Tb and Fz phages that are predominantly lytic for Brucella abortus and Brucella neotomae; Group II included Bk, R/C, and Pr phages that are lytic mainly for B. abortus, Brucella melitensis and Brucella suis; Group III was composed of Wb and S708 phages that are lytic for B. suis, B. abortus and B. neotomae. We found that the putative phage collar protein is a variable locus with features that may be contributing to the host specificities exhibited by different brucellaphage groups. The presence of several candidate host range determinants is illustrated herein for future dissection of the differential host specificity observed among these phages.
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Affiliation(s)
| | - Andrey A Filippov
- Department of Emerging Bacterial Infections, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Kirill V Sergueev
- Department of Emerging Bacterial Infections, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Adam Kotorashvili
- Richard G. Lugar Center for Public Health Research, Tbilisi, Georgia
| | - Mikeljon P Nikolich
- Department of Emerging Bacterial Infections, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
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Kotorashvili A, Ramnauth A, Liu C, Lin J, Ye K, Kim R, Hazan R, Rohan T, Fineberg S, Loudig O. Effective DNA/RNA co-extraction for analysis of microRNAs, mRNAs, and genomic DNA from formalin-fixed paraffin-embedded specimens. PLoS One 2012; 7:e34683. [PMID: 22514653 PMCID: PMC3326040 DOI: 10.1371/journal.pone.0034683] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/08/2012] [Indexed: 01/03/2023] Open
Abstract
Background Retrospective studies of archived human specimens, with known clinical follow-up, are used to identify predictive and prognostic molecular markers of disease. Due to biochemical differences, however, formalin-fixed paraffin-embedded (FFPE) DNA and RNA have generally been extracted separately from either different tissue sections or from the same section by dividing the digested tissue. The former limits accurate correlation whilst the latter is impractical when utilizing rare or limited archived specimens. Principal Findings For effective recovery of genomic DNA and total RNA from a single FFPE specimen, without splitting the proteinase-K digested tissue solution, we optimized a co-extraction method by using TRIzol and purifying DNA from the lower aqueous and RNA from the upper organic phases. Using a series of seven different archived specimens, we evaluated the total amounts of genomic DNA and total RNA recovered by our TRIzol-based co-extraction method and compared our results with those from two commercial kits, the Qiagen AllPrep DNA/RNA FFPE kit, for co-extraction, and the Ambion RecoverAll™ Total Nucleic Acid Isolation kit, for separate extraction of FFPE-DNA and -RNA. Then, to accurately assess the quality of DNA and RNA co-extracted from a single FFPE specimen, we used qRT-PCR, gene expression profiling and methylation assays to analyze microRNAs, mRNAs, and genomic DNA recovered from matched fresh and FFPE MCF10A cells. These experiments show that the TRIzol-based co-extraction method provides larger amounts of FFPE-DNA and –RNA than the two other methods, and particularly provides higher quality microRNAs and genomic DNA for subsequent molecular analyses. Significance We determined that co-extraction of genomic DNA and total RNA from a single FFPE specimen is an effective recovery approach to obtain high-quality material for parallel molecular and high-throughput analyses. Our optimized approach provides the option of collecting DNA, which would otherwise be discarded or degraded, for additional or subsequent studies.
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Affiliation(s)
- Adam Kotorashvili
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Andrew Ramnauth
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Christina Liu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Juan Lin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Kenny Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Ryung Kim
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Rachel Hazan
- Department of Pathology, Albert Einstein College of Medicine of Yeshiva University, Bronx , New York, United States of America
| | - Thomas Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Susan Fineberg
- Department of Pathology, Albert Einstein College of Medicine of Yeshiva University, Bronx , New York, United States of America
| | - Olivier Loudig
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
- Department of Pathology, Albert Einstein College of Medicine of Yeshiva University, Bronx , New York, United States of America
- * E-mail:
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11
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Beers MF, Hawkins A, Maguire JA, Kotorashvili A, Zhao M, Newitt JL, Ding W, Russo S, Guttentag S, Gonzales L, Mulugeta S. A nonaggregating surfactant protein C mutant is misdirected to early endosomes and disrupts phospholipid recycling. Traffic 2011; 12:1196-210. [PMID: 21707890 DOI: 10.1111/j.1600-0854.2011.01223.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interstitial lung disease in both children and adults has been linked to mutations in the lung-specific surfactant protein C (SFTPC) gene. Among these, the missense mutation [isoleucine to threonine at codon 73 = human surfactant protein C (hSP-C(I73T) )] accounts for ∼30% of all described SFTPC mutations. We reported previously that unlike the BRICHOS misfolding SFTPC mutants, expression of hSP-C(I73T) induces lung remodeling and alveolar lipoproteinosis without a substantial Endoplasmic Reticulum (ER) stress response or ER-mediated intrinsic apoptosis. We show here that, in contrast to its wild-type counterpart that is directly routed to lysosomal-like organelles for processing, SP-C(I73T) is misdirected to the plasma membrane and subsequently internalized to the endocytic pathway via early endosomes, leading to the accumulation of abnormally processed proSP-C isoforms. Functionally, cells expressing hSP-C(I73T) demonstrated both impaired uptake and degradation of surfactant phospholipid, thus providing a molecular mechanism for the observed lipid accumulation in patients expressing hSP-C(I73T) through the disruption of normal phospholipid recycling. Our data provide evidence for a novel cellular mechanism for conformational protein-associated diseases and suggest a paradigm for mistargeted proteins involved in the disruption of the endosomal/lysosomal sorting machinery.
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Affiliation(s)
- Michael F Beers
- Pulmonary, Allergy, and Critical Care Division, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Mulugeta S, Zhao M, Kotorashvili A, Shuman H, Beers MF. A Novel xLxxKN Targeting Motif of ATP Binding Cassette Class A Transporters. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.687.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Ming Zhao
- MedicineUniversity of PennsylvaniaPhiladelphiaPA
| | | | - Henry Shuman
- PhysiologyUniversilty of PennsylvaniaPhiladelphiaPA
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Kotorashvili A, Russo SJ, Mulugeta S, Guttentag S, Beers MF. Anterograde transport of surfactant protein C proprotein to distal processing compartments requires PPDY-mediated association with Nedd4 ubiquitin ligases. J Biol Chem 2009; 284:16667-16678. [PMID: 19366705 PMCID: PMC2713532 DOI: 10.1074/jbc.m109.002816] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 04/02/2009] [Indexed: 11/06/2022] Open
Abstract
Biosynthesis of surfactant protein C (SP-C) by alveolar type 2 cells requires proteolytic processing of a 21-kDa propeptide (proSP-C21) in post-Golgi compartments to yield a 3.7-kDa mature form. Scanning alanine mutagenesis, binding assays, and co-immunoprecipitation were used to characterize the proSP-C targeting domain. Delivery of proSP-C21 to distal processing organelles is dependent upon the NH2-terminal cytoplasmic SP-C propeptide, which contains a conserved PPDY motif. In A549 cells, transfection of EGFP/proSP-C21 constructs containing polyalanine substitution for Glu11-Thr18, 13PPDY16, or 14P,16Y produced endoplasmic reticulum retention of the fusion proteins. Protein-protein interactions of proSP-C with known WW domains were screened using a solid-phase array that revealed binding of the proSP-C NH2 terminus to several WW domains found in the Nedd4 family of E3 ligases. Specificity of the interaction was confirmed by co-immunoprecipitation of proSP-C and Nedd4 or Nedd4-2 in epithelial cell lines. By Western blotting and reverse transcription-PCR, both forms were detected in primary human type 2 cells. Knockdown of Nedd4-2 by small interference RNA transfection of cultured human type 2 cells blocked processing of 35S-labeled proSP-C21. Mutagenesis of potential acceptor sites for ubiquitination in the cytosolic domain of proSP-C (Lys6, Lys34, or both) failed to inhibit trafficking of EGFP/proSP-C21. These results indicate that PPDY-mediated interaction with Nedd4 E3-ligases is required for trafficking of proSP-C. We speculate that the Nedd4/proSP-C tandem is part of a larger protein complex containing a ubiquitinated component that further directs its transport.
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Affiliation(s)
- Adam Kotorashvili
- From the Surfactant Biology Laboratories, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Scott J Russo
- From the Surfactant Biology Laboratories, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Surafel Mulugeta
- From the Surfactant Biology Laboratories, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Susan Guttentag
- Division of Neonatology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Michael F Beers
- From the Surfactant Biology Laboratories, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104.
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14
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Mulugeta S, Maguire JA, Newitt JL, Russo SJ, Kotorashvili A, Beers MF. Misfolded BRICHOS SP-C mutant proteins induce apoptosis via caspase-4- and cytochrome c-related mechanisms. Am J Physiol Lung Cell Mol Physiol 2007; 293:L720-9. [PMID: 17586700 DOI: 10.1152/ajplung.00025.2007] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Several mutations within the BRICHOS domain of surfactant protein C (SP-C) have been linked to interstitial lung disease. Recent studies have suggested that these mutations cause misfolding of the proprotein (proSP-C), which initiates the unfolded protein response to resolve improper folding or promote protein degradation. We have reported that in vitro expression of one of these proteins, the exon 4 deletion mutant (hSP-CΔexon4), causes endoplasmic reticulum (ER) stress, inhibits proteasome function, and activates caspase-3-mediated apoptosis. To further elucidate mechanisms and common pathways for cellular dysfunction, various assays were performed by transiently expressing two SP-C BRICHOS domain mutant (BRISPC) proteins (hSP-CΔexon4, hSP-CL188Q) and control proteins in lung epithelium-derived A549 and kidney epithelium-derived (HEK-293) GFPu-1 cell lines. Compared with controls, cells expressing either BRICHOS mutant protein consistently exhibited increased formation of insoluble aggregates, enhanced promotion of inositol-requiring enzyme 1-dependent splicing of X-box binding protein-1 (XBP-1), significant inhibition of proteasome activity, enhanced induction of mitochondrial cytochrome c release, and increased activations of caspase-4 and caspase-3, leading to apoptosis. These results suggest common cellular responses, including initiation of cell-death signaling pathways, to these lung disease-associated BRISPC proteins.
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Affiliation(s)
- Surafel Mulugeta
- Pulmonary, Allergy, and Critical Care Division, Univ. of Pennsylvania School of Medicine, Vernon & Shirley Hill Pavilion, Suite H418, 380 South Univ. Ave., Philadelphia, PA 19104, USA.
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Kotorashvili A, Mulugeta S, Russo SJ, Beers MF. Surfactant Protein C Interacts with WW Domains of Nedd 4 Via an N‐terminal PPDY Motif. FASEB J 2007. [DOI: 10.1096/fasebj.21.5.a651-d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Adam Kotorashvili
- University of Pennsylvania, Abramson Research Center, 3615 Civic Center BoulevardPhiladelphiaPA19104‐4318
| | - Surafel Mulugeta
- University of Pennsylvania, Abramson Research Center, 3615 Civic Center BoulevardPhiladelphiaPA19104‐4318
| | - Scott J. Russo
- University of Pennsylvania, Abramson Research Center, 3615 Civic Center BoulevardPhiladelphiaPA19104‐4318
| | - Michael F. Beers
- University of Pennsylvania, Abramson Research Center, 3615 Civic Center BoulevardPhiladelphiaPA19104‐4318
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Solomonia RO, Kotorashvili A, Kiguradze T, McCabe BJ, Horn G. Ca2+/calmodulin protein kinase II and memory: learning-related changes in a localized region of the domestic chick brain. J Physiol 2005; 569:643-53. [PMID: 16179361 PMCID: PMC1464238 DOI: 10.1113/jphysiol.2005.098012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The role of calcium/calmodulin-dependent protein kinase II (CaMKII) in the recognition memory of visual imprinting was investigated. Domestic chicks were exposed to a training stimulus and learning strength measured. Trained chicks, together with untrained chicks, were killed either 1 h or 24 h after training. The intermediate and medial hyperstriatum ventrale/mesopallium (IMHV/IMM), a forebrain memory storage site, was removed together with a control brain region, the posterior pole of the neostriatum/nidopallium (PPN). Amounts of membrane total alphaCaMKII (tCaMKII) and Thr286-autophosphorylated alphaCaMKII (apCAMKII) were measured. For the IMHV/IMM 1 h group, apCaMKII amount and apCAMKII/tCaMKII increased as chicks learned. The magnitude of the molecular changes were positively correlated with learning strength. No learning-related effects were observed in PPN, or in either region at 24 h. These results suggest that CaMKII is involved in the formation of memory but not in its maintenance.
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Affiliation(s)
- Revaz O Solomonia
- Institute of Physiology, Georgian Academy of Sciences, Tbilisi, Republic of Georgia
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Solomonia RO, Morgan K, Kotorashvili A, McCabe BJ, Jackson AP, Horn G. Analysis of differential gene expression supports a role for amyloid precursor protein and a protein kinase C substrate (MARCKS) in long-term memory. Eur J Neurosci 2003; 17:1073-81. [PMID: 12653983 DOI: 10.1046/j.1460-9568.2003.02539.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Previous work has identified the intermediate and medial part of the hyperstriatum ventrale (IMHV) as a region of the chick brain storing information acquired through the learning process of imprinting. We have examined in this brain region changes in expression of candidate genes involved in memory. Chicks were exposed to a rotating red box and the strength of their preference for it, a measure of learning, determined. Brain samples were removed approximately 24 h after training. Candidate genes whose expressions were different in IMHV samples derived from strongly imprinted chicks relative to those from chicks showing little or no learning were identified using subtractive hybridization. The translation products of two candidate genes were investigated further in samples from the left and right IMHV and from two other brain regions not previously implicated in imprinting, the left and right posterior neostriatum. One of the proteins was the amyloid precursor protein (APP), the other was myristoylated alanine rich C kinase substrate (MARCKS). In the left IMHV the levels of the two proteins increased with the strength of learning. The effects in the right IMHV were not significantly different from those in the left. There were no effects of learning in the posterior neostriatum. This is the first study to relate changes in the amounts of MARCKS and APP proteins to the strength of learning in a brain region known to be a memory store and demonstrates that the systematic identification of protein molecules involved in memory formation is possible.
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Affiliation(s)
- R O Solomonia
- Institute of Physiology, Georgian Academy of Sciences, 14 Gotua St, Tbilisi 38600, Republic of Georgia
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