Organization of the channel-switching process in parallel computer systems based on a matrix optical switch

After a classification and analysis of electronic and optoelectronic switching devices, the design principles and structure of a matrix optical switch is described. The switching and pair-exclusion operations in this type of switch are examined, and a method for the optical switching of communication channels is elaborated. Finally, attention is given to the structural organization of a parallel computer system with a matrix optical switch

The G140S mutation in HIV integrases from raltegravir-resistant patients rescues catalytic defect due to the resistance Q148H mutation

Raltegravir (MK-0518) is the first integrase (IN) inhibitor to be approved by the US FDA and is currently used in clinical treatment of viruses resistant to other antiretroviral compounds. Virological failure of Raltegravir treatment is associated with mutations in the IN gene following two main distinct genetic pathways involving either the N155 or Q148 residue. Importantly, in most cases, an additional mutation at the position G140 is associated with the Q148 pathway. Here, we investigated the viral DNA kinetics for mutants identified in Raltegravir-resistant patients. We found that (i) integration is impaired for Q148H when compared with the wild-type, G140S and G140S/Q148H mutants; and (ii) the N155H and G140S mutations confer lower levels of resistance than the Q148H mutation. We also characterized the corresponding recombinant INs properties. Enzymatic performances closely parallel ex vivo studies. The Q148H mutation ‘freezes’ IN into a catalytically inactive state. By contrast, the conformational transition converting the inactive form into an active form is rescued by the G140S/Q148H double mutation. In conclusion, the Q148H mutation is responsible for resistance to Raltegravir whereas the G140S mutation increases viral fitness in the G140S/Q148H context. Altogether, these results account for the predominance of G140S/Q148H mutants in clinical trials using Raltegravir

Разработка и валидация методики пептидного картирования инновационного препарата ингибитора С1 эстеразы

Peptide mapping is a key method for studying the primary structure of proteins. With its sensitivity to the slightest changes in the covalent structure of a protein, this method is applicable both to medicinal product identification at the control stage and to production process stability monitoring.The aim of the study was to develop and validate a peptide-mapping procedure for the identification of a novel highly glycosylated recombinant C1 esterase inhibitor.Materials and methods. The authors studied recombinant human C1 esterase inhibitor products and trypsin. The study involved peptide mapping using reverse-phase high-performance liquid chromatography and high-resolution mass spectrometry. The following statistics were calculated to evaluate the results: mean, standard deviation, and coefficient of variation. The validation parameters included specificity, precision, and robustness.Results. The authors tested several variants of sample preparation for tryptic digests, including additional N-glycanase treatment and complete deglycosylation, and established the optimal conditions for sample preparation and chromatographic separation of C1 esterase inhibitor peptides to obtain consistent chromatographic profiles (peptide maps). The authors identified characteristic peaks and the corresponding relative retention time and area ranges. The absolute retention time of the second (characteristic) peak was approximately 16.5–16.9 minutes. The relative retention times were 2.14–2.21 for peak 9, 2.55–2.64 for peak 12, 2.97–3.14 for peak 14, 3.11–3.29 for peak 15, and 6.20–6.63 for peak 28.Conclusions. The authors developed a peptide-mapping procedure for C1 esterase inhibitors and optimised the conditions to achieve an over 18-hour reduction in sample preparation time. This procedure met the established acceptance criteria for specificity, precision, and robustness.Пептидное картирование является одним из ключевых методов изучения первичной структуры белка. Метод чувствителен даже к малейшим изменениям в ковалентной структуре белка, что позволяет использовать его для проверки подлинности препарата на стадии контроля и мониторинга стабильности производственного процесса.Цель работы: разработка и валидация методики пептидного картирования для подтверждения подлинности инновационного высокогликозилированного рекомбинантного белка — ингибитора С1 эстеразы.Материалы и методы: рекомбинантный ингибитор С1 эстеразы человека, трипсин. Исследование проводили методом пептидного картирования с использованием обращенно-фазовой высокоэффективной жидкостной хроматографии (ОФ ВЭЖХ) и метода масс-спектрометрии высокого разрешения. Результаты оценивали с применением статистических методов расчета среднего арифметического, стандартного отклонения, коэффициента вариации. Методику валидировали по показателям: специфичность, прецизионность и устойчивость.Результаты: апробированы разные варианты пробоподготовки трипсинолизатов, включая дополнительную обработку белка N-гликаназой и полное дегликозилирование. Подобраны условия пробоподготовки и хроматографического разделения пептидов ингибитора С1 эстеразы с получением стабильного профиля пептидной карты. Разработаны и определены реперные пики, а также диапазоны их относительных времен удерживания и относительной площади. Абсолютное время удерживания второго (референтного) пика составило 16,5–16,9 мин. Относительное время удерживания пика 9 — 2,14–2,21, пика 12 — 2,55–2,64, пика 14 — 2,97–3,14, пика 15 — 3,11–3,29 и пика 28 — 6,20–6,63.Выводы: разработана методика пептидного картирования ингибитора С1 эстеразы. Оптимизация условий методики позволила сократить время пробоподготовки более чем на 18 ч. Разработанная методика по валидационным характеристикам специфичности, прецизионности и устойчивости соответствовала установленным критериям приемлемости

Comparison of metal-dependent catalysis by HIV-1 and ASV integrase proteins using a new and rapid, moderate throughput assay for joining activity in solution

<p>Abstract</p> <p>Background</p> <p>HIV-1 integrase (IN) is an attractive target for the development of drugs to treat AIDS, and inhibitors of this viral enzyme are already in the clinic. Nevertheless, there is a continuing need to devise new approaches to block the activity of this viral protein because of the emergence of resistant strains. To facilitate the biochemical analysis of wild-type IN and its derivatives, and to measure the potency of prospective inhibitory compounds, a rapid, moderate throughput solution assay was developed for IN-catalyzed joining of viral and target DNAs, based on the detection of a fluorescent tag.</p> <p>Results</p> <p>A detailed, step-by-step description of the new joining assay is provided. The reactions are run in solution, the products captured on streptavidin beads, and activity is measured by release of a fluorescent tag. The procedure can be scaled up for the analysis of numerous samples, and is substantially more rapid and sensitive than the standard radioactive gel methods. The new assay is validated and its utility demonstrated via a detailed comparison of the Mg⁺⁺- and Mn⁺⁺-dependent activities of the IN proteins from human immunodeficiency virus type 1 (HIV-1) and the avian sarcoma virus (ASV). The results confirm that ASV IN is considerably more active than HIV-1 IN, but with both enzymes the initial rates of joining, and the product yields, are higher in the presence of Mn⁺⁺than Mg⁺⁺. Although the pH optima for these two enzymes are similar with Mn⁺⁺, they differ significantly in the presence of Mg⁺⁺, which is likely due to differences in the molecular environment of the binding region of this physiologically relevant divalent cation. This interpretation is strengthened by the observation that a compound that can inhibit HIV-1 IN in the presence of either metal cofactors is only effective against ASV in the presence of Mn⁺⁺.</p> <p>Conclusion</p> <p>A simplified, assay for measuring the joining activity of retroviral IN in solution is described, which offers several advantages over previous methods and the standard radioactive gel analyses. Based on comparisons of signal to background ratios, the assay is 10–30 times more sensitive than gel analysis, allows more rapid and accurate biochemical analyses of IN catalytic activity, and moderate throughput screening of inhibitory compounds. The assay is validated, and its utility demonstrated in a comparison of the metal-dependent activities of HIV-1 and ASV IN proteins.</p

Efficient and Specific Internal Cleavage of a Retroviral Palindromic DNA Sequence by Tetrameric HIV-1 Integrase

BACKGROUND: HIV-1 integrase (IN) catalyses the retroviral integration process, removing two nucleotides from each long terminal repeat and inserting the processed viral DNA into the target DNA. It is widely assumed that the strand transfer step has no sequence specificity. However, recently, it has been reported by several groups that integration sites display a preference for palindromic sequences, suggesting that a symmetry in the target DNA may stabilise the tetrameric organisation of IN in the synaptic complex. METHODOLOGY/PRINCIPAL FINDINGS: We assessed the ability of several palindrome-containing sequences to organise tetrameric IN and investigated the ability of IN to catalyse DNA cleavage at internal positions. Only one palindromic sequence was successfully cleaved by IN. Interestingly, this symmetrical sequence corresponded to the 2-LTR junction of retroviral DNA circles-a palindrome similar but not identical to the consensus sequence found at integration sites. This reaction depended strictly on the cognate retroviral sequence of IN and required a full-length wild-type IN. Furthermore, the oligomeric state of IN responsible for this cleavage differed from that involved in the 3'-processing reaction. Palindromic cleavage strictly required the tetrameric form, whereas 3'-processing was efficiently catalysed by a dimer. CONCLUSIONS/SIGNIFICANCE: Our findings suggest that the restriction-like cleavage of palindromic sequences may be a general physiological activity of retroviral INs and that IN tetramerisation is strongly favoured by DNA symmetry, either at the target site for the concerted integration or when the DNA contains the 2-LTR junction in the case of the palindromic internal cleavage

High-Level Synthesis versus Hardware Construction

Application-specific systems with FPGA accelerators are often designed using high-level synthesis or hardware construction tools. Nowadays, there are many frameworks available, both open-source and commercial. In this work, we aim at a fair comparison of several languages (and tools), including Verilog (our baseline), Chisel, Bluespec System Verilog (Bluespec Compiler), DSLX (XLS), MaxJ (MaxCompiler), and C (Bambu and Vivado HLS). Our analysis has been carried out using a representative example of 8×8 inverse discrete cosine transform (IDCT), a widely used algorithm engaged in JPEG and MPEG decoders. The metrics under consideration include: (a) the degree of automation (how much less code is required compared to Verilog), (b) the controllability (possibility to achieve given design characteristics, namely a given ratio of the performance and area), and (c) the flexibility (ease of design modifications to achieve certain characteristics). Rather than focusing on computational kernels only, we use AXI-Stream wrappers for the synthesized implementations, which allows adequately evaluating characteristics of the designs when they are used as parts of real systems. Our study shows clear examples of what impact specific optimizations (tool settings and source code modifications) have on the overall system performance and area. It emphasizes how important is to be able to control the balance between the communication interface utilization and the computational kernel performance and delivers clear guidelines for the next generation tools for designing FPGA-accelerator-based systems.</p

High-Level Synthesis versus Hardware Construction

Application-specific systems with FPGA accelerators are often designed using high-level synthesis or hardware construction tools. Nowadays, there are many frameworks available, both open-source and commercial. In this work, we aim at a fair comparison of several languages (and tools), including Verilog (our baseline), Chisel, Bluespec System Verilog (Bluespec Compiler), DSLX (XLS), MaxJ (MaxCompiler), and C (Bambu and Vivado HLS). Our analysis has been carried out using a representative example of 8×8 inverse discrete cosine transform (IDCT), a widely used algorithm engaged in JPEG and MPEG decoders. The metrics under consideration include: (a) the degree of automation (how much less code is required compared to Verilog), (b) the controllability (possibility to achieve given design characteristics, namely a given ratio of the performance and area), and (c) the flexibility (ease of design modifications to achieve certain characteristics). Rather than focusing on computational kernels only, we use AXI-Stream wrappers for the synthesized implementations, which allows adequately evaluating characteristics of the designs when they are used as parts of real systems. Our study shows clear examples of what impact specific optimizations (tool settings and source code modifications) have on the overall system performance and area. It emphasizes how important is to be able to control the balance between the communication interface utilization and the computational kernel performance and delivers clear guidelines for the next generation tools for designing FPGA-accelerator-based systems.</p