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41.
Vadim I. Nazarov Mikhail V. Pogorelyy Ekaterina A. Komech Ivan V. Zvyagin Dmitry A. Bolotin Mikhail Shugay Dmitry M. Chudakov Yury B. Lebedev Ilgar Z. Mamedov 《BMC bioinformatics》2015,16(1)
Background
The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is required for the rational analysis of massive data generated by next-generation sequencing.Results
Here we introduce tcR, a new R package, representing a platform for the advanced analysis of T cell receptor repertoires, which includes diversity measures, shared T cell receptor sequences identification, gene usage statistics computation and other widely used methods. The tool has proven its utility in recent research studies.Conclusions
tcR is an R package for the advanced analysis of T cell receptor repertoires after primary TR sequences extraction from raw sequencing reads. The stable version can be directly installed from The Comprehensive R Archive Network (http://cran.r-project.org/mirrors.html). The source code and development version are available at tcR GitHub (http://imminfo.github.io/tcr/) along with the full documentation and typical usage examples. 相似文献42.
Mikhail O. Maksimov A. James Link 《Journal of industrial microbiology & biotechnology》2014,41(2):333-344
Genome mining has unlocked a veritable treasure chest of natural compounds. However, each family of natural products requires a genome-mining approach tailored to its unique features to be successful. Lasso peptides are ribosomally synthesized and posttranslationally modified products with a unique three-dimensional structure. Advances in the understanding of these molecules have informed the design of strategies to identify new members of the class in sequenced genomes. This review presents the bioinformatic methods used to discover novel lasso peptides and describes how such analyses have afforded insights into the biosynthesis and evolution of this peptide class. 相似文献
43.
44.
Evgenia V. Dolgova Yaroslav R. Efremov Konstantin E. Orishchenko Oleg M. Andrushkevich Ekaterina A. Alyamkina Anastasia S. Proskurina Sergey I. Bayborodin Valeriy P. Nikolin Nelly A. Popova Elena R. Chernykh Alexandr A. Ostanin Oleg S. Taranov Vladimir V. Omigov Alexandra M. Minkevich Vladimir A. Rogachev Sergey S. Bogachev Mikhail A. Shurdov 《Gene》2013
We previously reported that fragments of exogenous double-stranded DNA can be internalized by mouse bone marrow cells without any transfection. Our present analysis shows that only 2% of bone marrow cells take up the fragments of extracellular exogenous DNA. Of these, ~ 45% of the cells correspond to CD34 + hematopoietic stem cells. Taking into account that CD34 + stem cells constituted 2.5% of the total cell population in the bone marrow samples analyzed, these data indicate that as much as 40% of CD34 + cells readily internalize fragments of extracellular exogenous DNA. This suggests that internalization of fragmented dsDNA is a general feature of poorly differentiated cells, in particular CD34 + bone marrow cells. 相似文献
45.
Efremova Agrafena Senzacqua Martina Venema Wiebe Isakov Evgeny Di Vincenzo Angelica Zingaretti Maria Cristina Protasoni Marina Thomski Mikhail Giordano Antonio Cinti Saverio 《Journal of physiology and biochemistry》2020,76(2):185-192
Journal of Physiology and Biochemistry - Many deleterious consequences for health of excessive fat accumulation are due to visceral fat. Browning of visceral fat is mainly cold dependent and has... 相似文献
46.
Two simple, selective and accurate methods were developed and validated for the determination of brimonidine tartrate (BT) in pure state and pharmaceutical formulations. Both methods are based on the coupling of the drug with 4‐chloro‐7‐nitro‐2,1,3‐benzoxadiazole in borate buffer (pH 8.5) at 70 °C and measurement of the reaction product spectrophotometrically at 407 nm (method I) or spectrofluorimetrically at 528 nm upon excitation at 460 nm (method II). The calibration graphs were rectilinear over the concentration ranges of 1.0–16.0 and 0.1–4.0 µg/mL with lower detection limits of 0.21 and 0.03, and lower quantification limits of 0.65 and 0.09 µg/mL for methods I and II, respectively. Both methods were successfully applied to the analysis of commercial ophthalmic solution with mean recovery of 99.50 ± 1.00 and 100.13 ± 0.71%, respectively. Statistical analysis of the results obtained by the proposed methods revealed good agreement with those obtained using a comparison method. The proposed spectrofluorimetric method was extended to a stability study of BT under different ICH‐outlined conditions such as alkaline, acidic, oxidative and photolytic degradation. Furthermore, the kinetics of oxidative degradation of the drug was investigated and the apparent first‐order reaction rate constants, half‐life times and Arrhenius equation were estimated. The proposed methods are practical and valuable for routine applications in quality control laboratories for the analysis of BT. Copyright © 2014 John Wiley & Sons, Ltd. 相似文献
47.
Shtyrlin Valery G. Borissenok Valery A. Serov Nikita Yu. Simakov Vladimir G. Bragunets Vyacheslav A. Trunin Ivan R. Tereshkina Irina A. Koshkin Sergey A. Bukharov Mikhail S. Gilyazetdinov Edward M. Shestakov Evgeny E. Sirotkina Anna G. Zakharov Alexey V. 《Origins of life and evolution of the biosphere》2019,49(1-2):1-18
Origins of Life and Evolution of Biospheres - Syntheses under shock in nitrogen bubbled samples of the water – formamide – bicarbonate – sodium hydroxide system at... 相似文献
48.
Ivanchenko MV Thomas Nowotny Selverston AI Rabinovich MI 《Journal of theoretical biology》2008,253(3):452-461
The origin of rhythmic activity in brain circuits and CPG-like motor networks is still not fully understood. The main unsolved questions are (i) What are the respective roles of intrinsic bursting and network based dynamics in systems of coupled heterogeneous, intrinsically complex, even chaotic, neurons? (ii) What are the mechanisms underlying the coexistence of robustness and flexibility in the observed rhythmic spatio-temporal patterns? One common view is that particular bursting neurons provide the rhythmogenic component while the connections between different neurons are responsible for the regularisation and synchronisation of groups of neurons and for specific phase relationships in multi-phasic patterns. We have examined the spatio-temporal rhythmic patterns in computer-simulated motif networks of H-H neurons connected by slow inhibitory synapses with a non-symmetric pattern of coupling strengths. We demonstrate that the interplay between intrinsic and network dynamics features either cooperation or competition, depending on three basic control parameters identified in our model: the shape of intrinsic bursts, the strength of the coupling and its degree of asymmetry. The cooperation of intrinsic dynamics and network mechanisms is shown to correlate with bistability, i.e., the coexistence of two different attractors in the phase space of the system corresponding to different rhythmic spatio-temporal patterns. Conversely, if the network mechanism of rhythmogenesis dominates, monostability is observed with a typical pattern of winnerless competition between neurons. We analyse bifurcations between the two regimes and demonstrate how they provide robustness and flexibility to the network performance. 相似文献
49.