Computational Design of β Sheet Proteins

Computational protein design has become a very powerful approach to test our understanding of the forces and energetics of macromolecular systems. The ability to design proteins that have specific structures and functions will be very valuable to future protein drug discovery. Protein design technology has been successfully applied to stabilize proteins, increase protein-protein binding affinity and create new protein structures. However, de novo design remains very challenging, especially for β-sheet proteins. Most de novo designed β-sheet proteins tested to date either misfold or aggregate. In this thesis, we use a hierarchical approach to search for the bottleneck in β-sheet design. First, we tested our ability to redesign the sequence of a naturally occurring β-sheet protein. The molecular modeling program Rosetta was used to design new sequences for the β-sheet protein tenascin. The redesigned proteins are well-folded and have thermal melting temperatures that are 40 °C higher than the wild type. These results indicate that given a designable backbone we can create a well-folded β-sheet protein. To move towards complete de novo design we next asked if we could design a portion of a β-sheet protein from scratch. We tested our ability to design loops by removing a ten-residue loop from tenascin and rebuilding it to have a new but specific conformation. These studies involved the simultaneous search of conformational and sequence space. Two of the designed loops were crystallized, and one of them adopts a structure that is very similar to the design model. Lastly, we have explored designing whole β-sheet proteins from scratch. Four generations of designs have been tested to date, and unfortunately, none of the designs appear to be well folded. To lay the groundwork for future success, we have been comparing the design models to naturally occurring β- sheet proteins to identify structural features that may be missing from the designs. We find that naturally occurring proteins include fewer voids accessible to small probes (~ 0.7 Å ) than our design models. It remains to be seen if more conformational sampling is need to remove these voids or if the energy function requires changes

Valuing changes in welfare to individuals and society resulting from the government's provision of children's social services in England: final report

Measurement for National Accounts purposes of the output attributable to government-provided services requires a different approach from that used for private sector goods and services. Public services, including Children’s Social Services (CSS), are mostly supplied free of charge and therefore there are no market prices by which their value can be measured. To advance the methodologies used in the measurement of government output, an independent review led by Professor Sir Tony Atkinson was set up. Its recommendations for the measurement of government output, productivity and associated price indices are set out in the Atkinson Review: Final Report (2005). Overall the Review’s recommended approach is to directly measure output using indicators that capture the full range of public services provided. In addition, ideally, these indicators should measure the incremental impact of these services on client outcomes. As part of a move towards implementing this approach for CSS output, the Department for Education and Skills (DfES) commissioned this study to explore how one might measure the contribution that CSS activities make to the welfare of service users and society more generally. The study’s remit was to advise on how the recommendations of the Atkinson review might be implemented, and on any improvements to data collections that might be required. Indicators to represent the various categories of CSS interventions were to be identified and combined into a single annual index. The study’s aim was therefore highly challenging: to recommend a methodology for producing a robust annual output measure that fully reflects the change in welfare to individuals and society from CSS provision. This final report presents the overall findings of the study. It sets out principles to be followed in the measurement of CSS output and specific recommendations for changes. The conclusions from the first stage of this study, which are reported in detail in the Interim Report, are summarised in paragraphs 1.8 to 1.12 below

Spatiotemporal Distribution of Eutrophication in Lake Tai as Affected by Wind

One common hypothesis is that wind can affect concentrations of nutrients (i.e., nitrogen and phosphorus) and chlorophyll-a (Chl-a) in shallow lakes. However, the tests of this hypothesis have yet to be conclusive in existing literature. The objective of this study was to use long-term data to examine how wind direction and wind speed affect the spatiotemporal variations of total nitrogen (TN), total phosphorus (TP) and Chl-a in Lake Tai, a typical shallow lake located in east China. The results indicated that the concentrations of nutrients and Chl-a tended to decrease from the northwest to the southeast of Lake Tai, with the highest concentrations in the two leeward bays (namely Meiliang Bay and Zhushan Bay) in the northwestern part of the lake. In addition to possible artificial reasons (e.g., wastewater discharge), the prevalent southeastward winds in warm seasons (i.e., spring and summer) and northwestward winds in cool seasons (i.e., fall and winter) might be the major natural factor for such a northwest-southeast decreasing spatial pattern. For the lake as a whole, the concentrations of TN, TP and Chl-a were highest for a wind speed between 2.1 and 3.2 m·s-1, which can be attributed to the idea that the wind-induced drifting and mixing effects might be dominant in the bays while the wind-induced drifting and resuspension effects could be more important in the other parts of the lake. Given that the water depth of the bays was relatively larger than that of the other parts, the drifting and mixing effects were likely dominant in the bays, as indicated by the negative relationships between the ratios of wind speed to lake depth, which can be a surrogate for the vertical distribution of wind-induced shear stress and the TN, TP and Chl-a concentration. Moreover, the decreasing temporal trend of wind speed in combination with the ongoing anthropogenic activities will likely increase the challenge for dealing with the eutrophication problem of Lake Tai. © 2017 by the authors

Genome-wide characterization and expression of two-component system genes in cytokinin-regulated gall formation in Zizania latifolia

The thickening of Zizania latifolia shoots, referred to as gall formation, depends on infection with the fungal endophyte Ustilago esculenta. The swollen and juicy shoots are a popular vegetable in Asia. A key role for cytokinin action in this process was postulated. Here, trans-zeatin stimulated swelling in fungi-infected Z. latifolia. A two-component system (TCS) linked cytokinin binding to receptors with transcriptional regulation in the nucleus and played important roles in diverse biological processes. We characterized 69 TCS genes encoding for 25 histidine kinase/histidine-kinase-like (HK(L)) (21 HKs and 4 HKLs), 8 histidine phosphotransfer proteins (HP) (5 authentic and 3 pseudo), and 36 response regulators (RR; 14 type A, 14 type B, 2 type C, and 6 pseudo) in the genome of Z. latifolia. These TCS genes have a close phylogenetic relationship with their rice counterparts. Nineteen duplicated TCS gene pairs were found and the ratio of nonsynonymous to synonymous mutations indicated that a strong purifying selection acted on these duplicated genes, leading to few mutations during evolution. Finally, ZlCHK1, ZlRRA5, ZIRRA9, ZlRRA10, ZlPRR1, and ZlPHYA expression was associated with gall formation. Among them, ARR5, ARR9, and ZlPHYA are quickly induced by trans-zeatin, suggesting a role for cytokinin signaling in shoot swelling of Z. latifolia. Keywords: two-component system; Z. latifolia; shoot swelling; cytokinin signal

Computer-Based Redesign of a β Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo β Sheet Design

The de novo design of globular β-sheet proteins remains largely an unsolved problem. It is unclear if most designs are failing because the designed sequences do not have favorable energies in the target conformations or if more emphasis should be placed on negative design, i.e. explicitly identifying sequences that have poor energies when adopting undesired conformations. We tested if we could redesign the sequence of a naturally occurring β-sheet protein, tenascin, with a design algorithm that does not include explicit negative design. Denaturation experiments indicate that the designs are significantly more stable than the wild type protein and the crystal structure of one design closely matches the design model. These results suggest that extensive negative design is not required to create well-folded β-sandwich proteins. However, it is important to note that negative design elements may be encoded in the conformation of the protein backbone which was preserved from the wild type protein

Time-lapse change pattern and mechanism of resistivity of coal seam floor mining damage based on inter-hole DC perspective

During the coal mining process, the change in the floor stress state of coal seam will produce deformation and failure. The seam floor failure in different coal mining processes has a certain law. At present, the water disaster monitoring of coal seam floors based on the DC resistivity method mainly focuses on the resistivity response characteristics of floor deformation and damage. To investigate the temporal changes in the electrical properties of the coal seam floor during mining, this study employs the inter-hole DC perspective observation system and the time-lapse resistivity reflection coefficient method. Through numerical simulation and field tests, the study uncovers the temporal variation law of the resistivity of coal seam floor induced by mining activities. First, this paper compares the results of individual inversion and time-lapse resistivity change rates for a typical geoelectric model to validate the reliability of the inter-hole DC perspective time-lapse method. Next, considering the mining-induced damage to the coal seam floor, this paper analyzes the electrical response patterns and charac-teristics of the rise of confined water and the damage zone in the floor during the mining process. It also discusses the feasibility of using a time-lapse resistivity reflection coefficient to assess the depth of coal seam floor damage, offering a theoretical basis for field construction. Finally, , the on-site monitoring tests reveal the electrical change characteristics of coal seam floor during the coal mining process. The time-lapse resistivity reflection coefficient R is utilized to determine the damage depth of the rock layer of the working face floor, which is found to be 15 m. The study results demonstrate that the time-lapse characteristics of the resistivity of coal seam floor mining damage obtained by the inter-hole DC perspective method can mitigate the influence of formation factors and random noise in the monitoring data to a certain extent. Additionally, the time-lapse resistivity reflection coefficient can be utilized to determine the depth of coal seam floor failure. This method transforms the detection target from the single study of geological anomalies to the full life cycle dynamic monitoring of the floor damage of the working face in the process of coal mining and then realizes the detailed depiction of structural damage to the working surface floor

A review of chemotherapeutic drugs-induced arrhythmia and potential intervention with traditional Chinese medicines

Significant advances in chemotherapy drugs have reduced mortality in patients with malignant tumors. However, chemotherapy-related cardiotoxicity increases the morbidity and mortality of patients, and has become the second leading cause of death after tumor recurrence, which has received more and more attention in recent years. Arrhythmia is one of the common types of chemotherapy-induced cardiotoxicity, and has become a new risk related to chemotherapy treatment, which seriously affects the therapeutic outcome in patients. Traditional Chinese medicine has experienced thousands of years of clinical practice in China, and has accumulated a wealth of medical theories and treatment formulas, which has unique advantages in the prevention and treatment of malignant diseases. Traditional Chinese medicine may reduce the arrhythmic toxicity caused by chemotherapy without affecting the anti-cancer effect. This paper mainly discussed the types and pathogenesis of secondary chemotherapeutic drug-induced arrhythmia (CDIA), and summarized the studies on Chinese medicine compounds, Chinese medicine Combination Formula and Chinese medicine injection that may be beneficial in intervention with secondary CDIA including atrial fibrillation, ventricular arrhythmia and sinus bradycardia, in order to provide reference for clinical prevention and treatment of chemotherapy-induced arrhythmias

Polysaccharide Extracted from Laminaria japonica

This study aimed to determine the effect of topically applied Laminaria polysaccharide (LP) on skin aging. We applied ointment containing LP (10, 25, and 50 μg/g) or vitamin E (10 μg/g) to the dorsal skin of aging mice for 12 months and young control mice for 4 weeks. Electron microscopy analysis of skin samples revealed that LP increased dermal thickness and skin collagen content. Tissue inhibitor of metalloprotease- (TIMP-) 1 expression was upregulated while that of matrix metalloproteinase- (MMP-) 1 was downregulated in skin tissue of LP-treated as compared to untreated aging mice. Additionally, phosphorylation of c-Jun N-terminal kinase (JNK) and p38 was higher in aging skin than in young skin, while LP treatment suppressed phospho-JNK expression. LP application also enhanced the expression of antioxidative enzymes in skin tissue, causing a decrease in malondialdehyde levels and increases in superoxide dismutase, catalase, and glutathione peroxidase levels relative to those in untreated aging mice. These results indicate that LP inhibits MMP-1 expression by preventing oxidative stress and JNK phosphorylation, thereby delaying skin collagen breakdown during aging

Interpretable surface-based detection of focal cortical dysplasias:a Multi-centre Epilepsy Lesion Detection study

One outstanding challenge for machine learning in diagnostic biomedical imaging is algorithm interpretability. A key application is the identification of subtle epileptogenic focal cortical dysplasias (FCDs) from structural MRI. FCDs are difficult to visualize on structural MRI but are often amenable to surgical resection. We aimed to develop an open-source, interpretable, surface-based machine-learning algorithm to automatically identify FCDs on heterogeneous structural MRI data from epilepsy surgery centres worldwide. The Multi-centre Epilepsy Lesion Detection (MELD) Project collated and harmonized a retrospective MRI cohort of 1015 participants, 618 patients with focal FCD-related epilepsy and 397 controls, from 22 epilepsy centres worldwide. We created a neural network for FCD detection based on 33 surface-based features. The network was trained and cross-validated on 50% of the total cohort and tested on the remaining 50% as well as on 2 independent test sites. Multidimensional feature analysis and integrated gradient saliencies were used to interrogate network performance. Our pipeline outputs individual patient reports, which identify the location of predicted lesions, alongside their imaging features and relative saliency to the classifier. On a restricted 'gold-standard' subcohort of seizure-free patients with FCD type IIB who had T1 and fluid-attenuated inversion recovery MRI data, the MELD FCD surface-based algorithm had a sensitivity of 85%. Across the entire withheld test cohort the sensitivity was 59% and specificity was 54%. After including a border zone around lesions, to account for uncertainty around the borders of manually delineated lesion masks, the sensitivity was 67%. This multicentre, multinational study with open access protocols and code has developed a robust and interpretable machine-learning algorithm for automated detection of focal cortical dysplasias, giving physicians greater confidence in the identification of subtle MRI lesions in individuals with epilepsy