title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=785 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Macrophage immunomodulatory activity of Acanthopanax senticousus polysaccharide nanoemulsion via activation of P65/JNK/ikkαsignaling pathway and regulation of Th1/Th2 Cytokines link: https://peerj.com/articles/12575 last-modified: 2021-12-24 description: Nanoemulsions (NE) are used widely in pharmaceutical drug formulations and vaccine preparation, and Acanthopanax senticousus polysaccharide (ASPS) is a natural bioactive compound with immunostimulatory activity. Therefore, NE-loaded ASPS is expected to provide immunological enhancement for effective treatment. In the present study, Acanthopanax senticousus polysaccharide (ASPS was encapsulated into nanoemulsions, the resultant ASPS–NE were coated with a negative charge, and the immune enhancement mechanism of these ASPS-NE formulations was analyzed. The immunosuppressive animal models (70 ICR mice, male) for the study were established using cyclophosphamide. In addition, the activation of splenocyte proliferation, phagocytosis of the macrophages, the ratio of CD4+ to CD8+, the concentrations of the cytokines in serum, Western blot analysis was used for the analysis of the P65/JNK/ikk α signaling pathway in the peritoneal macrophage s. The results revealed that the ASPS-NE could stimulated the proliferation of splenocytes and enhance immunity. The ASPS-NE induced the expression of different cytokines (TNF-α, IFN-γ, IL-2, and IL-6), could activate the expressions of P65, JNK, and ikkα, and regulated the Th1/Th2 cytokines. These findings demonstrated the potential of ASPS-NE formulations for drug delivery and to induce potent and sustained immune responses. creator: Xianghui Li creator: Zhiqiang Zhang creator: Zhenhuan Guo creator: Li Zhao creator: Yonglu Liu creator: Xia Ma creator: Qigai He uri: https://doi.org/10.7717/peerj.12575 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Three new species of Byrsopteryx Flint microcaddisflies from Peru (Insecta: Trichoptera) including DNA-based larval associations link: https://peerj.com/articles/12645 last-modified: 2021-12-24 description: In this paper, we have described and illustrated three new species of Byrsopteryx from Peru: Byrsopteryx inti, sp. nov.Byrsopteryx mamaocllosp. nov., and Byrsopteryx mancocapacsp. nov. Larvae of the latter two were also associated to male specimens based on comparison of a fragment of COI gene and pharate male identification. Byrsopteryx intisp. nov. and Byrsopteryx mamaocllosp. nov. share a unique feature: a semi-dome process formed by a thickened area on male forewings. The three species can be easily identified by wing coloration and male genitalia. Furthermore, Byrsopteryx intisp. nov. can be recognized by its sternum VIII with a median digitate process on posterior margin, slightly capitate; and by long dorsolateral processes from segment VIII, which cross each other apically in dorsal view. Byrsopteryx mamaocllosp. nov. can be distinguished by sternum VIII bearing a pair of short, posterior, spinelike processes, which are curved inwards and bordered by a rounded, membranous structure, and by a pair of short, heavily sclerotized, dorsolateral processes. Byrsopteryx mancocapacsp. nov. can be distinguished by strong spine-like processes arising dorsally from subgenital plate and by sternum VIII with posterior margin divided into two plate-like lobes. Larvae of B. mamaocllosp. nov. and B. mancocapacsp. nov. are similar to other Byrsopteryx larvae known. They can be distinguished from each other by the shape of the operculum formed by terga VIII and IX, and number of setae on the second abdominal pleurite. Maximum likelihood analyses of 20 COI sequences, including nine Byrsopteryx species, placed B. intisp. nov. and B. mamaocllosp. nov. as sister species and related to a clade including B. gomezi, B. tapanti, and B. esparta, while B. mancocapacsp. nov. was found as sister to B. abrelata. Despite the close phylogenetic relationship found between B. intisp. nov. and B. mamaocllosp. nov., they are separated by 14.9% minimum K2P divergence of COI. The highest intraspecific distance observed was 1.4% for B. mancocapacsp. nov. individuals. Although the Peruvian caddisfly fauna has around 320 known species and almost a third of them are microcaddisflies, in this paper we present the first descriptions of Byrsopteryx species for the country. creator: Allan P.M. Santos creator: Daniela Maeda Takiya uri: https://doi.org/10.7717/peerj.12645 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Santos and Takiya title: Living on the edge: genetic structure and geographic distribution in the threatened Markham’s Storm-Petrel (Hydrobates markhami) link: https://peerj.com/articles/12669 last-modified: 2021-12-24 description: Migratory birds are threatened by habitat loss and degradation, illegal killings, ineffective conservation policies, knowledge gaps and climate change. These threats are particularly troubling in the Procellariiformes (Aves), one of the most endangered bird groups. For “storm-petrels”, their cryptic breeding behavior, asynchrony between populations, and light pollution pose additional threats that contribute to increased mortality.Markham’s Storm-Petrel (Hydrobates markhami), a poorly known migratory species, is a pelagic bird that breeds in dispersed colonies in the Sechura and Atacama Deserts, with asynchronous reproduction between colonies, and is highly affected by artificial lights. Considering its complex conservation scenario and singular breeding, we expected to find narrow habitat distribution conditions, strong geographic genetic structure, and spatially differentiation related to human population activities (e.g., light pollution) and the climate global change. To evaluate these predictions, we analyzed the phylogeography, current and future potential distribution based on mitochondrial gene ND1 and geographic records.The phylogeographic analyses revealed three well-supported clades (i.e., Paracas, Arica, and Salar Grande), and the geographical distribution modeled using an intrinsic conditional model (iCAR) suggests a positive relationship with the mean temperature of the wettest quarter and of the driest quarter, solar radiation, and anthropogenic disturbance. The future predictions under moderate and severe scenarios of global change indicated a drastic distribution area reduction, especially in the southern zone around Tarapacá and Antofagasta in Chile. These suggest a potential loss of unique genetic diversity and the need for conservation actions particularly focused at the edges of the H. markhami distribution. creator: Heraldo V. Norambuena creator: Reinaldo Rivera creator: Rodrigo Barros creator: Rodrigo Silva creator: Ronny Peredo creator: Cristián E. Hernández uri: https://doi.org/10.7717/peerj.12669 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Norambuena et al. title: Integrated analysis and the identification of a circRNA-miRNA-mRNA network in the progression of abdominal aortic aneurysm link: https://peerj.com/articles/12682 last-modified: 2021-12-24 description: BackgroundAbdominal aortic aneurysm (AAA) is a disease commonly seen in the elderly. The aneurysm diameter increases yearly, and the larger the AAA the higher the risk of rupture, increasing the risk of death. However, there are no current effective interventions in the early stages of AAA.MethodsFour gene expression profiling datasets, including 23 normal artery (NOR) tissue samples and 97 AAA tissue samples, were integrated in order to explore potential molecular biological targets for early intervention. After preprocessing, differentially expressed genes (DEGs) between AAA and NOR were identified using LIMMA package. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis were conducted using the DAVID database. The protein-protein interaction network was constructed and hub genes were identified using the STRING database and plugins in Cytoscape. A circular RNA (circRNA) profile of four NOR tissues versus four AAA tissues was then reanalyzed. A circRNA-miRNA-mRNA interaction network was constructed after predictions were made using the Targetscan and Circinteractome databases.ResultsA total of 440 DEGs (263 up-regulated and 177 down-regulated) were identified in the AAA group, compared with the NOR group. The majority were associated with the extracellular matrix, tumor necrosis factor-α, and transforming growth factor-β. Ten hub gene-encoded proteins (namely IL6, RPS27A, JUN, UBC, UBA52, FOS, IL1B, MMP9, SPP1 and CCL2) coupled with a higher degree of connectivity hub were identified after protein‐protein interaction network analysis. Our results, in combination with the results of previous studies revealed that miR-635, miR-527, miR-520h, miR-938 and miR-518a-5p may be affected by circ_0005073 and impact the expression of hub genes such as CCL2, SPP1 and UBA52. The miR-1206 may also be affected by circ_0090069 and impact RPS27A expression.ConclusionsThis circRNA-miRNA-mRNA network may perform critical roles in AAA and may be a novel target for early intervention. creator: Ke Si creator: Da Lu creator: Jianbo Tian uri: https://doi.org/10.7717/peerj.12682 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Si et al. title: Spatiotemporal patterns of the COVID-19 epidemic in Mexico at the municipality level link: https://peerj.com/articles/12685 last-modified: 2021-12-24 description: In recent history, Coronavirus Disease 2019 (COVID-19) is one of the worst infectious disease outbreaks affecting humanity. The World Health Organization has defined the outbreak of COVID-19 as a pandemic, and the massive growth of the number of infected cases in a short time has caused enormous pressure on medical systems. Mexico surpassed 3.7 million confirmed infections and 285,000 deaths on October 23, 2021. We analysed the spatio-temporal patterns of the COVID-19 epidemic in Mexico using the georeferenced confirmed cases aggregated at the municipality level. We computed weekly Moran’s I index to assess spatial autocorrelation over time and identify clusters of the disease using the “flexibly shaped spatial scan” approach. Finally, we compared Euclidean, cost, resistance distances and gravitational model to select the best-suited approach to predict inter-municipality contagion. We found that COVID-19 pandemic in Mexico is characterised by clusters evolving in space and time as parallel epidemics. The gravitational distance was the best model to predict newly infected municipalities though the predictive power was relatively low and varied over time. This study helps us understand the spread of the epidemic over the Mexican territory and gives insights to model and predict the epidemic behaviour. creator: Jean-François Mas creator: Azucena Pérez-Vega uri: https://doi.org/10.7717/peerj.12685 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Mas and Pérez-Vega title: Bacterial diversity and potential risk factors associated with Salmonella contamination of seafood products sold in retail markets in Bangkok, Thailand link: https://peerj.com/articles/12694 last-modified: 2021-12-24 description: Consumption of contaminated food causes 600 million cases, including 420,000 of fatal infections every year. Estimated cost from food-borne illnesses is USD 110 billion per year, which is an economic burden to low- and middle-income countries. Thailand is a leading producer and consumer of seafood, but little is known about bacterial contamination in seafood. In particular, public health agencies need to know the relationship between Salmonella contamination in seafood and risk factors, as assessed with readily available culture-dependent and bacterial phenotyping methods. To address this, levels of indicator bacteria, Salmonella and Vibrio in various seafood products were determined to identify risk factors associated with Salmonella contamination. A total of 335 samples were collected from October 2018 to July 2019 at seafood markets throughout Bangkok, Thailand; overall sample composition was Pacific white shrimp (n = 85), oysters (n = 82), blood cockles (n = 84), and Asian seabass (n = 84). Prevalence was 100% for fecal coliforms and 85% for E. coli. In contrast, prevalence was 59% for V. parahaemolyticus, 49% for V. cholerae, 19% for V. alginolyticus, 18% for V. vulnificus, and 36% for Salmonella. Highest concentrations of fecal coliforms and E. coli were in oysters. Highest concentrations of Salmonella with Matopeni (31%) being the predominant serotype were in shrimp. Salmonella contamination was significantly associated with type of seafood, sampling location, retail conditions, and the presence of E. coli, V. alginolyticus and V. vulnificus. A cutoff value for E. coli concentration of 1.3 × 104 MPN/g predicted contamination of Salmonella, with a sensitivity of 84% and specificity of 61%. Displaying seafood products on ice, presence of E. coli and Vibrio, and seafood derived from Eastern Thailand were associated with an increased risk of Salmonella contamination. creator: Edward R. Atwill creator: Saharuetai Jeamsripong uri: https://doi.org/10.7717/peerj.12694 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Atwill and Jeamsripong title: Quantification of antibiotic resistance genes and mobile genetic in dairy manure link: https://peerj.com/articles/12408 last-modified: 2021-12-23 description: BackgroundAntibiotic resistance genes (ARGs) are considered to be emerging environmental contaminants of concern potentially posing risks to human and animal health, and this research studied the prevalence of antimicrobial resistance in dairy manure.MethodsThis study is focused on investigating prevalence of ARGs in California dairy farm manure under current common different manure management. A total of 33 manure samples were collected from multiple manure treatment conditions: (1) flushed manure (FM), (2) fresh pile (FP), (3) compost pile (CP), (4) primary lagoon (PL), and (5) secondary lagoon (SL). After DNA extraction, all fecal samples were screened by PCR for the presence of eight ARGs: four sulfonamide ARGs (sulI, sulII, sulIII, sulA), two tetracycline ARGs (tetW, tetO), two macrolide-lincosamide-streptogramin B (MLSB) ARGs (ermB, ermF). Samples were also screened for two mobile genetic elements (MGEs) (intI1, tnpA), which are responsible for dissemination of ARGs. Quantitative PCR was then used to screen all samples for five ARGs (sulII, tetW, ermF, tnpA and intI1).ResultsPrevalence of genes varied among sample types, but all genes were detectable in different manure types. Results showed that liquid-solid separation, piling, and lagoon conditions had limited effects on reducing ARGs and MGEs, and the effect was only found significant on tetW (p = 0.01). Besides, network analysis indicated that sulII was associated with tnpA (p < 0.05), and Psychrobacter and Pseudomonas as opportunistic human pathogens, were potential ARG/MGE hosts (p < 0.05). This research indicated current different manure management practices in California dairy farms has limited effects on reducing ARGs and MGEs. Improvement of different manure management in dairy farms is thus important to mitigate dissemination of ARGs into the environment. creator: Yi Wang creator: Pramod Pandey creator: Colleen Chiu creator: Richard Jeannotte creator: Sundaram Kuppu creator: Ruihong Zhang creator: Richard Pereira creator: Bart C. Weimer creator: Nitin Nitin creator: Sharif S. Aly uri: https://doi.org/10.7717/peerj.12408 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wang et al. title: A journey through the Corynebacterium pseudotuberculosis proteome promotes insights into its functional genome link: https://peerj.com/articles/12456 last-modified: 2021-12-23 description: BackgroundCorynebacterium pseudotuberculosis is a Gram-positive facultative intracellular pathogen and the etiologic agent of illnesses like caseous lymphadenitis in small ruminants, mastitis in dairy cattle, ulcerative lymphangitis in equines, and oedematous skin disease in buffalos. With the growing advance in high-throughput technologies, genomic studies have been carried out to explore the molecular basis of its virulence and pathogenicity. However, data large-scale functional genomics studies are necessary to complement genomics data and better understating the molecular basis of a given organism. Here we summarize, MS-based proteomics techniques and bioinformatics tools incorporated in genomic functional studies of C. pseudotuberculosis to discover the different patterns of protein modulation under distinct environmental conditions, and antigenic and drugs targets.MethodologyIn this study we performed an extensive search in Web of Science of original and relevant articles related to methods, strategy, technology, approaches, and bioinformatics tools focused on the functional study of the genome of C. pseudotuberculosis at the protein level.ResultsHere, we highlight the use of proteomics for understating several aspects of the physiology and pathogenesis of C. pseudotuberculosis at the protein level. The implementation and use of protocols, strategies, and proteomics approach to characterize the different subcellular fractions of the proteome of this pathogen. In addition, we have discussed the immunoproteomics, immunoinformatics and genetic tools employed to identify targets for immunoassays, drugs, and vaccines against C. pseudotuberculosis infection.ConclusionIn this review, we showed that the combination of proteomics and bioinformatics studies is a suitable strategy to elucidate the functional aspects of the C. pseudotuberculosis genome. Together, all information generated from these proteomics studies allowed expanding our knowledge about factors related to the pathophysiology of this pathogen. creator: Wanderson Marques da Silva creator: Nubia Seyffert creator: Artur Silva creator: Vasco Azevedo uri: https://doi.org/10.7717/peerj.12456 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Marques da Silva et al. title: Rediscovery of Laura’s glassfrog Nymphargus laurae (Anura: Centrolenidae) with new data on its morphology, colouration, phylogenetic position and conservation in Ecuador link: https://peerj.com/articles/12644 last-modified: 2021-12-23 description: We report the rediscovery of Laura’s Glassfrog, Nymphargus laurae Cisneros-Heredia & McDiarmid, 2007, based on two specimens collected at the Colonso-Chalupas Biological Reserve, province of Napo, Ecuador. The species was described and known from a single male specimen collected in 1955 at Loreto, north-eastern Andean foothills of Ecuador. Limited information was available about the colouration, systematics, ecology, and biogeography of N. laurae. We provide new data on the external morphology, colouration, distribution and comment on its conservation status and extinction risk. We discuss the phylogenetic relationships of N. laurae, which forms a clade together with N. siren and N. humboldti. The importance of research in unexplored areas must be a national priority to document the biodiversity associated, especially in protected areas. creator: María José Sánchez-Carvajal creator: Grace C. Reyes-Ortega creator: Diego F. Cisneros-Heredia creator: H. Mauricio Ortega-Andrade uri: https://doi.org/10.7717/peerj.12644 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Sánchez-Carvajal et al. title: Identification and molecular characterization of the alternative spliced variants of beta carbonic anhydrase 1 (βCA1) from Arabidopsis thaliana link: https://peerj.com/articles/12673 last-modified: 2021-12-23 description: Carbonic anhydrases (CAs) are ubiquitous zinc metalloenzymes that catalyze the interconversion of carbon dioxide and bicarbonate. Higher plants mainly contain the three evolutionarily distinct CA families αCA, βCA, and γCA, with each represented by multiple isoforms. Alternative splicing (AS) of the CA transcripts is common. However, there is little information on the spliced variants of individual CA isoforms. In this study, we focused on the characterization of spliced variants of βCA1 from Arabidopsis. The expression patterns and subcellular localization of the individual spliced variants of βCA1 were examined. The results showed that the spliced variants of βCA1 possessed different subcellular and tissue distributions and responded differently to environmental stimuli. Additionally, we addressed the physiological role of βCA1 in heat stress response and its protein-protein interaction (PPI) network. Our results showed that βCA1 was regulated by heat stresses, and βca1 mutant was hypersensitive to heat stress, indicating a role for βCA1 in heat stress response. Furthermore, PPI network analysis revealed that βCA1 interacts with multiple proteins involved in several processes, including photosynthesis, metabolism, and the stress response, and these will provide new avenues for future investigations of βCA1. creator: Jinyu Shen creator: Zhiyong Li creator: Yajuan Fu creator: Jiansheng Liang uri: https://doi.org/10.7717/peerj.12673 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Shen et al.