Studies of the structure of potassium channel KcsA in the open conformation and the effect of anionic lipids on channel inactivation

Membrane proteins play a vital role in cellular processes. In this thesis, we use KcsA, a prokaryotic potassium channel, as a model to investigate the gating mechanism of ion channels and the effect of anionic lipids on the channel activity using solid-state NMR spectroscopy. KcsA activity is known to be highly dependent on the presence of negatively charged lipids. Multiple crystal structures combined with biochemistry assays suggest that KcsA is co-purified with anionic lipids with phosphatidylglycerol headgroup. Here, we identified this specifically bound, isotopically labeled lipid in the protein 13C-13C correlation spectra. Our results reveal that the lipid cross peaks show stronger intensity when the channel is in the inactivated state compared to the activated state, which indicates a stronger protein-lipid interaction when KcsA is inactivated. In addition, our data shows that including anionic lipids into proteoliposomes leads to a weaker potassium ion affinity at the selectivity filter. Considering ion loss as a model of inactivation, our results suggest anionic lipids promote channel inactivation. However, the surface charge is not the only physical parameter that regulates channel gating or conformational preference. We found that the channel adapted to different conformations when reconstituted into liposome either made of DOPC or DOPE, two zwitterionic lipids. Also, we were able to stabilize the open-conformation of KcsA in 3:1 DOPE/DOPG liposome at pH 4.0 and acquired several multi-dimensional solid-state NMR experiments for site-specific resonance assignments. This is the first time that we obtain wild-type full-length KcsA structural information on the transient state. The structure is not only important for understanding channel gating, but can also serve as a homology model for investigating drug binding with more complicated potassium channels such as human voltage gated channel (hERG)

Tea consumption, oxidative stress, and breast cancer risk

Purpose: Oxidative stress, which features the imbalance between reactive oxygen species and antioxidant defenses, is associated with carcinogenesis. Tea contains natural antioxidants and has anti-tumor properties. However, limited epidemiologic studies investigated the association between tea and oxidative stress. Previous epidemiologic studies investigating tea and breast cancer risk have not addressed the potential for associations to vary by breast cancer subtype. Methods: The Sister Study is a nationwide cohort study that enrolled women across the US and Puerto Rico from 2003-2009. In aim 1, we included 889 premenopausal women from a nested case-control study within the Sister Study and investigated associations between black or green tea and oxidative stress which was measured by urinary F2-isoprostane (F2-IsoP) and a primary metabolite, 2,3-dinor-5,6-dihydro-15-F2t-isoprostane (15-F2t-IsoP-M). In aim 2, we investigated the association between black or green tea and breast cancer risk in the full cohort of 49,214 women. The analysis addressed variation by estrogen receptor (ER) status and other biologically important factors. Results: (Aim 1) We observed green tea was not associated with urinary F2-IsoP and 15-F2t-IsoP-M. Black tea was not associated with urinary F2-IsoP. However, drinking at least 5 cups of black tea per week (compared to 0 cup/week) was associated with a higher level of urinary 15-F2t-IsoP-M (geometric mean difference (GMD)=0.09, 95% CI 0.01, 0.17). Additionally adjusting for caffeine intake attenuated the association towards null (GMD=0.07, 95% CI -0.02, 0.16). (Aim 2) A total of 3,044 breast cancer patients were diagnosed from 49,214 participants. High-level black (hazard ratio (HR)=0.86, 95% CI 0.76, 0.98, ≥5 compared to 0 cups/week) and green tea (HR=0.84, 95% CI 0.73, 0.97, ≥5 compared to 0 cups/week) consumption were associated with a lower breast cancer risk. Both black and green tea consumption were inversely associated with ER+ breast cancer risk. Associations with ER- breast cancer risk were similarly inverse but non-significant. Conclusions: Contrary to previous experimental and clinical studies, we did not find an inverse association between black or green tea and oxidative stress. However, drinking at least 5 cups of black or green tea per week (compared to 0) was associated with a lower breast cancer risk.Doctor of Philosoph

CoLafier: Collaborative Noisy Label Purifier With Local Intrinsic Dimensionality Guidance

Deep neural networks (DNNs) have advanced many machine learning tasks, but their performance is often harmed by noisy labels in real-world data. Addressing this, we introduce CoLafier, a novel approach that uses Local Intrinsic Dimensionality (LID) for learning with noisy labels. CoLafier consists of two subnets: LID-dis and LID-gen. LID-dis is a specialized classifier. Trained with our uniquely crafted scheme, LID-dis consumes both a sample's features and its label to predict the label - which allows it to produce an enhanced internal representation. We observe that LID scores computed from this representation effectively distinguish between correct and incorrect labels across various noise scenarios. In contrast to LID-dis, LID-gen, functioning as a regular classifier, operates solely on the sample's features. During training, CoLafier utilizes two augmented views per instance to feed both subnets. CoLafier considers the LID scores from the two views as produced by LID-dis to assign weights in an adapted loss function for both subnets. Concurrently, LID-gen, serving as classifier, suggests pseudo-labels. LID-dis then processes these pseudo-labels along with two views to derive LID scores. Finally, these LID scores along with the differences in predictions from the two subnets guide the label update decisions. This dual-view and dual-subnet approach enhances the overall reliability of the framework. Upon completion of the training, we deploy the LID-gen subnet of CoLafier as the final classification model. CoLafier demonstrates improved prediction accuracy, surpassing existing methods, particularly under severe label noise. For more details, see the code at https://github.com/zdy93/CoLafier.Comment: This work is accepted by SIAM International Conference on Data Mining (SDM24

Boeravinone B promotes fracture healing in ovariectomyinduced osteoporotic rats via the regulation of NF-κB p65/IκB-α/SIRT-1 signaling pathway

Purpose: To investigate the fracture-healing effect of boeravinone B in ovariectomy-induced (OVX) osteoporotic rats. Methods: Adult female Wistar rats (n = 30) were ovariectomized and after three months, the unilateral cross-tibial fractures were fixed with intramedullary nails. The rats were then randomly assigned to three groups of 10 rats each: normal control group, OVX group and 100 mg/kg body weight boeravinone B group. Boeravinone B was orally administered for a period of 5 weeks. The effect of boeravinone B on indices of bone formation and resorption was assessed. Levels of inflammatory cytokines including tumor necrosis factor- α (TNF-α) and interleukin-1β (IL-1β) were determined using enzyme-linked immunosorbent assay (ELISA). Western blotting was used to determine the expression levels of NF-κB p65, IкB-α and SIRT1 proteins. Results: There were significant increases in the activities of tartrate-resistant acid phosphatase (TRAP) and alkaline phosphatase (ALP), and collagen type I fragment (CTX) level and serum osteocalcin (OC) of OVX group, when compared with normal control group (p < 0.05). However, treatment with boeravinone B significantly reduced the activities and levels of these parameters, relative to OVX group (p < 0.05). The levels of TNF-α and IL-1β significantly increased in OVX group, relative normal control group, but were significantly lower following treatment with boeravinone B (p < 0.05). Bone mineral content (BMC) was not significantly altered in OVX and boeravinone B-treated groups, when compared with normal control group (p > 0.05). There was significant reduction in bone mineral density (BMD) of OVX group relative to normal control group (p < 0.05). However, treatment with boeravinone B significantly increased the BMD, when compared with OVX group (p < 0.05). After Week 5 of treatment, boeravinone B significantly enhanced bone remodeling and formation of callus. Treatment with boeravinone B significantly reduced the expression levels of NF-κB p65 and IκB-α proteins, and significantly upregulated the expression of SIRT-1 (p < 0.05). Conclusion: The results obtained in this study suggest that boeravinone B promotes the healing of fracture caused by osteoporosis via a mechanism involving NF-κB p65/IκB-α/SIRT-1 signaling pathway

Expressing metaphorically, writing creatively: Metaphor identification for creativity assessment

Metaphor, which can implicitly express profound meanings and emotions, is a unique writing technique frequently used in human language. In writing, meaningful metaphorical expressions can enhance the literariness and creativity of texts. Therefore, the usage of metaphor is a significant impact factor when assessing the creativity and literariness of writing. However, little to no automatic writing assessment system considers metaphorical expressions when giving the score of creativity. For improving the accuracy of automatic writing assessment, this paper proposes a novel creativity assessment model that imports a token-level metaphor identification method to extract metaphors as the indicators for creativity scoring. The experimental results show that our model can accurately assess the creativity of different texts with precise metaphor identification. To the best of our knowledge, we are the first to apply automatic metaphor identification to assess writing creativity. Moreover, identifying features (e.g., metaphors) that influence writing creativity using computational approaches can offer fair and reliable assessment methods for educational settings

Facilitating Interskin Communication in Artificial Polymer Systems through Liquid Transfer

Chemical communication is a ubiquitous process in nature, and it has sparked interest in the development of electric-sense-based robotic perception systems with chemical components. Here, a novel liquid crystal polymer is introduced that combines the transferring, receiving, and sensing of chemical signals, providing a new principle to achieve chemical communication in robotic systems. This approach allows for the transfer of cargo between two polymer coatings, and the transfer can be monitored through an electrical signal. Additionally, cascade transfer can be achieved through this approach, as the transfer of cargo is not limited to only two coatings, but can continue from the second to a third coating. Furthermore, the two coatings can be infused with different reagents, and upon exchange, a reaction takes place to generate the desired species. The novel method of chemical communication that is developed presents a notable improvement in embodied perception. This advancement facilitates human–robot and robot–robot interactions and enhances the ability of robots to efficiently and accurately perform complex tasks in their environment.</p