On the classical description of the recombination of dark matter particles with a Coulomb-like interaction

Cold dark matter (DM) scenario may be cured of several problems by involving self-interaction of dark matter. Viability of the models of long-range interacting DM crucially depends on the effectiveness of recombination of the DM particles, making thereby their interaction short-range. Usually in numeric calculations, recombination is described by cross section obtained on a feasible quantum level. However in a wide range of parameter values, a classical treatment, where the particles are bound due to dipole radiation, is applicable. The cross sections, obtained in both approaches, are very different and lead to diverse consequences. Classical cross section has a steeper dependence on relative velocity, what leads to the fact that, after decoupling of DM particles from thermal background of "dark photons" (carriers of DM long-range interaction), recombination process does not "freeze out", diminishing gradually density of unbound DM particles. Our simplified estimates show, that at the taken parameter values (the mass of DM particle is $100$ GeV, interaction constant is $100^{-1}$, and quite natural assumptions on initial conditions, from which the result is very weakly dependent) the difference in residual density reaches about $5$ orders of magnitude on pre-galactic stage. This estimate takes into account thermal effects induced by dipole radiation and recombination, which resulted in the increase of both temperature and density of DM particles by a half order of magnitude.Comment: 11 pages, 4 figures. V3 has tiny corrections, matches published versio

Protein-DNA interactions: statistical analysis of interatomic contacts in major and minor grooves

The interactions between protein and DNA in essence underlie all processes in a living cell. Understanding the principles of specific recognition of DNA sites will open the way to understand how these processes are controlled and to interfere in their operation. In the paper we studied contacts between the protein and DNA at the atomic level in the structures of all the 3 518 protein­DNA complexes available in PDB by the Voronoi–Delaunay tessellation method. The method unambiguously defines contacts between atoms without any parameters, and characterizes each contact by the distance between atoms and the contact area, which is determined by the corresponding face of the Voronoi polyhedron. It was shown that most contacts are formed between the protein atoms and the sugarphosphate backbone of the DNA (72.9 %). The contact with the atoms of the nucleic bases emerging into the grooves of DNA is 17.0 % for a major groove and 10.1 % for all atomic contacts for a minor groove. Totally, the interaction between protein atoms and nucleic base atoms accounts for 27.1 % of all contacts. Analysis of the accessible surface area of atoms in the major and the minor grooves showed a correlation with the number of contacts (coefficient of linear correlation 0.94 and 0.93, respectively), however, nucleic acid atoms forming hydrogen bonds make contacts more often than may be expected from statistical considerations. It was shown that conformationally stable peptides occur sometimes in the binding regions with DNA. Analysis of the residues in a predefined conformation in 3 518 protein­DNA complexes revealed 159 amino acid residues in a predefined β­bend type I conformation, 15 residues in the conformation of β­bend type I’, and 6 residues in the conformation of β­bend type II. No residues in the conformation of β­bend type II’ were found. Analysis of contacts showed that such residues virtually do not form contacts with DNA. Contacts with nucleic base atoms are found only in the two homologous structures 3qea and 3qe9, where threonine atoms form contacts with atoms of nucleotide bases of the AT­pair

Tumor Blood Flow Differs between Mouse Strains: Consequences for Vasoresponse to Photodynamic Therapy

Fluctuations in tumor blood flow are common and attributed to factors such as vasomotion or local vascular structure, yet, because vessel structure and physiology are host-derived, animal strain of tumor propagation may further determine blood flow characteristics. In the present report, baseline and stress-altered tumor hemodynamics as a function of murine strain were studied using radiation-induced fibrosacomas (RIF) grown in C3H or nude mice. Fluctuations in tumor blood flow during one hour of baseline monitoring or during vascular stress induced by photodynamic therapy (PDT) were measured by diffuse correlation spectroscopy. Baseline monitoring revealed fluctuating tumor blood flow highly correlated with heart rate and with similar median periods (i.e., ∼9 and 14 min in C3H and nudes, respectively). However, tumor blood flow in C3H animals was more sensitive to physiologic or stress-induced perturbations. Specifically, PDT-induced vascular insults produced greater decreases in blood flow in the tumors of C3H versus nude mice; similarly, during baseline monitoring, fluctuations in blood flow were more regular and more prevalent within the tumors of C3H mice versus nude mice; finally, the vasoconstrictor L-NNA reduced tumor blood flow in C3H mice but did not affect tumor blood flow in nudes. Underlying differences in vascular structure, such as smaller tumor blood vessels in C3H versus nude animals, may contribute to strain-dependent variation in vascular function. These data thus identify clear effects of mouse strain on tumor hemodynamics with consequences to PDT and potentially other vascular-mediated therapies

Синтез мономеров γ-замещенных полиамидных миметиков нуклеиновых кислот

Universal efficient preparative approach for obtaining of γ-substitued polyamide DNA-mimics on the base of L-alanine and L-glycine derivates was presented. As result of research cytosine and adenine-containing final monomers were synthesised. It was found that both allyl and methyl C-terminal protecting group can be used in the synthesis as example of cytosine-containing derivates.редставлен универсальный эффективный препаративный способ получения мономеров γ-замещенных полиамидных ДНК-миметиков на основе производных L-аланина и глицина. В результате исследования были синтезированы цитозин- и аденинсодржащие целевые мономеры и показана возможность использования в их синтезе как аллильной, так и метильной С-терминальных защитных групп на примере цитозинсодержащих производных

Разработка непрямого метода определения энантиомерной чистоты мономеров хиральных полиамидных миметиков нуклеиновых кислот (ПАНКМ)

An indirect approach for the determination of enantiomeric purity of chiral α-(benzyl)-carboxyethyl- and γ-methyl-substituted monomers of polyamide nucleic acids mimics (PANAM) is described. The test consist in the synthesis of C-terminal diastereomers with methyl ester of L- or DL-isoleucine for each PANAM monomer and estimation of the relative content (abundance ratio) of main and minor diastereomers by means of reverse phase HPLC and 1H-NMR spectroscopy.Описан подход для определения энантиомерной чистоты хиральных α-(бензил)-карбоксиэтил- и γ-метилзамещенных мономеров полиамидных миметиков нуклеиновых кислот (ПАНКМ) непрямым методом. Способ основан на получении C-концевых производных с метиловым эфиром L- или DL-изолейцина с последующим определением относительного содержания основного и минорного диастереомеров с помощью обращенно-фазовой ВЭЖХ. Также представлен анализ 1Н-ЯМР-спектров диастереомерных смесей

Разработка нового малообъемного оксигенатора и создание гидродинамического стенда для ex vivo перфузии легких на мелких животных

Small animal models are widely used in basic research. However, experimental hydrodynamic test benches, which include extracorporeal circuits, often have limitations associated with the size and filling volume of equipment. Thus, we aimed at developing and validating a miniature oxygenator as well as a low-volume hydrodynamic system for ex vivo perfusion of small animal lungs. A series of low-volume membrane oxygenators (n = 10) with 90–100 aligned microporous polypropylene hollow fibers, placed inside a sheath that is sealed at both ends to isolate the perfusing solution, was designed and manufactured. This design makes gas to flow through the hollow fibers and perfusate to circulate around the fibers. A low-volume hydrodynamic test bench was designed and assembled for isolated ex vivo lung perfusion and for evaluation of the performance characteristics of the oxygenators: gas and perfusate flow, perfusion pressure and temperature at 5–70 ml/min flow range.В фундаментальных исследованиях широко используются модели мелких животных. Однако экспериментальные гидродинамические стенды, в состав которых входят экстракорпоральные контуры, часто имеют ограничения, связанные с размерами и объемами заполнения оборудования. Таким образом, мы стремились разработать и апробировать миниатюрный оксигенатор, а также малообъемную гидродинамическую систему для проведения ex vivo перфузии легких мелких животных. Была разработана и изготовлена серия малообъемных мембранных оксигенаторов (n = 10) с 90–100 выровненными микропористыми полипропиленовыми полыми волокнами, помещенными внутрь оболочки, запечатанной с обоих концов для изоляции перфузирующего раствора. Благодаря такой конструкции газ проходит через полые волокна, в то время как перфузат циркулирует вокруг волокон. Был разработан и собран гидродинамический стенд с малым объемом заполнения для проведения изолированной ex vivo перфузии легких, а также оценки рабочих характеристик оксигенаторов: потока газа и перфузата, перфузионного давления и температуры при диапазоне расхода 5–70 мл/мин

Определение отношения 8-оксо-2'-дезоксигуанозина к 2'-дезоксигуанозину в ДНК с помощью обращенно-фазовой ВЭЖХ в сочетании с амперометрической детекцией

The article presents an optimized method for the determination of the ratio of 8-oxo-2'-deoxyguanosine (formed in DNA due to the action of active forms of oxygen) to 2'-deoxyguanosine. The ratio was determined by reverse phase HPLC combined with amperometric detection. It was shown that the ratio increases upon oxidative stress caused by the action of large doses of ascorbic acid in samples of DNA isolated from the liver of experimental rats.В работе проведена оптимизация метода определения отношения 8-оксо-2'-дезоксигуанозина, образующегося в ДНК в результате действия активных форм кислорода, к 2'-дезоксигуанозину методом обращенно-фазовой ВЭЖХ в сочетании с амперометрической детекцией. Показано увеличение этого отношения при окислительном стрессе, вызванном действием больших доз аскорбиновой кислоты, в образцах ДНК, выделенных из печени экспериментальных крыс