Structural effects of clinically observed mutations in JAK2 exons 13-15: comparison with V617F and exon 12 mutations

<p>Abstract</p> <p>Background</p> <p>The functional relevance of many of the recently detected JAK2 mutations, except V617F and exon 12 mutants, in patients with chronic myeloproliferative neoplasia (MPN) has been significantly overlooked. To explore atomic-level explanations of the possible mutational effects from those overlooked mutants, we performed a set of molecular dynamics simulations on clinically observed mutants, including newly discovered mutations (K539L, R564L, L579F, H587N, S591L, H606Q, V617I, V617F, C618R, L624P, whole exon 14-deletion) and control mutants (V617C, V617Y, K603Q/N667K).</p> <p>Results</p> <p>Simulation results are consistent with all currently available clinical/experimental evidence. The simulation-derived putative interface, not possibly obtained from static models, between the kinase (JH1) and pseudokinase (JH2) domains of JAK2 provides a platform able to explain the mutational effect for all mutants, including presumably benign control mutants, at the atomic level.</p> <p>Conclusion</p> <p>The results and analysis provide structural bases for mutational mechanisms of JAK2, may advance the understanding of JAK2 auto-regulation, and have the potential to lead to therapeutic approaches. Together with recent mutation profiling results demonstrating the breadth of clinically observed JAK2 mutations, our findings suggest that molecular testing/diagnostics of JAK2 should extend beyond V617F and exon 12 mutations, and perhaps should encompass most of the pseudo-kinase domain-coding region.</p

JAK2 Exon 14 Deletion in Patients with Chronic Myeloproliferative Neoplasms

BACKGROUND: The JAK2 V617F mutation in exon 14 is the most common mutation in chronic myeloproliferative neoplasms (MPNs); deletion of the entire exon 14 is rarely detected. In our previous study of >10,000 samples from patients with suspected MPNs tested for JAK2 mutations by reverse transcription-PCR (RT-PCR) with direct sequencing, complete deletion of exon 14 (Deltaexon14) constituted <1% of JAK2 mutations. This appears to be an alternative splicing mutation, not detectable with DNA-based testing. METHODOLOGY/PRINCIPAL FINDINGS: We investigated the possibility that MPN patients may express the JAK2 Deltaexon14 at low levels (<15% of total transcript) not routinely detectable by RT-PCR with direct sequencing. Using a sensitive RT-PCR-based fluorescent fragment analysis method to quantify JAK2 Deltaexon14 mRNA expression relative to wild-type, we tested 61 patients with confirmed MPNs, 183 with suspected MPNs (93 V617F-positive, 90 V617F-negative), and 46 healthy control subjects. The Deltaexon14 variant was detected in 9 of the 61 (15%) confirmed MPN patients, accounting for 3.96% to 33.85% (mean = 12.04%) of total JAK2 transcript. This variant was also detected in 51 of the 183 patients with suspected MPNs (27%), including 20 of the 93 (22%) with V617F (mean [range] expression = 5.41% [2.13%-26.22%]) and 31 of the 90 (34%) without V617F (mean [range] expression = 3.88% [2.08%-12.22%]). Immunoprecipitation studies demonstrated that patients expressing Deltaexon14 mRNA expressed a corresponding truncated JAK2 protein. The Deltaexon14 variant was not detected in the 46 control subjects. CONCLUSIONS/SIGNIFICANCE: These data suggest that expression of the JAK2 Deltaexon14 splice variant, leading to a truncated JAK2 protein, is common in patients with MPNs. This alternatively spliced transcript appears to be more frequent in MPN patients without V617F mutation, in whom it might contribute to leukemogenesis. This mutation is missed if DNA rather than RNA is used for testing

Significant association between polymorphism of the erythropoietin gene promoter and myelodysplastic syndrome

<p>Abstract</p> <p>Background</p> <p>Myelodysplastic syndrome (MDS) may be induced by certain mutagenic environmental or chemotherapeutic toxins; however, the role of susceptibility genes remains unclear. The G/G genotype of the single-nucleotide polymorphism (SNP) rs1617640 in the erythropoietin (<it>EPO</it>) promoter has been shown to be associated with decreased EPO expression. We examined the association of rs1617640 genotype with MDS.</p> <p>Methods</p> <p>We genotyped the EPO rS1617640 SNP in 189 patients with MDS, 257 with acute myeloid leukemia (AML), 106 with acute lymphoblastic leukemia, 97 with chronic lymphocytic leukemia, 353 with chronic myeloid leukemia, and 95 healthy controls.</p> <p>Results</p> <p>The G/G genotype was significantly more common in MDS patients (47/187; 25.1%) than in controls (6/95; 6.3%) or in patients with other leukemias (101/813; 12.4%) (all <it>P </it>< 0.001). Individuals with the G/G genotype were more likely than those with other genotypes to have MDS (odd ratio = 4.98; 95% CI = 2.04-12.13). Clinical and follow up data were available for 112 MDS patients and 186 AML patients. There was no correlation between EPO promoter genotype and response to therapy or overall survival in MDS or AML. In the MDS group, the GG genotype was significantly associated with shorter complete remission duration, as compared with the TT genotype (<it>P </it>= 0.03). Time to neutrophils recovery after therapy was significantly longer in MDS patients with the G/G genotype (<it>P </it>= 0.02).</p> <p>Conclusions</p> <p>These findings suggest a strong association between the rs1617640 G/G genotype and MDS. Further studies are warranted to investigate the utility of screening for this marker in individuals exposed to environmental toxins or chemotherapy.</p

Effects of Clinically Relevant MPL Mutations in the Transmembrane Domain Revealed at the Atomic Level through Computational Modeling

BACKGROUND: Mutations in the thrombopoietin receptor (MPL) may activate relevant pathways and lead to chronic myeloproliferative neoplasms (MPNs). The mechanisms of MPL activation remain elusive because of a lack of experimental structures. Modern computational biology techniques were utilized to explore the mechanisms of MPL protein activation due to various mutations. RESULTS: Transmembrane (TM) domain predictions, homology modeling, ab initio protein structure prediction, and molecular dynamics (MD) simulations were used to build structural dynamic models of wild-type and four clinically observed mutants of MPL. The simulation results suggest that S505 and W515 are important in keeping the TM domain in its correct position within the membrane. Mutations at either of these two positions cause movement of the TM domain, altering the conformation of the nearby intracellular domain in unexpected ways, and may cause the unwanted constitutive activation of MPL's kinase partner, JAK2. CONCLUSIONS: Our findings represent the first full-scale molecular dynamics simulations of the wild-type and clinically observed mutants of the MPL protein, a critical element of the MPL-JAK2-STAT signaling pathway. In contrast to usual explanations for the activation mechanism that are based on the relative translational movement between rigid domains of MPL, our results suggest that mutations within the TM region could result in conformational changes including tilt and rotation (azimuthal) angles along the membrane axis. Such changes may significantly alter the conformation of the adjacent and intrinsically flexible intracellular domain. Hence, caution should be exercised when interpreting experimental evidence based on rigid models of cytokine receptors or similar systems

Simulations in the Topography Effects of Tianshan Mountains on an Extreme Precipitation Event in the Ili River Valley, China

Xinjiang is located in an arid and semi-arid climate region in China, but Xinjiang Ili river valley is more humid, with higher precipitation intensity and precipitation, which is closely related to the role of the Tianshan Mountains. In this paper, through the NCRP 1° × 1° reanalysis data and the conventional observation data of the Ili River Valley in Xinjiang, the terrain sensitivity experiment conducted by the WRF model is used to analyze the short-term extreme precipitation event of the Ili River Valley from 18–19 of May 2017, to reveal the influence of Tianshan Mountains on the extreme precipitation event of the Ili River Valley. The results show that: (1) The reduction or removal of the terrain will cause a wide range of wind field changes, weaken the vertical upward movement of the windward slope, and the accumulation of water vapor before the windward slope will also be reduced; a large-scale change of the terrain will also affect the direction of water vapor transportation. These effects together lead to a decrease or increase in regional precipitation. (2) “Fuzzy” (smooth) terrain will affect the precipitation simulated by changing the local vertical movement and water vapor transport, which shows that the WRF model’s accurate description of the terrain structure characteristics of mountainous areas is beneficial to accurately simulate the precipitation process on the windward slope area

Experimental and numerical investigation of heat transfer performance and sustainability of deep borehole heat exchangers coupled with ground source heat pump systems

Deep borehole heat exchangers (DBHEs) are a state-of-the-art and feasible apparatus for building heating and renewable energy utilization. Conventional BHEs with long-term operation may experience notable performance degradation, DBHE may provide an alternative way to overcome this issue. In this paper, a numerical model was developed by considering the ground temperature gradient in the axial direction and multilayer thermal properties of rock and soil and was used to simulate the temperature distribution and the performance characteristics of coaxial DBHEs. The effectiveness of the model was validated against the experimental data collected from a demonstration project. It was shown that the simulation results agreed well with the experimental data. The DBHEs could offer a higher heat exchange capacity in comparison to conventional BHEs. In the intermittent operation for 10 years, the decreasing proportions of the outlet temperature under four different operation modes with the run-stop ratio (i.e. the ratio of the running time to the stopping time in a day) of 8:16, 12:12, 16:8 and 24:0, were no more than 3.57%. The rock temperature profiles in the heating mode of both commercial and residential buildings were presented and the annual decreasing proportions were less than 4.0%. The findings obtained from this study could be used as a reference for sustainability research of DBHEs under different working conditions and operation modes

Effect of poly-β-hydroxybutyrate on growth, enzyme activity and intestinal microbial community of Chinese mitten crab, Eriocheir sinensis (Milne-Edwards) juveniles

Poly-beta-hydroxybutyrate (PHB) is microbial carbon and energy storage polymer, which can be degraded into water-soluble beta-hydroxybutyric acid in the gastrointestinal tract of aquatic animals. A 60-day culture experiment was performed using Chinese mitten crab, Eriocheir sinensis (Milne-Edwards) juveniles with an average initial body weight of 0.74 +/- 0.06 g which were fed a diet supplemented with 0%, 0.5%, 1%, 3% or 5% PHB. A PHB dietary supplementation of 1% and 3% significantly improved the body weight gain, moulting frequency and concomitantly reduced 2nd-3rd moulting intervals of the crabs (P < 0.05). The dietary PHB level positively related to hepatopan-creatic pepsin, trypsin and lipase activity (P < 0.05). Increasing the dietary PHB also improved total superoxide dismutase activity, but reduced alkaline phosphatase and acid phosphatase activity in the serum of hemolymph (P < 0.05). A 16S rRNA gene analysis by denaturing gradient gel electrophoresis indicated that PHB supplementation led to a significantly higher range-weighted richness, diversity and evenness of the gut bacterial community when dosed at 3% in the feed. The beneficial effects of PHB are discussed in terms of immune defense, metabolism and gut microbiota of the crabs

Enhancing Pixel Charging Efficiency by Optimizing Thin-Film Transistor Dimensions in Gate Driver Circuits for Active-Matrix Liquid Crystal Displays

Flat panel displays are electronic displays that are thin and lightweight, making them ideal for use in a wide range of applications, from televisions and computer monitors to mobile devices and digital signage. The Thin-Film Transistor (TFT) layer is responsible for controlling the amount of light that passes through each pixel and is located behind the liquid crystal layer, enabling precise image control and high-quality display. As one of the important parameters to evaluate the display performance, the faster response time provides more frames in a second, which benefits many high-end applications, such as applications for playing games and watching movies. To further improve the response time, the single-pixel charging efficiency is investigated in this paper by optimizing the TFT dimensions in gate driver circuits in active-matrix liquid crystal displays. The accurate circuit simulation model is developed to minimize the signal’s fall time (Tf) by optimizing the TFT width-to-length ratio. Our results show that using a driving TFT width of 6790 μm and a reset TFT width of 640 μm resulted in a minimum Tf of 2.6572 μs, corresponding to a maximum pixel charging ratio of 90.61275%. These findings demonstrate the effectiveness of our optimization strategy in enhancing pixel charging efficiency and improving display performance