Background Short tandem repeats (STRs) are genetic markers with a greater mutation rate than single nucleotide polymorphisms (SNPs) and are widely used in genetic studies and forensics. However, most studies in pigs have focused only on SNPs or on a limited number of STRs. Results This study screened 394 deep-sequenced genomes from 22 domesticated pig breeds/populations worldwide, wild boars from both Europe and Asia, and numerous outgroup Suidaes, and identified a set of 878,967 polymorphic STRs (pSTRs), which represents the largest repository of pSTRs in pigs to date. We found multiple lines of evidence that pSTRs in coding regions were affected by purifying selection. The enrichment of trinucleotide pSTRs in coding sequences (CDS), 5′UTR and H3K4me3 regions suggests that trinucleotide STRs serve as important components in the exons and promoters of the corresponding genes. We demonstrated that, compared to SNPs, pSTRs provide comparable or even greater accuracy in determining the breed identity of individuals. We identified pSTRs that showed significant population differentiation between domestic pigs and wild boars in Asia and Europe. We also observed that some pSTRs were significantly associated with environmental variables, such as average annual temperature or altitude of the originating sites of Chinese indigenous breeds, among which we identified loss-of-function and/or expanded STRs overlapping with genes such as AHR , LAS1L and PDK1 . Finally, our results revealed that several pSTRs show stronger signals in domestic pig—wild boar differentiation or association with the analysed environmental variables than the flanking SNPs within a 100-kb window. Conclusions This study provides a genome-wide high-density map of pSTRs in diverse pig populations based on genome sequencing data, enabling a more comprehensive characterization of their roles in evolutionary and environmental adaptation.
T cells are crucial for the control of persistent EBV infection and the development of EBV-associated diseases. The EBV gB protein is essential for virus entry into B cells and epithelial cells and is thus a target antigen for vaccine development. ABSTRACT Glycoprotein B (gB) is an essential fusion protein for Epstein-Barr virus (EBV) infection of both B cells and epithelial cells and is thus a promising target antigen for a prophylactic vaccine to prevent or reduce EBV-associated disease. T cell responses play key roles in the control of persistent EBV infection and the efficacy of a vaccine. However, to date, T cell responses to gB have been characterized for only a limited number of human leukocyte antigen (HLA) alleles. Here, we screened gB T cell epitopes in 23 healthy EBV carriers and 10 patients with nasopharyngeal cancer (NPC) using a peptide library spanning the entire gB sequence. We identified 12 novel epitopes in the context of seven new HLA restrictions that are common in Asian populations. Two epitopes, gB214–223 and gB840–849, restricted by HLA-B*58:01 and -B*38:02, respectively, elicited specific CD8+ T cell responses to inhibit EBV-driven B cell transformation. Interestingly, gB-specific CD8+ T cells were more frequent in healthy viral carriers with EBV reactivation than in those without EBV reactivation, indicating that EBV reactivation in vivo stimulates both humoral (VCA-gp125-IgA) and cellular responses to gB. We further found that most gB epitopes are conserved among different EBV strains. Our study broadens the diversity and HLA restrictions of gB epitopes and suggests that gB is a common target of T cell responses in healthy viral carriers with EBV reactivation. In particular, the precisely mapped and conserved gB epitopes provide valuable information for prophylactic vaccine development. IMPORTANCE T cells are crucial for the control of persistent EBV infection and the development of EBV-associated diseases. The EBV gB protein is essential for virus entry into B cells and epithelial cells and is thus a target antigen for vaccine development. Understanding T cell responses to gB is important for subunit vaccine design. Here, we comprehensively characterized T cell responses to full-length gB. Our results expand the available gB epitopes and HLA restrictions, particularly those common in Asian populations. Furthermore, we showed that gB-specific CD8+ T cells inhibit B cell transformation ex vivo and that gB-specific CD8+ T cell responses in vivo may be associated with intermittent EBV reactivation in asymptomatic viral carriers. These gB epitopes are highly conserved among geographically separated EBV strains. Precisely mapped and conserved T cell epitopes may contribute to immune monitoring and the development of a gB subunit vaccine.
The Geostationary Ocean Color Imager (GOCI) has been used for many remote sensing applications to observe and monitor the ocean color of East Asia around the Korean Peninsula. However, to date, its geometric accuracy has not been thoroughly investigated; the only studies conducted so far have focused on verifying its radiometric quality. This study investigates the geometric accuracy of the Level 1B (L1B) product created from the GOCI geometric correction. The paper contains a brief description of the geometric correction process and an analysis of the positioning accuracy of GOCI L1B. Independent check points to assess accuracy were extracted from L1B and compared to their corresponding features in Google Maps, whose positioning accuracy has been thoroughly verified. Our analysis showed that, on average, the positioning accuracy of the GOCI L1B is ∼500-600 m, although there are differences in accuracy throughout the coverage area. It was confirmed that the GOCI L1B's overall accuracy fully meets geometrical image quality requirements (about 1 km). No specific bias pattern was identified, and there was little difference in accuracy throughout the acquisition time. The accuracy of the GOCI when landmark determination failed, e.g. due to a cloud, was further analyzed, and analysis showed that geometric quality was maintained even in the case of failure, although a slightly higher number of errors was observed. The experimental results support the hypothesis that the GOCI's geometric correction works well and provides sufficiently accurate positional information on ocean properties to be used for remote sensing applications.
Transforming Monkey by Hongmei Sun is an enlightening study of adaptation, tracing the rewritings, reconfigurations, and reincarnations of the Monkey King Sun Wukong from Wu Cheng’en’s Journey of the West. In fact, these adaptations can be summarized as three types of journey. First, Transforming Monkey maps a journey across time from traditional China into the twenty-first century. After all, Journey to the West in itself is a work of adaptation from various sources into what is today known as the canonical classic. The temporal journey of Transforming Monkey covers two chapters each on adaptations in premodern China, on those from the twentieth century and on those from the first decade of the twenty-first century. Second, Transforming Monkey maps a journey around the globe, varying the motif inscribed in the original title of the Journey to the West. While the “West” in the original referred to India as the origin of Buddhism, the twenty-first-century adaptations of the epic take the Monkey King from the PRC to Hong Kong and the United States. Third, Sun studies a journey across media, starting with a sutra and a drama that were among the sources of Wu’s novel, through fiction, drama adaptations, Peking opera, animated films, lianhuan hua, movies, Internet literature, and graphic novels. The twentiethand twenty-first-century works covered include the first animated feature film in China, Princess Iron Fan (1941); the Mao-era Havoc in Heaven adapted into opera, graphic forms, and animated film (1961–64); the comedy A Chinese Odyssee (1995, Hong Kong); the Internet fan fiction Story of Wukong; the television mini-series The Lost Empire (2001); the movie The Forbidden Kingdom (2008); and, lastly, with Gene Luan Yang’s graphic novel American Born Chinese (2006), which tackles the issue of Asian American identity. With its focus on the transformations of Sun Wukong in the adaptations, Transforming Monkey attains neat analytical conciseness, in terms of both content and theoretical considerations. After all, the Monkey King is essentially about transformation; he is conceptualized as a “transforming monkey” not only by Sun, but by Wu Cheng’en. He changes form and appearance, and he maneuvers between the human world and that of the gods. This renders him multivalent, allowing readers to identify with (parts of) him, which in turn explains the fascination the character has exerted over readers, as well as over other authors: with multivalence engraved into his character, he lends himself particularly well for adaptation. Unsurprisingly, then, transformations of the character continued after the “original” epic through adaptations of the text. Transforming Monkey thus feeds into an emerging stream of recent scholarship that engages with issues of rewriting, adaptation, translation, and the power of models, such as Pang Laikwan’s The Art of Cloning or Xing Fan’s Staging Revolution. While these discuss cultural production during and leading up to the Cultural Revolution, Sun traces one figure and the myth surrounding it through its various adaptations and rewritings over time. This approach brings to light two observations that may be applied more broadly to adaptation studies. First, each adaptation is a representation of the original myth; it
Cephalopods have the most advanced nervous systems and intelligent behavior among all invertebrates. Their brains provide comparative insights for understanding the molecular and functional origins of the human brain. Although brain maps that contain information on the organization of each subregion are necessary for a study on the brain, no whole brain atlas for adult cephalopods has been constructed to date. Here, we obtained sagittal and coronal sections covering the entire brain of adult Octopus minor (Sasaki), which belongs to the genus with the most species in the class Cephalopoda and is commercially available in East Asia throughout the year. Sections were stained using Hematoxylin and Eosin (H&E) to visualize the cellular nuclei and subregions. H&E images of the serial sections were obtained at 30~70-µm intervals for the sagittal plain and at 40~80-µm intervals for the coronal plain. Setting the midline point of the posterior end as the fiducial point, we also established the distance coordinates of each image. We found that the brain had the typical brain structure of the Octopodiformes. A number of subregions were discriminated by a Hematoxylin-positive layer, the thickness and neuronal distribution pattern of which varied markedly depending upon the region. We identified more than 70 sub-regions based on delineations of representative H&E images. This is the first brain atlas, not only for an Octopodiformes species but also among adult cephalopods, and we anticipate that this atlas will provide a valuable resource for comparative neuroscience research.
Abstract Due to the spatial variability of soil resources in rapidly changing landscapes, such as rubber expansion areas in mountainous South East Asia, landscape based soil organic carbon (SOC) stock assessments need new approaches to obtain cost effective high-resolution soil maps. 3D modelling presents the opportunity to model changes of soil properties with soil depth and in space in one single model. While most 3D models make use of spatial autocorrelation to create soil maps, it might be feasible for upscaling to neglect the spatial autocorrelation and only model autocorrelation within the soil profiles. We propose a “mixed model over continuous depth” (MMCD), which uses a linear and quadratic term to model changes of soil properties with depth and predicts the spatial distribution of soil properties at the landscape level. As the study area of 43 km2 in South West China was subject to multiple constraints such as sparse road networks, steep terrain, and poor infrastructure, we applied the cost-constrained conditioned Latin hypercube sampling (CCLHS) scheme for soil sampling at 120 locations to a depth of 1 m. The MMCD provides information on the most important drivers of selected soil properties, and their relative importance. In this study, SOC was strongly linked to an interaction of elevation with mean horizon depth (p
Abstract This study outlines a consistent methodology for identifying glacier surfaces from Landsat 5, 7 and 8 imagery that is applied to map all mainland North Asian glaciers, providing the first methodologically consistent and complete glacier inventory for the region ~2010. We identify 5065 glaciers covering a planimetric area of 2326 ± 186 km2, most of which is located in the Altai mountain subregion. The total glacier count is 15% higher, but the total glacier area is 32 ±11.6% lower, than the estimated glacier coverage provided in version 4.0 of the Randolph Glacier Inventory. We investigate the distribution of glacier size within North Asia and find that the majority of glaciers (82%) are smaller than 0.5 km2 but only account for a third of the total glacier area, with the largest 1 % (60 glaciers ≥ 5 km2 ) accounting for 28% of the total area. We present hypsometric characterizations of North Asian glaciers, largely substantiating existing findings that glaciers in this region are dominated by cold, relatively dry conditions. We provide a detailed assessment of errors and determine the uncertainty in our area estimate to be ±8.0%, with snow-cover uncertainty the largest contributing factor. Based on this assessment, the new glacier inventory presented here is more complete and of higher quality than other currently available data sources.