Mark Zhang

Objective: Fragile X premutation carriers have an expansion of 55 -200 CGG repeats in the FMR1 gene. Male fXPCs are at risk for developing a neurodegenerative motor disorder often accompanied by inhibitory control impairments, even in fXPCs without motor symptoms. Inhibitory control impairments might precede, and thus indicate elevated risk for motor impairment associated with FXTAS. We tested whether inhibitory impairments are observable in fXPCs by assessing oculomotor performance. Method: Participants were males aged 18-48 years asymptomatic for FXTAS. FXPCs and healthy age-matched controls performed four oculomotor tasks. In a Fixation task, participants fixated on a central cross and maintained gaze position when a peripheral stimulus appeared. In a Pursuit task, participants maintained gaze on a square moving at constant velocity. In a Prosaccade task, participants fixated on a central cross, then looked at a peripheral stimulus. An Antisaccade task was identical to the Prosaccade task, except participants looked in the direction opposite the stimulus. Inhibitory cost was the difference in saccade latency between the Antisaccade and Prosaccade tasks. Results: Relative to controls, fXPCs had longer saccade latency in the Antisaccade task. In fXPCs, inhibitory cost was positively associated with vermis area in lobules VI-VII. Conclusion: Antisaccades require inhibitory control to inhibit reflexive eye movements. We found that eye movements are sensitive to impaired inhibitory control in fXPCs asymptomatic for FXTAS. Thus, eye movements may be useful in assessing FXTAS risk or disease progression. © 2014 American Psychological Association.

Accurate quantification of dissolved oxygen is critically important for managing water resources and controlling pollution. Artificial intelligence models have been successfully applied for modeling DO content in aquatic ecosystems with limited data. However, the efficacy of these AI models in predicting DO levels in the hypoxic river systems having multiple pollution sources and complicated pollutants behaviors is unclear. Given this dilemma, we developed a promising AI model, known as support vector machine, to predict the DO concentration in a hypoxic river in southeastern China. Four different calibration models, specifically, multiple linear regression, back propagation neural network, general regression neural network, and SVM, were established, and their prediction accuracy was systemically investigated and compared. A total of 11 hydro-chemical variables were used as model inputs. These variables were measured bimonthly at eight sampling sites along the rural-suburban-urban portion of Wen-Rui Tang River from 2004 to 2008. The performances of the established models were assessed through the mean square error, determination coefficient ), and Nash-Sutcliffe model efficiency. The results indicated that the SVM model was superior to other models in predicting DO concentration in Wen-Rui Tang River. For SVM, the MSE, R, and NS values for the testing subset were 0.9416 mg/L, 0.8646, and 0.8763, respectively. Sensitivity analysis showed that ammonium-nitrogen was the most significant input variable of the proposal SVM model. Overall, these results demonstrated that the proposed SVM model can efficiently predict water quality, especially for highly impaired and hypoxic river systems.

Common bean is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.

Copyright © 2016 by the American Society for Biochemistry and Molecular Biology, Inc.Human VLDLs assembled in the liver and secreted into the circulation supply energy to peripheral tissues. VLDL lipolysis yields atherogenic LDLs and VLDL remnants that strongly correlate with CVD. Although the composition of VLDL particles has been well-characterized, their 3D structure is elusive because of their variations in size, heterogeneity in composition, structural flexibility, and mobility in solution. Here, we employed cryo-electron microscopy and individual-particle electron tomography to study the 3D structure of individual VLDL particles at both below and above their lipid phase transition temperatures. The 3D reconstructions of VLDL and VLDL bound to antibodies revealed an unexpected polyhedral shape, in contrast to the generally accepted model of a spherical emulsion-like particle. The smaller curvature of surface lipids compared with HDL may also reduce surface hydrophobicity, resulting in lower binding affinity to the hydrophobic distal end of the N-terminal β-barrel domain of cholesteryl ester transfer protein compared with HDL. The directional binding of CETP to HDL and VLDL may explain the function of CETP in transferring TGs and cholesteryl esters between these particles. This first visualization of the 3D structure of VLDL could improve our understanding of the role of VLDL in atherogenesis.

Knowledge of three-dimensional structures of each individual particles of asymmetric and flexible proteins is essential in understanding those proteins' functions; but their structures are difficult to determine. Electron tomography provides a tool for imaging a single and unique biological object from a series of tilted angles, but it is challenging to image a single protein for three-dimensional reconstruction due to the imperfect mechanical control capability of the specimen goniometer under both a medium to high magnification and an optimized beam coherence condition. Here, we report a fully mechanical control method for automating ET data acquisition without using beam tilt/shift processes. This method could reduce the accumulation of beam tilt/shift that used to compensate the error from the mechanical control, but downgraded the beam coherence. Our method was developed by minimizing the error of the target object center during the tilting process through a closed-loop proportional-integral control algorithm. The validations by both negative staining and cryo-electron microscopy suggest that this method has a comparable capability to other ET methods in tracking target proteins while maintaining optimized beam coherence conditions for imaging.

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtain 14 density maps at ~ 2-nm resolution. Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.

Cholesteryl ester transfer protein mediates the transfer of cholesterol esters from atheroprotective high-density lipoproteins to atherogenic low-density lipoproteins. CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases. Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobic environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.

Trend and change-point analyses of water quality time series data have important implications for pollution control and environmental decision-making. This paper developed a new approach to assess trends and change-points of water quality parameters by integrating locally weighted polynomial regression and segmented regression. Firstly, LWPR was used to pretreat the original water quality data into a smoothed time series to represent the long-term trend of water quality. Then, SegReg was used to identify the long-term trends and change-points of the smoothed time series. Finally, statistical tests were applied to determine the significance of the long-term trends and change-points. The efficacy of this approach was validated using a 10-year record of total nitrogen and chemical oxygen demand from Shanxi Reservoir watershed in eastern China. Results showed that this approach was straightforward and reliable for assessment of long-term trends and change-points on irregular water quality datasets. The reliability was verified by statistical tests and practical considerations for Shanxi Reservoir watershed. The newly developed integrated LWPR-SegReg approach is not only limited to the assessment of trends and change-points of water quality parameters but also has a broad application to other fields with long-term time series records.