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Of all publications in the section: 600
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Article
Ivanenko V., et a., Gelfand M. S. et al. PeerJ. 2016. Vol. 10. No. 4. P. e2305-1-e2305-20.

This study describes the segmentation and setation at different developmental stages of the homonomous trunk limbs of the remipede Speleonectes tulumensis Yager, 1987 collected in anchialine caves of the Yucatan Peninsula. Most homonomous trunk limbs originate ventrolaterally and are composed of two protopodal segments, three exopodal segments and four endopodal segments; contralateral limb pairs are united by a sternal bar. However, the last few posterior limbs originate ventrally, are smaller sized, and have regressively fewer segments, suggesting that limb development passes through several intermediate steps beginning with a limb bud. A terminal stage of development is proposed for specimens on which the posterior somite bears a simple bilobate limb bud, and the adjacent somite bears a limb with a protopod comprised of a coxapod and basipod, and with three exopodal and four endopodal segments. On each trunk limb there are 20 serially homologous groups of setae, and the numbers of setae on different limbs usually varies. These groups of setae are arranged linearly and are identified based on the morphology of the setae and their position on the segments. The number of setae in these groups increases gradually from the anterior homonomous limb to a maximum between limbs 8-12; the number then decreases sharply on the more posterior limbs. Changes in the number of setae, which reach a maximum between trunk limbs 8-12, differ from changes in segmentation which vary only over the last few posterior trunk limbs. Following a vector analysis that identified a spatial pattern for these 20 groups of setae among the different homonomous limbs, the hypothesis was confirmed that the number of setae in any given group and any given limb is correlated with the group, with the position of the somite along the body axis, and with the number of somites present on the specimens. This is the first vector analysis used to analyze a pattern of developmental changes in serially homologs of an arthropod. Development of remipede limbs are compared and contrasted with similar copepod limbs. Architecture, particularly the sternal bar uniting contralateral limb pairs, proposed as homologous, and development of trunk limb segmentation of the remipede is generally similar to that of copepods, but the remipede limb differs in several ways including an additional endopodal segment, the proximal, that appears simultaneously with the protopod during development.

Added: Mar 13, 2017
Article
Zhang B., Gelfand M. S., Khaitovich P. et al. Genome Biology and Evolution. 2016. Vol. 8. No. 3. P. 840-850.

Small nuclear and nucleolar RNAs (snRNAs and snoRNAs) are known to be functionally and evolutionarily conserved elements of transcript processing machinery. Here, we investigated the expression evolution of snRNAs and snoRNAs by measuring their abundance in the frontal cortex of humans, chimpanzees, rhesus monkeys, and mice. Although snRNA expression is largely conserved, 44% of the 185 measured snoRNA and 40% of the 134 snoRNA families showed significant expression divergence among species. The snRNA and snoRNA expression divergence included drastic changes unique to humans: A 10-fold elevated expression of U1snRNA and a 1,000-fold drop in expression ofSNORA29 The decreased expression of SNORA29 might be due to two mutations that affect secondary structure stability. Using in situ hybridization, we further localizedSNORA29expression to nucleolar regions of neuronal cells. Our study presents the first observation of snoRNA abundance changes specific to the human lineage and suggests a possible mechanism underlying these changes.

Added: Mar 13, 2017
Article
Safonov G. Law360's Expert Analysis special series. 2016.

In December 2015, nearly 200 countries reached a historic agreement in Paris to limit greenhouse gas emissions in hopes of curbing global warming. Law360's Expert Analysis special series looks at the impact the agreement will have on policies in various regions and countries.

Added: Jul 20, 2016
Article
Chugunov A. O., Koromyslova A. D., Berkut A. A. et al. Journal of biological chemistry. 2013. Vol. 88. No. 26. P. 19014-19027.

To gain success in the evolutionary “arms race”, venomous animals such as scorpions produce diverse neurotoxins selected to hit targets in the nervous system of prey. Scorpion α-toxins affect insect and/or mammalian voltage-gated sodium channels (Nav’s) and thereby modify the excitability of muscle and nerve cells. Although more than a hundred α-toxins are known and a number of them have been studied into detail, the molecular mechanism of their interaction with Nav’s is still poorly understood. Here, we employ extensive molecular dynamics simulations and spatial mapping of hydrophobic/hydrophilic properties distributed over the molecular surface of α-toxins. It is revealed that in spite of the small size and relatively rigid structure, these toxins possess modular organization from structural, functional and evolutionary perspectives. The more conserved and rigid “core module” is supplemented with the “specificity module” (SM) that is comparatively flexible and variable, and determines the taxon (mammal vs. insect) specificity of α-toxin activity. We further show that SMs in mammal toxins are more flexible and hydrophilic than in insect toxins. Concomitant sequence-based analysis of Nav’s extracellular loops suggests that α-toxins recognize the channels using both modules. We propose that the core module binds to the voltage-sensing domain of repeat IV, whereas the more versatile SM interacts with the pore domain in repeat I of Nav’s. These findings corroborate and expand the hypothesis on different functional epitopes of toxins that has been reported previously. In effect, we propose that the modular structure in toxins evolved to match the domain architecture of Nav’s.

Added: Nov 13, 2013
Article
Vendina O., Makhrova A., Mkrtchyan N. V. et al. Regional Research of Russia. 2014. Vol. 4. No. 2. P. 95-104.

Some categories used in Russian geography to analyze spatial aspects of social processes in cities are considered. The possibility to interpret the same terms differently is shown depending on scientific approaches and the investigation scopes applied. This paper is part of a topical collection of five articles published in this issue of the journal under the rubric “Urban Geography” and dedicated to key terms and notions used in urban studies in Russia, France, and other European countries (in addition, see also the following articles: “Cities, Rural Areas and Urbanization: Russia and the World”, “City and Countryside under WorldWide Urbanization”, “Integrated Forms of Urban Settlement Pattern in Russia, Europe, and Worldwide”, “Types of Cities in Russia and Across the Globe”).

Added: Oct 20, 2014
Article
Salukvadze J., Golubchikov O. Cities. 2016. Vol. 52. P. 39-54.

Tbilisi, a city of over a million, is the national capital of Georgia. Although little explored in urban studies, the city epitomizes a fascinating assemblage of processes that can illuminate the interplay of geopolitics, political choices, globalization discourses, histories, and urban contestations in shaping urban transformations. Tbilisi's strategic location in the South Caucasus, at the juncture of major historical empires and religions in Eurasia, has ensured its turbulent history and a polyphony of cultural influences. Following Georgia's independence in 1991, Tbilisi found itself as the pivot of Georgian nation-building. Transition to a market economy also exposed the city to economic hardship, ethnical homogenization, and the informalization of the urban environment. The economic recovery since the early 2000s has activated urban regeneration. Georgia's government has recently promoted flagship urban development projects in pursuit of making Tbilisi as a modern globalizing metropolis. This has brought contradictions, such as undermining the city's heritage, contributing to socio-spatial polarization, and deteriorating the city's public spaces. The elitist processes of decision-making and a lack of a consistent urban policy and planning regimes are argued to be among major impediments for a more sustainable development of this city.

Added: Feb 23, 2016
Article
Loganathan N., Bowers G. M., Yazaydin A. O. et al. The Journal of Physical Chemistry C. 2018. Vol. 122. No. 8. P. 4391-4402.

In situ XRD and NMR experiments combined with molecular dynamics simulations using the grand canonical ensemble (GCMD) show that cation size, charge and solvation energy play critical roles in determining the interlayer expansion of smectite clay minerals when exposed to dry supercritical CO2 under conditions relevant to the earth’s upper crust, petroleum reservoirs, and geological CO2 sequestration conditions (323 K and 90 bar). The GCMD results show that the smectite mineral, hectorite, containing interlayer alkali and alkaline earth cations with relatively small ionic radii and high solvation and hydration energies (e.g., Li+, Na+ Mg2+, and Ca2+) does not intercalate dry CO2 and that the fully collapsed interlayer structure is the energetically most stable configuration. With increasing cation size and decreasing cation solvation energy, the energy barrier to CO2 intercalation decreases. With K+, Rb+, Cs+, Sr2+, and Ba2+ the monolayer structure is the stable configuration, and CO2 should spontaneously enter the interlayer. With Cs+ there is not even an energy barrier for CO2 intercalation, in agreement with the experimental XRD and NMR results that show clay layer expansion and CO2 incorporation. The number of intercalated CO2 molecules decreases with increasing size of the alkali cation but does not vary with ion size for the alkaline earth cations. 13C NMR spectroscopy and the GCMD simulations show that the average orientation of the intercalated CO2 molecules is with their O-C-O axes parallel to the basal clay surface and that they undergo a combination of rapid rotation about an axis perpendicular to the main molecular axis and wobbling motion with respect to the basal surface. Incorporation of CO2 in the interlayer decreases the coordination of Cs+ by the oxygen atoms of the basal surfaces, which is compensated by CO2 molecules entering their solvation shell, as predicted based on previously published NMR results. The GCMD simulations show that the strength of the interaction between the exchangeable cation and the clay structure dominates the intercalation energetics in dry scCO2. With relatively small cations, the cation-clay interactions outcompete cation solvation by CO2 molecules. The computed residence times for coordination among of interlayer species are consistent with the computed energetics.

Added: May 31, 2018
Article
Safonov G. ERINA Business News. 2016. No. 117. P. 33-40.

A comprehensive review of the climate change mitigation and low carbon development issues in the Northeast Asia, including Russia, China, Japan, Mongolia, Republic of Korea and DPR of Korea. The countries face an outstanding challenge of using their huge reserves of fossil fuels while committing to prevent global warming by over 2 degree Celsius. Their resources of renewable energy, technological potential and investment resources can help to deeply decarbonize their economies by 2050, and the international cooperation projects in the region can speed up this process.

Added: Sep 27, 2016
Article
Deck C., Wiles G., Sara Frederick F. et al. Forests. 2017. Vol. 8. No. 9. P. 1-11.

Kamchatka’s forests span across the peninsula’s diverse topography and provide a wide range of physiographic and elevational settings that can be used to investigate how forests are responding to climate change and to anticipate future response. Birch (Betula ermanii Cham.) and larch (Larix gmelinii (Rupr.) Kuzen) were sampled at eight new sites and together with previous collections were compared with monthly temperature and precipitation records to identify their climate response. Comparisons show that tree-ring widths in both species are primarily influenced by May through August temperatures of the current growth year, and that there is a general increase in temperature sensitivity with altitude. The ring-width data for each species were also combined into regional chronologies. The resulting composite larch chronology shows a strong resemblance to a Northern Hemisphere (NH) tree-ring based temperature reconstruction with the larch series tracking NH temperatures closely through the past 300 years. The composite birch ring-width series more closely reflects the Pacific regional coastal late summer temperatures. These new data improve our understanding of the response of forests to climate and show the low frequency warming noted in other, more continental records from high latitudes of the Northern Hemisphere. Also evident in the ring-width record is that the larch and birch forests continue to track the strong warming of interior Kamchatka. View Full-Text

Added: Nov 1, 2019
Article
Lajus J., Kraikovski A., Lajus D. Plos One. 2013. Vol. 8. No. 10.

The paper describes and analyzes original data, extracted from historical documents and scientific surveys, related to Russian fisheries in the southeastern part of the Gulf of Finland and its inflowing rivers during the 15- early 20th centuries. The data allow tracing key trends in fisheries development and in the abundance of major commercial species. In particular, results showed that, over time, the main fishing areas moved from the middle part of rivers downstream towards and onto the coastal sea. Changes in fishing patterns were closely interrelated with changes in the abundance of exploited fish. Anadromous species, such as Atlantic sturgeon, Atlantic salmon, brown trout, whitefish, vimba bream, smelt, lamprey, and catadromous eel were the most important commercial fish in the area because they were abundant, had high commercial value and were easily available for fishing in rivers. Due to intensive exploitation and other human-induced factors, populations of most of these species had declined notably by the early 20th century and have now lost commercial significance. The last sturgeon was caught in 1996, and todayonly smelt and lamprey support small commercial fisheries. According to historical sourcescatches of freshwater species such as roach, ide, pike, perch, ruffe and burbot regularly occurred, in some areas exceeding half of the total catch, but they were not as important as migrating fish and no clear trends in abundance are apparent. Of documented marine catch, Baltic herring appeared in the 16th century, but did not become commerciallysignificant until the 19th century. From then until now herring have been the dominant catch.

Added: Nov 18, 2013
Article
Zaytsev A., Belyakov V., Beresnev P. et al. Science of Tsunami Hazards. 2017. Vol. 36. No. 1. P. 1-12.
Added: Mar 15, 2018
Article
Долгих А., Мацковский В., Воронин К. и др. Доклады Академии Наук. Науки о Земле. 2017. Т. 474. № 2. С. 706-708.
Added: Nov 1, 2019
Article
Polyanovsky V. O., Roytberg M. A., Tumanyan V. G. Algorithms for Molecular Biology. 2011. Vol. 6. No. 25. P. 1-12.

 

Background: Algorithms of sequence alignment are the key instruments for computer-assisted studies of biopolymers. Obviously, it is important to take into account the “quality” of the obtained alignments, i.e. how closely the algorithms manage to restore the “gold standard” alignment (GS-alignment), which superimposes positions originating from the same position in the common ancestor of the compared sequences. As an approximation of the GS-alignment, a 3D-alignment is commonly used not quite reasonably. Among the currently used algorithms of a pair-wise alignment, the best quality is achieved by using the algorithm of optimal alignment based on affine penalties for deletions (the Smith-Waterman algorithm). Nevertheless, the expedience of using local or global versions of the algorithm has not been studied. Results: Using model series of amino acid sequence pairs, we studied the relative “quality” of results produced by local and global alignments versus (1) the relative length of similar parts of the sequences (their “cores”) and their nonhomologous parts, and (2) relative positions of the core regions in the compared sequences. We obtained numerical values of the average quality (measured as accuracy and confidence) of the global alignment method and the local alignment method for evolutionary distances between homologous sequence parts from 30 to 240 PAM and for the core length making from 10% to 70% of the total length of the sequences for all possible positions of homologous sequence parts relative to the centers of the sequences. Conclusion: We revealed criteria allowing to specify conditions of preferred applicability for the local and the global alignment algorithms depending on positions and relative lengths of the cores and nonhomologous parts of the sequences to be aligned. It was demonstrated that when the core part of one sequence was positioned above the core of the other sequence, the global algorithm was more stable at longer evolutionary distances and larger nonhomologous parts than the local algorithm. On the contrary, when the cores were positioned asymmetrically, the local algorithm was more stable at longer evolutionary distances and larger nonhomologous parts than the global algorithm.
Added: Mar 5, 2012
Article
Loganathan N., Bowers G. M., Yazaydin A. O. et al. The Journal of Physical Chemistry C. 2018. Vol. 122. No. 41. P. 23460-23469.

The intercalation of H2O, CO2, and other fluid species in expandable clay minerals (smectites) may play a significant role in controlling the behavior of these species in geological C-sequestration and enhanced petroleum production and has been the subject of intensive study in recent years. This paper reports the results of a computational study of the effects of the properties of the charge balancing, exchangeable cations on H2O and CO2 intercalation in the smectite mineral, hectorite, in equilibrium with an H2O-saturated supercritical CO2 fluid under reservoir conditions using Grand Canonical Molecular Dynamics (GCMD) methods. The results show that the intercalation behavior is greatly different with cations with relatively low hydration energies and high affinities for CO2 (here Cs+) than with cations with higher hydration energies (here Ca2+). With Cs+, CO2 intercalation occurs in a 1-layer structure and does not require H2O intercalation, whereas with Ca2+ the presence of a sub-monolayer of H2O is required for CO2 intercalation. The computational results provide detailed structural, dynamical and energetic insight into the differences in intercalation behavior and are in excellent agreement with in situ experimental XRD, IR, quartz crystal microbalance, and NMR results for smectite materials obtained under reservoir conditions.

Added: Oct 20, 2018
Article
Permogorskiy M. S. Biology Bulletin Reviews. 2015. Vol. 5. No. 3. P. 213-219.
The contemporary state of the competitive intransitivity hypothesis is considered. Intransitive competition among species occurs when, for example, species A outcompetes species B, B outcompetes C, and C outcompetes A (sometimes written as A > B > C > A). In the first part of the article, a summary of the studies of competitive intransitivity is given. Examples of actually existing intransitive loops, as well as simulation models that provide a theoretical explanation for these processes, are discussed. For competitive intransitivity to emerge, it is necessary (but is it enough?) that the community has sufficient potential diver sity, that species interactions are carried out in a relatively stable limited space, and that there is a penalty for the acquisition of competitive ability. In the second part, the competitive intransitivity hypothesis is compared with neutral theory and niche theory. The results are believed to make it possible to form some generalizations, which could stimulate a deeper understanding of the species coexistence phenomenon.
Added: Jul 13, 2015
Article
Ossadtchi A. Journal of Neuroscience Methods. 2012. Vol. 207. No. 1. P. 1-16.

Connectivity measures are (typically bivariate) statistical measures that may be used to estimate interactions between brain regions from electrophysiological data. We review both formal and informal descriptions of a range of such measures, suitable for the analysis of human brain electrophysiological data, principally electro- and magnetoencephalography. Methods are described in the space–time,space–frequency, and space–time–frequency domains. Signal processing and information theoretic measures are considered, and linear and nonlinear methods are distinguished. A novel set of crosstime–frequency measures is introduced, including a cross-time–frequency phase synchronization measure.

Added: Oct 23, 2014
Article
Mazin P., Jiang X., Fu N. et al. RNA. 2018. P. 585-596.

Changes in splicing are known to affect the function and regulation of genes. We analyzed splicing events that take place during the postnatal development of the prefrontal cortex in humans, chimpanzees, and rhesus macaques based on data obtained from 168 individuals. Our study revealed that among the 38,822 quantified alternative exons, 15% are differentially spliced among species, and more than 6% splice differently at different age. Mutations in splicing acceptor and/or donor sites might explain more than 14% of all splicing differences among species and up to 64% of high-amplitude differences. A reconstructed trans- regulatory network containing 21 RNA-binding proteins explain a further 4% of splicing variations within species. While most age-dependent splicing patterns are conserved among the three species, developmental changes in intron retention are substantially more pronounced in humans.

Added: Mar 5, 2018
Article
Poptsova M., Grechishnikova D. BMC Genomics. 2016. Vol. 17. No. 1. P. 992.

Abstract BACKGROUND:

In the process of retrotransposition LINEs use their own machinery for copying and inserting themselves into new genomic locations, while SINEs are parasitic and require the machinery of LINEs. The exact mechanism of how a LINE-encoded reverse transcriptase (RT) recognizes its own and SINE RNA remains unclear. However it was shown for the stringent-type LINEs that recognition of a stem-loop at the 3'UTR by RT is essential for retrotransposition. For the relaxed-type LINEs it is believed that the poly-A tail is a common recognition element between LINE and SINE RNA. However polyadenylation is a property of any messenger RNA, and how the LINE RT recognizes transposon and non-transposon RNAs remains an open question. It is likely that RNA secondary structures play an important role in RNA recognition by LINE encoded proteins.

RESULTS:

Here we selected a set of L1 and Alu elements from the human genome and investigated their sequences for the presence of position-specific stem-loop structures. We found highly conserved stem-loop positions at the 3'UTR. Comparative structural analyses of a human L1 3'UTR stem-loop showed a similarity to 3'UTR stem-loops of the stringent-type LINEs, which were experimentally shown to be recognized by LINE RT. The consensus stem-loop structure consists of 5-7 bp loop, 8-10 bp stem with a bulge at a distance of 4-6 bp from the loop. The results show that a stem loop with a bulge exists at the 3'-end of Alu. We also found conserved stem-loop positions at 5'UTR and at the end of ORF2 and discuss their possible role.

CONCLUSIONS:

Here we presented an evidence for the presence of a highly conserved 3'UTR stem-loop structure in L1 and Alu retrotransposons in the human genome. Both stem-loops show structural similarity to the stem-loops of the stringent-type LINEs experimentally confirmed as essential for retrotransposition. Here we hypothesize that both L1 and Alu RNA are recognized by L1 RT via the 3'-end RNA stem-loop structure. Other conserved stem-loop positions in L1 suggest their possible functions in protein-RNA interactions but to date no experimental evidence has been reported.

 

Added: Mar 8, 2017
Article
Daryin A., Alexandrin M., Grachev A. et al. Bulletin of the Russian Academy of Sciences: Physics. 2019. Vol. 83. No. 2. P. 190-193.

Cores of bottom sediments of Lake Karakel (Northern Caucasus) were obtained in 2010 and 2014 to perform geochemical studies for reconstructing the regional paleoclimate of the late Holocene. Solid sam- ples of bottom sediments were scanned via micro-XRF with a step of 1 mm at the shared resource center of the Siberian Synchrotron and Terahertz Radiation Center. The contents of more than 20 elements were deter- mined. The scan profiles are used to construct a single reference section with correction for a sediment layer dated via radiocarbon analysis, and to create a sediment core age–depth model.

Added: Oct 23, 2019
Article
Mazin P., Gelfand M. S. Proceedings of the National Academy of Sciences of the United States of America. 2018. P. E2477-E2486.

Polypedilum vanderplanki is a striking and unique example of an insect that can survive almost complete desiccation. Its genome and a set of dehydration-rehydration transcriptomes, together with the genome of Polypedilum nubifer (a congeneric desiccation-sensitive midge), were recently released. Here, using published and newly generated datasets reflecting detailed transcriptome changes during anhydrobiosis, as well as a developmental series, we show that the TCTAGAA DNA motif, which closely resembles the binding motif of the Drosophila melanogaster heat shock transcription activator (Hsf), is significantly enriched in the promoter regions of desiccation-induced genes in P. vanderplanki, such as genes encoding late embryogenesis abundant (LEA) proteins, thioredoxins, or trehalose metabolism-related genes, but not in P. nubifer Unlike P. nubiferP. vanderplanki has double TCTAGAA sites upstream of the Hsf gene itself, which is probably responsible for the stronger activation of Hsf in P. vanderplanki during desiccation compared with P. nubifer To confirm the role of Hsf in desiccation-induced gene activation, we used the Pv11 cell line, derived from P. vanderplanki embryo. After preincubation with trehalose, Pv11 cells can enter anhydrobiosis and survive desiccation. We showed that Hsf knockdown suppresses trehalose-induced activation of multiple predicted Hsf targets (including P. vanderplanki-specific LEA protein genes) and reduces the desiccation survival rate of Pv11 cells fivefold. Thus, cooption of the heat shock regulatory system has been an important evolutionary mechanism for adaptation to desiccation in P. vanderplanki.

Added: Mar 5, 2018
Article
Dubois J., Kulikova S., Hertz-Pannier L. et al. Magnetic Resonance Imaging. 2014. Vol. 32. No. 8. P. 981-992.
Objective

Diffusion imaging techniques such as DTI and HARDI are difficult to implement in infants because of their sensitivity to subject motion. A short acquisition time is generally preferred, at the expense of spatial resolution and signal-to-noise ratio. Before estimating the local diffusion model, most pre-processing techniques only register diffusion-weighted volumes, without correcting for intra-slice artifacts due to motion or technical problems. Here, we propose a fully automated strategy, which takes advantage of a high orientation number and is based on spherical-harmonics decomposition of the diffusion signal.

Material and methods

The correction strategy is based on two successive steps: 1) automated detection and resampling of corrupted slices; 2) correction for eddy current distortions and realignment of misregistered volumes. It was tested on DTI data from adults and non-sedated healthy infants.

Results

The methodology was validated through simulated motions applied to an uncorrupted dataset and through comparisons with an unmoved reference. Second, we showed that the correction applied to an infant group enabled to improve DTI maps and to increase the reliability of DTI quantification in the immature cortico-spinal tract.

Conclusion

This automated strategy performed reliably on DTI datasets and can be applied to spherical single- and multiple-shell diffusion imaging.

Added: Oct 22, 2015