Публикации ИЦиГ СО РАН в журналах с высоким импакт-фактором 2016-2017 годы

Публикации ИЦиГ в журналах с высоким импакт-фактором в 2017 году


1) Chaos and Hyperchaos in a Model of Ribosome Autocatalytic Synthesis

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5151018/

Likhoshvai VA, Kogai VV, Fadeev SI, Khlebodarova TM

SCIENTIFIC REPORTS
Том: 6
Номер статьи: 38870
DOI: 10.1038/srep38870
Опубликовано: DEC 12 2016
iF 5.228

2) A quantitative method for determination of PPDK concentration in miscanthus leaves

http://onlinelibrary.wiley.com/doi/10.1111/gcbb.12361/full

Meshcheryakova IA, Bannikova SV, Rozanov AS, Demidova EV, Demidov EA, Goryachkovskaya TN, Burmakina NV, Shekhovtsov SV, Bryanskaya AV, Kolchanov NA, Peltek SE

GLOBAL CHANGE BIOLOGY BIOENERGY
Том: 9 Выпуск: 1 Стр.: 262-269 Специальный выпуск: SI
DOI: 10.1111/gcbb.12361
Опубликовано: JAN 2017
iF 6.151

Abstract:

          In this study, we used ELISA for quantification of PPDK in photosynthesizing leaves of miscanthus. We cloned a fragment of the gene encoding PPDK, purified the resulting protein by affinity chromatography, identified it using MALDI mass spectrometry, and obtained monoclonal antibodies by immunizing BALB/c mice. Selectivity of monoclonal antibodies was assessed by Western blot using the protein extracts of Soranovskii. The presence of PPDK was again verified by MALDI mass spectrometry. Therefore, we developed and tested the method for determining PPDK quantity in miscanthus using ELISA.

3) Evaluation of the SeedCounter, A Mobile Application for Grain Phenotyping

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5151018/

Komyshev E, Genaev M, Afonnikov D

FRONTIERS IN PLANT SCIENCE
Том: 7
Номер статьи: 1990
DOI: 10.3389/fpls.2016.01990
Опубликовано: JAN 4 2017
iF 4.495

Abstract:

Grain morphometry in cereals is an important step in selecting new high-yielding plants. Manual assessment of parameters such as the number of grains per ear and grain size is laborious. One solution to this problem is image-based analysis that can be performed using a desktop PC. Furthermore, the effectiveness of analysis performed in the field can be improved through the use of mobile devices. In this paper, we propose a method for the automated evaluation of phenotypic parameters of grains using mobile devices running the Android operational system. The experimental results show that this approach is efficient and sufficiently accurate for the large-scale analysis of phenotypic characteristics in wheat grains. Evaluation of our application under six different lighting conditions and three mobile devices demonstrated that the lighting of the paper has significant influence on the accuracy of our method, unlike the smartphone type.

4) The Interplay of Chromatin Landscape and DNA-Binding Context Suggests Distinct Modes of EIN3 Regulation in Arabidopsis thaliana

http://onlinelibrary.wiley.com/doi/10.1111/gcbb.12361/full

Zemiyanskaya EV, Leyitsky VG, Oshchepkov DY, Grosse I, Mironova VV

FRONTIERS IN PLANT SCIENCE
Том: 7
Номер статьи: 2044
DOI: 10.3389/fpls.2016.02044
Опубликовано: JAN 9 2017
iF 4.495

Abstract:

The plant hormone ethylene regulates numerous developmental processes and stress responses. Ethylene signaling proceeds via a linear pathway, which activates transcription factor (TF) EIN3, a primary transcriptional regulator of ethylene response. EIN3 influences gene expression upon binding to a specific sequence in gene promoters. This interaction, however, might be considerably affected by additional co-factors. In this work, we perform whole genome bioinformatics study to identify the impact of epigenetic factors in EIN3 functioning. The analysis of publicly available ChIP-Seq data on EIN3 binding in Arabidopsis thaliana showed bimodality of distribution of EIN3 binding regions (EBRs) in gene promoters. Besides a sharp peak in close proximity to transcription start site, which is a common binding region for a wide variety of TFs, we found an additional extended peak in the distal promoter region. We characterized all EBRs with respect to the epigenetic status appealing to previously published genome-wide map of nine chromatin states in A. thaliana. We found that the implicit distal peak was associated with a specific chromatin state (referred to as chromatin state 4 in the primary source), which was just poorly represented in the pronounced proximal peak. Intriguingly, EBRs corresponding to this chromatin state 4 were significantly associated with ethylene response, unlike the others representing the overwhelming majority of EBRs related to the explicit proximal peak. Moreover, we found that specific EIN3 binding sequences predicted with previously described model were enriched in the EBRs mapped to the chromatin state 4, but not to the rest ones. These results allow us to conclude that the interplay of genetic and epigenetic factors might cause the distinct modes of EIN3 regulation.


5) Contributions of age-related alterations of the retinal pigment epithelium and of glia to the AMD-like pathology in OXYS rats

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5278403/

Telegina, DV, Kozhevnikova, OS, Bayborodin, SI, Kolosova, NG

SCIENTIFIC REPORTS
Том: 7
Номер статьи: 41533
DOI: 10.1038/srep41533
Опубликовано: JAN 30 2017
iF 5.228

Abstract:

Age-related macular degeneration (AMD) is a major cause of blindness in developed countries, and the molecular pathogenesis of early events of AMD is poorly understood. It is known that age-related alterations of retinal pigment epithelium (RPE) cells and of glial reactivity are early hallmarks of AMD. Here we evaluated contributions of the age-related alterations of the RPE and of glia to the development of AMD-like retinopathy in OXYS rats. We showed that destructive alterations in RPE cells are a primary change during the development of retinopathy in OXYS rats. Furthermore, a defect of retinal maturation and decreased immune function at the preclinical stage of retinopathy were observed in OXYS rats in addition to the impairment of RPE cell proliferation and of their capacity for division. At the active stage of the disease, the atrophic alterations increased, and reactive gliosis was observed when disease progressed, but immune function stayed weakened. Unexpectedly, we did not observe migration of microglia and macrophages into the photoreceptor layer. These results and the wide spectrum of age-related retinal alterations in humans as well as individual differences in the risk of AMD may be attributed to genetic factors and to differences in the underlying molecular events.

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Публикации ИЦиГ в журналах с высоким импакт-фактором в 2016 году


1) Whole exome sequencing links dental tumor to an autosomal-dominant mutation in ANO5 gene associated with gnathodiaphyseal dysplasia and muscle dystrophies

https://www.ncbi.nlm.nih.gov/pubmed/27216912

Andreeva TV; Tyazhelova TV; Rykalina VN; Gusev FE; Goltsov AY; Zolotareva OI; Aliseichik MP; Borodina TA; Grigorenko AP; Reshetov DA; Ginter EK; Amelina SS; Zinchenko RA; Rogaev EI

SCIENTIFIC REPORTS
Том: 6
Номер статьи: 26440
DOI: 10.1038/srep26440
Опубликовано: MAY 24 2016
IF 5.228

2) Apoptosis-mediated endothelial toxicity but not direct calcification or functional changes in anti-calcification proteins defines pathogenic effects of calcium phosphate bions

https://www.ncbi.nlm.nih.gov/pubmed/27251104

Kutikhin A. G., Velikanova E. A., Mukhamadiyarov R. A., Glushkova T. V., Borisov V. V., Matveeva V. G., Antonova L. V., Filip'ev D. E., Golovkin A. S., Shishkova D. K., Burago A. Y., Frolov A. V., Dolgov V. Y., Efimova O. S., Popova A. N., Malysheva V. Y., Vladimirov A. A., Sozinov S. A., Ismagilov Z. R., Russakov D. M., Lomzov A. A., Pyshnyi D. V., Gutakovsky A. K., Zhivodkov Y. A., Demidov E. A., Peltek S. E., Dolganyuk V. F., Babich O. O., Grigoriev E. V., Brusina E. B., Barbarash O. L., Yuzhalin A. E.

SCIENTIFIC REPORTS
Том: 6
Номер статьи: 27255
DOI: 10.1038/srep27255
Опубликовано: JUN 2 2016
IF 5.228

3) Some pitfalls in application of functional data analysis approach to association studies

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4819216/

Svishcheva G. R., Belonogova N. M., Axenovich T. I.

SCIENTIFIC REPORTS
Том: 6
Номер статьи: 23918
DOI: 10.1038/srep23918
Опубликовано: APR 4 2016
IF 5.228

4) Cytological basis of sterility in male and female hybrids between sibling species of grey voles Microtus arvalis and M. levis

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5109913/

Torgasheva A. A., Borodin P. M

SCIENTIFIC REPORTS
Том: 6
Номер статьи: 36564
DOI: 10.1038/srep36564
Опубликовано: NOV 4 2016
IF 5.228

5) Combined effects of social stress and liver fluke infection in a mouse model

https://www.ncbi.nlm.nih.gov/pubmed/26778779

Avgustinovich D. F., Marenina M. K., Zhanaeva S. Y., Tenditnik M. V., Katokhin A. V., Pavlov K. S., Sivkov A. Y., Vishnivetskaya G. B., Lvova M. N., Tolstikova T. G., Mordvinov V. A.

BRAIN BEHAVIOR AND IMMUNITY
Том: 53 Стр.: 262-272
DOI: 10.1016/j.bbi.2016.01.012
Опубликовано: MAR 2016
IF 5.874

6) Comparison of the three-dimensional organization of sperm and fibroblast genomes using the Hi-C approach

https://www.ncbi.nlm.nih.gov/pubmed/25886366

Battulin N., Fishman V. S., Mazur A. M., Pomaznoy M., Khabarova A. A., Afonnikov D. A., Prokhortchouk E. B., Serov O. L.

GENOME BIOLOGY
Том: 17
Номер статьи: 6
DOI: 10.1186/s13059-016-0868-5
Опубликовано: JAN 14 2016
IF 11.313

7) FREGAT: an R package for region-based association analysis

https://www.ncbi.nlm.nih.gov/pubmed/27153598

Belonogova N. M., Svishcheva G. R., Axenovich T. I.

BIOINFORMATICS
Том: 32 Выпуск: 15 Стр.: 2392-2393
DOI: 10.1093/bioinformatics/btw160
Опубликовано: AUG 1 2016
IF 5.766

8) Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster

https://www.ncbi.nlm.nih.gov/pubmed/26429969

Chereji R. V., Kan T. W., Grudniewska M. K., Romashchenko A. V., Berezikov E., Zhimulev I. F., Guryev V., Morozov A. V., Moshkin Y. M.

NUCLEIC ACIDS RESEARCH
Том: 44 Выпуск: 3 Стр.: 1036-1051
DOI: 10.1093/nar/gkv978
Опубликовано: FEB 18 2016
IF 9.202

9) Guanine quadruplex structures localize to heterochromatin

https://www.ncbi.nlm.nih.gov/pubmed/26384414

Hoffmann R. F., Moshkin Y. M., Mouton S., Grzeschik N. A., Kalicharan R. D., Kuipers J., Wolters A. H. G., Nishida K., Romashchenko A. V., Postberg J., Lipps H., Berezikov E., Sibon O. C. M., Giepmans B. N. G., Lansdorp P. M.

NUCLEIC ACIDS RESEARCH
Том: 44 Выпуск: 1 Стр.: 152-163
DOI: 10.1093/nar/gkv900
Опубликовано: JAN 8 2016
IF 9.202

10) p53 coordinates base excision repair to prevent genomic instability

https://www.ncbi.nlm.nih.gov/pubmed/26773055

Poletto M., Legrand A. J., Fletcher S. C., Dianov G. L.

NUCLEIC ACIDS RESEARCH
Том: 44 Выпуск: 7 Стр.: 3165-3175
DOI: 10.1093/nar/gkw015
Опубликовано: APR 20 2016
IF 9.202

11) Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

https://www.ncbi.nlm.nih.gov/pubmed/27001520

St Laurent G., Vyatkin Y., Antonets D., Ri M., Qi Y., Saik O., Shtokalo D., de Hoon M. J. L., Kawaji H., Itoh M., Lassmann T., Arner E., Forrest A. R. R., Nicolas E., McCaffrey T. A., Carninci P., Hayashizaki Y., Wahlestedt C., Kapranov P., Consortium F.

NUCLEIC ACIDS RESEARCH
Том: 44 Выпуск: 7 Стр.: 3233-3252
DOI: 10.1093/nar/gkw162
Опубликовано: APR 20 2016
IF 9.202

12) Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families

https://www.ncbi.nlm.nih.gov/pubmed/27392075

Ilumae A. M., Reidla M., Chukhryaeva M., Jarve M., Post H., Karmin M., Saag L., Agdzhoyan A., Kushniarevich A., Litvinov S., Ekomasova N., Tambets K., Metspalu E., Khusainova R., Yunusbayev B., Khusnutdinova E. K., Osipova L. P., Fedorova S., Utevska O., Koshel S., Balanovska E., Behar D. M., Balanovsky O., Kivisild T., Underhill P. A., Villems R., Rootsi S.

AMERICAN JOURNAL OF HUMAN GENETICS
Том: 99 Выпуск: 1 Стр.: 163-173
DOI: 10.1016/j.ajhg.2016.05.025
Опубликовано: JUL 7 2016
IF 10.794

13) Alterations in pharmacological and behavioural responses in recombinant mouse line with an increased predisposition to catalepsy: role of the 5-HT1A receptor

https://www.ncbi.nlm.nih.gov/pubmed/27004983

Kulikova E. A., Bazovkina D. V., Akulov A. E., Tsybko A. S., Fursenko D. V., Kulikov A. V., Naumenko V. S., Ponimaskin E., Kondaurova E. M.

BRITISH JOURNAL OF PHARMACOLOGY
Том: 173 Выпуск: 13 Стр.: 2147-2161 Специальный выпуск: SI
DOI: 10.1111/bph.13484
Опубликовано: JUL 2016
IF 5.259

14) The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

https://www.ncbi.nlm.nih.gov/pubmed/27654912

Mallick S., Li H., Lipson M., Mathieson I., Gymrek M., Racimo F., Zhao M. Y., Chennagiri N., Nordenfelt S., Tandon A., Skoglund P., Lazaridis I., Sankararaman S., Fu Q. M., Rohland N., Renaud G., Erlich Y., Willems T., Gallo C., Spence J. P., Song Y. S., Poletti G., Balloux F., van Driem G., de Knijff P., Romero I. G., Jha A. R., Behar D. M., Bravi C. M., Capelli C., Hervig T., Moreno-Estrada A., Posukh O. L., Balanovska E., Balanovsky O., Karachanak-Yankova S., Sahakyan H., Toncheva D., Yepiskoposyan L., Tyler-Smith C., Xue Y., Abdullah M. S., Ruiz-Linares A., Beall C. M., Di Rienzo A., Jeong C., Starikovskaya E. B., Metspalu E., Parik J., Villems R., Henn B. M., Hodoglugil U., Mahley R., Sajantila A., Stamatoyannopoulos G., Wee J. T. S., Khusainova R., Khusnutdinova E., Litvinov S., Ayodo G., Comas D., Hammer M. F., Kivisild T., Klitz W., Winkler C. A., Labuda D., Bamshad M., Jorde L. B., Tishkoff S. A., Watkins W. S., Metspalu M., Dryomov S., Sukernik R., Singh L., Thangaraj K., Paabo S., Kelso J., Patterson N., Reich D.

NATURE
Том: 538 Выпуск: 7624 Стр.: 201-+
DOI: 10.1038/nature18964
Опубликовано: OCT 13 2016
IF 38.138

15) Manifestation of Huntington's disease pathology in human induced pluripotent stem cell-derived neurons

https://www.ncbi.nlm.nih.gov/pubmed/27080129

Nekrasov E. D., Vigont V. A., Klyushnikov S. A., Lebedeva O. S., Vassina E. M., Bogomazova A. N., Chestkov I. V., Semashko T. A., Kiseleva E., Suldina L. A., Bobrovsky P. A., Zimina O. A., Ryazantseva M. A., Skopin A. Y., Illarioshkin S. N., Kaznacheyeva E. V., Lagarkova M. A., Kiselev S. L

MOLECULAR NEURODEGENERATION
Том: 11
Номер статьи: 27
DOI: 10.1186/s13024-016-0092-5
Опубликовано: APR 14 2016
IF 6.51

16) Genomic analyses inform on migration events during the peopling of Eurasia

https://www.ncbi.nlm.nih.gov/pubmed/27654910

Pagani L., Lawson D. J., Jagoda E., Morseburg A., Eriksson A., Mitt M., Clemente F., Hudjashov G., DeGiorgio M., Saag L., Wall J. D., Cardona A., Magi R., Sayres M. A. W., Kaewert S., Inchley C., Scheib C. L., Jarve M., Karmin M., Jacobs G. S., Antao T., Iliescu F. M., Kushniarevich A., Ayub Q., Tyler-Smith C., Xue Y. L., Yunusbayev B., Tambets K., Mallick C. B., Pocheshkhova E., Andriadze G., Muller C., Westaway M. C., Lambert D. M., Zoraqi G., Turdikulova S., Dalimova D., Sabitov Z., Sultana G. N. N., Lachance J., Tishkoff S., Momynaliev K., Isakova J., Damba L. D., Gubina M., Nymadawa P., Evseeva I., Atramentova L., Utevska O., Ricaut F. X., Brucato N., Sudoyo H., Letellier T., Cox M. P., Barashkov N. A., Skaro V., Mulahasanovic L., Primorac D., Sahakyan H., Mormina M., Eichstaedt C. A., Lichman D. V., Abdullah S., Chaubey G., Wee J. T. S., Mihailov E., Karunas A., Litvinov S., Khusainova R., Ekomasova N., Akhmetova V., Khidiyatova I., Marjanovi D., Yepiskoposyan L., Behar D. M., Balanovska E., Metspalu A., Derenko M., Malyarchuk B., Voevoda M., Fedorova S. A., Osipova L. P., Mirazon M., Gerbault P., Leavesley M., Migliano A. B., Petraglia M., Balanovsky O., Khusnutdinova E. K., Metspalu E., Thomas M. G., Manica A., Nielsen R., Villems R., Willerslev E., Kivisild T., Metspalu M.

NATURE
Том: 538 Выпуск: 7624 Стр.: 238-+
DOI: 10.1038/nature19792
Опубликовано: OCT 13 2016
IF 38.138

17) Candidate SNP Markers of Gender-Biased Autoimmune Complications of Monogenic Diseases Are Predicted by a Signification Change in the Affinity of TATA-Binding Protein for Human Gene Promoters

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4819121/

Ponomarenko M. P., Arkova O., Rasskazov D., Ponomarenko P., Savinkova L., Kolchanov N.

FRONTIERS IN IMMUNOLOGY
Том: 7
Номер статьи: 130
DOI: 10.3389/fimmu.2016.00130
Опубликовано: APR 4 2016
IF 5.695

18) A strategy to eradicate well-developed Krebs-2 ascites in mice

https://www.ncbi.nlm.nih.gov/pubmed/26872383

Potter E. A., Dolgova E. V., Proskurina A. S., Minkevich A. M., Efremov Y. R., Taranov O. S., Omigov V. V., Nikolin V. P., Popova N. A., Bayborodin S. I., Ostanin A. A., Chernykh E. R., Kolchanov N. A., Shurdov M. A., Bogachev S.S.

ONCOTARGET
Том: 7 Выпуск: 10 Стр.: 11580-11594
Опубликовано: MAR 8 2016
IF 5.008

19) Molecular architecture of the DED chains at the DISC: regulation of procaspase-8 activation by short DED proteins c-FLIP and procaspase-8 prodomain

https://www.ncbi.nlm.nih.gov/pubmed/26494467

Schleich K., Buchbinder J. H., Pietkiewicz S., Kahne T., Warnken U., Ozturk S., Schnolzer M., Naumann M., Krammer P. H., Lavrik I. N.

CELL DEATH AND DIFFERENTIATION
Том: 23 Выпуск: 4 Стр.: 681-694
DOI: 10.1038/cdd.2015.137
Опубликовано: APR 2016
IF 8.218

20) Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

https://www.ncbi.nlm.nih.gov/pubmed/27126040

Zhernakova A., Kurilshikov A., Bonder M. J., Tigchelaar E. F., Schirmer M., Vatanen T., Mujagic Z., Vila A. V., Falony G., Vieira-Silva S., Wang J., Imhann F., Brandsma E., Jankipersadsing S. A., Joossens M., Cenit M. C., Deelen P., Swertz M. A., Weersma R. K., Feskens E. J. M., Netea M. G., Gevers D., Jonkers D., Franke L., Aulchenko Y. S., Huttenhower C., Raes J., Hofker M. H., Xavier R. J., Wijmenga C., Fu J. Y.

SCIENCE
Том: 352 Выпуск: 6285 Стр.: 565-569
DOI: 10.1126/science.aad3369
Опубликовано: APR 29 2016
IF 34.661

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