A set of RT-PCR assays for detection of all known avian paramyxoviruses and application in surveillance of avian paramyxoviruses in China
Background Avian paramyxoviruses (APMVs), also termed avian avulaviruses, are of a vast diversity and great significance in poultry. Detection of all known APMVs is challenging, and distribution of APMVs have not been well investigated. Methods A set of reverse transcription polymerase chain reaction (RT-PCR) assays for detection of all known APMVs were established using degenerate primers targeting the viral polymerase L gene. The assays were preliminarily evaluated using in-vitro transcribed double-stranded RNA controls and 24 known viruses, and then they were employed to detect 4,346 avian samples collected from 11 provinces. Results The assays could detect 20–200 copies of the double-stranded RNA controls, and detected correctly the 24 known viruses. Of the 4,346 avian samples detected using the assays, 72 samples were found positive. Of the 72 positives, 70 were confirmed through sequencing, indicating the assays were specific for APMVs. The 4,346 samples were also detected using a reported RT-PCR assay, and the results showed this RT-PCR assay was less sensitive than the assays reported here. Of the 70 confirmed positives, 40 were class I Newcastle disease virus (NDV or APMV-1) and 27 were class II NDV from poultry including chickens, ducks, geese, and pigeons, and three were APMV-2 from parrots. The surveillance identified APMV-2 in parrots for the first time, and revealed that prevalence of NDVs in live poultry markets was higher than that in poultry farms. The surveillance also suggested that class I NDVs in chickens could be as prevalent as in ducks, and class II NDVs in ducks could be more prevalent than in chickens, and class II NDVs could be more prevalent than class I NDVs in ducks. Altogether, we developed a set of specific and sensitive RT-PCR assays for detection of all known APMVs, and conducted a large-scale surveillance using the assays which shed novel insights into APMV epidemiology.
Jin et al. (2021) A set of RT-PCR assays for detection of all known avian paramyxoviruses and application in surveillance of avian paramyxoviruses in China. PeerJ 9:e10748 https://doi.org/10.7717/peerj.10748
Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L.
Background Seed coat color is an important horticultural trait in Brassica crops, which is divided into two categories: brown/black and yellow. Seeds with yellow seed coat color have higher oil quality, higher protein content and lower fiber content. Yellow seed coat color is therefore considered a desirable trait in hybrid breeding of Brassica rapa, Brassica juncea and Brassica napus. Methods Comprehensive analysis of the abundance transcripts for seed coat color at three development stages by RNA-sequencing (RNA-seq) and corresponding flavonoids compounds by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were carried out in B. rapa. Results We identified 41,286 unigenes with 4,989 differentially expressed genes between brown seeds (B147) and yellow seeds (B80) at the same development stage. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified 19 unigenes associated with the phenylpropanoid, flavonoid, flavone and flavonol biosynthetic pathways as involved in seed coat color formation. Interestingly, expression levels of early biosynthetic genes (BrCHS, BrCHI, BrF3H, BrF3’H and BrFLS) in the flavonoid biosynthetic pathway were down-regulated while late biosynthetic genes (BrDFR, BrLDOX and BrBAN) were hardly or not expressed in seeds of B80. At the same time, BrTT8 and BrMYB5 were down-regulated in B80. Results of LC-MS also showed that epicatechin was not detected in seeds of B80. We validated the accuracy of our RNA-seq data by RT-qPCR of nine critical genes. Epicatechin was not detected in seeds of B80 by LC-MS/MS. Conclusions The expression levels of flavonoid biosynthetic pathway genes and the relative content of flavonoid biosynthetic pathway metabolites clearly explained yellow seed color formation in B. rapa. This study provides a foundation for further research on the molecular mechanism of seed coat color formation.
Ren et al. (2021) Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L.. PeerJ 9:e10770 https://doi.org/10.7717/peerj.10770
CoViD-19: an automatic, semiparametric estimation method for the population infected in Italy
To date, official data on the number of people infected with the SARS-CoV-2—responsible for the Covid-19—have been released by the Italian Government just on the basis of a non-representative sample of population which tested positive for the swab. However a reliable estimation of the number of infected, including asymptomatic people, turns out to be crucial in the preparation of operational schemes and to estimate the future number of people, who will require, to different extents, medical attentions. In order to overcome the current data shortcoming, this article proposes a bootstrap-driven, estimation procedure for the number of people infected with the SARS-CoV-2. This method is designed to be robust, automatic and suitable to generate estimations at regional level. Obtained results show that, while official data at March the 12th report 12.839 cases in Italy, people infected with the SARS-CoV-2 could be as high as 105.789.
Fenga (2021) CoViD-19: an automatic, semiparametric estimation method for the population infected in Italy. PeerJ 9:e10819 https://doi.org/10.7717/peerj.10819
Maniraptoran pelvic musculature highlights evolutionary patterns in theropod locomotion on the line to birds
Locomotion is a fundamental aspect of palaeobiology and often investigated by comparing osteological structures and proportions. Previous studies document a stepwise accumulation of avian-like features in theropod dinosaurs that accelerates in the clade Maniraptora. However, the soft tissues that influenced the skeleton offer another perspective on locomotory adaptations. Examination of the pelvis for osteological correlates of hind limb and tail musculature allowed reconstruction of primary locomotory muscles across theropods and their closest extant relatives. Additionally, the areas of pelvic muscle origins were quantified to measure relative differences within and between taxa, to compare morphological features associated with cursoriality, and offer insight into the evolution of locomotor modules. Locomotory inferences based on myology often corroborate those based on osteology, although they occasionally conflict and indicate greater complexity than previously appreciated. Maniraptoran pelvic musculature underscores previous studies noting the multifaceted nature of cursoriality and suggests that a more punctuated step in caudal decoupling occurred at or near the base of Maniraptora.
Rhodes et al. (2021) Maniraptoran pelvic musculature highlights evolutionary patterns in theropod locomotion on the line to birds. PeerJ 9:e10855 https://doi.org/10.7717/peerj.10855
Prevalence and clinical correlates of insomnia symptoms and their association with quality of life in Chinese patients with HBV-related liver disease
Objective This study aimed to describe the one-month prevalence of insomnia symptoms (insomnia hereafter) and the demographic and clinical correlates, and its association with quality of life (QOL) in Chinese patients with HBV-related liver disease. Method A total of 689 patients with HBV-related liver disease in Beijing, China formed the study sample. Three forms of insomnia including difficulty initiating sleep (DIS), difficulty maintaining sleep (DMS) and early morning awakening (EMA) were assessed using standardized questions. QOL was measured using the Medical Outcomes Study Short Form 12 (SF-12). Results The one-month prevalence of at least one type of insomnia was 69.5%, while DIS, DMS and EMA were 60.4%, 54.7% and 50.9%, respectively. Only 4.8% of patients suffering from insomnia received treatment. Multiple logistic regression analyses revealed that pre-existing medical conditions were positively associated with DIS and EMA; patients with more severe depressive symptoms were more likely to have DIS, DMS and EMA; local residents were less likely to have DIS; and those who were married and older were more likely to have DMS. Insomnia was not independently associated with QOL. Conclusions Insomnia is common in Chinese patients with HBV-related liver disease with a very low rate of treatment. Greater attention should be given to identify and treat insomnia in this patient population.
Zhao et al. (2021) Prevalence and clinical correlates of insomnia symptoms and their association with quality of life in Chinese patients with HBV-related liver disease. PeerJ 9:e10956 https://doi.org/10.7717/peerj.10956
The influence of fish farm activity on the social structure of the common bottlenose dolphin in Sardinia (Italy)
In a wide variety of habitats, including some heavily urbanised areas, the adaptability of populations of common bottlenose dolphin (Tursiops truncatus) may depend on the social structure dynamics. Nonetheless, the way in which these adaptations take place is still poorly understood. In the present study we applied photo-identification techniques to investigate the social structure of the common bottlenose dolphin population inhabiting the Gulf of Alghero (Sardinia, Italy), analysing data recorded from 2008 to 2019. The social structure analysis showed a division of the entire population into five different communities and the presence of non-random associations, while there was no evidence of segregation between sexes. Furthermore, results highlighted an important change in social structure through time, likely due to a reduction in fish farm activity since 2015. The division of the population into different communities, the presence of segregation based on the foraging strategy (inside or outside the fish farm area) and the social network measures were evaluated by analysing independently the two datasets: the intense and low farm activity periods: 2008–2014 and 2015–2020, respectively. Segregation among individuals belonging to the same foraging strategy class was found only in the earlier period, and the composition of the four communities was consistent with this result. Our study improves the knowledge about bottlenose dolphin adaptation, as a lower complexity in social structure was linked to a reduction in anthropogenic food availability.
Frau et al. (2021) The influence of fish farm activity on the social structure of the common bottlenose dolphin in Sardinia (Italy). PeerJ 9:e10960 https://doi.org/10.7717/peerj.10960
A review of the diagnosis and geographical distribution of the recently described flea toad Brachycephalus sulfuratus in relation to B. hermogenesi (Anura: Brachycephalidae)
Background The flea toad Brachycephalus sulfuratus was recently described from southeastern and southern Brazil. In its description, the authors overlooked previous records of flea toads that had been identified as “Brachycephalus sp. nov.” and B. hermogenesi occurring in the same regions, which could suggest the possibility of up to three flea toads coexisting in southern Brazil. In addition, B. sulfuratus is characterized by substantial phenotypic variability, to an extent that compromises its current diagnosis with respect to its congener B. hermogenesi. Therefore, the current state-of-affairs regarding the geographical distribution of these two species and the identification of previously known populations is hitherto uncertain. Our goals are to reassess previous records of flea toads attributable to B. hermogenesi, B. sulfuratus and “Brachycephalus sp. nov.”, considering the description of B. sulfuratus, and to review the diagnosis of B. sulfuratus. Methods A critical analysis of the species identity of flea toad specimens attributable to B. hermogenesi, B. sulfuratus, or to a potentially undescribed species from southeastern and southern Brazil was based either on the analysis of morphology or on their advertisement calls. These analyses include our independent examinations of specimens and, when not possible, examinations of published descriptions. To allow for a consistent comparison of advertisement calls between B. hermogenesi and B. sulfuratus, we made recordings of both species, including in the type locality of the former. Results We found that morphological and call characters originally proposed as diagnostic for B. sulfuratus in relation to B. hermogenesi vary intraspecifically. Live individuals with ventral yellow spots correspond to B. sulfuratus; individuals without yellow spots can be either B. sulfuratus or B. hermogenesi. In preservative, they are indistinguishable. Previous records of Brachycephalus sp. nov. correspond to B. sulfuratus. We propose that the reduced number of notes per call and the presence of only isolated notes in the call of B. sulfuratus, as opposed to a high number of notes per call with isolated notes and note groups in the call of B. hermogenesi, as the only diagnostic characters between them. Regarding their distributions and based in our assessment, only B. sulfuratus occurs in southern Brazil, without any overlap with B. hermogenesi. There is a narrow gap between the distributions of these species around the southeast of the city of São Paulo. Our revision also revealed that some records previously attributed to B. hermogenesi in Rio de Janeiro and north São Paulo represent a distinct, unidentified flea toad that is not B. sulfuratus. Both species occur side by side in Corcovado, São Paulo, a locality from where five paratypes of B. hermogenesi were obtained. Biogeographic events that might have led to vicariance between B. hermogenesi and B. sulfuratus are discussed.
Bornschein et al. (2021) A review of the diagnosis and geographical distribution of the recently described flea toad Brachycephalus sulfuratus in relation to B. hermogenesi (Anura: Brachycephalidae). PeerJ 9:e10983 https://doi.org/10.7717/peerj.10983
Changes in diversity and community assembly of jumping spiders (Araneae: Salticidae) after rainforest conversion to rubber and oil palm plantations
Rainforest conversion into monoculture plantations results in species loss and community shifts across animal taxa. The effect of such conversion on the role of ecophysiological properties influencing communities, and conversion effects on phylogenetic diversity and community assembly mechanisms, however, are rarely studied in the same context. Here, we compare salticid spider (Araneae: Salticidae) communities between canopies of lowland rainforest, rubber agroforest (“jungle rubber”) and monoculture plantations of rubber or oil palm, sampled in a replicated plot design in Jambi Province, Sumatra, Indonesia. Overall, we collected 912 salticid spider individuals and sorted them to 70 morphospecies from 21 genera. Salticid richness was highest in jungle rubber, followed by rainforest, oil palm and rubber, but abundance of salticids did not differ between land-use systems. Community composition was similar in jungle rubber and rainforest but different from oil palm and rubber, which in turn were different from each other. The four investigated land-use systems differed in aboveground plant biomass, canopy openness and land use intensity, which explained 12% of the observed variation in canopy salticid communities. Phylogenetic diversity based on ~850 bp 28S rDNA fragments showed similar patterns as richness, that is, highest in jungle rubber, intermediate in rainforest, and lowest in the two monoculture plantations. Additionally, we found evidence for phylogenetic clustering of salticids in oil palm, suggesting that habitat filtering is an important factor shaping salticid spider communities in monoculture plantations. Overall, our study offers a comprehensive insight into the mechanisms shaping communities of arthropod top predators in canopies of tropical forest ecosystems and plantations, combining community ecology, environmental variables and phylogenetics across a land-use gradient in tropical Asia.
Junggebauer et al. (2021) Changes in diversity and community assembly of jumping spiders (Araneae: Salticidae) after rainforest conversion to rubber and oil palm plantations. PeerJ 9:e11012 https://doi.org/10.7717/peerj.11012
Differential gene expression in a tripartite interaction: Drosophila, Spiroplasma and parasitic wasps
Background Several facultative bacterial symbionts of insects protect their hosts against natural enemies. Spiroplasma poulsonii strain sMel (hereafter Spiroplasma), a male-killing heritable symbiont of Drosophila melanogaster, confers protection against some species of parasitic wasps. Several lines of evidence suggest that Spiroplasma-encoded ribosome inactivating proteins (RIPs) are involved in the protection mechanism, but the potential contribution of the fly-encoded functions (e.g., immune response), has not been deeply explored. Methods Here we used RNA-seq to evaluate the response of D. melanogaster to infection by Spiroplasma and parasitism by the Spiroplasma-susceptible wasp Leptopilina heterotoma, and the Spiroplasma-resistant wasp Ganaspis sp. In addition, we used quantitative (q)PCR to evaluate the transcript levels of the Spiroplasma-encoded Ribosomal inactivation protein (RIP) genes. Results In the absence of Spiroplasma infection, we found evidence of Drosophila immune activation by Ganaspis sp., but not by L. heterotoma, which in turn negatively influenced functions associated with male gonad development. As expected for a symbiont that kills males, we detected extensive downregulation in the Spiroplasma-infected treatments of genes known to have male-biased expression. We detected very few genes whose expression patterns appeared to be influenced by the Spiroplasma-L. heterotoma interaction, and these genes are not known to be associated with immune response. For most of these genes, parasitism by L. heterotoma (in the absence of Spiroplasma) caused an expression change that was at least partly reversed when both L. heterotoma and Spiroplasma were present. It is unclear whether such genes are involved in the Spiroplasma-mediated mechanism that leads to wasp death and/or fly rescue. Nonetheless, the expression pattern of some of these genes, which reportedly undergo expression shifts during the larva-to-pupa transition, is suggestive of an influence of Spiroplasma on the development time of L. heterotoma-parasitized flies. One of the five RIP genes (RIP2) was consistently highly expressed independently of wasp parasitism, in two substrains of sMel. Finally, the RNAseq data revealed evidence consistent with RIP-induced damage in the ribosomal (r)RNA of the Spiroplasma-susceptible, but not the Spiroplasma-resistant, wasp. Acknowledging the caveat that we lacked adequate power to detect the majority of DE genes with fold-changes lower than 3, we conclude that immune priming is unlikely to contribute to the Spiroplasma-mediated protection against wasps, and that the mechanism by which Ganaspis sp. resists/tolerates Spiroplasma does not involve inhibition of RIP transcription.
Higareda Alvear et al. (2021) Differential gene expression in a tripartite interaction: Drosophila, Spiroplasma and parasitic wasps. PeerJ 9:e11020 https://doi.org/10.7717/peerj.11020
Characterizing avian pathogenic Escherichia coli (APEC) from colibacillosis cases, 2018
Colibacillosis caused by avian pathogenic Escherichia coli (APEC) is a devastating disease of poultry that results in multi-million-dollar losses annually to the poultry industry. Disease syndromes associated with APEC includes colisepticemia, cellulitis, air sac disease, peritonitis, salpingitis, omphalitis, and osteomyelitis among others. A total of 61 APEC isolates collected during the Fall of 2018 (Aug–Dec) from submitted diagnostic cases of poultry diagnosed with colibacillosis were assessed for the presence of 44 virulence-associated genes, 24 antimicrobial resistance genes and 17 plasmid replicon types. Each isolate was also screened for its ability to form biofilm using the crystal violet assay and antimicrobial susceptibility to 14 antimicrobials using the NARMS panel. Overall, the prevalence of virulence genes ranged from 1.6% to >90% with almost all strains harboring genes that are associated with the ColV plasmid—the defining trait of the APEC pathotype. Overall, 58 strains were able to form biofilms and only three strains formed negligible biofilms. Forty isolates displayed resistance to antimicrobials of the NARMS panel ranging from one to nine agents. This study highlights that current APEC causing disease in poultry possess virulence and resistance traits and form biofilms which could potentially lead to challenges in colibacillosis control.
Newman et al. (2021) Characterizing avian pathogenic Escherichia coli (APEC) from colibacillosis cases, 2018. PeerJ 9:e11025 https://doi.org/10.7717/peerj.11025