Molecular Modeling of the HR2 and Transmembrane Domains of the SARS-CoV-2 S Protein in the Prefusion State.

SARS-CoV-2, the causative agent of COVID-19, remains the focus of research worldwide. SARS-CoV-2 entry into the cell starts with its S protein binding to the angiotensin-converting enzyme-2 (ACE2) expressed on the cell surface. The knowledge of the S protein's spatial structure is indispensable for understanding the molecular principles of its work. The S protein structure has been almost fully described using experimental approaches with the only exception for the protein's endodomain, the transmembrane domain, and the ectodomain parts adjacent to the latter. The paper reports molecular modelling of the S protein fragment corresponding to its coiled coil HR2 domain and fully palmitoylated transmembrane domain. Model stability in lipid bilayer was confirmed by all-atom and coarse-grained molecular dynamics simulations. It has been demonstrated that palmitoylation leads to a significant decrease in transmembrane domain mobility and local bilayer thickening, which may be relevant for protein trimerization.

The role of nelarabine in the treatment of T-cell acute lymphoblastic leukemia: literature review and own experience.

AIM: The analysis of experience of nelarabine use in refractory/relapsed T-cell acute lymphoblastic leukemia (T-ALL) depending on the immunophenotype and the line of therapy. MATERIALS AND METHODS: All the patients with relapsed or refractory T-ALL aged from 0 to 18 years who received treatment with nelarabine as a part of the therapeutic element R6 were included in the study. For all patients a detailed immunological analysis of leukemia cells with discrimination of immunological variants TI, TII, TIII or TIV was performed. Patients administered with nelarabine as a first therapeutic element were referred to the first-line therapy group, other patients were referred to the second-line therapy group. Nelarabine was ad- ministered as intravenous infusion at a dose of 650 mg/m2, on days 1-5. Allogeneic hematopoietic stem cells transplantation (allo-HSCT) was considered for all patients. RESULTS: From 2009 to 2017, 54 patients with refractory/relapsed T-ALL were treated with nelarabine. Five-year event-free survival (EFS) and overall survival (OS) was 28% for all patients, cumulative risk of relapse (CIR) was 27%. EFS was significantly higher in nelarabine first-line therapy group in comparison with second-line therapy group (34±8% vs 8±8%, p=0,05). In patients after allo-HSCT EFS, OS and CIR were 51±10%, 50±10% and 39,1±9,5% accordingly. The best results were achieved in patients with TI immunophenotype. No toxicity-related mortality as well as severe neurologic complications or discontinuation of therapy associated with use of nelarabine were reported. CONCLUSION: The use of nelarabine is an effective strategy for the treatment of relapsed and refractory T-ALL. The best treatment outcomes were obtained in patients with TI immunophenotype and in the first-line therapy group. Optimal dosage regimens can be established dur- ing controlled clinical trials.

[Age-related characteristics of the efficacy of different glucocorticosteroids in the therapy of acute lymphoblastic leukemia].

AIM: To determine predictors for decision-making on a differential approach to choosing glucocorticosteroids (GCS) for children and adolescents with acute lymphoblastic leukemia (ALL). SUBJECTS AND METHODS: The analysis covered 1064 primary patients aged to 1 to 18 years with ALL who had been registered at the clinics of Russia and Belorussia in April 2002 to November 2006. Before induction therapy, the patients were randomized into a dexamethasone (DEXA) 6 mg/m2 group (n=539) and a methylprednisolone (MePRED) 60 mg/m2 one (n=525). RESULTS: The entire group showed no statistically significant differences in survival rates between the patients receiving DEXA or MePRED. However, an analysis of age groups revealed the benefits of DEXA in children younger than 14 years (the event-free survival (EFS) was 76±2 and 71±2%, respectively (p=0.048); the overall survival (OS) was 81±2 and 77±2%, respectively (p=0.046); therapy-induced mortality was 6.4% (DEXA) andl 1.1% (MePRED) (p=0.01 4); the rate of isolated extramedullary relapses was 1.5% (DEXA) and 4.4% (MePRED) (p=0.009). At the same time, EFS and OS in 14-to-18-year-old adolescents were statistically significantly higher than in those who used MePRED (EFS, 65±6 and 52±6%, respectively (p=0.087); OS, 72±6 and 61±6%, respectively; (p=0.l 7). CONCLUSION: The findings suggest that it is possible that the choice of a GCS for ALL therapy must be also based on a patient's age. There is a need for further studies of this matter in prospective randomized multicenter trials in children and adolescents.

Graded bit patterned magnetic arrays fabricated via angled low-energy He ion irradiation.

A bit patterned magnetic array based on Co/Pd magnetic multilayers with a binary perpendicular magnetic anisotropy distribution was fabricated. The binary anisotropy distribution was attained through angled helium ion irradiation of a bit edge using hydrogen silsesquioxane (HSQ) resist as an ion stopping layer to protect the rest of the bit. The viability of this technique was explored numerically and evaluated through magnetic measurements of the prepared bit patterned magnetic array. The resulting graded bit patterned magnetic array showed a 35% reduction in coercivity and a 9% narrowing of the standard deviation of the switching field.

[Efficiency of the ALL-MB-2002 protocol in children with acute lymphoblastic leukemia].

AIM: To evaluate the efficiency of the original ALL-MB-2002 protocol within the multicenter study of treatment of acute lymphoblastic leukemia (ALL) in children. SUBJECTS AND METHODS: A total of 1873 primary patients with ALL aged 1 to 18 years, of whom 1544 patients were enrolled in this study, were notified at 36 clinics of Russia and Belarus from April 15, 2002, to January 1, 2008. RESULTS: With the median observation of 4.12 years, 7-year event-free survival (EFS) was 73 +/- 13%; overall survival (OS) 78 +/- 2%; relapse-free survival 82 +/- 1%. The rates of EFS and OS were equal and amounted to 76 +/- 2 and 80 +/- 2% in the standard-risk group (SRG) and intermediate-risk group (ImRG), respectively. In the high-risk group (HRG) patients, EFS and OS were as high as 30 +/- 6 and 37 +/- 6%, respectively. The frequency of relapses with central nervous system lesion was as much as 4.7% in all the patients, 6-year cumulative risk for isolated neurorecurrences being 2.5% in the SRG patients. Adolescents, patients with the baseline leukocytosis (more than 100 x 10(9)/l), and those with a splenic size of over 4 cm or more from the costal arch margin had substantially worse survival rates. A poor early response to therapy (on induction days 8 and 15) was also associated with its lower efficiency. CONCLUSION: Despite a considerable rise in the number of centers and a slight increase in the intensity of therapy, the results of the new ALL-MB-2002 protocol are as minimum equivalents obtained in the use of the previous ALL-MB-91 protocol. A significant improvement in the overall results of therapy and a reduction in the cumulative risk for isolated neurorecurrences were noted in the ImRG patients.

Attempts to grow optically coupled Fibonacci-spaced InGaAs/GaAs quantum wells result in surface gratings.

An instability in the growth of nonperiodic InGaAs/GaAs multiple quantum well samples, ordinarily of high-quality when grown with equal periods of order of half the wavelength of light in the material, leads to a dramatic microscopic, self-organized surface grating. This effect was discovered while growing quantum wells with two unequal barrier lengths arranged in a Fibonacci sequence to form an optical quasicrystal. A laser beam incident normal to the surface of the sample is diffracted into a propeller-shaped pattern. The sample surface has a distinctly cloudy appearance when viewed along one crystal axis but is mirror-like when the sample is rotated 90 degrees. The instability results in a five-fold increase in the absorption linewidth of the heavy-hole exciton transition. Atomic force microscopy, transmission electron microscopy, and scanning electron microscopy were used to study the samples.

[Clinico-laboratory variants of the course and results of therapy of hepatitis-associated aplastic anemias in children].

AIM: To study clinical and laboratory characteristics of hepatitides and evaluate efficacy of immunosuppressive therapy and transplantation of the bone marrow in hepatitis-associated aplastic anemia (HAAA). MATERIAL AND METHODS: A retrospective analysis of case histories of children with HAAA was made. For all the patients standard tests for detection of aquired aplastic anemia and hepatitis were conducted. Transplantation of hemopoietic stem cells (THSC) from HLA-identical donors was made in 4 patients, 25 patients were treated with combined immunosuppressive therapy (antithymocytic globulin--ATG plus cyclosporin A -CsA), one patients received monotherapy with CsA, two--prednisolone and a short course of CsA, one child was untreated. RESULTS: Of 260 children admitted to hospital from April 1989 to July 2005 for aquired aplastic anemia, 33 (12.7%) met diagnostic criteria of HAAA. Boys to girls ratio was 267. Hepatitides were severe: median of alaninaminotransferase concentration was 1215 IU/l, aspartataminotransferase--789 IU/l, bilirubin--152.5 mcmol/l. Median of the interval from hepatitis symptoms to documentation of pancytopenia was 66 days (0-204 days). All four patients after THSC are alive for 30-72 months. Probability of complete remission after the first course of ATG+CsA is 0.72 +/- 0.09, probability of survival 0.81 +/- 0.07, median of the interval to transfusion independence--50 days. CONCLUSION: HAAA prognosis is good only in administration of up-to-date therapy. After seronegative hepatitis it is necessary to control hemogram parameters and in the presence of minimal cytopenia patients should be directed to hematological hospital.

Submonolayer quantum dots for high speed surface emitting lasers.

We report on progress in growth and applications of submonolayer (SML) quantum dots (QDs) in high-speed vertical-cavity surface-emitting lasers (VCSELs). SML deposition enables controlled formation of high density QD arrays with good size and shape uniformity. Further increase in excitonic absorption and gain is possible with vertical stacking of SML QDs using ultrathin spacer layers. Vertically correlated, tilted or anticorrelated arrangements of the SML islands are realized and allow QD strain and wavefunction engineering. Respectively, both TE and TM polarizations of the luminescence can be achieved in the edge-emission using the same constituting materials. SML QDs provide ultrahigh modal gain, reduced temperature depletion and gain saturation effects when used in active media in laser diodes. Temperature robustness up to 100 °C for 0.98 µm range vertical-cavity surface-emitting lasers (VCSELs) is realized in the continuous wave regime. An open eye 20 Gb/s operation with bit error rates better than 10-12has been achieved in a temperature range 25-85 °Cwithout current adjustment. Relaxation oscillations up to ∼30 GHz have been realized indicating feasibility of 40 Gb/s signal transmission.

Hybrid epitaxial-colloidal semiconductor nanostructures.

We present a growth technique which combines wet-chemical growth and molecular beam epitaxy (MBE) to create complex semiconductor nanostructures with nanocrystals as active optical material. The obtained results show that wet-chemically prepared semiconductor nanocrystals can be incorporated in an epitaxally grown crystalline cap layer. As an exemplary system we chose CdSe nanorods and CdSe(ZnS) core-shell nanocrystals in ZnSe and discuss the two limits of thin (d approximately 2R) and thick (d>2R) ZnSe cap layers of thickness d for CdSe nanorods and nanodots of radii R between 2 and 4 nm. In contrast to the strain-induced CdSe/ZnSe Stranski-Krastanow growth of a quantum dot layer in a semiconductor heterostructure, the technique proposed here does not rely on strain and thus results in additional degrees of freedom for choosing composition, concentration, shape, and size of the nanocrystals. Transmission electron microscopy and X-ray diffractometry show that the ZnSe cap layer is of high crystalline quality and provides all parameters for a consecutive growth of Bragg structures, waveguides, or diode structures for electrical injection.

[Effect of the antioxidants on NO-dependent induction of heme oxigenase 1 gene in U937 monocytes].

Previously it was shown that thiol antioxidants are potent inhibitors of the NO-dependent induction of heme oxygenase 1 (HOX-1) gene. However, the mechanism of HOX-1 gene down-regulation by thiol antioxidants and underlying signaling pathway remain unclear. In this study we have examined, whether the scavenging of reactive oxygen and reactive nitrogen species (ROS and RNS) is the major cause for thiol-mediated suppression of the HOX-1 induction by NO. Further, to identify the ROS family members implicated in the HOX-1 induction, we also exposed cells to various non-thiol antioxidants: dimethyl sulfoxide, dimetylthiourea, sodium salicylate, sodium formate, uric acid, catalase, and superoxide dismutase. A partial inhibition of HOX-1 induction occurred in the presence of non-polar hydroxyl radical scavengers, dimethyl sulfoxide and dimetylthiourea. The other non-thiol antioxidants were ineffective towards HOX-1 expression. Then, in order to determine, whether RNS scavenging is implicated in the HOX-1 down-regulation by thiol antioxidants, we took advantage of the capacity of suboptimal concentrations of the NO scavenger PTIO (2-phenyl-4,4,5,5-tetramethylimidazole-1-oxyl-3-oxide) to oxidize NO to nitrosating species. We showed that simultaneous cell treatment with NO donor and PTIO significantly enhanced the rate of the HOX-1 gene NO-dependent induction indicating that RNS are mediators of HOX-1 gene transcriptional activation. Thiol antioxidants completely suppressed PTIO stimulatory action. These findings imply that inhibitory action of thiol antioxidants is mediated by RNS scavenging. The study provides an approach for pharmacologycal modulation of cell response to NO and its derivatives through the use of antioxidants.

[Redox-dependent regulation of gene expression induced by nitric oxide]. / Redoks-zavisimaia reguliatsiia ékspressii genov, indutsiruemykh okis'iu azota.

Nitric oxide (NO) is a mobile, highly reactive signal molecule, and changes the expression of specific genes in effector cells. Under physiological conditions, NO reacts with molecular oxygen and with reactive oxygen species (ROS) to produce intermediates known as reactive nitrogen species (RNS). The production of NO and RNS in the cell is controlled by hormones, neurotransmitters, cytokines, and growth factors. Hence NO and its derivatives act as secondary paracrinous factors and transmit the signal from NO-producing to neighboring cells. Intracellular reception of NO and RNS is due to Src-related tyrosine protein kinases, G-protein Ras, cytochrome oxidase, and guanylate cyclase. Receptor proteins mostly contain heme, active thiol, or iron-sulfur groups, and are both on the plasma membrane and in internal cell compartments. Many of the NO receptors are the key components of cell regulatory systems controlling the transcription factors AP-1, HIF-1, NF-kappa B, and p53 and the expression of their target genes. A distinguishing feature of NO signaling is that changes in redox potential of the cell switch the NO receptor and, consequently, modify the NO effect. Depending on the ROS level, NO activates different signal transduction pathways to induce (or suppress) different gene sets. The data considered indicate that antioxidants may be used to directionally change the transcriptional response of the cell to NO.

Phorbol ester stimulates expression of the human tryptophanyl-tRNA synthetase gene.

The effect of the phorbol ester phorbol 12-myristate 13-acetate (PMA) on expression of the human interferon (IFN)-inducible tryptophanyl-tRNA synthetase (WRS) gene was studied. PMA caused an increase in the basal and IFNgamma-induced WRS protein content in HeLa and HEK293 cultured cells. Besides, PMA upregulated WRS mRNA level in HeLa cells. Since PMA is known as a selective activator of protein kinase C (PKC) and is widely used to study the PKC-related pathways, these results show possible PKC involvement in regulation of the WRS gene expression. PKC inhibition by staurosporine (10 and 100 nM) had no effect on either basal or IFNgamma-induced expression of WRS in either cell line. Consequently, PKC is not an indispensable element in WRS induction by IFNgamma. Rather, PKC may activate WRS gene expression only by a distinct pathway.

[Identification of genes induced to chondrocytes by nitric oxide]. / Poisk i identifikatsiia genov, indutsiruemykh v khondrotsitakh pod deistviem okisi azota.

Nitric oxide (NO) acts as a short-lived paracrine factor and selectively activates transcription of certain genes. The spectrum of inducible genes was studied in primary chondrocytes. A cDNA library was obtained by subtraction hybridization with RNAs isolated from rabbit chondrocytes before and after treatment with nitrosoglutathione, an NO-generating agent. Some of the cloned cDNAs were homologous to known mammalian genes and human EST. NO-dependent transcriptional activation was demonstrated for the stromelysin 1 and cyclooxygenase 2 genes and, for the first time, for mcl1 coding for an apoptosis suppressor.

[Time course changes in the count of peripheral granulocytes in children with acquired aplastic anemias treated with antithymocyte globulin, cyclosporin A and granulocytic colony stimulating factor]. / Dinamika kolichestva granulotsitov v perifericheskoi krovi u detei s priobretennymi aplasticheskimi anemiiami, poluchivshikh lechenie antitimotsitarnym globulinom, tsiklosporinom A i granulotsitarnym koloniestimuliruiushchim faktorom.

AIM: To examine the pattern of changes in the count of peripheral granulocytes in children with aplastic anemias (AA), receiving a combined immunosuppressive therapy with antithymocytic globulin (ATG) and cyclosporin A in combination with granulocytic colony-stimulating factor (G-CSF). MATERIALS AND METHODS: 31 children (17 boys and 14 girls) aged 2-15 years (median 9 years) with newly diagnosed severe and very severe acquired AA took a combined immunosuppressive therapy with ATG and cyclosporin A in combination with G-CSF in an initial dose of 10 micrograms/kg a day. RESULTS: A three-linear and response was recorded in 19 (61%) children, an isolated granulocytic response was in 26 (84%). The interval median before the recovery of granulocytes to 1.5 x 10(9)/l and 5 x 10(9)/l was 19 and 38 days, respectively. CONCLUSION: Use of G-CSF may increase the count of granulocytes in the vast majority of patients with AA, without dramatic influence on the frequency of a three-linear response. Intermittent use of G-CSF may maintain the count of granulocytes long at the safe level and reduce the cost of treatment.

Induction of vascular endothelial growth factor by nitric oxide in cultured human articular chondrocytes.

We investigated the role of nitric oxide (NO) in the control of vascular endothelial growth factor A (VEGF) gene expression in cultured human articular chondrocytes. Cell treatment with the NO-generating compound nitrosoglutathione (GSNO) caused a significant accumulation of 4.4 kb VEGF mRNA, a major VEGF mRNA isoform expressing in chondrocytes. This is the first demonstration that NO can induce VEGF mRNA expression in chondrocytes. VEGF mRNA level was not affected in cells exposed to dibutyryl cGMP, a non-hydrolyzable analog of cGMP, suggesting that the cGMP system is not involved in NO-dependent transcriptional activation of VEGF gene. The GSNO-stimulated induction of VEGF mRNA was slightly attenuated by MAP protein kinase inhibitors PD98058 and SB203580, but was completely blocked in cells incubated with GSNO in the presence of catalase and superoxide dismutase, enzymes scavenging reactive oxygen species (ROS), or in the presence of thiol-containing antioxidants, N-acetyl cysteine and reduced glutathione. These results suggest that in articular chondrocytes the GSNO-induced VEGF gene transcriptional activation is dependent on endogenous ROS production and oxidative thiol modifications.

Autocorrelation spectroscopy on single ultrathin layers of CdSe/ZnSe: hints for a non-thermal distribution of excitons in quantum islands.

Autocorrelation spectroscopy on the basis of thousands of individual near-field photoluminescence spectra of single ultrathin CdSe layers at low temperatures exhibits a strong positive correlation peak around 18 meV energy with a width of 5 meV. Using simulations and experiments as a function of temperature and laser intensity, we can exclude interpretations along the lines of biexcitons or phonon sidebands. We attribute this feature to the splitting of ground state and an excited state in individual quantum islands. This interpretation implies that the potential minima are rather uniform in size and that the distribution of excitons is nonthermal.

Results at a single centre of immunosuppression with cyclosporine A in 66 children with aplastic anaemia.

A retrospective analysis of cyclosporine A (CsA) monotherapy administered to 66 children with aplastic anaemia (AA) at a single centre was carried out. The study was conducted on 66 children (F34/M32) with a median age of 10.5 years. 30 children (45%) achieved complete or partial remission within a median of 8 weeks. The response rate was 3/19 (16%) in cases of very severe aplastic anaemia (vSAA), 16/34 (47%) in severe aplastic anaemia (SAA) and 11/13 (85%) in nonSAA. 10 remitters (33%) relapsed after CsA cessation or dose tapering and six of those responded again on CsA alone. The only variable predictive for response was granulocyte count before treatment. The actuarial probability of survival was 51% at 4 years (85% in moderate AA, 50% in SAA and 32% in vSAA). The optimal dosage of CsA has yet to be established.