Rule-based modeling and simulations of the inner kinetochore structure

Background

Combinatorial complexity is a central problem when modeling biochemical reaction networks, since the association of a few components can give rise to a large variation of protein complexes. Available classical modeling approaches are often insufficient for the analysis of very large and complex networks in detail. Recently, we developed a new rule-based modeling approach that facilitates the analysis of spatial and combinatorially complex problems. Here, we explore for the first time how this approach can be applied to a specific biological system, the human kinetochore, which is a multi-protein complex involving over 100 proteins.

Results

Applying our freely available SRSim software to a large data set on kinetochore proteins in human cells, we construct a spatial rule-based simulation model of the human inner kinetochore. The model generates an estimation of the probability distribution of the inner kinetochore 3D architecture and we show how to analyze this distribution using information theory. In our model, the formation of a bridge between CenpA and an H3 containing nucleosome only occurs efficiently for higher protein concentration realized during S-phase but may be not in G1. Above a certain nucleosome distance the protein bridge barely formed pointing towards the importance of chromatin structure for kinetochore complex formation. We define a metric for the distance between structures that allow us to identify structural clusters. Using this modeling technique, we explore different hypothetical chromatin layouts.

Conclusions

Applying a rule-based network analysis to the spatial kinetochore complex geometry allowed us to integrate experimental data on kinetochore proteins, suggesting a 3D model of the human inner kinetochore architecture that is governed by a combinatorial algebraic reaction network. This reaction network can serve as bridge between multiple scales of modeling. Our approach can be applied to other systems beyond kinetochores.     

Engineering the acceptor substrate specificity in the xyloglucan endotransglycosylase TmXET6.3 from nasturtium seeds (Tropaeolum majus L.)

Plant Molecular Biology - The knowledge of substrate specificity of XET enzymes is important for the general understanding of metabolic pathways to challenge the established notion that these...     

Contrasting strategies for wing‐moult and pre‐migratory fuelling in western and eastern populations of Common Whitethroat Sylvia communis

Trade‐offs between moult and fuelling in migrant birds vary with migration distance and the environmental conditions they encounter. We compared wing moult and fuelling at the northern and southern ends of migration in two populations of adult Common Whitethroats Sylvia communis. The western population moults most remiges at the breeding grounds in Europe (e.g. Poland) and migrates 4000–5000 km to western Africa (e.g. Nigeria). The eastern population moults all remiges at the non‐breeding grounds and migrates 7000–10 000 km from western Asia (e.g. southwestern Siberia) to eastern and southern Africa. We tested the hypotheses that: (1) Whitethroats moult their wing feathers slowly in South Africa, where they face fewer time constraints than in Poland, and (2) fuelling is slower when it coincides with moulting (Poland, South Africa) than when it occurs alone (Siberia, Nigeria). We estimated moult timing of primaries, secondaries and tertials from moult records of Polish and South African Whitethroats ringed in 1987–2017 and determined fuelling patterns from the body mass of Whitethroats ringed in all four regions. The western population moulted wing feathers in Poland over 55 days (2 July–26 August) at a varying rate, up to 13 feathers simultaneously, but fuelled slowly until departure in August–mid‐September. In Nigeria, during the drier period of mid‐February–March they fuelled slowly, but the fuelling rate increased three‐fold in April–May after the rains before mid‐April–May departure. The eastern population did not moult in Siberia but fuelled three times faster before mid‐July–early August departure than did the western birds moulting in Poland. In South Africa, the Whitethroats moulted over 57 days (2 January–28 February) at a constant rate of up to nine feathers simultaneously and fuelled slowly from mid‐December until mid‐April–May departure. These results suggest the two populations use contrasting strategies to capitalize on food supplies before departure from breeding and non‐breeding grounds.     

Impact of the zebra mussel Dreissena polymorpha invasion on the budget of suspended material in a shallow lagoon ecosystem

The role of the zebra mussel Dreissena polymorpha in redistribution of total particulate material (TPM) between the water column and bottom sediment was estimated using the TPM budget for a mussel bed in the Curonian lagoon, the Baltic Sea. Seasonal clearance rates were derived from the TPM budget assuming two resuspension scenarios: no resuspension and full resuspension of biodeposits. Estimated clearance rates for both scenarios were compared with the rates calculated from the population clearance rate model. Seasonal clearance rates estimated using the population model (1.1 and 11.8 l g⁻¹ SFDW day⁻¹) fitted well into the interval of seasonal clearance rates calculated from TPM budgets assuming no resuspension of biodeposits (3.2 and 21.4 l g SFDW⁻¹ day⁻¹). In the scenario with biodeposits resuspension clearance rates were much higher (57.4 and 148.9 g SFDW⁻¹ day⁻¹). The ratio of clearance to residence time was highly dependent on the fate of biodeposits. Therefore its use in interpretation of the species impact on TPM was limited. An alternative measure based on the ratio of the amount of TPM biodeposited to TPM transported into the bed was used. It was found that zebra mussels are able to deposit between 10 and 30% of the incoming TPM, and the amount of biodeposited material was correlated with water residence time. Results indicate that the impact of zebra mussels on TPM in the lagoon is small relative to the high transport rates of TPM over the bed. However, annual biosedimentation rate (~590 g m⁻²) in the mussel bed was higher than physical deposition rate (~380 g m⁻²) in accumulation areas devoid of large suspension feeders. We suggest that a local impact due to enhanced availability of organic material to other trophic groups of associated benthic organisms may be more significant than effects on TPM pathways at an ecosystem scale.     

Characterization of reproductive activity in captive male Eurasian lynx (Lynx lynx)

This study characterizes the reproductive activity of male European lynx kept in Central Russia. Four captive adult males were subjected to an electroejaculation prior to (November), during (March) and after (June) the breeding season. Concentration, motility and morphological integrity of spermatozoa as well as testis diameter and testosterone levels in serum were evaluated. Additionally, fecal samples were collected for 2 years to determine the fecal testosterone secretion. Testis sizes and serum testosterone concentrations were characterized by little changes with highest levels in March (2.98 mm³; 1.96 ng/ml testosterone) and lowest in June (2.34 mm³; 0.75 ng/ml testosterone). In faeces, the highest testosterone concentrations were measured in February followed by a second increase in May. The volume of ejaculates and percentages of motile and intact spermatozoa reached the maxima in March. By performing two-male mating experiments, we could prove multiple paternity within three litters. Paternity analysis of litter also revealed that 26 of 31 cubs (84%) were sired from the same male, independently from being the first or second mating partner of the respective female. This particular male showed the most developed and activated reproductive tract and also had the best semen quality, which seems to be important for sperm competition.     

Pronounced hypoxia in models of murine and human leukemia: high efficacy of hypoxia-activated prodrug PR-104

Recent studies indicate that interactions between leukemia cells and the bone marrow (BM) microenvironment promote leukemia cell survival and confer resistance to anti-leukemic drugs. There is evidence that BM microenvironment contains hypoxic areas that confer survival advantage to hematopoietic cells. In the present study we investigated whether hypoxia in leukemic BM contributes to the protective role of the BM microenvironment. We observed a marked expansion of hypoxic BM areas in immunodeficient mice engrafted with acute lymphoblastic leukemia (ALL) cells. Consistent with this finding, we found that hypoxia promotes chemoresistance in various ALL derived cell lines. These findings suggest to employ hypoxia-activated prodrugs to eliminate leukemia cells within hypoxic niches. Using several xenograft models, we demonstrated that administration of the hypoxia-activated dinitrobenzamide mustard, PR-104 prolonged survival and decreased leukemia burden of immune-deficient mice injected with primary acute lymphoblastic leukemia cells. Together, these findings strongly suggest that targeting hypoxia in leukemic BM is feasible and may significantly improve leukemia therapy.