PIE-1, SUMOylation, and Epigenetic Regulation of Germline Specification in Caenorhabditis elegans

In many organisms, the most fundamental event during embryogenesis is differentiating between germline cells and specialized somatic cells. In C. elegans, PIE-1 functions to protect the germline from somatic differentiation and appears to do so by blocking transcription and by preventing chromatin remodeling in the germline during early embryogenesis. Yet the molecular mechanisms by which PIE-1 specifies germline remain poorly understood. Our work shows that SUMOylation facilitates PIE-1-dependent germline maintenance and specification. In vivo SUMO purification in various CRISPR strains revealed that PIE-1 is SUMOylated at lysine 68 in the germline and that this SUMOylation is essential for forming NuRD complex and preserving HDA-1 activity. Moreover, HDA-1 SUMOylation is dependent on PIE-1 and enhanced by PIE-1 SUMOylation, which is required for protecting germline integrity. Our results suggest the importance of SUMOylation in the germline maintenance and exemplify simultaneous SUMOylation of proteins in the same functional pathway

KAYAGŬM SHIN'GOK: COMPOSITION, PERFORMANCE, AND REPRESENTATION OF NEW KAYAGŬM MUSIC IN CONTEMPORARY SOUTH KOREA

This dissertation focuses on kayagŭm shin'gok, newly composed music for the kayagŭm, a Korean 12-stringed long board zither. The work examines the relationship between composition, performance and representation of kayagŭm shin'gok in contemporary South Korea. Practitioners of kayagŭm shin'gok have developed new musical repertoire, instruments, and techniques for this genre since the 1960s. This dissertation is the first treatise in any language on kayagŭm shin'gok which contextualizes the genre within the changing social and cultural conditions that have underpinned musical life in modern South Korea. This study is the first English-language dissertation written by a kayagŭm practitioner who has worked with the major performers and composers of this genre.This dissertation is organized around four categories of kayagŭm shin'gok composition and performance. Those include kayagŭm as a living tradition; the boundaries of musical style in kayagŭm shin'gok; kayagŭm shin'gok as a modern high art form; and the social matrix of kayagŭm shin'gok production. Musical analysis focuses on the compositional style and development of Hwang Byung-ki and Yi Sung-chun, composers who are widely recognized as the most influential composers of this genre. Theoretical issues that are examined include composers and composition in an Asian context, musical change, and the role of music in processes of identity formation.As the kayagŭm represents an authentic Korean sound, the social value of this traditional instrument is highly emphasized and legitimized in South Korea. Thus the discourse of "tradition" lives with practices of kayagŭm in contemporary Korean culture. Modernity in kayagŭm shin'gok is defined as being opposed to the music of the "past." Through kayagŭm shin'gok, the meaning attached to kayagŭm music has been changed from a form of entertainment in the early 20th century to a symbol of the nation. Social networks have been important in keeping kayagŭm shin'gok alive, and are made up of diverse layers of relationships within the cultural system of Korean music: composers and performers; teachers and students; patrons and practitioners. Social values and meanings of kayagŭm shin'gok are constantly being negotiated, reaffirmed, and reinforced by these social actors through the institutions that engage the music

Unknown Domain Inconsistency Minimization for Domain Generalization

The objective of domain generalization (DG) is to enhance the transferability of the model learned from a source domain to unobserved domains. To prevent overfitting to a specific domain, Sharpness-Aware Minimization (SAM) reduces source domain's loss sharpness. Although SAM variants have delivered significant improvements in DG, we highlight that there's still potential for improvement in generalizing to unknown domains through the exploration on data space. This paper introduces an objective rooted in both parameter and data perturbed regions for domain generalization, coined Unknown Domain Inconsistency Minimization (UDIM). UDIM reduces the loss landscape inconsistency between source domain and unknown domains. As unknown domains are inaccessible, these domains are empirically crafted by perturbing instances from the source domain dataset. In particular, by aligning the loss landscape acquired in the source domain to the loss landscape of perturbed domains, we expect to achieve generalization grounded on these flat minima for the unknown domains. Theoretically, we validate that merging SAM optimization with the UDIM objective establishes an upper bound for the true objective of the DG task. In an empirical aspect, UDIM consistently outperforms SAM variants across multiple DG benchmark datasets. Notably, UDIM shows statistically significant improvements in scenarios with more restrictive domain information, underscoring UDIM's generalization capability in unseen domains. Our code is available at \url{https://github.com/SJShin-AI/UDIM}.Comment: 25 pages, 7 figures, Accepted to the twelfth International Conference on Learninig Representations (ICLR 24

Leveraging the COVID-19 fermentation trend to enhance nutrition and food safety Extension efforts

Our program aimed to increase knowledge related to fermented foods. Over 400 stakeholders registered for a webinar series that focused on defining fermented foods, health benefits of fermenting foods, and the safety of fermented foods. Participants indicated increases in knowledge and overall satisfaction with the content of the fermentation curriculum. The impact of the COVID-19 pandemic on the program outcomes are discussed

Label-Noise Robust Diffusion Models

Conditional diffusion models have shown remarkable performance in various generative tasks, but training them requires large-scale datasets that often contain noise in conditional inputs, a.k.a. noisy labels. This noise leads to condition mismatch and quality degradation of generated data. This paper proposes Transition-aware weighted Denoising Score Matching (TDSM) for training conditional diffusion models with noisy labels, which is the first study in the line of diffusion models. The TDSM objective contains a weighted sum of score networks, incorporating instance-wise and time-dependent label transition probabilities. We introduce a transition-aware weight estimator, which leverages a time-dependent noisy-label classifier distinctively customized to the diffusion process. Through experiments across various datasets and noisy label settings, TDSM improves the quality of generated samples aligned with given conditions. Furthermore, our method improves generation performance even on prevalent benchmark datasets, which implies the potential noisy labels and their risk of generative model learning. Finally, we show the improved performance of TDSM on top of conventional noisy label corrections, which empirically proving its contribution as a part of label-noise robust generative models. Our code is available at: https://github.com/byeonghu-na/tdsm.Comment: Accepted at ICLR 202

A co-CRISPR strategy for efficient genome editing in Caenorhabditis elegans

Genome editing based on CRISPR (clustered regularly interspaced short palindromic repeats)-associated nuclease (Cas9) has been successfully applied in dozens of diverse plant and animal species, including the nematode Caenorhabditis elegans. The rapid life cycle and easy access to the ovary by micro-injection make C. elegans an ideal organism both for applying CRISPR-Cas9 genome editing technology and for optimizing genome-editing protocols. Here we report efficient and straightforward CRISPR-Cas9 genome-editing methods for C. elegans, including a Co-CRISPR strategy that facilitates detection of genome-editing events. We describe methods for detecting homologous recombination (HR) events, including direct screening methods as well as new selection/counterselection strategies. Our findings reveal a surprisingly high frequency of HR-mediated gene conversion, making it possible to rapidly and precisely edit the C. elegans genome both with and without the use of co-inserted marker genes

Comparative cardiovascular outcomes in type 2 diabetes patients taking dapagliflozin versus empagliflozin: a nationwide population-based cohort study

BACKGROUND: Sodium-glucose co-transporter-2 inhibitors displayed cardiovascular benefits in type 2 diabetes mellitus in previous studies; however, there were some heterogeneities regarding respective cardiovascular outcomes within the class. Furthermore, their efficacies in Asians, females, and those with low cardiovascular risks were under-represented. Thus, we compared the cardiovascular outcomes between new users of dapagliflozin and empagliflozin in a broad range of patients with type 2 diabetes mellitus using a nationwide population-based real-world cohort from Korea. METHODS: Korean National Health Insurance registry data between May 2016 and December 2018 were extracted, and an active-comparator new-user design was applied. The primary outcome was a composite of heart failure (HF)-related events (i.e., hospitalization for HF and HF-related death), myocardial infarction, ischemic stroke, and cardiovascular death. The secondary outcomes were individual components of the primary outcome. RESULTS: A total of 366,031 new users of dapagliflozin or empagliflozin were identified. After 1:1 nearest-neighbor propensity score matching, 72,752 individuals (mean age approximately 56 years, 42% women) from each group were included in the final analysis, with a follow-up of 150,000 ~ person-years. Approximately 40% of the patients included in the study had type 2 diabetes mellitus as their sole cardiovascular risk factor, with no other risk factors. The risk of the primary outcome was not different significantly between dapagliflozin and empagliflozin users (hazard ratio [HR] 0.93, 95% confidence interval [CI] 0.855-1.006). The risks of secondary outcomes were also similar, with the exception of the risks of HF-related events (HR 0.84, 95% CI 0.714-0.989) and cardiovascular death (HR 0.76, 95% CI 0.618-0.921), which were significantly lower in the dapagliflozin users. CONCLUSIONS: This large-scale nationwide population-based real-world cohort study revealed no significant difference in composite cardiovascular outcomes between new users of dapagliflozin and empagliflozin. However, dapagliflozin might be associated with lower risks of hospitalization or death due to HF and cardiovascular death than empagliflozin in Asian patients with type 2 diabetes mellitus

Relationship between metformin use and mortality in tuberculosis patients with diabetes: a nationwide cohort study

Background/Aims To determine whether metformin, which is considered a host-directed therapy for tuberculosis (TB), is effective in improving the prognosis of patients with TB and diabetes mellitus (DM), who have higher mortality than those without DM. Methods This cohort study included patients who were registered as having TB in the National Tuberculosis Surveillance System. The medical and death records of matched patients were obtained from the National Health Information Database and Statistics Korea, respectively, and data from 2011 to 2017 were collected retrospectively. We classified patients according to metformin use among participants who used diabetes drugs for more than 28 days. The primary outcome was all-cause mortality during TB treatment. Double propensity score adjustment was applied to reduce the effects of confounding and multivariable Cox proportional hazard models were used to estimate adjusted hazard ratio (aHR) with 95% confidence interval (CI). Results The all-cause mortality rate during TB treatment was lower (9.5% vs. 12.4%, p < 0.01) in the metformin user group. The hazard of death due to all causes after double propensity score adjustment was also lower in the metformin user group (aHR 0.76, 95% CI 0.67–0.86, p < 0.01). There was no significant difference in mortality between metformin users and non-users for TB-related deaths (p = 0.22); however, there was a significant difference in the non-TB-related deaths (p < 0.01). Conclusions Metformin use in patients with TB–DM co-prevalence is associated with reduced all-cause mortality, suggesting the potential for metformin adjuvant therapy in these patients

Preventable Cancer Burden Associated With Poor Diet in the United States.

BACKGROUND: Diet is an important risk factor for cancer that is amenable to intervention. Estimating the cancer burden associated with diet informs evidence-based priorities for nutrition policies to reduce cancer burden in the United States. METHODS: Using a comparative risk assessment model that incorporated nationally representative data on dietary intake, national cancer incidence, and estimated associations of diet with cancer risk from meta-analyses of prospective cohort studies, we estimated the annual number and proportion of new cancer cases attributable to suboptimal intakes of seven dietary factors among US adults ages 20 years or older, and by population subgroups. RESULTS: An estimated 80 110 (95% uncertainty interval [UI] = 76 316 to 83 657) new cancer cases were attributable to suboptimal diet, accounting for 5.2% (95% UI = 5.0% to 5.5%) of all new cancer cases in 2015. Of these, 67 488 (95% UI = 63 583 to 70 978) and 4.4% (95% UI = 4.2% to 4.6%) were attributable to direct associations and 12 589 (95% UI = 12 156 to 13 038) and 0.82% (95% UI = 0.79% to 0.85%) to obesity-mediated associations. By cancer type, colorectal cancer had the highest number and proportion of diet-related cases (n = 52 225, 38.3%). By diet, low consumption of whole grains (n = 27 763, 1.8%) and dairy products (n = 17 692, 1.2%) and high intake of processed meats (n = 14 524, 1.0%) contributed to the highest burden. Men, middle-aged (45-64 years) and racial/ethnic minorities (non-Hispanic blacks, Hispanics, and others) had the highest proportion of diet-associated cancer burden than other age, sex, and race/ethnicity groups. CONCLUSIONS: More than 80 000 new cancer cases are estimated to be associated with suboptimal diet among US adults in 2015, with middle-aged men and racial/ethnic minorities experiencing the largest proportion of diet-associated cancer burden in the United States.This work was supported by NIH/ NIMHD 1R01MD011501 (FFZ), NIH/ NHLBI R01HL115189 (DM), United Kingdom Medical Research Council Epidemiology Unit Core Support (MC_UU_12015/5) (FI), and American Heart Association postdoctoral fellowship (JXL)

Acetylation changes tau interactome to degrade tau in Alzheimer’s disease animal and organoid models

© 2019 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.Alzheimer&apos;s disease (AD) is an age-related neurodegenerative disease. The most common pathological hallmarks are amyloid plaques and neurofibrillary tangles in the brain. In the brains of patients with AD, pathological tau is abnormally accumulated causing neuronal loss, synaptic dysfunction, and cognitive decline. We found a histone deacetylase 6 (HDAC6) inhibitor, CKD-504, changed the tau interactome dramatically to degrade pathological tau not only in AD animal model (ADLPAPT) brains containing both amyloid plaques and neurofibrillary tangles but also in AD patient-derived brain organoids. Acetylated tau recruited chaperone proteins such as Hsp40, Hsp70, and Hsp110, and this complex bound to novel tau E3 ligases including UBE2O and RNF14. This complex degraded pathological tau through proteasomal pathway. We also identified the responsible acetylation sites on tau. These dramatic tau-interactome changes may result in tau degradation, leading to the recovery of synaptic pathology and cognitive decline in the ADLPAPT mice11Nsciescopu