CWAS-Plus: estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data.

Variants in cis-regulatory elements link the noncoding genome to human pathology; however, detailed analytic tools for understanding the association between cell-level brain pathology and noncoding variants are lacking. CWAS-Plus, adapted from a Python package for category-wide association testing (CWAS), enhances noncoding variant analysis by integrating both whole-genome sequencing (WGS) and user-provided functional data. With simplified parameter settings and an efficient multiple testing correction method, CWAS-Plus conducts the CWAS workflow 50 times faster than CWAS, making it more accessible and user-friendly for researchers. Here, we used a single-nuclei assay for transposase-accessible chromatin with sequencing to facilitate CWAS-guided noncoding variant analysis at cell-type-specific enhancers and promoters. Examining autism spectrum disorder WGS data (n = 7280), CWAS-Plus identified noncoding de novo variant associations in transcription factor binding sites within conserved loci. Independently, in Alzheimer's disease WGS data (n = 1087), CWAS-Plus detected rare noncoding variant associations in microglia-specific regulatory elements. These findings highlight CWAS-Plus's utility in genomic disorders and scalability for processing large-scale WGS data and in multiple-testing corrections. CWAS-Plus and its user manual are available at https://github.com/joonan-lab/cwas/ and https://cwas-plus.readthedocs.io/en/latest/, respectively.

High-Frequency Vestibular Function Is Vulnerable to Presbyvestibulopathy.

INTRODUCTION: In 2019, mild vestibular function deficiency in elder populations was defined as presbyvestibulopathy (PVP) by the Classification Committee of the Bárány Society. The diagnostic criteria include tests for low-, mid-, and high-frequency vestibular function, represented by caloric testing, rotary chair testing, and head impulse testing, respectively. However, there is still a lack of large-scale reports supporting the relationship between vestibular function tests (VFTs) and aging. In this study, we evaluated whether each test is correlated with aging in the elderly population aged over 50. METHODS: This study retrospectively enrolled 1043 subjects from a single university hospital database after excluding those with unilateral and bilateral vestibulopathy, central dizziness, and acute dizziness. Enrolled subjects had caloric canal paresis <20%, vHIT lateral canal gain >0.6, vHIT interaural difference <0.3, and age >50 years old. RESULTS: Significant negative correlations with age were identified in the vHIT (p < 0.001) and rotary chair test (RCT) 1.0 Hz gain (p = 0.030). However, the caloric test (p = 0.739 and 0.745 on the left and right sides, respectively) and RCT 0.12 Hz gain (p = 0.298) did not show a significant correlation with age. A total of 4.83% of subjects aged 70 years or older showed sub-normal vHIT gain that met the criteria of PVP, whereas only 0.50% of subjects aged 60 to 69 did. The prevalence of sub-normal caloric test results, however, was not significantly different between the two age groups (21.55% in the 60-69 age group and 26.59% in the >70 age group). CONCLUSIONS: The high-frequency range vestibular function seems vulnerable to aging, and this is more discernible at age >70 years. The weak correlation between age and low-frequency vestibular function tests, such as the caloric test and low-frequency rotary chair testing, suggests the need to revisit the diagnostic criteria for PVP.

CWAS-Plus: Estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data.

Variants in cis-regulatory elements link the noncoding genome to human brain pathology; however, detailed analytic tools for understanding the association between cell-level brain pathology and noncoding variants are lacking. CWAS-Plus, adapted from a Python package for category-wide association testing (CWAS) employs both whole-genome sequencing and user-provided functional data to enhance noncoding variant analysis, with a faster and more efficient execution of the CWAS workflow. Here, we used single-nuclei assay for transposase-accessible chromatin with sequencing to facilitate CWAS-guided noncoding variant analysis at cell-type specific enhancers and promoters. Examining autism spectrum disorder whole-genome sequencing data (n = 7,280), CWAS-Plus identified noncoding de novo variant associations in transcription factor binding sites within conserved loci. Independently, in Alzheimer's disease whole-genome sequencing data (n = 1,087), CWAS-Plus detected rare noncoding variant associations in microglia-specific regulatory elements. These findings highlight CWAS-Plus's utility in genomic disorders and scalability for processing large-scale whole-genome sequencing data and in multiple-testing corrections. CWAS-Plus and its user manual are available at https://github.com/joonan-lab/cwas/ and https://cwas-plus.readthedocs.io/en/latest/, respectively.

Light-Dependent High Ambient Temperature-Induced Senescence Assay Using Whole Seedlings.

High ambient temperature affects various plant developmental and physiological processes, including senescence. Here, we present a protocol for assaying light-dependent high ambient temperature-induced senescence using whole seedlings. The protocol covers all steps, from inducing senescence by darkness at high ambient temperature to determining the degree of senescence, and includes experimental tips and notes. The onset of senescence is established by quantifying the increased expression of senescence marker genes by quantitative real-time PCR (RT-qPCR). The degree of senescence is determined by measuring the loss of chlorophyll and the increase of ion leakage. This protocol can be adapted to study light-dependent high ambient temperature-induced senescence in other plant species by adjusting the temperature and duration of darkness.

Isolation of Phytochrome B Photobodies.

Phytochrome B (phyB), a plant photoreceptor, forms a membraneless organelle known as a photobody. Here, we present a protocol for the isolation of phyB photobodies through fluorescence-activated particle sorting from mature transgenic Arabidopsis leaves expressing phyB-GFP. This protocol involves the isolation of nuclei from frozen ground leaves using sucrose gradient centrifugation, the disruption of nuclear envelopes by sonication, and the subsequent isolation of phyB photobodies through fluorescence-activated particle sorting. We include experimental tips and notes for each step.

"Meaning in Life" Mediates the Relationship between Loneliness and Depressive Symptoms among Older Adults during the COVID-19 Pandemic.

BACKGROUND: Loneliness was found to be a commonly experienced feeling among older adults during the COVID-19 pandemic and is considered to be a high-risk factor for depressive symptoms. Maintaining meaning in life has been found to be a protective resource for mental health among older adults. The purpose of this study was to examine the mediating effects of an individual's meaning in life in the relationship between loneliness and depressive symptoms among older Korean adults. METHODS: The data were obtained from a sample of 213 community-dwelling older adults aged over 65. The instruments were the UCLA Loneliness Scale, the Center for Epidemiologic Studies Depression Scale, and the Meaning in Life Questionnaire. RESULTS: Loneliness was positively associated with depressive symptoms and negatively associated with the presence of and search for meaning among older adults. The presence of meaning mediated the relationship between loneliness and depressive symptoms but the search for meaning did not. The search for meaning mediated the relationship between loneliness and depressive symptoms through the presence of meaning. CONCLUSIONS: Our study findings suggest that efforts to reduce loneliness and improve meaning in life should be undertaken to prevent depressive symptoms among older adults.

Phytochrome B photobody components.

Phytochrome B (phyB) is a red and far-red photoreceptor that promotes light responses. Upon photoactivation, phyB enters the nucleus and forms a molecular condensate called a photobody through liquid-liquid phase separation. Phytochrome B photobody comprises phyB, the main scaffold molecule, and at least 37 client proteins. These clients belong to diverse functional categories enriched with transcription regulators, encompassing both positive and negative light signaling factors, with the functional bias toward the negative factors. The functionally diverse clients suggest that phyB photobody acts either as a trap to capture proteins, including negatively acting transcription regulators, for processes such as sequestration, modification, or degradation or as a hub where proteins are brought into close proximity for interaction in a light-dependent manner.

Epigenetic Modulations for Prevention of Infectious Diseases in Shrimp Aquaculture.

Aquaculture assumes a pivotal role in meeting the escalating global food demand, and shrimp farming, in particular, holds a significant role in the global economy and food security, providing a rich source of nutrients for human consumption. Nonetheless, the industry faces formidable challenges, primarily attributed to disease outbreaks and the diminishing efficacy of conventional disease management approaches, such as antibiotic usage. Consequently, there is an urgent imperative to explore alternative strategies to ensure the sustainability of the industry. In this context, the field of epigenetics emerges as a promising avenue for combating infectious diseases in shrimp aquaculture. Epigenetic modulations entail chemical alterations in DNA and proteins, orchestrating gene expression patterns without modifying the underlying DNA sequence through DNA methylation, histone modifications, and non-coding RNA molecules. Utilizing epigenetic mechanisms presents an opportunity to enhance immune gene expression and bolster disease resistance in shrimp, thereby contributing to disease management strategies and optimizing shrimp health and productivity. Additionally, the concept of epigenetic inheritability in marine animals holds immense potential for the future of the shrimp farming industry. To this end, this comprehensive review thoroughly explores the dynamics of epigenetic modulations in shrimp aquaculture, with a particular emphasis on its pivotal role in disease management. It conveys the significance of harnessing advantageous epigenetic changes to ensure the long-term viability of shrimp farming while deliberating on the potential consequences of these interventions. Overall, this appraisal highlights the promising trajectory of epigenetic applications, propelling the field toward strengthening sustainability in shrimp aquaculture.

Sources of meaning in life among older adults during the COVID-19 pandemic: A qualitative study.

AIM: This study aims to explore the sources of meaning in life (MIL) and its impact on South Korean older adults during the coronavirus disease 2019 (COVID-19) pandemic. DESIGN: This study had a qualitative descriptive study design. METHODS: The study participants included 18 older adults. Six focus group interviews were conducted. Data were analysed using content analysis. RESULTS: The subcategories 'Continued learning and growth', 'Self-transcending practices' and 'Efforts to maintain good health' were extracted under the category 'Sources of MIL for older adults'. Similarly, the subcategories 'Tremendous changes brought about by the virus' and 'Varying patterns of adjustment to the pandemic' were extracted under the category 'Changes in the sources of MIL since the COVID-19 outbreak'. PUBLIC CONTRIBUTION: Our study provides an in-depth understanding of the changed sources of MIL for older adults during the COVID-19 pandemic. The findings serve as useful guidance for planning interventions for older adults to lead meaningful lives during the COVID-19 pandemic and post-pandemic crises.

Direct indicators of social distancing effectiveness in COVID-19 outbreak stages: a correlational analysis of case contacts and population mobility in Korea.

OBJECTIVES: The effectiveness of social distancing during the coronavirus disease 2019 (COVID-19) pandemic has been evaluated using the magnitude of changes in population mobility. This study aimed to investigate a direct indicator-namely, the number of close contacts per patient with confirmed COVID-19. METHODS: From week 7, 2020 to week 43, 2021, population movement changes were calculated from the data of two Korean telecommunication companies and Google in accordance with social distancing stringency levels. Data on confirmed cases and their close contacts among residents of Gyeonggi Province, Korea were combined at each stage. Pearson correlation analysis was conducted to compare the movement data with the change in the number of contacts for each confirmed case calculated by stratification according to age group. The reference value of the population movement data was set using the value before mid-February 2020, considering each data's characteristics. RESULTS: In the age group of 18 or younger, the number of close contacts per confirmed case decreased or increased when the stringency level was strengthened or relaxed, respectively. In adults, the correlation was relatively low, with no correlation between the change in the number of close contacts per confirmed case and the change in population movement after the commencement of vaccination for adults. CONCLUSIONS: The effectiveness of governmental social distancing policies against COVID-19 can be evaluated using the number of close contacts per confirmed case as a direct indicator, especially for each age group. Such an analysis can facilitate policy changes for specific groups.

Removal of evolutionarily conserved functional MYC domains in a tilapia cell line using a vector-based CRISPR/Cas9 system.

MYC transcription factors have critical roles in facilitating a variety of cellular functions that have been highly conserved among species during evolution. However, despite circumstantial evidence for an involvement of MYC in animal osmoregulation, mechanistic links between MYC function and osmoregulation are missing. Mozambique tilapia (Oreochromis mossambicus) represents an excellent model system to study these links because it is highly euryhaline and highly tolerant to osmotic (salinity) stress at both the whole organism and cellular levels of biological organization. Here, we utilize an O. mossambicus brain cell line and an optimized vector-based CRISPR/Cas9 system to functionally disrupt MYC in the tilapia genome and to establish causal links between MYC and cell functions, including cellular osmoregulation. A cell isolation and dilution strategy yielded polyclonal myca (a gene encoding MYC) knockout (ko) cell pools with low genetic variability and high gene editing efficiencies (as high as 98.2%). Subsequent isolation and dilution of cells from these pools produced a myca ko cell line harboring a 1-bp deletion that caused a frameshift mutation. This frameshift functionally inactivated the transcriptional regulatory and DNA-binding domains predicted by bioinformatics and structural analyses. Both the polyclonal and monoclonal myca ko cell lines were viable, propagated well in standard medium, and differed from wild-type cells in morphology. As such, they represent a new tool for causally linking myca to cellular osmoregulation and other cell functions.

Phytochrome B photobodies are comprised of phytochrome B and its primary and secondary interacting proteins.

Phytochrome B (phyB) is a plant photoreceptor that forms a membraneless organelle called a photobody. However, its constituents are not fully known. Here, we isolated phyB photobodies from Arabidopsis leaves using fluorescence-activated particle sorting and analyzed their components. We found that a photobody comprises ~1,500 phyB dimers along with other proteins that could be classified into two groups: The first includes proteins that directly interact with phyB and localize to the photobody when expressed in protoplasts, while the second includes proteins that interact with the first group proteins and require co-expression of a first-group protein to localize to the photobody. As an example of the second group, TOPLESS interacts with PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 (PCH1) and localizes to the photobody when co-expressed with PCH1. Together, our results support that phyB photobodies include not only phyB and its primary interacting proteins but also its secondary interacting proteins.

Improving Active Collaborative Clinical Learning Through a Mobile Application for Undergraduate Nursing Students.

Innovative teaching and learning strategies in pediatric clinical education are needed to ensure that learning outcomes are achieved efficiently and to improve students' satisfaction with the learning process. We developed a mobile application to enhance the clinical learning of nursing students during pediatric clinical practice and explored the participants' perceptions of the learning method. A mixed-method design and an online survey were used to assess participants' perceived achievement of learning objectives and satisfaction with the clinical practicum. Focus groups explored the participants' experience of using the application. The overall achievement of learning outcomes was 4.1 out of 5, and participants reported high satisfaction with the clinical practicum using the mobile application. Qualitative analysis of the transcripts revealed four major themes: (1) facilitation of collaborative learning through real-time interactions and communication; (2) engagement in active learning through an application; (3) a useful tool for enhancing critical thinking; and (4) the "curate's egg" nature of the application. The mobile application can be incorporated into the clinical education of nursing students to promote self-regulated learning and collaboration with faculty. Clear guidance on how to use the application in a clinical environment should be provided to students and preceptors to achieve better learning outcomes.

Mixture and individual effects of benzene, toluene, and formaldehyde in zebrafish (Danio rerio) development: Metabolomics, epigenetics, and behavioral approaches.

In this study, we aimed to investigate the potential hazards of volatile organic compounds (VOCs) on the development of zebrafish. To this end, zebrafish embryos were exposed in two different windows, either alone or in a mixture with VOCs (benzene, toluene, and formaldehyde) [EW1: 4 ± 2 h post-fertilization (hpf) to 24 hpf and EW2: 24 ± 2 hpf to 48 hpf]. Alterations in global DNA methylation and related gene expression, behavioral responses, and stress-related gene expression were observed. In addition to these endpoints, non-targeted NMR-based global metabolomics followed by pathway analysis showed significant changes in the metabolism of various amino acids during VOC exposure. Regardless of the analyzed endpoints, toluene was the most toxic chemical when exposed individually and possibly played the most pivotal role in the mixture treatment conditions. In conclusion, our data show that exposure to VOCs at embryonic developmental stages causes physiological perturbations and adverse outcomes at later life stages.

Prediction and Experimental Validation of a New Salinity-Responsive Cis-Regulatory Element (CRE) in a Tilapia Cell Line.

Transcriptional regulation is a major mechanism by which organisms integrate gene x environment interactions. It can be achieved by coordinated interplay between cis-regulatory elements (CREs) and transcription factors (TFs). Euryhaline tilapia (Oreochromis mossambicus) tolerate a wide range of salinity and thus are an appropriate model to examine transcriptional regulatory mechanisms during salinity stress in fish. Quantitative proteomics in combination with the transcription inhibitor actinomycin D revealed 19 proteins that are transcriptionally upregulated by hyperosmolality in tilapia brain (OmB) cells. We searched the extended proximal promoter up to intron1 of each corresponding gene for common motifs using motif discovery tools. The top-ranked motif identified (STREME1) represents a binding site for the Forkhead box TF L1 (FoxL1). STREME1 function during hyperosmolality was experimentally validated by choosing two of the 19 genes, chloride intracellular channel 2 (clic2) and uridine phosphorylase 1 (upp1), that are enriched in STREME1 in their extended promoters. Transcriptional induction of these genes during hyperosmolality requires STREME1, as evidenced by motif mutagenesis. We conclude that STREME1 represents a new functional CRE that contributes to gene x environment interactions during salinity stress in tilapia. Moreover, our results indicate that FoxL1 family TFs are contribute to hyperosmotic induction of genes in euryhaline fish.

COVID-19 outbreak response at a nursing hospital in South Korea in the post-vaccination era, including an estimation of the effectiveness of the first shot of the Oxford-AstraZeneca COVID-19 vaccine (ChAdOx1-S).

OBJECTIVES: We descriptively reviewed a coronavirus disease 2019 (COVID-19) outbreak at a nursing hospital in Gyeonggi Province (South Korea) and assessed the effectiveness of the first dose of the Oxford-AstraZeneca vaccine in a real-world population. METHODS: The general process of the epidemiological investigation included a public health intervention. The relative risk (RR) of vaccinated and unvaccinated groups was calculated and compared to confirm the risk of severe acute respiratory syndrome coronavirus-2 (SARSCoV-2) infection, and vaccine effectiveness was evaluated based on the calculated RR. RESULTS: The population at risk was confined to ward E among 8 wards of Hospital X, where the outbreak occurred. This population comprised 55 people, including 39 patients, 12 nurses, and 4 caregivers, and 19 cases were identified. The RR between the vaccinated and unvaccinated groups was 0.04, resulting in a vaccine effectiveness of 95.3%. The vaccination rate of the nonpatients in ward E was the lowest in the entire hospital, whereas the overall vaccination rate of the combined patient and non-patient groups in ward E was the third lowest. CONCLUSION: The first dose of the Oxford-AstraZeneca vaccine (ChAdOx1-S) was effective in preventing SARS-CoV-2 infection. To prevent COVID-19 outbreaks in medical facilities, it is important to prioritize the vaccination of healthcare providers.

Effectiveness of Lifestyle Modification in Polycystic Ovary Syndrome Patients with Obesity: A Systematic Review and Meta-Analysis.

(1) Background: Polycystic ovary syndrome (PCOS) is the most common cause of anovulatory infertility and endocrine disorders among women of reproductive age. Previous studies have employed lifestyle interventions to manage anovulatory infertility and endocrine disorders. However, the effect of lifestyle interventions on the metabolic index remains ambiguous; (2) Methods: Data were obtained through a systematic search of the Ovid-Medline, Ovid-EMBASE, and Cochrane Library databases. Two reviewers independently reviewed the literature in two stages. A consensus was achieved through discussions regarding the final selection of the literature; (3) Results: This study observed that the group that underwent lifestyle modifications displayed significant improvement in reproductive function compared to the control group. Combination therapy with diet and exercise resulted in improved fasting insulin levels, compared to monotherapy with diet or exercise. Moreover, moderate weight loss (a minimum of 5%) resulted in an improved metabolic index. The subgroup analysis revealed that the group that underwent lifestyle modifications had a significantly higher number of patients with improved menstrual cycles, compared to the control groups; (4) Conclusions: Lifestyle modification using combination therapy is a promising therapeutic approach that can be employed in the management of PCOS patients with obesity. This scenario warrants further studies with larger sample sizes to develop ideal treatment protocols.

Experience of a COVID-19 outbreak response in a general hospital in Gyeonggi Province, Korea.

OBJECTIVES: Coronavirus disease 2019 (COVID-19) outbreaks in general hospitals are particularly risky because they not only overburden the regional healthcare delivery system, but also increase the possibility of community transmission. This study shares an experience of a COVID-19 outbreak response in a general hospital in Gyeonggi Province, Korea. METHODS: Since the first COVID-19 confirmed case was recognized in Hospital A on March 29, 2020, the Immediate Response Team of Gyeonggi Province and Korea Disease Control and Prevention Agency devised a plan to conduct an epidemiological investigation and minimize the paralysis of hospital functions. Apart from the epidemiological investigation, a risk assessment of the hospital and management of contacts, including patients and workers, were also undertaken. RESULTS: In total, 72 confirmed cases were identified, including 26 hospitalized patients, 16 healthcare personnel, 7 visitors, and 22 cases identified externally. The majority of the confirmed cases were exposed in Ward B or were contacts of people exposed in Ward A (58.3% of 72 cases). Among healthcare personnel, caregivers were found to be the most vulnerable to COVID-19 in this outbreak. CONCLUSIONS: Preparation for all possible situations in medical facilities is important because it is difficult to find alternative resources. The findings of this study provide information on controlling the further transmission of COVID-19 and furnish evidence of the importance of ordinary management skills to be prepared for COVID-19.

Importation and Transmission of SARS-CoV-2 B.1.1.529 (Omicron) Variant of Concern in Korea, November 2021.

In November 2021, 14 international travel-related severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (omicron) variant of concern (VOC) patients were detected in South Korea. Epidemiologic investigation revealed community transmission of the omicron VOC. A total of 80 SARS-CoV-2 omicron VOC-positive patients were identified until December 10, 2021 and 66 of them reported no relation to the international travel. There may be more transmissions with this VOC in Korea than reported.

Hepatitis A Outbreak in a Facility for the Disabled, Gyeonggi Province, Korea: An Epidemiological Investigation.

OBJECTIVES: The number of cases of hepatitis A virus (HAV) infections has sharply increased in Korea, especially among young adults. In this study, an HAV outbreak in a facility for disabled people was investigated, and we found epidemiological differences both between 2 different generations and between generally abled and disabled groups. METHODS: We analyzed the incubation period and attack rate of an HAV outbreak and investigated the prevalence of HAV antibodies among the staff and residents of a facility for the disabled. We performed a retrospective cohort study during the HAV outbreak, which lasted from February 8 to 25, 2019, including examinations of HAV antibody tests and post-exposure HAV vaccination for the staff or residents of the facility. RESULTS: There were 9 confirmed cases in 2 staff members and 7 residents. Among 53 people (30 staff and 23 residents), except for the 9 confirmed cases and 1 staff member with a known history of HAV infection, HAV seroprevalence was seen in 16.7% of the staff under 40 years of age and 95.2% of those over 40 years of age, while the corresponding rates in the residents were 0.0% and 58.8%, respectively. CONCLUSIONS: This result implies that it is necessary to prioritize HAV vaccination for vulnerable groups and workers of residential care facilities.