Deletion of MGF505-2R Gene Activates the cGAS-STING Pathway Leading to Attenuation and Protection against Virulent African Swine Fever Virus.

African swine fever virus (ASFV) is the etiological agent causing African swine fever (ASF), affecting domestic pigs and wild boar, which is currently the biggest animal epidemic in the world and a major threat to the swine sector. At present, some safety concerns about using LAVs against ASFV still exist despite a commercial vaccine licensed in Vietnam. Therefore, the efforts to identify virulence factors and their mechanisms, as well as to generate new vaccine prototypes, are of major interest. In this work, we have identified the MGF505-2R gene product as an inhibitor of the cGAS/STING pathway, specifically through its interaction with STING protein, controlling IFN-ß production. In addition, immunization of a recombinant virus lacking this gene, Arm/07-ΔMGF505-2R, resulted in complete attenuation, demonstrating its involvement in ASFV virulence. Finally, immunization with Arm/07-ΔMGF505-2R induced the generation of antibodies and proved to be partially protective against virulent ASFV strains. These results identify MGF505-2R, as well as its mechanism of action, as a gene contributing to understanding the molecular mechanisms of ASFV virulence, which will be of great value in the design of future vaccine prototypes.

The genomic signatures of evolutionary stasis.

Evolutionary stasis characterizes lineages that seldom speciate and show little phenotypic change over long stretches of geological time. Although lineages that appear to exhibit evolutionary stasis are often called living fossils, no single mechanism is thought to be responsible for their slow rates of morphological evolution and low species diversity. Some analyses of molecular evolutionary rates in a handful of living fossil lineages have indicated that these clades exhibit slow rates of genomic change. Here, we investigate mechanisms of evolutionary stasis using a dataset of 1,105 exons for 481 vertebrate species. We demonstrate that two ancient clades of ray-finned fishes classically called living fossils, gars and sturgeons, exhibit the lowest rates of molecular substitution in protein-coding genes among all jawed vertebrates. Comparably low rates of evolution are observed at fourfold degenerate sites in gars and sturgeons, implying a mechanism of stasis decoupled from selection that we speculate is linked to a highly effective DNA repair apparatus. We show that two gar species last sharing common ancestry over 100 million years ago produce morphologically intermediate and fertile hybrids in the wild. This makes gars the oldest naturally hybridizing divergence among eukaryotes and supports a theoretical prediction that slow rates of nucleotide substitution across the genome slow the accumulation of genetic incompatibilities, enabling hybridization across deeply divergent lineages and slowing the rate of speciation over geological timescales. Our results help establish molecular stasis as a barrier to speciation and phenotypic innovation and provide a mechanism to explain the low species diversity in living fossil lineages.

Genome characterization of a Korean isolate of porcine epidemic diarrhea virus.

Porcine epidemic diarrhea (PED) outbreaks occur annually in the Republic of Korea. The complete genome sequence of the PED virus isolate CKK1-1 obtained from an infected pig was determined. The genome is 28,037 nt long, excluding the poly(A) tail, and contains seven open reading frames flanked by two untranslated regions.

Erosional exhumation of carbonate rock facilitates dispersal-mediated allopatric speciation in freshwater fishes.

A fundamental goal of evolutionary biology is to understand the mechanisms that generate and maintain biodiversity. Discovery and delimitation of species represent essential prerequisites for such investigations. We investigate a freshwater fish species complex comprising Etheostoma bellator and the endangered E. chermocki, which is endemic to the Black Warrior River system in Alabama, USA, a global hotspot of temperate freshwater biodiversity. Phylogenomic analyses delimit five geographically disjunct species masquerading as E. bellator. Three of these new species exhibit microendemic distributions comparable to that of E. chermocki raising the possibility that they also require protection. The species of the complex are found in streams flowing over carbonate rock and they are separated by waterways flowing over siliciclastic rock, a geographic pattern dictated by the underlying stratigraphy and structural geology. Over time, rivers have eroded downward through layers of siliciclastic rocks in the basin, gradually exposing underlying carbonate rock, the substrate of suitable habitat today. Our results suggest that episodic dispersal to patches of suitable habitat set the stage for allopatric speciation in the species complex. Our study suggests that the presence of heterogeneous rock can facilitate dispersal-mediated allopatric speciation in freshwater organisms in the absence of external tectonic or climatic perturbations.

Alteration of the Gut Microbiota in Pigs Infected with African Swine Fever Virus.

The factors that influence the pathogenicity of African swine fever (ASF) are still poorly understood, and the host's immune response has been indicated as crucial. Although an increasing number of studies have shown that gut microbiota can control the progression of diseases caused by viral infections, it has not been characterized how the ASF virus (ASFV) changes a pig's gut microbiome. This study analyzed the dynamic changes in the intestinal microbiome of pigs experimentally infected with the high-virulence ASFV genotype II strain (N = 4) or mock strain (N = 3). Daily fecal samples were collected from the pigs and distributed into the four phases (before infection, primary phase, clinical phase, and terminal phase) of ASF based on the individual clinical features of the pigs. The total DNA was extracted and the V4 region of the 16 s rRNA gene was amplified and sequenced on the Illumina platform. Richness indices (ACE and Chao1) were significantly decreased in the terminal phase of ASF infection. The relative abundances of short-chain-fatty-acids-producing bacteria, such as Ruminococcaceae, Roseburia, and Blautia, were decreased during ASFV infection. On the other hand, the abundance of Proteobacteria and Spirochaetes increased. Furthermore, predicted functional analysis using PICRUSt resulted in a significantly reduced abundance of 15 immune-related pathways in the ASFV-infected pigs. This study provides evidence for further understanding the ASFV-pig interaction and suggests that changes in gut microbiome composition during ASFV infection may be associated with the status of immunosuppression.

Erosion of heterogeneous rock drives diversification of Appalachian fishes.

The high levels of biodiversity supported by mountains suggest a possible link between geologic processes and biological evolution. Freshwater biodiversity is high not only in tectonically active settings but also in tectonically quiescent montane regions such as the Appalachian Mountains. We show that erosion through different rock types drove allopatric divergence between lineages of the Greenfin Darter (Nothonotus chlorobranchius), a fish species endemic to rivers draining metamorphic rocks in the Tennessee River basin in the United States. In the past, metamorphic rock preferred by N. chlorobranchius was more widespread, but as erosion exposed other rock types, lineages of this species were progressively isolated in tributaries farther upstream, where metamorphic rock remained. Our results suggest a geologic mechanism for initiating allopatric diversification in mountains long after tectonic activity ceases.

Development of Effective PEDV Vaccine Candidates Based on Viral Culture and Protease Activity.

Porcine epidemic diarrhea (PED) is a highly contagious disease that has been reported annually in several Asian countries, causing significant economic losses to the swine livestock industry. Although vaccines against the porcine epidemic diarrhea virus (PEDV) are available, their efficacy remains questionable due to limitations such as viral genome mutation and insufficient intestinal mucosal immunity. Therefore, the development of a safe and effective vaccine is necessary. In this study, a virulent Korean strain of PEDV, CKT-7, was isolated from a piglet with severe diarrhea, and six different conditions were employed for serial passage of the strain in a cell culture system to generate effective live attenuated vaccine (LAV) candidates. The characteristics of these strains were analyzed in vitro and in vivo, and the CKT-7 N strain was identified as the most effective vaccine candidate, with a viral titer peak of 8.67 ± 0.29 log10TCID50/mL, and no mortality or diarrhea symptoms were observed in five-day-old piglets. These results indicate that LAV candidates can be generated through serial passage with different culture conditions and provide valuable insights into the development of a highly effective LAV against PEDV.

Delta (B1.617.2) variant of SARS-CoV-2 induces severe neurotropic patterns in K18-hACE2 mice.

A highly contagious virus, severe acute respiratory syndrome coronavirus 2, caused the coronavirus disease 19 (COVID-19) pandemic (SARS-CoV-2). SARS-CoV-2 genetic variants have been reported to circulate throughout the COVID-19 pandemic. COVID-19 symptoms include respiratory symptoms, fever, muscle pain, and breathing difficulty. In addition, up to 30% of COVID-19 patients experience neurological complications such as headaches, nausea, stroke, and anosmia. However, the neurotropism of SARS-CoV-2 infection remains largely unknown. This study investigated the neurotropic patterns between the B1.617.2 (Delta) and Hu-1 variants (Wuhan, early strain) in K18-hACE2 mice. Despite both the variants inducing similar pathogenic patterns in various organs, B1.617.2-infected K18-hACE2 mice demonstrated a higher range of disease phenotypes such as weight loss, lethality, and conjunctivitis when compared to those in Hu-1-infected mice. In addition, histopathological analysis revealed that B1.617.2 infects the brain of K18-hACE2 mice more rapidly and effectively than Hu-1. Finally, we discovered that, in B1.617.2-infected mice, the early activation of various signature genes involved innate cytokines and that the necrosis-related response was most pronounced than that in Hu-1-infected mice. The present findings indicate the neuroinvasive properties of SARS-CoV-2 variants in K18-hACE2 mice and link them to fatal neuro-dissemination during the disease onset.

Recombinant African Swine Fever Virus Arm/07/CBM/c2 Lacking CD2v and A238L Is Attenuated and Protects Pigs against Virulent Korean Paju Strain.

African swine fever (ASF) is an obligated declaration swine disease, provoking farm isolation measures and the closing of affected country boarders. ASF virus (ASFV) is currently the cause of a pandemic across China and Eurasia. By the end of 2019, ASF was detected in nine EU Member States: Bulgaria, Romania, Slovakia, Estonia, Hungary, Latvia, Lithuania, Poland and Belgium. The affected area of the EU extended progressively, moving mostly in a southwestern direction (EFSA). Inactivated and/or subunit vaccines have proven to fail since certain virus replication is needed for protection. LAVs are thus the most realistic option, which must be safe, effective and industrially scalable. We here generated a vaccine prototype from the Arm/07/CBM/c2 genotype II strain, in which we have deleted the EP402R (CD2v) and A238L genes by CRISPR/Cas9 in COS-1 cells, without detectable further genetic changes. The successful immunization of pigs has proven this vaccine to be safe and fully protective against the circulating Korean Paju genotype II strain, opening the possibility of a new vaccine on the market in the near future.

Hidden species diversity in an iconic living fossil vertebrate.

Ancient, species-poor lineages persistently occur across the Tree of life. These lineages are likely to contain unrecognized species diversity masked by the low rates of morphological evolution that characterize living fossils. Halecomorphi is a lineage of ray-finned fishes that diverged from its closest relatives before 200 Ma and is represented by only one living species in eastern North America, the bowfin, Amia calva Linnaeus. Here, we use double digest restriction-site-associated DNA sequencing and morphology to illuminate recent speciation in bowfins. Our results support the delimitation of a second living species of Amia, with the timing of diversification dating to the Plio-Pleistocene. This delimitation expands the species diversity of an ancient lineage that is integral to studies of vertebrate genomics and development, yet is facing growing conservation threats driven by the caviar fishery.

Phylogenomics and species delimitation of the economically important Black Basses (Micropterus).

Informed management and conservation efforts are vital to sustainable recreational fishing and biodiversity conservation. Because the taxonomic rank of species is important in conservation and management strategies, success of these efforts depends on accurate species delimitation. The Black Basses (Micropterus) are an iconic lineage of freshwater fishes that include some of the world's most popular species for recreational fishing and world's most invasive species. Despite their popularity, previous studies to delimit species and lineages in Micropterus suffer from insufficient geographic coverage and uninformative molecular markers. Our phylogenomic analyses of ddRAD data result in the delimitation of 19 species of Micropterus, which includes 14 described species, the undescribed but well-known Altamaha, Bartram's, and Choctaw basses, and two additional undescribed species currently classified as Smallmouth Bass (M. dolomieu). We provide a revised delimitation of species in the Largemouth Bass complex that necessitates a change in scientific nomenclature: Micropterus salmoides is retained for the Florida Bass and Micropterus nigricans is elevated from synonymy for the Largemouth Bass. The new understanding of diversity, distribution, and systematics of Black Basses will serve as important basis for the management and conservation of this charismatic and economically important clade of fishes.

Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae).

Introgression and hybridization are major impediments to genomic-based species delimitation because many implementations of the multispecies coalescent framework assume no gene flow among species. The sunfish genus Lepomis, one of the world's most popular groups of freshwater sport fish, has a complicated taxonomic history. The results of ddRAD phylogenomic analyses do not provide support for the current taxonomy that recognizes two species, Lepomis megalotis and Lepomis peltastes, in the L. megalotis complex. Instead, evidence from phylogenomics and phenotype warrants recognizing six relatively ancient evolutionary lineages in the complex. The introgressed and hybridizing populations in the L. megalotis complex are localized and appear to be the result of secondary contact or rare hybridization events between nonsister species. Segregating admixed populations from our multispecies coalescent analyses identifies six species with moderate to high genealogical divergence, whereas including admixed populations drives all but one lineage below the species threshold of genealogical divergence. Segregation of admixed individuals also helps reveal phenotypic distinctiveness among the six species in morphological traits used by ichthyologists to discover and delimit species over the last two centuries. Our protocols allow for the identification and accommodation of hybridization and introgression in species delimitation. Genomic-based species delimitation validated with multiple lines of evidence provides a path towards the discovery of new biodiversity and resolving long-standing taxonomic problems.[ddRAD; genealogical divergence index; hybridization; integrative species delimitation; phylogeny; secondary contact; systematics; taxonomy.].

Phylogeny and time scale of diversification in the fossil-rich sunfishes and black basses (Teleostei: Percomorpha: Centrarchidae).

Species of the North American freshwater fish lineage Centrarchidae are apex predators in their habitats and are among the world's most popular sport fishes. Centrarchids boast a rich fossil record that extends from the latest Eocene to the Pleistocene. To investigate the phylogeny and timing of diversification of Centrarchidae, we deploy a dataset of DNA sequences of 16 nuclear genes sampled from nearly all of the recognized and undescribed species. We also utilize previously published morphological datasets to assess the phylogenetic placement of one of the oldest known centrarchid fossils, †Plioplarchus whitei. A Bayesian multispecies coalescent species tree analysis provides insight on relationships that evaded resolution in earlier studies, such as the relationships of Acantharchus pomotis, the resolution of a clade consisting of species previously synonymized under the Spotted Bass, Micropterus punctulatus, and a clade of recently described species previously considered populations of the Redeye Bass, Micropterus coosae. This new molecular phylogeny and the inclusion of †P. whitei and other centrarchid fossils in the tip-dated fossilized birth-death analysis results in a new hypothesis of the timing of diversification in Centrarchidae that contextualizes the ages of centrarchid fossils to the timing of speciation among the extant species. In addition to providing new temporal perspectives on the diversification of freshwater fishes in North America, this study may close of the chapter of centrarchid phylogeny inferred using Sanger-sequenced genes, as the use of genomic-scale datasets becomes mainstream in the phylogenetics of fishes.

Application of AULA Risk Assessment Tool by Comparison with Other Ergonomic Risk Assessment Tools.

Agricultural upper limb assessment (AULA), which was developed for evaluating upper limb body postures, was compared with the existing assessment tools such as rapid upper limb assessment (RULA), rapid entire body assessment (REBA), and ovako working posture analysis system (OWAS) based on the results of experts' assessments of 196 farm tasks in this study. The expert group consisted of ergonomists, industrial medicine experts, and agricultural experts. As a result of the hit rate analysis, the hit rate (average: 48.6%) of AULA was significantly higher than those of the other assessment tools (RULA: 33.3%, REBA: 30.1%, and OWAS: 34.4%). The quadratic weighted kappa analysis also showed that the kappa value (0.718) of AULA was significantly higher than those of the other assessment tools (0.599, 0.578, and 0.538 for RULA, REBA, and OWAS, respectively). Based on the results, AULA showed a better agreement with expert evaluation results than other evaluation tools. In general, other assessment tools tended to underestimate the risk of upper limb posture in this study. AULA would be an appropriate evaluation tool to assess the risk of various upper limb postures.

The effect of tablet use on trunk posture while sitting.

BACKGROUND: The use of tablet during the office work is on the rise, but the biomechanical response of tablet use under various sitting postures is not well understood. OBJECTIVE: This study quantitatively measured changes in trunk kinematics under three sitting conditions (raised leg, neutral leg, and lowered leg) while using a tablet. METHODS: Fifteen participants were asked to sit on a chair with three different postures while staring at a handheld tablet or gazing straight ahead with a bare hand, and the head flexion, lumbar flexion and trunk inclination were captured with electrical goniometers. RESULTS: The results revealed significantly less lumbar flexion (12.8%) and trunk inclination (28.0%) while using the tablet compared to the empty hand condition (p < 0.001), but at a significant cost of increased head flexion (90.8%; p < 0.001). Further, while using the tablet, participants showed less head flexion in the raised leg condition (p < 0.001) than in the others (9.7% and 7.5%, respectively), but larger trunk inclination and lumbar flexion were required (p < 0.001 in both). CONCLUSIONS: Collectively, the lower extremity sitting posture significantly changed the way to observe the tablet by adopting more head flexion in neutral and lowered leg conditions or more trunk flexion in raised leg condition.

A comparison of biomechanical workload between smartphone and smartwatch while sitting and standing.

Increasing concerns about musculoskeletal disorders in the upper back arising from excessive daily use of the smartwatch have been widely validated by the rising prevalence of discomfort. This study explored the smartwatch as a potential ergonomic intervention over the smartphone. Fourteen healthy participants completed five tasks (application setting, calling, message typing, message checking and vocal message entry) with smartphone and smartwatch in both sitting and standing postures. The neck-shoulder kinematics and muscle activation levels were monitored to assess the effects of the tasks, devices, and postures. The results indicated greater head flexion, head rotation and shoulder abduction and greater muscle activities for smartwatch use compared to smartphone use, but the performance measure (i.e., elapsed time) was superior for smartwatch use in all tasks except message typing. Collectively, only short and simple tasks such as message checking and application setting should be conducted with the smartwatch.

Evaluation of the controlled grip force exertion tasks associated with age, gender, handedness and target force level.

INTRODUCTION: Force control of the hand is an essential factor for operating tools and moving objects. Therefore, a method for quantifying hand functionality more accurately and objectively is very important. METHODS: The present study included 60 healthy participants (30 elderly and 30 young adults) to evaluate the effects of age, gender and target force levels on tracking performance. Tracking performance was quantified by measuring the difference between target force levels and exerted force. RESULTS: Females exerted 59.6% of the maximum grip strength of males and the elderly group exerted 70.5% of maximum grip strength compared with the young group. The elderly group showed 3.1 times larger tracking error than the young group. There was a significant difference in females between the young and elderly groups, indicating age-related decline in hand function is more pronounced in females. The difference in grip force control ability between the elderly and young groups was significant at the low target force level (5% maximum voluntary contraction). CONCLUSIONS: The results of this study could be used for hand function evaluation guidelines. In addition, this study could be used as a tool for physiotherapy to improve hand function and prevent its decline in elderly people.

Comparisons of ergonomic evaluation tools (ALLA, RULA, REBA and OWAS) for farm work.

INTRODUCTION: The purpose of this study was to validate the agricultural lower limb assessment (ALLA) ergonomic checklist, which was developed for various agricultural tasks in Korea. METHODS: One hundred and ninety-six working postures were selected from the real agricultural tasks to verify ALLA, a lower limb body posture assessment tool, and then evaluated by 16 ergonomic experts. Hit rate, quadratic weighted κ, one-way analysis of variance and t-test analyses were applied to compare ALLA with other assessment tools. RESULTS: ALLA analysis had a superior hit rate with ergonomic expert assessment compared with other assessment tools. Quadratic weighted κ analysis also showed that ALLA provided superior estimates of risk levels for farm working postures. DISCUSSION: ALLA would be an appropriate assessment tool to estimate risk factors for various lower limb body postures which frequently occur in agricultural tasks in Korea. ALLA is a simple and accurate risk assessment tool that could be usefully applied to identify and mitigate risk factors and work-related musculoskeletal disorders in agricultural tasks, and also to evaluate the effects of control and intervention for working conditions.