Substrate-mediated regulation of the arginine transporter of Toxoplasma gondii

Intracellular parasites, such as the apicomplexan Toxoplasma gondii, are adept at scavenging nutrients from their host. However, there is little understanding of how parasites sense and respond to the changing nutrient environments they encounter during an infection. TgApiAT1, a member of the apicomplexan ApiAT family of amino acid transporters, is the major uptake route for the essential amino acid L-arginine (Arg) in T. gondii. Here, we show that the abundance of TgApiAT1, and hence the rate of uptake of Arg, is regulated by the availability of Arg in the parasite's external environment, increasing in response to decreased [Arg]. Using a luciferase-based 'biosensor' strain of T. gondii, we demonstrate that the expression of TgApiAT1 varies between different organs within the host, indicating that parasites are able to modulate TgApiAT1-dependent uptake of Arg as they encounter different nutrient environments in vivo. Finally, we show that Arg-dependent regulation of TgApiAT1 expression is post-transcriptional, mediated by an upstream open reading frame (uORF) in the TgApiAT1 transcript, and we provide evidence that the peptide encoded by this uORF is critical for mediating regulation. Together, our data reveal the mechanism by which an apicomplexan parasite responds to changes in the availability of a key nutrient

Investigation of Body Development in Growing Holstein Heifers With Special Emphasis on Body Fat Development Using Bioelectrical Impedance Analysis

This study analyzed skeletal development, body condition, and total body fat development of growing heifers. A total of 144 female primiparous Holstein cattle from four commercial dairy farms with different degrees of stillbirth rates were examined during the rearing period. This included measurements in body condition, fat tissue, metabolic, and endocrine factors. Pelvic measurements and the sacrum height were analyzed to assess skeletal development. The body condition was classified via body condition scoring, bioelectrical impedance analysis (BIA), back fat thickness measurements, and the body mass. For the first time, BIA was used as an appropriate method to evaluate the fat tissue content of cattle throughout the rearing period. This analysis technique can be performed on heifers aged 8–15 months. Throughout that period, the fat content decreased while the skeletal development increased. In addition, high free fatty acid concentrations in serum of the animals with high frame development were found, supporting our hypothesis that stored energy of body fat deposits is used for skeletal growth. Furthermore, we were able to demonstrate complex endocrine relationships between fat metabolism and skeletal growth by using specific markers, such as leptin, insulin growth factor-1 (IGF-1), and estradiol (E2). Food analysis showed high crude protein (CP) levels in the total mixed ration above recommendation for daily protein intake of all farms. However, there was a positive correlation between CP and the body frame measurements in our study. In summary, we established a novel regression formula for BIA analysis (“BIA-Heine”) in heifers to evaluate the body composition throughout different ages and physiological stages in the development of heifers. This special formula allows the evaluation of fat tissue without a whole-body analysis and therefore provides an innovative technique for animal welfare support

A hybrid approach to protein folding problem integrating constraint programming with local search

<p>Abstract</p> <p>Background</p> <p>The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy function have been proposed to ease the computational hardness of this optimization problem. Heuristic search algorithms and constraint programming are two common techniques to approach this problem. The present study introduces a novel hybrid approach to simulate the protein folding problem using constraint programming technique integrated within local search.</p> <p>Results</p> <p>Using the face-centered-cubic lattice model and 20 amino acid pairwise interactions energy function for the protein folding problem, a constraint programming technique has been applied to generate the neighbourhood conformations that are to be used in generic local search procedure. Experiments have been conducted for a few small and medium sized proteins. Results have been compared with both pure constraint programming approach and local search using well-established local move set. Substantial improvements have been observed in terms of final energy values within acceptable runtime using the hybrid approach.</p> <p>Conclusion</p> <p>Constraint programming approaches usually provide optimal results but become slow as the problem size grows. Local search approaches are usually faster but do not guarantee optimal solutions and tend to stuck in local minima. The encouraging results obtained on the small proteins show that these two approaches can be combined efficiently to obtain better quality solutions within acceptable time. It also encourages future researchers on adopting hybrid techniques to solve other hard optimization problems.</p

Calcification, skeletal structure and composition of the cold-water coral Desmophyllum dianthus

In the naturally acidified Comau Fjord (Chile), high densities of the cosmopolitan cold-water coral (CWC) Desmophyllum dianthus are found at or below aragonite saturation (Ωar ≤ 1). However, it is not known so far if seasonal changes in Ωar lead to seasonal differences in calcification rates and the corals’ ability to up-regulate the pH in the calcifying fluid (pHcf). In the present study, corals were sampled along both horizontal and vertical pH gradients (pHT = 7.6-7.9, Ωar = 0.76-1.45) in Comau Fjord. We compared D. dianthus’ calcification rates (buoyant weight technique) with the physico-chemical conditions in the water column (T, Ωar) in austral summer 2016/2017 and winter 2017. In order to determine the biological pHcf up-regulation of D. dianthus, the skeletal boron isotopic composition (δ11B) was measured in the upper part of the calyx between the septa, using a UV femtosecond laser ablation system connected to a multicollector inductively coupled plasma mass spectrometer (LA-MC-ICP-MS). Higher growth rates of D. dianthus were found in summer than in winter. Surprisingly, growth of D. dianthus was highest in undersaturated waters in both seasons (Ωar = 0.76 and 0.84) and cross-transplanted specimens were able to acclimatise to Ωar < 1. Therefore, the present study shows that Ωar alone is a poor predictor of D. dianthus growth. Skeletal analyses show a complex relationship between δ11B and the structure of the coral skeletons. δ11B measurements were highly variable, which may be attributed to the high calcification rates in the upper part of the coral calyx. Therefore, high resolution analyses of the skeletal composition and micro-structure will be conducted along the entire longitudinal section of D. dianthus skeletons using Raman microscopy and scanning electron microscopy (SEM). In addition, δ11B will be measured in different skeletal parts and compared to skeletal structure analyses for a reliable reconstruction of seawater pH at high temporal resolution using skeletons of D. dianthus grown under laboratory and field conditions (Comau Fjord, Chile)

Substrate-mediated regulation of the arginine transporter of Toxoplasma gondii

ABSTRACTIntracellular parasites, such as the apicomplexanToxoplasma gondii, are adept at scavenging nutrients from their host. However, there is little understanding of how parasites sense and respond to the changing nutrient environments they encounter during an infection.TgApiAT1, a member of the apicomplexan ApiAT family of amino acid transporters, is the major uptake route for the essential amino acid L-arginine (Arg) inT. gondii. Here, we show that the abundance ofTgApiAT1, and hence the rate of uptake of Arg, is regulated by the availability of Arg in the parasite’s external environment, increasing in response to decreased [Arg]. Using a luciferase-based ‘biosensor’ strain ofT. gondii, we demonstrate that parasites vary the expression ofTgApiAT1 in different organs within their host, indicating that parasites are able to modulateTgApiAT1-dependent uptake of Arg as they encounter different nutrient environmentsin vivo. Finally, we show that Arg-dependent regulation ofTgApiAT1 expression is post-transcriptional, mediated by an upstream open reading frame (uORF) in theTgApiAT1 transcript, and we provide evidence that the peptide encoded by this uORF is critical for mediating regulation. Together, our data reveal the mechanism by which an apicomplexan parasite responds to changes in the availability of a key nutrient.</jats:p

A framework for high-throughput gene signatures with microarray-based brain cancer gene expression profiling data

Cancer classification through high-throughput gene expression profiles has been widely used in biomedical research. Most recently, we portrayed a multivariate method for large scale gene selection based on information theory with the central issue of feature interdependence, and we validated its effectiveness using a colon cancer benchmark. The present paper further develops our previous work on feature interdependence. Firstly, we have refined the method and proposed a complete framework to select a gene signature for a certain disease phenotype prediction under high-throughput technologies. The framework has then been applied to a brain cancer gene expression profile derived from Affymetrix Human Genome U95Av2 Array, where the number of interrogated genes is six times larger than that in the previously studied colon cancer data set. Three information theory based filters were used for comparison. Our experimental results show that the framework outperforms them in terms of classification performance based upon three performance measures. Additionally, to demonstrate how effectively feature interdependence can be tackled within the framework, two sets of enrichment analysis have also been performed. The results also show that more statistically significant gene sets and regulatory interactions could be found in our gene signature. Therefore, this framework could be promising for high-throughput gene selection around gene synergy

Sa based power efficient FPGA LUT mapping

Look up Table (LUT) based Field Programmable Gate Arrays (FPGAs) are commonly used in mobile devices due to their efficient signal processing capabilities and flexibility to be reprogrammed in situ. However the mechanisms which enable a FPGA to be re-programmable make it require more power than an Application Specific Integrated Circuit. In this paper we consider the power reduction of a FPGA by optimising the mapping the underlying boolean circuit onto the LUT based FPGA with respect to cumulative switching. We formulate the power minimisation problem as a combinatorial optimisation problem. To tackle this NP hard problem we propose the application of a local search method. Here we introduce a complete a neighborhood function and apply heuristic simulated annealing in conjunction with the objective function from [20] 'cumulative switching'. Our experimental results show a 42.96% average reduction in power consumption compared to SIS based mapping and 27.44% average reduction in power consumption compared to a genetic algorithm

Stochastic protein folding simulation in the three-dimensional HP-model

We present results from three-dimensional protein folding simulations in the HP-model on ten benchmark problems. The simulations are executed by a simulated annealing-based algorithm with a time-dependent cooling schedule. The neighbourhood relation is determined by the pull-move set. The results provide experimental evidence that the maximum depth D of local minima of the underlying energy landscape can be upper bounded by D<n2/3D<n2/3. The local search procedure employs the stopping criterion (m/δ)D/γ(m/δ)D/γ, where m is an estimation of the average number of neighbouring conformations, γγ relates to the mean of non-zero differences of the objective function for neighbouring conformations, and 1−δ1−δ is the confidence that a minimum conformation has been found. The bound complies with the results obtained for the ten benchmark problems