Применение алгоритмов биоинформатики для обнаружения мутирующих кибератак

The functionality of any system can be represented as a set of commands that lead to a change in the state of the system. The intrusion detection problem for signature-based intrusion detection systems is equivalent to matching the sequences of operational commands executed by the protected system to known attack signatures. Various mutations in attack vectors (including replacing commands with equivalent ones, rearranging the commands and their blocks, adding garbage and empty commands into the sequence) reduce the effectiveness and accuracy of the intrusion detection. The article analyzes the existing solutions in the field of bioinformatics and considers their applicability for solving the problem of identifying polymorphic attacks by signature-based intrusion detection systems. A new approach to the detection of polymorphic attacks based on the suffix tree technology applied in the assembly and verification of the similarity of genomic sequences is discussed. The use of bioinformatics technology allows us to achieve high accuracy of intrusion detection at the level of modern intrusion detection systems (more than 0.90), while surpassing them in terms of cost-effectiveness of storage resources, speed and readiness to changes in attack vectors. To improve the accuracy indicators, a number of modifications of the developed algorithm have been carried out, as a result of which the accuracy of detecting attacks increased by up to 0.95 with the level of mutations in the sequence up to 10%. The developed approach can be used for intrusion detection both in conventional computer networks and in modern reconfigurable network infrastructures with limited resources (Internet of Things, networks of cyber-physical objects, wireless sensor networks).Функционал любой системы может быть представлен в виде совокупности команд, которые приводят к изменению состояния системы. Задача обнаружения атаки для сигнатурных систем обнаружения вторжений эквивалентна сопоставлению последовательностей команд, выполняемых защищаемой системой, с известными сигнатурами атак. Различные мутации в векторах атак (включая замену команд на равносильные, перестановку команд и их блоков, добавление мусорных и пустых команд) снижают эффективность и точность обнаружения вторжений. В статье проанализированы существующие решения в области биоинформатики, рассмотрена их применимость для идентификации мутирующих атак. Предложен новый подход к обнаружению атак на основе технологии суффиксных деревьев, используемой при сборке и проверке схожести геномных последовательностей. Применение алгоритмов биоинформатики позволяет добиться высокой точности обнаружения мутирующих атак на уровне современных систем обнаружения вторжений (более 90%), при этом превосходя их по экономичности использования памяти, быстродействию и устойчивости к изменениям векторов атак. Для улучшения показателей точности проведен ряд модификаций разработанного решения, вследствие которых точность обнаружения атак увеличена до 95% при уровне мутаций в последовательности до 10%. Метод может применяться для обнаружения вторжений как в классических компьютерных сетях, так и в современных реконфигурируемых сетевых инфраструктурах с ограниченными ресурсами (Интернет вещей, сети киберфизических объектов, сенсорные сети)

Применение алгоритмов биоинформатики для обнаружения мутирующих кибератак

Функционал любой системы может быть представлен в виде совокупности команд, которые приводят к изменению состояния системы. Задача обнаружения атаки для сигнатурных систем обнаружения вторжений эквивалентна сопоставлению последовательностей команд, выполняемых защищаемой системой, с известными сигнатурами атак. Различные мутации в векторах атак (включая замену команд на равносильные, перестановку команд и их блоков, добавление мусорных и пустых команд) снижают эффективность и точность обнаружения вторжений. В статье проанализированы существующие решения в области биоинформатики, рассмотрена их применимость для идентификации мутирующих атак. Предложен новый подход к обнаружению атак на основе технологии суффиксных деревьев, используемой при сборке и проверке схожести геномных последовательностей. Применение алгоритмов биоинформатики позволяет добиться высокой точности обнаружения мутирующих атак на уровне современных систем обнаружения вторжений (более 90%), при этом превосходя их по экономичности использования памяти, быстродействию и устойчивости к изменениям векторов атак. Для улучшения показателей точности проведен ряд модификаций разработанного решения, вследствие которых точность обнаружения атак увеличена до 95% при уровне мутаций в последовательности до 10%. Метод может применяться для обнаружения вторжений как в классических компьютерных сетях, так и в современных реконфигурируемых сетевых инфраструктурах с ограниченными ресурсами (Интернет вещей, сети киберфизических объектов, сенсорные сети)

The role of parallel computing in bioinformatics

The need to intelligibly capture, manage and analyse the ever-increasing amount of publicly available genomic data is one of the challenges facing bioinformaticians today. Such analyses are in fact impractical using uniprocessor machines, which has led to an increasing reliance on clusters of commodity-priced computers. An existing network of cheap, commodity PCs was utilised as a single computational resource for parallel computing. The performance of the cluster was investigated using a whole genome-scanning program written in the Java programming language. The TSpaces framework, based on the Linda parallel programming model, was used to parallelise the application. Maximum speedup was achieved at between 30 and 50 processors, depending on the size of the genome being scanned. Together with this, the associated significant reductions in wall-clock time suggest that both parallel computing and Java have a significant role to play in the field of bioinformatics

Organic acid production in Aspergillus niger and other filamentous fungi

The aim of the thesis was to increase the understanding of organic acid production in Aspergillus niger and other filamentous fungi, with the ultimate purpose to improve A. niger as biotechnological production host. In Chapter 1, the use of microbial cell-factories for the production of various compounds of interest, with a focus on organic acid production in A. niger, is introduced. To convert A. niger into a cell-factory for the production of fumarate, an organic acid that this fungus does not naturally accumulate extracellularly, we need to know the key components that lead to high extracellular fumarate accumulation. This can be achieved by studying a natural fumarate producer, in our case the filamentous fungus Rhizopus delemar. To increase both the understanding of R. delemar fumarate production, and identify a possible candidate fumarate exporter protein for heterologuous expression in A. niger, we studied differences in the transcriptional and proteomic responses of R. delemar under high and low fumarate producing conditions, described in Chapter 2. Based on our analyses, we propose that a substantial part of the fumarate accumulated in R. delemar during nitrogen starvation results from the urea cycle due to amino acid catabolism. Thus, although we failed to identify the correct fumarte exporter (discussed in Chapter 8), the results of these analyses lead to a broader understanding of the mechanism underlying fumarate accumulation in R. delemar. In order to make A. niger a suitable production host for other organic acids, we also delved deeper into the understanding of why A. niger has an innate ability to secrete various organic acids, especially citrate, described in Chapter 3. We show that an increase in citrate secretion under iron limited conditions is a physiological response consistent with a role of citrate as A. niger iron siderophore. We found that A. niger citrate secretion increases with decreasing amounts of iron added to the culture medium and, in contrast to previous findings, this response is independent of the nitrogen source. Differential transcriptomics analyses of the two A. niger mutants NW305 (gluconate non-producer) and NW186 (gluconate and oxalate non-producer) revealed up-regulation of the citrate biosynthesis gene citA under iron limited conditions compared to iron replete conditions. In addition, we show that A. niger can utilise Fe(III) citrate as iron source. Finally, we discuss our findings in the general context of the pH-dependency of A. niger organic acid production, offering an explanation, besides competition, for why A. niger organic acid production is a sequential process influenced by the external pH of the culture medium. In Chapter 4, we further unravel the various different mechanisms underlying extracellular A. niger citrate accumulation. We show that the phenotype of increased extracellular citrate accumulation can have fundamentally different underlying mechanisms, depending on how this response was triggered. We found that varying the amount and supplement of an arginine auxotrophic A. niger strain induces increased citrate productivity. Transcriptomics analysis shows down-regulation of citrate metabolising enzymes in the conditions in which more citrate is accumulated extracellularly. This contrasts with the transcriptional adaptations triggered by iron limited conditions, described in Chapter 3. By combining data obtained from both experimental setups described in Chapters 3 and 4, we compiled a list of likely citrate transporter candidates. Two promising citrate exporter candidates were tested in the yeast Saccharomyces cerevisiae, of which one was successfully identified as citrate exporter. Our findings provide the first steps in untangling the complex interplay of different mechanisms underlying A. niger citrate accumulation, and we pinpoint, for the first time, a promising A. niger citrate exporter candidate, offering a valuable tool for improvement of A. niger as biotechnological cell-factory for citrate production. For the identification of different A. niger substrate importers, we combined in silico and in vivo approaches, and established a reliable pipeline to identify and test candidate transport proteins. The in silico approach, in which likely glucose transporter candidates are inferred from good matches with a glucose transporter specific Hidden Markov model (HMMgluT), and the in vivo approach, in which a sub-cellular proteomics approach is applied to isolate plasmalemmal glucose transporters, is described in Chapter 5. In the presented research work, a hidden Markov model (HMM), that shows a good performance in the identification and segmentation of functionally validated glucose transporters, was constructed. The model (HMMgluT) was used to analyse the A. niger membrane-associated proteome response to high and low glucose concentrations at a low pH. By combining the abundance patterns of the proteins found in the A. niger plasmalemma proteome with their HMMgluT scores, two new putative high affinity glucose transporters, denoted MstG and MstH, were identified. MstG and MstH were functionally validated and biochemically characterised by heterologous expression in a S. cerevisiae glucose transport null mutant. They were shown to be a high affinity glucose transporter (Km = 0.6 ± 0.1 mM) and a very high affinity glucose transporter (Km = 0.06 ± 0.005 mM) respectively. The concepts developed in Chapter 5 were applied in Chapter 6 to identify further substrate importer proteins in both A. niger and another filamentous fungus, Trichoderma reesei. Again a hidden Markov model, this time for the identification of xylose transporters, was constructed and used to analyse the A. niger and T. reesei in silico proteomes, yielding a list of candidate xylose transporters. From this list, three A. niger (XltA, XltB and XltC) and three T. reesei (Str1, Str2 and Str3) transporters were selected, functionally validated and biochemically characterised through their expression in a S. cerevisiae hexose transport null mutant, engineered to be able to metabolise xylose, but unable to transport this sugar. All six transporters were able to support growth of the engineered yeast on xylose, but varied in affinities and efficiencies in the uptake of the pentose. Amino acid sequence analysis of the selected transporters showed the presence of specific residues and motifs associated to xylose transporters. Transcriptional analysis of A. niger and T. reesei showed that XltA and Str1 were specifically induced by xylose and dependent on the XlnR/Xyr1 regulators, implying a biological role for these transporters in xylose utilisation. Thus, our findings show that our approach using HMMs is a robust pipeline to identify different substrate importer candidates. In Chapter 7, comparative plasmalemma proteomic analysis was used to identify candidate L-rhamnose transporters in A. niger. Further analysis was focused on protein ID 1119135 (RhtA) (JGI A. niger ATCC 1015 genome database). RhtA was classified as a Family 7 Fucose:H+ Symporter (FHS) within the Major Facilitator Superfamily. Family 7 currently includes exclusively bacterial transporters able to use different sugars. Strong indications for its role in L-rhamnose transport were obtained by functional complementation of the Saccharomyces cerevisiae EBY.VW.4000 strain in growth studies with a range of potential substrates. Biochemical analysis using L-[3H(G)]-rhamnose confirmed that RhtA is a L-rhamnose transporter. The RhtA gene is located in tandem with a hypothetical alpha-L-rhamnosidase gene (rhaB). Transcriptional analysis of rhtA and rhaB confirmed that both genes have a coordinated expression, being strongly and specifically induced by L-rhamnose, and controlled by RhaR, a transcriptional regulator involved in the release and catabolism of the methyl-pentose. RhtA is the first eukaryotic L-rhamnose transporter identified and functionally validated to date. In Chapter 8, the findings presented in this thesis with regards to our attempts at improving A. niger as biotechnological production host are summarised, and further implications for metabolic engineering approaches based on the conclusions drawn are discussed.</p

Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit

SUMMARY: PRALINE 2 is a toolkit for custom multiple sequence alignment workflows. It can be used to incorporate sequence annotations, such as secondary structure or (DNA) motifs, into the alignment scoring, as well as to customize many other aspects of a progressive multiple alignment workflow. AVAILABILITY AND IMPLEMENTATION: PRALINE 2 is implemented in Python and available as open source software on GitHub: https://github.com/ibivu/PRALINE/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Approaches in Enhancing Antioxidant Defense in Plants

This Special Issue, “Approaches in Enhancing Antioxidant Defense in Plants” published 13 original research works and a couple of review articles that discuss the various aspects of plant oxidative stress biology and ROS metabolism, as well as the physiological mechanisms and approaches to enhancing antioxidant defense and mitigating oxidative stress. These papers will serve as a foundation for plant oxidative stress tolerance and, in the long term, provide further research directions in the development of crop plants’ tolerance to abiotic stress in the era of climate change

Micro-costing study of rituximab subcutaneous injection versus intravenous infusion in dutch setting

Background: Rituximab for subcutaneous (SC) administration has recently been approved for use in common forms of diffuse large B-cell lymphoma (DLBCL). This form of rituximab is supplied in ready-to-use vials that do not require individual dose adjustment. It is expected that SC-injection will shorten the treatment time per administration of rituximab in comparison with currently available intravenous (IV) infusion. Aims: The goal of this study is to identify and compare all direct costs of IV and SC rituximab given to the DLBCL patients in the Netherlands. Methods: Using a prospective, observational, bottom up, micro-costing study we collected primary data on the direct medical costs of the preparation, administration and acquisition of rituximab. Drug costs and spillage, labor costs, material costs and remaining daycare costs were identified using standardized forms, structured using guideline prices and compared for the IV and SC forms of rituximab. Results: Measurements were done on 53 administrations (33 IV and 20 SC). The mean total costs of the IV infusion were €2174, and €1907 for the SC injection. The estimated difference of €267 per administration was mainly due to spillage costs and differences in chair time, related daycare costs and drug costs. Summary and Conclusions: Rituximab administered in the form of SC injection is less costly than its IV form. Taking into account their equal effectiveness, favorable pharmacoeconomic profile of SC rituximab can result in significant savings when transferred to the total DLBCL population in the Netherlands

Trial efficacy vs real world effectiveness in first line treatment of multiple myeloma

Background: Large randomized clinical trials (RCT) are the foundation of the registration of newly developed drugs. A potential problem with RCTs is that the inclusion/exclusion criteria will make the population different from the actual population treated in real life. Hence, it is important to understand how the results from the RCT can be generalized to a general population. Aims: The primary aim of the present study was to assess the generalizability of the large 1st line RCTs in Multiple Myeloma (MM) to the Nordic setting and to understand potential difference and magnitude in outcomes between RCTs and patients treated in standard care in the Nordics. Methods: A retrospective analysis was performed on an incident cohort of 2960 MM-patients from 24 hospitals in Denmark, Finland, Norway and Sweden. The database contained information on patient baseline characteristics, treatments and outcomes. Data from relevant 1st line MM RCTs was selected from the treatment MP (Waage, A., et al., Blood. 2010], MPT (Waage, A., et al., Blood. 2010) and VMP (San Miguel, J.F., et al., N Engl J Med, 2008) and baseline characteristics were compared to newly diagnosed Nordic MM treated patients. Potential difference in response and overall survival (OS) was estimated by adjusting the RWE population to the RCT population using matching adjusted indirect comparisons. Patients were matched on age (median approximated to mean), gender, calcium, beta2-microglobulin and ISS score 3. These variables were selected because they were reported in all trials and have previously been identified as having prognostic value. Results: Patients in the Nordic database treated with MP (n=880) had a response rate of (PD, NR, PR, VGPR, ≥nCR) of (13%, 39%, 38%, 6%, 4%). After matching (n=347), the response rate was slightly worse (12%, 43%, 36%, 6%, 3%). This can be compared to the response rate from the RCT of (7%, 53%, 33%, 3%, 4%). OS for Nordic MP treated patients was 2.67 years (2.25-3.17). After matching the OS was 3.37 years (2.86-3.96) and this can be compared to the trial with OS 2.40 years (2.23-2.66). Patients treated with MPT (n=283) in the Nordic countries had a response rate of (5%, 14%, 52%, 20%, 9%). After matching (n=179) the response rate was slightly changed to (6%, 20%, 50%, 13% 11%). The corresponding RCT response results were 14%, 29%, 34%, 10%, and 13% respectively. OS for Nordic MPT treated patients was 4.15 years (3.73- 4.74). After matching the OS was 4.28 years (3.98-NA) years and compared to 2.42 years (2.08-3.17) OS observed in the corresponding trial. Patients treated with VMP (n=59) in the Nordic countries had a response rate of (4%, 5%, 40%, 18%, 33%). After matching (n=31) the response rate was improved to (8%, 11%, 28%, 8%, 45%). This corresponding response rates shown in the trial are 1%, 23%, 33%, 8%, and 33% respectively. OS for Nordic MP treated patients was 4.86 years (3.79-NA). After matching the OS was 4.86 years (4.86-NA) and this can be compared to the trial with OS 4.70 years. Summary and Conclusions: Surprisingly Nordic treated MM patients do very well compared to, and even better than, patients treated in RCTs. Since the OS for all tested treatments improves after matching to the RCT baseline characteristics, patients recruited to the RCTs seems to be a bit better than ordinary Nordic patents. The database used in the present study, and the used method, can be valuable for generalizing the results to the Nordic setting and estimating potential difference for future RCTs and Nordic MM treated patients. Future research should include different data cuts to see whether the analyses are biased by differences subsequent treatments applied in RCTs and clinical practice