Analysis of the ABC transporter CG31731 in engulfment during programmed cell death in the Drosophila melanogaster ovary

Programmed cell death (PCD) is an essential biological process in animal development and tissue homeostasis that is necessary to ensure the physiological well-being of the organism. During PCD, phagocytes facilitate the selective removal of excess, damaged, and potentially deleterious cells, in a multi-step engulfment process. Genetic studies in Drosophila melanogaster, Caenorhabditis elegans, and mammals have identified two evolutionarily conserved signal transduction pathways that act redundantly to regulate engulfment: the CED-1/-6/-7 and CED-2/-5/-12 pathways. Of these cell death (CED) proteins, the ABC transporter CED-7 is the only protein reported to be required in both the engulfing cell and the dying cell. However, its function in the cell death process remains the most enigmatic and the ced-7 ortholog previously has not been identified in Drosophila. Homology searches revealed a family of putative ced-7 orthologs that encode transporters of the ABCA family in Drosophila. To determine which of these genes functions similarly to ced-7/ABCA1 in PCD, we analyzed their engulfment function in oogenesis, during which 15 germ cells in each egg chamber undergo programmed cell death and are removed by neighboring phagocytic follicle cells. It has been shown that genetically knocking down individual engulfment genes results in inefficient clearance of the germ cells, which then persist in late-stage egg chambers. Only two of the putative ced-7/ABCA1 genes are expressed significantly in the ovary, CG31731 and CG1718, and we have characterized these genes using transposon insertions, deficiencies, and RNAi knockdowns. Our genetic analysis reveals that CG31731 is necessary for germ cell clearance in the Drosophila ovary. Immunostaining shows that genetically knocking down CG31731 results in uncleared germ cells which persist in late-stage egg chambers. Altogether, our findings suggest that CED-7/ABCA1/CG31731 play evolutionarily conserved roles during engulfment

Guided discussion or immersive play? Influence of on-site presentation platform on visitor satisfaction in a heritage attraction

Extensive research has been conducted on visitor experience and visitor satisfaction at tourist attractions. Few studies have addressed the influence of different types of on-site factors on visitor satisfaction at heritage sites. This study combined observation, in-depth interview, and a survey to examine the underlying factors of visitors’ perceptions of on-site attributes and their effects on overall visitor satisfaction while considering the influence of visitors’ interest and visitor type at Iron Age Farm in Stavanger, Norway. The findings suggest four sub-categories of visitors’ perceptions of the presentation platform (technology, immersive play, guided discussion, and autonomy), in addition to one support service platform category. Guided discussion, autonomy orientation, and support service platforms have a significant influence on visitor satisfaction. The findings suggest that visitors’ perceptions of the on-site factors do not differ significantly by visitors’ interest or type. The results only partly confirmed previous research and provided a different perspective on the role of on-site presentation attributes in heritage attractions. Knowledge of presentation platforms can function as a practical framework to analyze heritage sites based on visitors’ experiences and expectations.publishedVersio

Enhanced yeast one-hybrid screens to identify transcription factor binding to human DNA sequences

Identifying the sets of transcription factors (TFs) that regulate each human gene is a daunting task that requires integrating numerous experimental and computational approaches. One such method is the yeast one-hybrid (Y1H) assay, in which interactions between TFs and DNA regions are tested in the milieu of the yeast nucleus using reporter genes. Y1H assays involve two components: a 'DNA-bait' (e.g., promoters, enhancers, silencers, etc.) and a 'TF-prey,' which can be screened for reporter gene activation. Most published protocols for performing Y1H screens are based on transforming TF-prey libraries or arrays into DNA-bait yeast strains. Here, we describe a pipeline, called enhanced Y1H (eY1H) assays, where TF-DNA interactions are interrogated by mating DNA-bait strains with an arrayed collection of TF-prey strains using a high density array (HDA) robotic platform that allows screening in a 1,536 colony format. This allows for a dramatic increase in throughput (60 DNA-bait sequences against >1,000 TFs takes two weeks per researcher) and reproducibility. We illustrate the different types of expected results by testing human promoter sequences against an array of 1,086 human TFs, as well as examples of issues that can arise during screens and how to troubleshoot them.Accepted manuscrip

THREATS AND CONSERVATION EFFORTS OF THE LAST REMAINING BANTENG (Bos javanicus lowi) IN UNPROTECTED AREAS AT BELANTIKAN HULU, CENTRAL KALIMANTAN

Bornean banteng is classified as endangered and found only in Borneo island. The existence of a wild population of Bornean Banteng in Belantikan Hulu, in the north-western part of Indonesia’s Central Kalimantan Province, has been confirmed from the results of camera-trap programme since 2013, but its population size has yet to be determined. The study aimed to identify the threats to the banteng population in Belantikan Hulu and describe the conservation efforts that have already been taken there. Although Belantikan Hulu is now one of the priority habitats for conserving banteng in Kalimantan, the area lies outside the nationally-designated conservation area network. Hunting is one of the greatest threats that can lead directly to failure in their population. Local informants were able to describe the location and number of 24 banteng that were killed over a 65-year period, from the 1950’s to 2015. The true number is likely to be much higher, since these data were derived from a sample representing only 30% of the local hunting community, and they did not include information from any outsiders. Logging, mining and shifting cultivation in around banteng habitats are important factors that are currently contributing to the destruction and degradation of their habitats in Belantikan Hulu. Conservation efforts have got a lot of supports from local stakeholders. These efforts have led to a customary regulation being adopted that prohibits hunting of banteng or degradation of their habitats around their key saltlicks and feeding sites, and the creation of local conservation area of 1,700 ha (on land voluntarily released by the logging company) that includes these key sites.   Keywords: bornean banteng, conservation, habitat, hunting, threa

Uncovering human transcription factor interactions associated with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays

Identifying transcription factor (TF) binding to noncoding variants, uncharacterized DNA motifs, and repetitive genomic elements has been difficult due to technical and computational challenges. Indeed, current experimental methods such as chromatin immunoprecipitation are capable of only testing one TF at a time and motif prediction algorithms often lead to false positive and false negative predictions. Here, we address these limitations by developing two approaches based on enhanced yeast one-hybrid assays. The first approach allows to interrogate the binding of >1,000 human TFs to single nucleotide variant alleles, short insertions and deletions (indels), and novel DNA motifs; while the second approach allows for the identification of TFs that bind to repetitive DNA elements. Using the former approach, we identified gain of TF interactions to a GG→AA mutation in the TERT promoter and an 18 bp indel in the TAL1 super-enhancer, both of which are associated with cancer, and identified the TFs that bind to three uncharacterized DNA motifs identified by the ENCODE Project in footprinting assays. Using the latter approach, we detected the binding of 75 TFs to the highly repetitive Alu elements. We anticipate that these approaches will expand our capabilities to study genetic variation and under-characterized genomic regions.https://doi.org/10.1101/459305First author draf

Virtual Tour Museum Application Using Flutter Framework

According to the Kamus Besar Bahasa Indonesia (KBBI), a museums function is to protect, develop, utilize collections, and communicate them to the public. The public often knows the word museum itself as a historical place or a place that has high cultural value. Usually, museums are also used as study tour places for students in Indonesia. In 2020, Indonesia has 439 museums spread across the country. However, not all of these museums can be visited by the public due to distance and time limitations. Therefore, media such as a mobile application is needed so that people can visit the museum virtually without being limited by distance and time. In its creation, the Virtual Tour Museum application will implement a framework using the Dart programming language. This application will also be useful as a means of promotion and introduction of Indonesian culture and history to the public, especially the younger generation through the Virtual Museum media

Global landscape of mouse and human cytokine transcriptional regulation

Cytokines are cell-to-cell signaling proteins that play a central role in immune development, pathogen responses, and diseases. Cytokines are highly regulated at the transcriptional level by combinations of transcription factors (TFs) that recruit cofactors and the transcriptional machinery. Here, we mined through three decades of studies to generate a comprehensive database, CytReg, reporting 843 and 647 interactions between TFs and cytokine genes, in human and mouse respectively. By integrating CytReg with other functional datasets, we determined general principles governing the transcriptional regulation of cytokine genes. In particular, we show a correlation between TF connectivity and immune phenotype and disease, we discuss the balance between tissue-specific and pathogen-activated TFs regulating each cytokine gene, and cooperativity and plasticity in cytokine regulation. We also illustrate the use of our database as a blueprint to predict TF–disease associations and identify potential TF–cytokine regulatory axes in autoimmune diseases. Finally, we discuss research biases in cytokine regulation studies, and use CytReg to predict novel interactions based on co-expression and motif analyses which we further validated experimentally. Overall, this resource provides a framework for the rational design of future cytokine gene regulation studies.National Institutes of Health (NIH) [R00 GM114296 and R35 GM128625 to J.I.F.B., 5T32HL007501-34 to J.A.S.]; National Science Foundation [NSF-REU BIO-1659605 to M.M.]. Funding for open access charge: NIH [R35 GM128625]. (R00 GM114296 - National Institutes of Health (NIH); R35 GM128625 - National Institutes of Health (NIH); 5T32HL007501-34 - National Institutes of Health (NIH); NSF-REU BIO-1659605 - National Science Foundation; R35 GM128625 - NIH)Published versio

Busan's Paradiplomacy: Aspiring to be the World's Premier Film City

This study explored the image transformation of Busan, South Korea, from an industrial hub to a globally recognized City of Film. By employing a paradiplomacy framework, the research examined how Busan utilized BIFF as both a cultural event and a strategic tool for international diplomacy, economic development, and city branding. This qualitative research focused on gathering data largely through a comprehensive evaluation of scientific literature, including books and papers relevant to the case study. The analyses delved into the evolution of the BIFF event and its significant role in rebranding Busan from a declining industrial city to the first "City of Film" in Asia, a title bestowed by UNESCO. The study highlighted how the festival had successfully stimulated local economic growth, bolstered creative industries, and facilitated cultural exchange. The result demonstrated that BIFF had been pivotal in repositioning Busan as a significant player in the international film industry and a vibrant cultural destination. In conclusion, Busan's status as Asia's "City of Film" should be sustained, and the ongoing significance of integrating cultural initiatives with wider urban development strategies should also be emphasized

Psikoedukasi Bahaya Perilaku Phubbing Dan Meningkatkan Self-Confidence Pada Remaja

Psikoedukasi dilakukan sebagai usaha untuk mendorong terjadinya perubahan perilaku pada individu, masyarakat, kelompok atau organisasi agar memiliki pengetahuan dan mampu menyelesaikan masalah yang sedang dihadapi. Psikoedukasi ini bertujuan untuk meminimalisir terjadinya perilaku phubbing dan memberikan edukasi kepada remaja tentang self-confidence. Metode psikoedukasi dilakukan dengan penyuluhan materi terkait perilaku phubbing dan materi self-confidence kepada remaja PIKR Tunas Bangsa RW 014 Perumahan Graha Melasti. Hal yang didapatkan yakni para remaja mampu memahami dampak dari perilaku phubbing sehingga meminimalisir terjadinya perilaku phubbing dan mengetahui self-confidece untuk mengoptimalkan kepercayaan diri dalam berkomunikasi

Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors

Cooperativity and antagonism between transcription factors (TFs) can drastically modify their binding to regulatory DNA elements. While mapping these relationships between TFs is important for understanding their context-specific functions, existing approaches either rely on DNA binding motif predictions, interrogate one TF at a time, or study individual TFs in parallel. Here, we introduce paired yeast one-hybrid (pY1H) assays to detect cooperativity and antagonism across hundreds of TF-pairs at DNA regions of interest. We provide evidence that a wide variety of TFs are subject to modulation by other TFs in a DNA region-specific manner. We also demonstrate that TF-TF relationships are often affected by alternative isoform usage and identify cooperativity and antagonism between human TFs and viral proteins from human papillomaviruses, Epstein-Barr virus, and other viruses. Altogether, pY1H assays provide a broadly applicable framework to study how different functional relationships affect protein occupancy at regulatory DNA regions.U01 CA232161 - NCI NIH HHSPublished versio