Search

Your search keyword '"Lobanov, Alexei"' showing total 155 results
Start Over Author "Lobanov, Alexei"
155 results on '"Lobanov, Alexei"'

2. HIV vaccine candidate efficacy in female macaques mediated by cAMP-dependent efferocytosis and V2-specific ADCC

Author

Bissa, Massimiliano, Kim, Sohyoung, Galli, Veronica, Fourati, Slim, Sarkis, Sarkis, Arakelyan, Anush, de Castro, Isabela Silva, Rahman, Mohammad Arif, Fujiwara, Saori, Vaccari, Monica, Tomalka, Jeffrey A., Stamos, James D., Schifanella, Luca, Gorini, Giacomo, Moles, Ramona, Gutowska, Anna, Ferrari, Guido, Lobanov, Alexei, Montefiori, David C., Nelson, George W., Cam, Margaret C., Chakhtoura, Marita, Haddad, Elias K., Doster, Melvin N., McKinnon, Katherine, Brown, Sophia, Venzon, David J., Choo-Wosoba, Hyoyoung, Breed, Matthew W., Killoran, Kristin E., Kramer, Joshua, Margolis, Leonid, Sekaly, Rafick P., Hager, Gordon L., and Franchini, Genoveffa

Published
2023
Full Text
View/download PDF

7. Genomic and ecosystem evidence demonstrate the importance of selenium for the harmful alga, Aureococcus anophagefferens

Author

Gobler, Christopher J, Lobanov, Alexei V, Tang, Ying-Zhong, Turanov, Anton A, Zhang, Yan, Doblin, Martina, Taylor, Gordon T, Sanudo-Wilhelmy, Sergio A, Grigoriev, Igor V, and Gladyshev, Vadim N

Subjects
selenium, selenoproteins, harmful algal blooms, HABs, genome sequence, Aureococcus anophagefferens
Abstract

The trace element selenium (Se) is required for the biosynthesis of selenocysteine (Sec), the 21st amino acid in the genetic code, but its role in the ecology of harmful algal blooms (HABs) is unknown. Here, we examined the role of Se in the biology and ecology of the harmful pelagophyte, Aureococcus anophagefferens, through cell culture, genomic analyses, and ecosystem studies. This organism has the largest and the most diverse selenoproteome identified to date that consists of at least 59 selenoproteins, including known eukaryotic selenoproteins, selenoproteins previously only detected in bacteria, and novel selenoproteins. The A. anophagefferens selenoproteome was dominated by the thioredoxin fold proteins and oxidoreductase functions were assigned to the majority of detected selenoproteins. Insertion of Sec in these proteins was supported by a unique Sec insertion sequence. Se was required for the growth of A. anophagefferens as cultures grew maximally at nanomolar Se concentrations. In a coastal ecosystem, dissolved Se concentrations were elevated before and after A. anophagefferens blooms, but were reduced by >95percent during the peak of blooms to 0.05 nM. Consistent with this pattern, enrichment of seawater with selenite before and after a bloom did not affect the growth of A. anophagefferens, but enrichment during the peak of the bloom significantly increased population growth rates. These findings demonstrate that Se inventories, which can be anthropogenically enriched, can support proliferation of HABs, such as A. anophagefferens through its synthesis of a large arsenal of Se-dependent oxidoreductases that fine-tune cellular redox homeostasis.

Published
2013

12. Reusable Single Cell for Iterative Epigenomic Analyses

Author

Ohnuki, Hidetaka, Venzon, David J., Lobanov, Alexei, and Tosato, Giovanna

Subjects
Epigenomics, Epigenome, General Immunology and Microbiology, General Chemical Engineering, General Neuroscience, DNA, DNA-Directed DNA Polymerase, DNA Probes, Article, General Biochemistry, Genetics and Molecular Biology
Abstract

Current single-cell epigenome analyses are designed for single use. The cell is discarded after a single use, preventing analysis of multiple epigenetic marks in a single cell and requiring data from other cells to distinguish signal from experimental background noise in a single cell. This paper describes a method to reuse the same single cell for iterative epigenomic analyses. In this experimental method, cellular proteins are first anchored to a polyacrylamide polymer instead of crosslinking them to protein and DNA, alleviating structural bias. This critical step allows repeated experiments with the same single cell. Next, a random primer with a scaffold sequence for proximity ligation is annealed to the genomic DNA, and the genomic sequence is added to the primer by extension using a DNA polymerase. Subsequently, an antibody against an epigenetic marker and control IgG, each labeled with different DNA probes, are bound to the respective targets in the same single cell. Proximity ligation is induced between the random primer and the antibody by adding a connector DNA with complementary sequences to the scaffold sequence of the random primer and the antibody-DNA probe. This approach integrates antibody information and nearby genome sequences in a single DNA product of proximity ligation. By enabling repeated experiments with the same single cell, this method allows an increase in data density from a rare cell and statistical analysis using only IgG and antibody data from the same cell. The reusable single cells prepared by this method can be stored for at least a few months and reused later to broaden epigenetic characterization and increase data density. This method provides flexibility to researchers and their projects.

Published
2022

15. Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics

Author

Gobler, Christopher J., Berry, Dianna L., Dyhrman, Sonya T., Wilhelm, Steven W., Salamov, Asaf, Lobanov, Alexei V., Zhang, Yan, Collier, Jackie L., Wurch, Louie L., Kustka, Adam B., Dill, Brian D., Shah, Manesh, VerBerkmoes, Nathan C., Kuo, Alan, Terry, Astrid, Pangilinan, Jasmyn, Lindquist, Erika A., Lucas, Susan, Paulsen, Ian T., Hattenrath-Lehmann, Theresa K., Talmage, Stephanie C., Walker, Elyse A., Koch, Florian, Burson, Amanda M., Marcoval, Maria Alejandra, Tang, Ying-Zhong, LeCleir, Gary R., Coyne, Kathryn J., Berg, Gry M., Bertrand, Erin M., Saito, Mark A., Gladyshev, Vadim N., Grigoriev, Igor V., and Karl, David M.

Published
2011

16. Ecdysoneless Protein Regulates Viral and Cellular mRNA Splicing to Promote Cervical Oncogenesis

Author

Mirza, Sameer, primary, Kalluchi, Achyuth, additional, Raza, Mohsin, additional, Saleem, Irfana, additional, Mohapatra, Bhopal, additional, Pal, Dhananjaya, additional, Ouellette, Michel M., additional, Qiu, Fang, additional, Yu, Lulu, additional, Lobanov, Alexei, additional, Zheng, Zhi-Ming, additional, Zhang, Ying, additional, Alsaleem, Mansour A., additional, Rakha, Emad A., additional, Band, Hamid, additional, Rowley, M. Jordan, additional, and Band, Vimla, additional

Published
2021
Full Text
View/download PDF

23. Genome sequencing reveals insights into physiology and longevity of the naked mole rat

Author

Kim, Eun Bae, Fang, Xiaodong, Fushan, Alexey A., Huang, Zhiyong, Lobanov, Alexei V., Han, Lijuan, Marino, Stefano M., Sun, Xiaoqing, Turanov, Anton A., Yang, Pengcheng, Yim, Sun Hee, Zhao, Xiang, Kasaikina, Marina V., Stoletzki, Nina, Peng, Chunfang, Polak, Paz, Xiong, Zhiqiang, Kiezun, Adam, Zhu, Yabing, Chen, Yuanxin, Kryukov, Gregory V., Zhang, Qiang, Peshkin, Leonid, Yang, Lan, Bronson, Roderick T., Buffenstein, Rochelle, Wang, Bo, Han, Changlei, Li, Qiye, Chen, Li, Zhao, Wei, Sunyaev, Shamil R., Park, Thomas J., Zhang, Guojie, Wang, Jun, and Gladyshev, Vadim N.

Subjects
Nucleotide sequencing -- Physiological aspects -- Research -- Genetic aspects, Genomics -- Research -- Physiological aspects -- Genetic aspects, Moles (Animals) -- Physiological aspects -- Genetic aspects -- Research, DNA sequencing -- Physiological aspects -- Research -- Genetic aspects, Longevity -- Physiological aspects -- Genetic aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The naked mole rat (Heterocephalusglaber) is a strictly subterranean, extraordinarily long-lived eusocial mammal (1). Although it is the size of a mouse, its maximum lifespan exceeds 30 years, making this animal the longest-living rodent. Naked mole rats show negligible senescence, no age-related increase in mortality, and high fecundity until death (2). In addition to delayed ageing, they are resistant to both spontaneous cancer and experimentally induced tumorigenesis (3,4). Naked mole rats pose a challenge to the theories that link ageing, cancer and redox homeostasis. Although characterized by significant oxidative stress (5), the naked mole rat proteome does not show age-related susceptibility to oxidative damage or increased ubiquitination (6). Naked mole rats naturally reside in large colonies with a single breeding female, the 'queen', who suppresses the sexual maturity of her subordinates (7). They also live in full darkness, at low oxygen and high carbon dioxide concentrations (8), and are unable to sustain thermogenesis (9) nor feel certain types of pain (10,11). Here we report the sequencing and analysis of the naked mole rat genome, which reveals unique genome features and molecular adaptations consistent with cancer resistance, poikilothermy, hairlessness and insensitivity to low oxygen, and altered visual function, circadian rythms and taste sensing. This information provides insights into the naked mole rat's exceptional longevity and ability to live in hostile conditions, in the dark and at low oxygen. The extreme traits of the naked mole rat, together with the reported genome and transcriptome information, offer opportunities for understanding ageing and advancing other areas of biological and biomedical research., We applied a whole-genome shotgun strategy to sequence the genome of an individual male naked mole rat (NMR) (Table 1 and Supplementary Tables 1-3). The sequencing depth of 98.6% of [...]

Published
2011
Full Text
View/download PDF

28. Pan genome of the phytoplankton Emiliania underpins its global distribution

Author

Read, Betsy A., Kegel, Jessica, Klute, Mary J., Kuo, Alan, Lefebvre, Stephane C., Maumus, Florian, Mayer, Christoph, Miller, John, Monier, Adam, Salamov, Asaf, Young, Jeremy, Aguilar, Maria, Claverie, Jean-Michel, Frickenhaus, Stephan, Gonzalez, Karina, Herman, Emily K., Lin, Yao-Cheng, Napier, Johnathan, Ogata, Hiroyuki, Sarno, Analissa F., Shmutz, Jeremy, Schroeder, Declan, de Vargas, Colomban, Verret, Frederic, von Dassow, Peter, Valentin, Klaus, Van de Peer, Yves, Wheeler, Glen, Allen, Andrew E., Bidle, Kay, Borodovsky, Mark, Bowler, Chris, Brownlee, Colin, Cock, Mark J., Elias, Marek, Gladyshev, Vadim N., Groth, Marco, Guda, Chittibabu, Hadaegh, Ahmad, Debora Iglesias-Rodriguez, Maria, Jenkins, Jerry, Jones, Bethan M., Lawson, Tracy, Leese, Florian, Lindquist, Erika, Lobanov, Alexei, Lomsadze, Alexandre, Malik, Shehre-Banoo, Marsh, Mary E., Mackinder, Luke, Mock, Thomas, Mueller-Roeber, Bernd, Pagarete, António, Parker, Micaela, Probert, Ian, Quesneville, Hadi, Raines, Christine, Rensing, Stefan A., Riaño-Pachón, Diego Mauricio, Richier, Sophie, Rokitta, Sebastian, Shiraiwa, Yoshihiro, Soanes, Darren M., van der Giezen, Mark, Wahlund, Thomas M., Williams, Bryony, Wilson, Willie, Wolfe, Gordon, Wurch, Louie L., Dacks, Joel B., Delwiche, Charles F., Dyhrman, Sonya T., Glöckner, Gernot, John, Uwe, Richards, Thomas, Worden, Alexandra Z., Zhang, Xiaoyu, and Grigoriev, Igor V.

Published
2013
Full Text
View/download PDF

29. Abstract 4221: Anti-Tumor activity of the multityrosine kinase inhibitor dasatinib in type 1 papillary renal cell carcinoma

Author

Pahwa, Roma, primary, Dubhashi, Janhavi, additional, Giri, Abhigya, additional, Thomas, Craig, additional, Ceribelli, Michele, additional, Jailwala, Parthav, additional, Lobanov, Alexei, additional, Singh, Anand, additional, Sourbier, Carole, additional, Ricketts, Christopher J., additional, Vocke, Cathy D., additional, Yang, Youfeng, additional, Linehan, W. Marston, additional, and Srinivasan, Ramaprasad, additional

Published
2020
Full Text
View/download PDF

36. Position-dependent termination and widespread obligatory frameshifting in Euplotes translation

Author

Lobanov, Alexei V, primary, Heaphy, Stephen M, additional, Turanov, Anton A, additional, Gerashchenko, Maxim V, additional, Pucciarelli, Sandra, additional, Devaraj, Raghul R, additional, Xie, Fang, additional, Petyuk, Vladislav A, additional, Smith, Richard D, additional, Klobutcher, Lawrence A, additional, Atkins, John F, additional, Miceli, Cristina, additional, Hatfield, Dolph L, additional, Baranov, Pavel V, additional, and Gladyshev, Vadim N, additional

Published
2016
Full Text
View/download PDF

37. Selenoprotein Gene Nomenclature

Author

Gladyshev, Vadim N., primary, Arnér, Elias S., additional, Berry, Marla J., additional, Brigelius-Flohé, Regina, additional, Bruford, Elspeth A., additional, Burk, Raymond F., additional, Carlson, Bradley A., additional, Castellano, Sergi, additional, Chavatte, Laurent, additional, Conrad, Marcus, additional, Copeland, Paul R., additional, Diamond, Alan M., additional, Driscoll, Donna M., additional, Ferreiro, Ana, additional, Flohé, Leopold, additional, Green, Fiona R., additional, Guigó, Roderic, additional, Handy, Diane E., additional, Hatfield, Dolph L., additional, Hesketh, John, additional, Hoffmann, Peter R., additional, Holmgren, Arne, additional, Hondal, Robert J., additional, Howard, Michael T., additional, Huang, Kaixun, additional, Kim, Hwa-Young, additional, Kim, Ick Young, additional, Köhrle, Josef, additional, Krol, Alain, additional, Kryukov, Gregory V., additional, Lee, Byeong Jae, additional, Lee, Byung Cheon, additional, Lei, Xin Gen, additional, Liu, Qiong, additional, Lescure, Alain, additional, Lobanov, Alexei V., additional, Loscalzo, Joseph, additional, Maiorino, Matilde, additional, Mariotti, Marco, additional, Sandeep Prabhu, K., additional, Rayman, Margaret P., additional, Rozovsky, Sharon, additional, Salinas, Gustavo, additional, Schmidt, Edward E., additional, Schomburg, Lutz, additional, Schweizer, Ulrich, additional, Simonović, Miljan, additional, Sunde, Roger A., additional, Tsuji, Petra A., additional, Tweedie, Susan, additional, Ursini, Fulvio, additional, Whanger, Philip D., additional, and Zhang, Yan, additional

Published
2016
Full Text
View/download PDF

40. Adaptations to a Subterranean Environment and Longevity Revealed by the Analysis of Mole Rat Genomes

Author

Fang, Xiaodong, primary, Seim, Inge, additional, Huang, Zhiyong, additional, Gerashchenko, Maxim V., additional, Xiong, Zhiqiang, additional, Turanov, Anton A., additional, Zhu, Yabing, additional, Lobanov, Alexei V., additional, Fan, Dingding, additional, Yim, Sun Hee, additional, Yao, Xiaoming, additional, Ma, Siming, additional, Yang, Lan, additional, Lee, Sang-Goo, additional, Kim, Eun Bae, additional, Bronson, Roderick T., additional, Šumbera, Radim, additional, Buffenstein, Rochelle, additional, Zhou, Xin, additional, Krogh, Anders, additional, Park, Thomas J., additional, Zhang, Guojie, additional, Wang, Jun, additional, and Gladyshev, Vadim N., additional

Published
2014
Full Text
View/download PDF

44. Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems.

Author

Mariotti, Marco, Lobanov, Alexei V., Manta, Bruno, Santesmasses, Didac, Bofill, Andreu, Guigó, Roderic, Gabaldón, Toni, and Gladyshev, Vadim N.

Abstract

Selenocysteine (Sec) is the 21st amino acid in the genetic code, inserted in response to UGA codons with the help of RNA structures, the SEC Insertion Sequence (SECIS) elements. The three domains of life feature distinct strategies for Sec insertion in proteins and its utilization.While bacteria and archaea possess similar sets of selenoproteins, Sec biosynthesis is more similar among archaea and eukaryotes. However, SECIS elements are completely different in the three domains of life. Here, we analyze the archaeon Lokiarchaeota that resolves the relationships among Sec insertion systems. This organism has selenoproteins representing five protein families, three of which have multiple Sec residues. Remarkably, these archaeal selenoprotein genes possess conserved RNA structures that strongly resemble the eukaryotic SECIS element, including key eukaryotic protein-binding sites. These structures also share similarity with the SECIS element in archaeal selenoprotein VhuD, suggesting a relation of direct descent. These results identify Lokiarchaeota as an intermediate form between the archaeal and eukaryotic Sec-encoding systems and clarify the evolution of the Sec insertion system. [ABSTRACT FROM AUTHOR]

Published
2016
Full Text
View/download PDF

46. Position-dependent termination and widespread obligatory frameshifting in Euplotes translation

Author

Lobanov, Alexei V, Heaphy, Stephen M, Turanov, Anton A, Gerashchenko, Maxim V, Pucciarelli, Sandra, Devaraj, Raghul R, Xie, Fang, Petyuk, Vladislav A, Smith, Richard D, Klobutcher, Lawrence A, Atkins, John F, Miceli, Cristina, Hatfield, Dolph L, Baranov, Pavel V, and Gladyshev, Vadim N

Abstract

The ribosome can change its reading frame during translation in a process known as programmed ribosomal frameshifting. These rare events are supported by complex mRNA signals. However, we found that the ciliates Euplotes crassus and Euplotes focardii exhibit widespread frameshifting at stop codons. 47 different codons preceding stop signals resulted in either +1 or +2 frameshifts, and +1 frameshifting at AAA was the most frequent. The frameshifts showed unusual plasticity and rapid evolution, and had little influence on translation rates. The proximity of a stop codon to the 3′ mRNA end, rather than its occurrence or sequence context, appeared to designate termination. Thus, a 'stop codon' is not a sufficient signal for translation termination, and the default function of stop codons in Euplotes is frameshifting, whereas termination is specific to certain mRNA positions and probably requires additional factors.

Published
2017
Full Text
View/download PDF

47. Reduced Utilization of Selenium by Naked Mole Rats Due to a Specific Defect in GPx1 Expression

Author

Kasaikina, Marina V., primary, Lobanov, Alexei V., additional, Malinouski, Mikalai Y., additional, Lee, Byung Cheon, additional, Seravalli, Javier, additional, Fomenko, Dmitri E., additional, Turanov, Anton A., additional, Finney, Lydia, additional, Vogt, Stefan, additional, Park, Thomas J., additional, Miller, Richard A., additional, Hatfield, Dolph L., additional, and Gladyshev, Vadim N., additional

Published
2011
Full Text
View/download PDF

49. Position dependent termination and widespread obligatory frameshifting in Euplotes translation

Author

Lobanov, Alexei V., Heaphy, Stephen M., Turanov, Anton A., Gerashchenko, Maxim V., Pucciarelli, Sandra, Devaraj, Raghul R., Xie, Fang, Petyuk, Vladislav A., Smith, Richard D., Klobutcher, Lawrence A., Atkins, John F., Miceli, Cristina, Hatfield, Dolph L., Baranov, Pavel V., and Gladyshev, Vadim N.

Abstract

The ribosome can change its reading frame during translation in a process known as programmed ribosomal frameshifting. These rare events are supported by complex mRNA signals. However, we found that the ciliates Euplotes crassus and Euplotes focardii exhibit widespread frameshifting at stop codons. 47 different codons preceding stop signals resulted in either +1 or +2 frameshifts, with the +1 frameshifting at AAA being the most frequent. The frameshifts show unusual plasticity and rapid evolution, and have little influence on translation rates. Proximity of a stop codon to the 3′-mRNA end rather than its occurrence or sequence context appeared to designate termination. Thus, a stop codon is not a sufficient signal for translation termination, and the default function of stop codons in Euplotes is frameshifting, whereas termination is specific to certain mRNA positions and likely requires additional factors.

Published
2016
Full Text
View/download PDF

50. Evidence that mutation accumulation does not cause aging in Saccharomyces cerevisiae

Author

Kaya, Alaattin, Lobanov, Alexei V, and Gladyshev, Vadim N

Subjects
aging, DNA damage, lifespan, mitochondria, mutations, thiol peroxidase, yeast
Abstract

The concept that mutations cause aging phenotypes could not be directly tested previously due to inability to identify age-related mutations in somatic cells and determine their impact on organismal aging. Here, we subjected Saccharomyces cerevisiae to multiple rounds of replicative aging and assessed de novo mutations in daughters of mothers of different age. Mutations did increase with age, but their low numbers, < 1 per lifespan, excluded their causal role in aging. Structural genome changes also had no role. A mutant lacking thiol peroxidases had the mutation rate well above that of wild-type cells, but this did not correspond to the aging pattern, as old wild-type cells with few or no mutations were dying, whereas young mutant cells with many more mutations continued dividing. In addition, wild-type cells lost mitochondrial DNA during aging, whereas shorter-lived mutant cells preserved it, excluding a causal role of mitochondrial mutations in aging. Thus, DNA mutations do not cause aging in yeast. These findings may apply to other damage types, suggesting a causal role of cumulative damage, as opposed to individual damage types, in organismal aging.

Published
2014
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results