Discovery of novel astrovirus genotype species in small ruminants
Astroviruses (AstV) are single-stranded, positive-sense RNA viruses, best known for causing diarrhea in humans and are also found in many other mammals; in those, the relevance in gastroenteritis remains unclear. Recently described neurotropic AstV showed associations with encephalitis in humans as well as in other mammals. In Switzerland, two different neurotropic AstV were identified in cattle, as well as one in a sheep. The high genetic similarity between the ovine and one of the bovine AstV strengthens the hypothesis of an interspecies transmission. In humans, AstV associated with encephalitis were found also in human stool samples, suggesting that in these patients the infection spreads from the gastrointestinal tract to the brain under certain conditions, such as immunosuppression. Whether a similar pathogenesis occurs in ruminants remains unknown. The aims of this study were (1) the investigation of the potential occurrence of neurotropic AstV in feces samples, (2) the discovery and analysis of so far unknown AstV in small ruminants and other ruminant species’ fecal samples and (3) the examination of a potential interspecies transmission of AstV. To achieve these aims, RNA extraction out of 164 fecal samples from different ruminant species was performed and all samples were screened for known neurotropic AstV occurring in Switzerland, as well as for various AstV using RT-PCR. Positive tested samples were submitted to next generation sequencing. The generated sequences were compared to nucleotide- and amino acid databases, virus properties were identified, and phylogenetic analyses as well as recombination analysis were performed. The excretion of neurotropic AstV in small ruminants’ feces could not be demonstrated, but this work suggests the first identification of AstV in goats as well as the discovery of multiple and highly diverse new genetic variants in small ruminants, which lead to a classification into novel genotype-species. Additionally, the prediction of multiple recombination events in four of five newly discovered full or almost full-length genome sequences suggests a plausible interspecies transmission. The findings point out the occurrence and fecal shedding of previously unknown AstV in sheep and goats and pave the way towards a better understanding of the diversity and transmission of AstV in small ruminants.
Kauer et al. (2019) Discovery of novel astrovirus genotype species in small ruminants. PeerJ 7:e7338 https://doi.org/10.7717/peerj.7338
TLR2 polymorphism (rs650082970) is associated with somatic cell count in goat milk
Pathogens invading the mammary gland are recognized through a range of pattern recognition receptors (PRRs), residing on the plasma membrane of mammary epithelial cells. Toll-like receptor 2 (TLR2) signalling is responsible for recognition of Gram-positive bacteria, which are the most common mastitis-causing pathogens in goats. Somatic cell counts (SCC) in milk are routinely determined in goat dairy flocks and serve as an indicator of milk quality, which is highly correlated to intramammary infections. Recently, a single nucleotide polymorphism of the TLR2 was suggested to be associated with SCC in goat milk. To further test the suggested association, we genotyped 61 Slovenian Alpine goats included in the dataset. The effect of the genotype was analysed using the general linear model (GLM) procedure of SAS/STAT software. We found the TLR2 genotypes significantly (p = 0.0007) associated with milk SCC. Animals with the A/G genotype had significantly (p ≤ 0.05) lower SCC value in milk compared to the G/G genotype. Our data suggest that the A allele is the minor one and is associated with lower milk SCC. In the current study, we provide a validated PCR-RFLP based genotyping assay for the TLR2 SNP (rs650082970) and confirm its association with milk SCC. Further studies to confirm the association on a larger number of animals of different breeds and to explain functional consequences of the polymorphism in relation to SCC are encouraged.
Ogorevc et al. (2019) TLR2 polymorphism (rs650082970) is associated with somatic cell count in goat milk. PeerJ 7:e7340 https://doi.org/10.7717/peerj.7340
Functional and evolutionary perspectives on gill structures of an obligate air-breathing, aquatic snail
Ampullariids are freshwater gastropods bearing a gill and a lung, thus showing different degrees of amphibiousness. In particular, Pomacea canaliculata (Caenogastropoda, Ampullariidae) is an obligate air-breather that relies mainly or solely on the lung for dwelling in poorly oxygenated water, for avoiding predators, while burying in the mud during aestivation, and for oviposition above water level. In this paper, we studied the morphological peculiarities of the gill in this species. We found (1) the gill and lung vasculature and innervation are intimately related, allowing alternation between water and air respiration; (2) the gill epithelium has features typical of a transporting rather than a respiratory epithelium; and (3) the gill has resident granulocytes within intraepithelial spaces that may serve a role for immune defence. Thus, the role in oxygen uptake may be less significant than the roles in ionic/osmotic regulation and immunity. Also, our results provide a morphological background to understand the dependence on aerial respiration of Pomacea canaliculata. Finally, we consider these findings from a functional perspective in the light of the evolution of amphibiousness in the Ampullariidae, and discuss that master regulators may explain the phenotypic convergence of gill structures amongst this molluscan species and those in other phyla.
Rodriguez et al. (2019) Functional and evolutionary perspectives on gill structures of an obligate air-breathing, aquatic snail. PeerJ 7:e7342 https://doi.org/10.7717/peerj.7342
A 3-mRNA-based prognostic signature of survival in oral squamous cell carcinoma
Background Oral squamous cell carcinoma (OSCC) is the most common type of head and neck squamous cell carcinoma with an unsatisfactory prognosis. The aim of this study was to identify potential prognostic mRNA biomarkers of OSCC based on analysis of The Cancer Genome Atlas (TCGA). Methods Expression profiles and clinical data of OSCC patients were collected from TCGA database. Univariate Cox analysis and the least absolute shrinkage and selection operator Cox (LASSO Cox) regression were used to primarily screen prognostic biomarkers. Then multivariate Cox analysis was performed to build a prognostic model based on the selected prognostic mRNAs. Nomograms were generated to predict the individual’s overall survival at 3 and 5 years. The model performance was assessed by the time-dependent receiver operating characteristic (ROC) curve and calibration plot in both training cohort and validation cohort (GSE41613 from NCBI GEO databases). In addition, machine learning was used to assess the importance of risk factors of OSCC. Finally, in order to explore the potential mechanisms of OSCC, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was completed. Results Three mRNAs (CLEC3B, C6 and CLCN1) were finally identified as a prognostic biomarker pattern. The risk score was imputed as: (−0.38602 × expression level of CLEC3B) + (−0.20632 × expression level of CLCN1) + (0.31541 × expression level of C6). In the TCGA training cohort, the area under the curve (AUC) was 0.705 and 0.711 for 3- and 5-year survival, respectively. In the validation cohort, AUC was 0.718 and 0.717 for 3- and 5-year survival. A satisfactory agreement between predictive values and observation values was demonstrated by the calibration curve in the probabilities of 3- and 5- year survival in both cohorts. Furthermore, machine learning identified the 3-mRNA signature as the most important risk factor to survival of OSCC. Neuroactive ligand-receptor interaction was most enriched mostly in KEGG pathway analysis. Conclusion A 3-mRNA signature (CLEC3B, C6 and CLCN1) successfully predicted the survival of OSCC patients in both training and test cohort. In addition, this signature was an independent and the most important risk factor of OSCC.
Cao et al. (2019) A 3-mRNA-based prognostic signature of survival in oral squamous cell carcinoma. PeerJ 7:e7360 https://doi.org/10.7717/peerj.7360
Biochar, that is, carbonized biomass similar to charcoal, has been used in acute medical treatment of animals for many centuries. Since 2010, livestock farmers increasingly use biochar as a regular feed supplement to improve animal health, increase nutrient intake efficiency and thus productivity. As biochar gets enriched with nitrogen-rich organic compounds during the digestion process, the excreted biochar-manure becomes a more valuable organic fertilizer causing lower nutrient losses and greenhouse gas emissions during storage and soil application. Scientists only recently started to investigate the mechanisms of biochar in the different stages of animal digestion and thus most published results on biochar feeding are based so far on empirical studies. This review summarizes the state of knowledge up to the year 2019 by evaluating 112 relevant scientific publications on the topic to derive initial insights, discuss potential mechanisms behind observations and identify important knowledge gaps and future research needs. The literature analysis shows that in most studies and for all investigated farm animal species, positive effects on different parameters such as toxin adsorption, digestion, blood values, feed efficiency, meat quality and/or greenhouse gas emissions could be found when biochar was added to feed. A considerable number of studies provided statistically non-significant results, though tendencies were mostly positive. Rare negative effects were identified in regard to the immobilization of liposoluble feed ingredients (e.g., vitamin E or Carotenoids) which may limit long-term biochar feeding. We found that most of the studies did not systematically investigate biochar properties (which may vastly differ) and dosage, which is a major drawback for generalizing results. Our review demonstrates that the use of biochar as a feed additive has the potential to improve animal health, feed efficiency and livestock housing climate, to reduce nutrient losses and greenhouse gas emissions, and to increase the soil organic matter content and thus soil fertility when eventually applied to soil. In combination with other good practices, co-feeding of biochar may thus have the potential to improve the sustainability of animal husbandry. However, more systematic multi-disciplinary research is definitely needed to arrive at generalizable recommendations.
Schmidt et al. (2019) The use of biochar in animal feeding. PeerJ 7:e7373 https://doi.org/10.7717/peerj.7373
Long-term warming results in species-specific shifts in seed mass in alpine communities
Background Global warming can cause variation in plant functional traits due to phenotypic plasticity or rapid microevolutionary change. Seed mass represents a fundamental axis of trait variation in plants, from an individual to a community scale. Here, we hypothesize that long-term warming can shift the mean seed mass of species. Methods We tested our hypothesis in plots that had been warmed over 18 years in alpine meadow communities with a history of light grazing (LG) and heavy grazing (HG) on the Qinghai-Tibet plateau. In this study, seeds were collected during the growing season of 2015. Results We found that warming increased the mean seed mass of 4 (n = 19) species in the LG meadow and 6 (n = 20) species in the HG meadow, while decreasing the mean seed mass of 6 species in the LG and HG meadows, respectively. For 7 species, grazing history modified the effect of warming on seed mass. Therefore, we concluded that long-term warming can shift the mean seed mass at the species level. However, the direction of this variation is species-specific. Our study suggests that mean seed mass of alpine plant species appears to decrease in warmer (less stressful) habitats based on life-history theory, but it also suggests there may be an underlying trade-off in which mean seed mass may increase due to greater thermal energy inputs into seed development. Furthermore, the physical and biotic environment modulating this trade-off result in complex patterns of variation in mean seed mass of alpine plant species facing global warming.
Zhang et al. (2019) Long-term warming results in species-specific shifts in seed mass in alpine communities. PeerJ 7:e7416 https://doi.org/10.7717/peerj.7416
Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples
Background Biological invasions are major drivers of environmental change that can significantly alter ecosystem function and diversity. In plants, soil microbes play an important role in plant establishment and growth; however, relatively little is known about the role they might play in biological invasions. A first step to assess whether root microbes may be playing a role in the invasion process is to find out if invasive plants host different microbes than neighbouring native plant species. Methods In this study we investigated differences in root associated microbes of native sugar maple (Acer saccharum Marsh.) and exotic Norway maple (A. platanoides L.) collected from a forested reserve in eastern Canada. We used microscopy to examine root fungi and high-throughput sequencing to characterize the bacterial, fungal and arbuscular mycorrhizal communities of both maple species over one growing season. Results We found differences in root associated bacterial and fungal communities between host species. Norway maple had a higher bacterial and fungal OTU (operational taxonomic units) richness compared to sugar maple, and the indicator species analysis revealed that nine fungal OTUs and three bacterial OTUs had a significant preference for sugar maple. The dominant bacterial phyla found on the roots of both maple species were Actinobacteria and Proteobacteria. The most common fungal orders associated with the Norway maple roots (in descending order) were Helotiales, Agaricales, Pleosporales, Hypocreales, Trechisporales while the Agaricales, Pleosporales, Helotiales, Capnodiales and Hypocreales were the dominant orders present in the sugar maple roots. Dark septate fungi colonization levels were higher in the sugar maple, but no differences in arbuscular mycorrhizal fungal communities and colonization rates were detected between maple species. Discussion Our findings show that two congeneric plant species grown in close proximity can harbor distinct root microbial communities. These findings provide further support for the importance of plant species in structuring root associated microbe communities. The high colonization levels observed in Norway maple demonstrates its compatibility with arbuscular mycorrhizal fungi in the introduced range. Plant-associated microbial communities can affect host fitness and function in many ways; therefore, the observed differences suggest a possibility that biotic interactions can influence the dynamics between native and invasive species.
DeBellis et al. (2019) Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples. PeerJ 7:e7295 https://doi.org/10.7717/peerj.7295
Three-dimensional facial development of children with unilateral cleft lip and palate during the first year of life in comparison with normative average faces
Background Stereophotogrammetry can be used to study facial morphology in both healthy individuals as well as subjects with orofacial clefts because it shows good reliability, ability to capture images rapidly, archival capabilities, and high resolution, and does not require ionizing radiation. This study aimed to compare the three-dimensional (3D) facial morphology of infants born with unilateral cleft lip and palate (UCLP) with an age-matched normative 3D average face before and after primary closure of the lip and soft palate. Methods Thirty infants with a non-syndromic complete unilateral cleft lip, alveolus, and palate participated in the study. Three-dimensional images were acquired at 3, 6, 9, and 12 months of age. All subjects were treated according to the primary surgical protocol consisting of surgical closure of the lip and the soft palate at 6 months of age. Three-dimensional images of UCLP patients at 3, 6 (pre-treatment), 9, and 12 months of age were superimposed on normative datasets of average facial morphology using the children’s reference frame. Distance maps of the complete 3D facial surface and the nose, upper lip, chin, forehead, and cheek regions were developed. Results Assessments of the facial morphology of UCLP and control subjects by using color-distance maps showed large differences in the upper lip region at the location of the cleft defect and an asymmetry at the nostrils at 3 and 6 months of age. At 9 months of age, the labial symmetry was completely restored although the tip of the nose towards the unaffected side showed some remnant asymmetry. At 12 months of age, the symmetry of the nose improved, with only some remnant asymmetry noted on both sides of the nasal tip. At all ages, the mandibular and chin regions of the UCLP patients were 2.5–5 mm posterior to those in the average controls. Conclusion In patients with UCLP deviations from the normative average 3D facial morphology of age-matched control subjects existed for the upper lip, nose, and even the forehead before lip and soft palate closure was performed. Compared to the controls symmetry in the upper lip was restored, and the shape of the upper lip showed less variation after primary lip and soft palate closure. At this early age, retrusion of the soft-tissue mandible and chin, however, seems to be developing already.
Brons et al. (2019) Three-dimensional facial development of children with unilateral cleft lip and palate during the first year of life in comparison with normative average faces. PeerJ 7:e7302 https://doi.org/10.7717/peerj.7302
Characterization of the karyotype and accumulation of repetitive sequences in Australian Darling hardyhead Craterocephalus amniculus (Atheriniformes, Teleostei)
Belonging to the order Atheriniformes, Craterocephalus is one of the most widespread genera of freshwater fishes in Australia, spanning along the northern coast from central Western Australia to central New South Wales and across the Murray-Darling and Lake Eyre basins. In this study, both conventional cytogenetic techniques (Giemsa, C-banding, CMA3/DAPI staining), and fluorescence in situ hybridization (FISH) with telomeric DNA and rDNA probes were used to examine the karyotypes and other chromosomal characteristics of Darling hardyhead (Craterocephalus amniculus) from New South Wales, Australia. We identified a diploid chromosome number 2n = 48 (NF = 58) in all studied individuals. FISH with rDNA probes showed a nonsyntenic pattern, with signals on one pair of subtelocentric chromosomes for 5S rDNA and one pair of submetacentric chromosomes for 28S rDNA. C-banding displayed the accumulation of constitutive heterochromatin in the centromeric regions of approximately 40 chromosomes. CMA3/DAPI fluorescence staining revealed extremely GC-rich signals in the pericentromeric region of one submetacentric chromosomal pair with size polymorphism. We detected telomeric signals at the end of all chromosomes and no interstitial signals.
Majtánová et al. (2019) Characterization of the karyotype and accumulation of repetitive sequences in Australian Darling hardyhead Craterocephalus amniculus (Atheriniformes, Teleostei). PeerJ 7:e7347 https://doi.org/10.7717/peerj.7347
Integrating phylogeographic and ecological niche approaches to delimitating cryptic lineages in the blue–green damselfish (Chromis viridis)
Species delimitation is challenging in sibling species/cryptic lineages because of the absence of clear diagnostic traits. However, integration of different approaches such as phylogeography and ecological niche comparison offers one potential approach to tease apart recently diverged lineages. In this study, we estimate the ecological niche divergence among lineages in Chromis viridis in a broad-scale phylogeographic framework to test whether the combination of these two approaches can effectively distinguish recently diverged lineages. Results from Cytb and Rag2 analyses identified two cryptic lineages (C. viridis A and C. viridis B) that diverged ∼3 Myr ago. Estimates of ecological niche divergence with 11 environmental parameters across the broad geographic range of these lineages showed overlapping ecological niches and niche conservatism. However, regardless of the incongruence between genetic and ecological niche divergence, the substantial genetic divergence between the two clades of C. viridis in both mtDNA and nuclear loci strong suggest that they are cryptic taxa.
Liu et al. (2019) Integrating phylogeographic and ecological niche approaches to delimitating cryptic lineages in the blue–green damselfish (Chromis viridis). PeerJ 7:e7384 https://doi.org/10.7717/peerj.7384