Partition System Research Articles

A conserved mechanism drives partition complex assembly on bacterial chromosomes and plasmids

Chromosome and plasmid segregation in bacteria are mostly driven by ParABS systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites (parS). However, the mechanism of how a few parS‐bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico‐mathematical models. We discriminated between these different models by varying some key parameters in vivo using the F plasmid partition system. We found that “Nucleation & caging” is the only coherent model recapitulating in vivo data. We also showed that the stochastic self‐assembly of partition complexes (i) is a robust mechanism, (ii) does not directly involve ParA ATPase, (iii) results in a dynamic structure of discrete size independent of ParB concentration, and (iv) is not perturbed by active transcription but is by protein complexes. We refined the “Nucleation & caging” model and successfully applied it to the chromosomally encoded Par system of Vibrio cholerae, indicating that this stochastic self‐assembly mechanism is widely conserved from plasmids to chromosomes.

PYR4 From a Norwegian Isolate of Yersinia ruckeri Is a Putative Virulence Plasmid Encoding Both a Type IV Pilus and a Type IV Secretion System.

Enteric redmouth disease caused by the pathogen Yersinia ruckeri is a significant problem for fish farming around the world. Despite its importance, only a few virulence factors of Y. ruckeri have been identified and studied in detail. Here, we report and analyze the complete DNA sequence of pYR4, a plasmid from a highly pathogenic Norwegian Y. ruckeri isolate, sequenced using PacBio SMRT technology. Like the well-known pYV plasmid of human pathogenic Yersiniae, pYR4 is a member of the IncFII family. Thirty-one percent of the pYR4 sequence is unique compared to other Y. ruckeri plasmids. The unique regions contain, among others genes, a large number of mobile genetic elements and two partitioning systems. The G+C content of pYR4 is higher than that of the Y. ruckeri NVH_3758 genome, indicating its relatively recent horizontal acquisition. pYR4, as well as the related plasmid pYR3, comprises operons that encode for type IV pili and for a conjugation system (tra). In contrast to other Yersinia plasmids, pYR4 cannot be cured at elevated temperatures. Our study highlights the power of PacBio sequencing technology for identifying mis-assembled segments of genomic sequences. Comparative analysis of pYR4 and other Y. ruckeri plasmids and genomes, which were sequenced by second and the third generation sequencing technologies, showed errors in second generation sequencing assemblies. Specifically, in the Y. ruckeri 150 and Y. ruckeri ATCC29473 genome assemblies, we mapped the entire pYR3 plasmid sequence. Placing plasmid sequences on the chromosome can result in erroneous biological conclusions. Thus, PacBio sequencing or similar long-read methods should always be preferred for de novo genome sequencing. As the tra operons of pYR3, although misplaced on the chromosome during the genome assembly process, were demonstrated to have an effect on virulence, and type IV pili are virulence factors in many bacteria, we suggest that pYR4 directly contributes to Y. ruckeri virulence.

Social microbial inocula confer functional stability in a methyl tert-butyl ether extractive membrane biofilm bioreactor

Methyl tert-butyl ether (MTBE) degradation technologies based on two-phase partitioning systems such as extractive membrane biofilm reactors (EMBFR) permit separation of biological and contaminant compartments, thus allowing optimization of the biological section. In this study, we set-up an EMBFR with three MTBE-degrading and cooperating strains (termed social biofilm: Agrobacterium sp. MS2, Paenibacillus etheri SH7T and Rhodococcus ruber EE6). The removal efficiency of the social-biofilm EMBFR was 80%, and functional stability was observed in the reactor, i.e. more efficient than previous studies (single-strain inoculated EMBFR, <50% removal efficiency and unstable function). Metabolite tert-butyl alcohol was not observed, and the EC50 values were higher than those observed in single-strain EMBFRs. Comparative analysis of the MTBE enzymatic pathway and the social-biofilm was performed, where the mechanism of cooperation observed within the social-biofilm is likely due to enzymatic redundancy. Functional outcomes were equal to previous batch tests, hence 100% scalability was obtained. Overall, higher functional and stability outcomes are obtained with the use of the social-biofilm in an MTBE-EMBFR.

Fighting CPS Complexity by Component-Based Software Development of Multi-Mode Systems

Growing software complexity is an increasing challenge for the software development of modern cyber-physical systems. A classical strategy for taming this complexity is to partition system behaviors into different operational modes specified at design time. Such a multi-mode system can change behavior by switching between modes at run-time. A complementary approach for reducing software complexity is provided by component-based software engineering (CBSE), which reduces complexity by building systems from composable, reusable and independently developed software components. CBSE and the multi-mode approach are fundamentally conflicting in that component-based development conceptually is a bottom-up approach, whereas partitioning systems into operational modes is a top-down approach with its starting point from a system-wide perspective. In this article, we show that it is possible to combine and integrate these two fundamentally conflicting approaches. The key to simultaneously benefiting from the advantages of both approaches lies in the introduction of a hierarchical mode concept that provides a conceptual linkage between the bottom-up component-based approach and system level modes. As a result, systems including modes can be developed from reusable mode-aware components. The conceptual drawback of the approach—the need for extensive message exchange between components to coordinate mode-switches—is eliminated by an algorithm that collapses the component hierarchy and thereby eliminates the need for inter-component coordination. As this algorithm is used from the design to implementation level (“compilation”), the CBSE design flexibility can be combined with efficiently implemented mode handling, thereby providing the complexity reduction of both approaches, without inducing any additional design or run-time costs. At the more specific level, this article presents (1) a mode mapping mechanism that formally specifies the mode relation between composable multi-mode components and (2) a mode transformation technique that transforms component modes to system-wide modes to achieve efficient implementation.

A Causal Model for Safety Assessment Purposes in Opening the Low-Altitude Urban Airspace of Chinese Pilot Cities

China has been gradually relaxing its ban on the use of low-altitude airspace across the country. To guarantee the high reliability of air traffic management (ATM), conflict detection and conflict resolution (CDR) approaches are indispensable to maintain safe separation between neighbouring small fixed-wing aircraft. In this study, we analyse a temporal and spatial integrated strategy for safety assessment purposes in opening the low-altitude urban airspace of Chinese pilot cities. First, we present a detailed mathematical description of the proposed algorithms based on a spatial grid partitioning system (SGPS). For our system, a conflict detection (CD) algorithm is designed to determine if two trajectories pass through the same grid space within overlapping time windows. A conflict resolution (CR) algorithm integrates a proposed time scheduling-based technique (TST) and vertical change-based technique (VCT), which operate under predetermined basic principles. Then, based on our novel CDR algorithms, a causal model is constructed in graphical modelling and analysis software (GMAS) to generate a state space that can provide a global perspective on scenario dynamics and better understanding of induced conflict occurrences. Finally, simulation results demonstrate that the proposed approach is practical and efficient.

Aqueous two phase partitioning of Pisum sativum lectin in PEG/citrate salt system

Pisum sativum lectin (Psl) is a metalloprotein which is in the center of research interest because of its HIV-1 reverse transcriptase inhibitory activity and mitogenic activity. The application of this lectin in various fields demands the economically feasible and scalable purification strategy other than affinity chromatography. The suitability of aqueous two phase system (ATPS) composed of poly ethylene glycol (PEG) with different salts (sodium citrate, potassium citrate, and ammonium citrate) was evaluated for better partitioning of Psl. The significant factors such as molar mass and concentration of PEG, type and concentration of salts, the effect of tie line length (TLL), ionic strength, and pH were studied to select a suitable system for better partitioning of Psl. ATPS comprising of 18% PEG 6000, 16% sodium citrate, 1% NaCl at the operating condition of pH 8, 40.23% of TLL, and the volume ratio of 1.32 was found to be the best system which gave a maximum partition coefficient and yield of 14.5% and 98.66%, respectively.

Investigation of betacyanins stability from peel and flesh of red-purple pitaya with food additives supplementation and pH treatments

Betacyanins are potential source of natural red dyes. Generally, natural plant pigments, such as betacyanins, are highly unstable and prone to degradation due to internal and external factors. Hence, this study investigated the stability of betacyanins extracted from peel and flesh of red-purple pitaya using alcohol/salt-based liquid biphasic partitioning system (LBPS) over a 10-days storage period. Various stability treatments, including addition of food additives, pH treatments and different storage conditions were conducted. Overall, the results reveal that the peel and flesh extract added with 0.5% (w/v) of ascorbic acid and without any pH adjustments showed an optimum betacyanins stability under all storage conditions. The betacyanins retentions of the peel and flesh extract at 4 °C dark storage (4 °C D) were the highest, as indicated at 114.98 ± 1.11% and 105.90 ± 1.59%, respectively. In addition, kinetic analysis of the degradation of betacyanins was studied, and the extracts at 4 °C D showed no degradation sign of betacyanins. Stabilised betacyanins with low degradation rate would be beneficial to be used in food science processing.

Betacyanins extraction from Hylocereus polyrhizus using alcohol/salt-based liquid biphasic partitioning system and antioxidant activity evaluation

ABSTRACTBetacyanins have gained increasing interest as natural food dye because of their health-promoting effects. This study investigated the betacyanins extraction from peel and flesh of red–purple pitaya using ethanol/K2HPO4-based liquid biphasic partitioning system (LBPS) by optimised concentrations of ethanol, K2HPO4, NaCl and crude. Overall, the highest values of betacyanins concentration in alcohol-rich top phase (Ct), phase volume ratio (Vr) and partition coefficient (K) of betacyanins that represented an optimum betacyanins extraction from the peel (98.080%, 1.667 and 51.097, respectively) and flesh (96.256%, 2.167 and 25.764, respectively) were achieved. Lastly, conventional solvent extractions, colour characterisation and antioxidant activity evaluation were conducted.

The incidence of alternative minimum load values in masonry partition and lightweight partition systems with a cost analysis in Barranquilla, Colombia

This paper presents the structural behaviour of a 11-storey tall rectangular building for residential use in three configurations with different partition systems. The three partition systems considered were as follows: masonry partitions made from clay brick, masonry partitions made from concrete block and lightweight partitions made from drywall. The structural analysis was carried out considering dead, live and earthquake loads. For the calculation of the dead loads generated by the non-structural elements such as partition walls two type of analysis were considered for each partition system. The first one with the alternative minimum loads suggested by the Colombian Earthquake Resistant Building Regulations, NSR-10 and the second one with the real calculated loads. In total six structural analyses were carried out. Lower values as much as 17% for maximum vertical deformations and 18% for story drifts have been obtained for the analysis with the alternative minimum loads compared to the real calculated loads. For both type of analysis, the building with lightweight partition system behaved best, lower values as much as 12% for deformations and 19% for drifts have been obtained. Also, the cost analysis shows that it is more economical to construct the building with drywall partitions, the reduction in cost being 12% in comparison to masonry partitions.

In Vivo Labelling of Adenovirus DNA Identifies Chromatin Anchoring and Biphasic Genome Replication.

Adenoviruses are DNA viruses with a lytic infection cycle. Following the fate of incoming as well as recently replicated genomes during infections is a challenge. In this study, we used the ANCHOR3 technology based on a bacterial partitioning system to establish a versatile in vivo imaging system for adenoviral genomes. The system allows the visualization of both individual incoming and newly replicated genomes in real time in living cells. We demonstrate that incoming adenoviral genomes are attached to condensed cellular chromatin during mitosis, facilitating the equal distribution of viral genomes in daughter cells after cell division. We show that the formation of replication centers occurs in conjunction with in vivo genome replication and determine replication rates. Visualization of adenoviral DNA revealed that adenoviruses exhibit two kinetically distinct phases of genome replication. Low-level replication occurred during early replication, while high-level replication was associated with late replication phases. The transition between these phases occurred concomitantly with morphological changes of viral replication compartments and with the appearance of virus-induced postreplication (ViPR) bodies, identified by the nucleolar protein Mybbp1A. Taken together, our real-time genome imaging system revealed hitherto uncharacterized features of adenoviral genomes in vivo The system is able to identify novel spatiotemporal aspects of the adenovirus life cycle and is potentially transferable to other viral systems with a double-stranded DNA phase.IMPORTANCE Viruses must deliver their genomes to host cells to ensure replication and propagation. Characterizing the fate of viral genomes is crucial to understand the viral life cycle and the fate of virus-derived vector tools. Here, we integrated the ANCHOR3 system, an in vivo DNA-tagging technology, into the adenoviral genome for real-time genome detection. ANCHOR3 tagging permitted the in vivo visualization of incoming genomes at the onset of infection and of replicated genomes at late phases of infection. Using this system, we show viral genome attachment to condensed host chromosomes during mitosis, identifying this mechanism as a mode of cell-to-cell transfer. We characterize the spatiotemporal organization of adenovirus replication and identify two kinetically distinct phases of viral genome replication. The ANCHOR3 system is the first technique that allows the continuous visualization of adenoviral genomes during the entire virus life cycle, opening the way for further in-depth study.

Insights into the chromosome partitioning system, ParABS

Insights into the chromosome partitioning system, ParABS

The effectiveness of phase change materials in relation to summer thermal comfort in air-conditioned office buildings

The incorporation of Phase Change Materials (PCMs) into the opaque envelope of lightweight buildings is a good solution to compensate for the small thermal inertia, which usually entails pronounced overheating and high space cooling load in summer. However, the position and the thickness of the PCMs, as well as their thermal properties, must be attentively selected in order to ensure their effective operation. This paper shows a comprehensive investigation about the effectiveness of a commercial PCM, available in the form of mats, when installed within drywall partition systems in air-conditioned lightweight office buildings. The study is based on dynamic simulations carried out with EnergyPlus on a typical office building, with the aim to calculate the indoor operative temperature and the cooling load under thermostatic control. The performance for the base case (without PCM) is then compared with the case where PCM mats with various thickness and melting temperature are applied. The analysis is repeated in three different locations, ranging from Southern Europe (Rome, Italy), Continental Europe (Wien, Austria) and Northern Europe (London, UK). The results of the simulations highlight that in lightweight air-conditioned office buildings PCMs contribute to attenuate the inside surface temperature peak by around 0.5 °C, while also reducing the peak cooling load by 10% or even 15%, depending on the PCM thickness and on the outdoor climate. The conclusions may help designers to make the correct choices in terms of thickness of the PCMs, scheduled rate of nighttime ventilation and value of the peak melting temperature.

STRUCTURAL CHARACTERISATION OF 5-HYDROXYTRYPTAMINE2A RECEPTOR IN HOMO SAPIENS BY IN - SILICO METHOD

Objective: Structural characterization of 5-hydroxytryptamine (5-HT)2A receptor in homo sapiens using in silico method.Methods: In silico approach has particularly providing a realistic representation needed to understand the fundamental molecular structure of a serotonin receptor. The structure has been generated using Swiss model, Modeller 9.14, Phyre2, and Geno three-dimensional, which was visualized using PyMol, and validated by Procheck and ERRAT analysis along with the values of different secondary structures mapping to diverse sections of the Ramachandran plot.Results: We compared all different models. Further structural analysis suggested that the structure of 5-HT2A is a monomer with 18 alpha helices, seven beta sheets, and one disulfide bridge. There is no signal peptide region in the protein sequence. The structure contains mostly polar and aromatic amino acid as suggested by using hydropathy plot. However, in both partitioning systems bilayer to water and water to bilayer, there are some hydropathy predicted segments, which are also transmembrane segments. Finally, the pore features, including diameter profile, size, and shape, were determined by porewalker, and the shape of the pore was found to be UDSD.Conclusion: This study suggested that 5-HT2A receptor interaction with its natural ligand serotonin and other inhibitor compounds would further additional information about G protein-coupled receptors. The 5-HT2A receptor could be an important target for therapeutics development.

Significance of combination therapy between Euclea crispa (Thunb.) (leaf and stem bark) extracts and standard antibiotics against drug resistant bacteria

This study evaluates the probable effect of combination therapy between the extracts of Euclea crispa and standard antibiotics against selected resistant strains of bacterial isolates. The crude extracts were partitioned using a solvent partitioning system. The isolates were screened via determination of minimum inhibitory concentrations (MICs) using broth micro-dilution method and the combination assessment was carried out via time-kill assay to determine the probable synergisms. The MICs by the plant extracts range from 310 to 630 μg/ml (leaf extract) and from 630 to 1250 μg/ml (stem bark extract). The MICs by erythromycin and chloramphenicol range between 31 and 250 μg/ml, while that of ampicillin is between 63 and 500 μg/ml. The range exhibited by streptomycin and tetracycline is between 8 and 250 μg/ml and 6 and 100 μg/ml respectively. Out of 130 different combination tests between the leaf extract and antibiotics, 91.5% express synergy while 8.5% are indifferent. On the other hand, 88.5% of the same number of combination tests show synergism between the stem bark extract and standard antibiotics with no record of antagonism in both cases. The leaf and stem bark extracts of E. crispa have been confirmed, in the course of this study, to possess some bioactive principles which may serve to enhance potency of the available antibiotics against multidrug resistant organisms. Thus, it indicates a source of alternative therapy in combating infectious diseases.

Binary Covering Arrays on Tournaments

We introduce graph-dependent covering arrays which generalize covering arrays on graphs, introduced by Meagher and Stevens (2005), and graph-dependent partition systems, studied by Gargano, Körner, and Vaccaro (1994). A covering array $\hbox{CA}(n; 2, G, H)$ (of strength 2) on column graph $G$ and alphabet graph $H$ is an $n\times |V(G)|$ array with symbols $V(H)$ such that for every arc $ij \in E(G)$ and for every arc $ab\in E(H)$, there exists a row $\vec{r} = (r_{1},\dots, r_{|V(G)|})$ such that $(r_{i}, r_{j}) = (a,b)$. We prove bounds on $n$ when $G$ is a tournament graph and $E(H)$ consists of the edge $(0,1)$, which corresponds to a directed version of Sperner's 1928 theorem. For two infinite families of column graphs, transitive and so-called circular tournaments, we give constructions of covering arrays which are optimal infinitely often.

On Instability in Componentwise Partitioned Systems

On Instability in Componentwise Partitioned Systems

Going around in circles: virulence plasmids in enteric pathogens.

Plasmids have a major role in the development of disease caused by enteric bacterial pathogens. Virulence plasmids are usually large (>40 kb) low copy elements and encode genes that promote host-pathogen interactions. Although virulence plasmids provide advantages to bacteria in specific conditions, they often impose fitness costs on their host. In this Review, we discuss virulence plasmids in Enterobacteriaceae that are important causes of diarrhoea in humans, Shigella spp., Salmonella spp., Yersinia spp and pathovars of Escherichia coli. We contrast these plasmids with those that are routinely used in the laboratory and outline the mechanisms by which virulence plasmids are maintained in bacterial populations. We highlight examples of virulence plasmids that encode multiple mechanisms for their maintenance (for example, toxin-antitoxin and partitioning systems) and speculate on how these might contribute to their propagation and success.

Evaluation of Ion-pair Formation of Adefovir to Improve Permeation across Artificial and Biological Membranes.

Adefovir is an antiviral drug that exhibits high hydrophilic properties and negligible bioavailability (less than 12%). It is only applied in the form of the ester prodrug adefovir dipivoxil (ADV). The oral bioavailability of ADV is limited (32% to 45%) by its low permeability (Class 3) and biological conversion of the prodrug to adefovir. Ion-pair formation is considered as an alternative approach to a covalent prodrug (ADV) to enhance intestinal permeation of adefovir. The effect of various counter-ions (anionic, cationic and two quaternary ammonium salts) on the lipophilicity of adefovir was investigated by means of the n-octanol/buffer partitioning system, an in vitro transport model (PAMPA) and a biological membrane (everted gut sac). Quaternary ammonium salts, cetylpyridinium chloride (CPC) and cetrimide enhanced the lipophilicity of adefovir 136- and 87-fold, respectively. The apparent permeability of adefovir in combination with CPC (counter-ion) was 2.5-fold greater than ADV permeability in the PAMPA model. The apparent permeability of adefovir-CPC (counter-ion) was 1.3-fold greater than that of adefovir dipivoxil permeability in a biologic membrane (everted gut sac). These results suggest that the adefovir-CPC ion-paired system has potential for improving the permeation of adefovir across the intestinal membrane.This article is open to POST-PUBLICATION REVIEW. Registered readers (see "For Readers") may comment by clicking on ABSTRACT on the issue's contents page.

The TubR-centromere complex adopts a double-ring segrosome structure in Type III partition systems.

In prokaryotes, the centromere is a specialized segment of DNA that promotes the assembly of the segrosome upon binding of the Centromere Binding Protein (CBP). The segrosome structure exposes a specific surface for the interaction of the CBP with the motor protein that mediates DNA movement during cell division. Additionally, the CBP usually controls the transcriptional regulation of the segregation system as a cell cycle checkpoint. Correct segrosome functioning is therefore indispensable for accurate DNA segregation. Here, we combine biochemical reconstruction and structural and biophysical analysis to bring light to the architecture of the segrosome complex in Type III partition systems. We present the particular features of the centromere site, tubC, of the model system encoded in Clostridium botulinum prophage c-st. We find that the split centromere site contains two different iterons involved in the binding and spreading of the CBP, TubR. The resulting nucleoprotein complex consists of a novel double-ring structure that covers part of the predicted promoter. Single molecule data provides a mechanism for the formation of the segrosome structure based on DNA bending and unwinding upon TubR binding.

Study on Multi-Scale Window Determination for GLCM Texture Description in High-Resolution Remote Sensing Image Geo-Analysis Supported by GIS and Domain Knowledge

Texture features based on the gray-level co-occurrence matrix (GLCM) can effectively improve classification accuracy in geographical analyses of optical remote sensing (RS) images, with the parameters of scale of the GLCM texture window greatly affecting the validity. By analyzing human visual attention characteristics for geo-texture cognition, it was found that there is a strong correlation between the texture scale parameters and the domain shape knowledge in a specified geo-scene. Therefore, a new approach for quickly determining the multi-scale parameters of the texture with the assistance of a geographic information system (GIS) and domain knowledge is proposed in this paper. First, the validity of domain knowledge from an existing GIS database is measured by spatial data mining algorithms, including spatial partitioning, image segmentation, and space-time system evaluation. Second, the general domain shape knowledge of each category is described by the GIS minimum enclosing rectangle indices and rectangular-degree indices. Then, the corresponding multi-scale texture windows can be quickly determined for each category by a correlation analysis with the shape indices. Finally, the Fisher function is used to evaluate the validity of the scale parameters. The experimental results show that the multi-scale value keeps a one-to-one relationship with the classified objects, and their value ranges are from a few to tens, instead of the smaller values of a traditional analysis; thus, effective texture features at such a scale can be built to identify categories in a geo-scene. In this way, the proposed method can increase the total number of categories for a certain geo-scene and reduce the classification uncertainty, as well as better meet the requirements of large-scale image geo-analysis. It also has as high a calculation efficiency and as good a performance as the traditional enumeration method.