Transcriptome analysis and identification of key genes involved in 1-deoxynojirimycin biosynthesis of mulberry (Morus alba L.)
Mulberry (Morus alba L.) represents one of the most commonly utilized plants in traditional medicine and as a nutritional plant used worldwide. The polyhydroxylated alkaloid 1-deoxynojirimycin (DNJ) is the major bioactive compounds of mulberry in treating diabetes. However, the DNJ content in mulberry is very low. Therefore, identification of key genes involved in DNJ alkaloid biosynthesis will provide a basis for the further analysis of its biosynthetic pathway and ultimately for the realization of synthetic biological production. Here, two cDNA libraries of mulberry leaf samples with different DNJ contents were constructed. Approximately 16 Gb raw RNA-Seq data was generated and de novo assembled into 112,481 transcripts, with an average length of 766 bp and an N50 value of 1,392. Subsequently, all unigenes were annotated based on nine public databases; 11,318 transcripts were found to be significantly differentially regulated. A total of 38 unique candidate genes were identified as being involved in DNJ alkaloid biosynthesis in mulberry, and nine unique genes had significantly different expression. Three key transcripts of DNJ biosynthesis were identified and further characterized using RT-PCR; they were assigned to lysine decarboxylase and primary-amine oxidase genes. Five CYP450 transcripts and two methyltransferase transcripts were significantly associated with DNJ content. Overall, the biosynthetic pathway of DNJ alkaloid was preliminarily speculated.
Wang et al. (2018) Transcriptome analysis and identification of key genes involved in 1-deoxynojirimycin biosynthesis of mulberry (Morus alba L.). PeerJ 6:e5443 https://doi.org/10.7717/peerj.5443
Setting the stage: reviewing current knowledge on the health of New Zealand immigrants—an integrative review
The growth of migrant communities continues to rise globally, creating unique and complex health challenges. Literature on immigrant health in New Zealand (NZ) remains scant. This integrative literature review was conducted drawing on peer-reviewed research articles on immigrant health in NZ published between 2012 and 2018. The objectives were to: (i) provide a critical overview of immigrant health in NZ; (ii) identify general trends in health research conducted in NZ on immigrants; (iii) compare, contrast, and evaluate the quality of the information; (iv) develop a summary of research results and; (v) identify priorities and recommendations for future research. A search yielded more than 130 articles with 28 articles constituting the foundation of the review. This review is timely following the rapid increase in the scale, speed, and spread of immigration and its potential for changing NZ’s national health patterns and priorities. This integrative review led to the four primary conclusions. Firstly, migration in NZ is a gendered phenomenon, as there has been more women and girls arriving as migrants in NZ and being at risk of poor health in comparison with their male counterparts. Secondly, studies on infectious diseases take precedence over other health problems. Thirdly, research methodologies used to collect data may not be relevant to the cultural and traditional customs of the migrant populations. Furthermore, a number of research findings implemented have failed to meet the needs of NZ migrants. Lastly, policy initiatives are inclined more towards supporting health practitioners and lack a migrant centred approach. What is already known about this topic? Despite NZ becoming more ethnically and linguistically diverse, there is limited literature on the health of migrants living in NZ. What this paper adds? This integrative literature review provides a critical overview of refugee and migrant health in NZ through reviewing and critiquing the current literature available. This paper identifies research trends, the general health of migrants in NZ, recommendations that could inform future migrant and refugee health research and health policies and initiatives to ensure effective and relevant health service provision to migrants.
Kanengoni et al. (2018) Setting the stage: reviewing current knowledge on the health of New Zealand immigrants—an integrative review. PeerJ 6:e5184 https://doi.org/10.7717/peerj.5184
Fine-scale differentiation between Bacillus anthracis and Bacillus cereus group signatures in metagenome shotgun data
Background It is possible to detect bacterial species in shotgun metagenome datasets through the presence of only a few sequence reads. However, false positive results can arise, as was the case in the initial findings of a recent New York City subway metagenome project. False positives are especially likely when two closely related are present in the same sample. Bacillus anthracis, the etiologic agent of anthrax, is a high-consequence pathogen that shares >99% average nucleotide identity with Bacillus cereus group (BCerG) genomes. Our goal was to create an analysis tool that used k-mers to detect B. anthracis, incorporating information about the coverage of BCerG in the metagenome sample. Methods Using public complete genome sequence datasets, we identified a set of 31-mer signatures that differentiated B. anthracis from other members of the B. cereus group (BCerG), and another set which differentiated BCerG genomes (including B. anthracis) from other Bacillus strains. We also created a set of 31-mers for detecting the lethal factor gene, the key genetic diagnostic of the presence of anthrax-causing bacteria. We created synthetic sequence datasets based on existing genomes to test the accuracy of a k-mer based detection model. Results We found 239,503 B. anthracis-specific 31-mers (the Ba31 set), 10,183 BCerG 31-mers (the BCerG31 set), and 2,617 lethal factor k-mers (the lef31 set). We showed that false positive B. anthracis k-mers—which arise from random sequencing errors—are observable at high genome coverages of B. cereus. We also showed that there is a “gray zone” below 0.184× coverage of the B. anthracis genome sequence, in which we cannot expect with high probability to identify lethal factor k-mers. We created a linear regression model to differentiate the presence of B. anthracis-like chromosomes from sequencing errors given the BCerG background coverage. We showed that while shotgun datasets from the New York City subway metagenome project had no matches to lef31 k-mers and hence were negative for B. anthracis, some samples showed evidence of strains very closely related to the pathogen. Discussion This work shows how extensive libraries of complete genomes can be used to create organism-specific signatures to help interpret metagenomes. We contrast “specialist” approaches to metagenome analysis such as this work to “generalist” software that seeks to classify all organisms present in the sample and note the more general utility of a k-mer filter approach when taxonomic boundaries lack clarity or high levels of precision are required.
Petit III et al. (2018) Fine-scale differentiation between Bacillus anthracis and Bacillus cereus group signatures in metagenome shotgun data. PeerJ 6:e5515 https://doi.org/10.7717/peerj.5515
Unveiling community patterns and trophic niches of tropical and temperate ants using an integrative framework of field data, stable isotopes and fatty acids
Background The use and partitioning of trophic resources is a central aspect of community function. On the ground of tropical forests, dozens of ant species may be found together and ecological mechanisms should act to allow such coexistence. One hypothesis states that niche specialization is higher in the tropics, compared to temperate regions. However, trophic niches of most species are virtually unknown. Several techniques might be combined to study trophic niche, such as field observations, fatty acid analysis (FAA) and stable isotope analysis (SIA). In this work, we combine these three techniques to unveil partitioning of trophic resources in a tropical and a temperate community. We describe patterns of resource use, compare them between communities, and test correlation and complementarity of methods to unveil both community patterns and species’ niches. Methods Resource use was assessed with seven kinds of bait representing natural resources available to ants. Neutral lipid fatty acid (NLFA) profiles, and δ15N and δ13C isotope signatures of the species were also obtained. Community patterns and comparisons were analyzed with clustering, correlations, multivariate analyses and interaction networks. Results Resource use structure was similar in both communities. Niche breadths (H′) and network metrics (Q and H2′) indicated similar levels of generalization between communities. A few species presented more specialized niches, such as Wasmannia auropunctata and Lasius fuliginosus. Stable isotope signatures and NLFA profiles also indicated high generalization, although the latter differed between communities, with temperate species having higher amounts of fat and proportions of C18:1n9. Bait use and NLFA profile similarities were correlated, as well as species’ specialization indices (d′) for the two methods. Similarities in δ15N and bait use, and in δ13C and NLFA profiles, were also correlated. Discussion Our results agree with the recent view that specialization levels do not change with latitude or species richness. Partition of trophic resources alone does not explain species coexistence in these communities, and might act together with behavioral and environmental mechanisms. Temperate species presented NLFA patterns distinct from tropical ones, which may be related to environmental factors. All methods corresponded in their characterization of species’ niches to some extent, and were robust enough to detect differences even in highly generalized communities. However, their combination provides a more comprehensive picture of resource use, and it is particularly important to understand individual niches of species. FAA was applied here for the first time in ant ecology, and proved to be a valuable tool due to its combination of specificity and temporal representativeness. We propose that a framework combining field observations with chemical analysis is valuable to understand resource use in ant communities.
Rosumek et al. (2018) Unveiling community patterns and trophic niches of tropical and temperate ants using an integrative framework of field data, stable isotopes and fatty acids. PeerJ 6:e5467 https://doi.org/10.7717/peerj.5467
Contrasting gene flow at different spatial scales revealed by genotyping-by-sequencing in Isocladus armatus, a massively colour polymorphic New Zealand marine isopod
Understanding how genetic diversity is maintained within populations is central to evolutionary biology. Research on colour polymorphism (CP), which typically has a genetic basis, can shed light on this issue. However, because gene flow can homogenise genetic variation, understanding population connectivity is critical in examining the maintenance of polymorphisms. In this study we assess the utility of genotyping-by-sequencing to resolve gene flow, and provide a preliminary investigation into the genetic basis of CP in Isocladus armatus, an endemic New Zealand marine isopod. Analysis of the genetic variation in 4,000 single nucleotide polymorphisms (SNPs) within and among populations and colour morphs revealed large differences in gene flow across two spatial scales. Marine isopods, which lack a pelagic larval phase, are typically assumed to exhibit greater population structuring than marine invertebrates possessing a biphasic life cycle. However, we found high gene flow rates and no genetic subdivision between two North Island populations situated 8 km apart. This suggests that I. armatus is capable of substantial dispersal along coastlines. In contrast, we identified a strong genetic disjunction between North and South Island populations. This result is similar to those reported in other New Zealand marine species, and is congruent with the presence of a geophysical barrier to dispersal down the east coast of New Zealand. We also found some support for a genetic basis to colouration evidenced by positive FST outlier tests, with two SNPs in particular showing strong association to the expression of a striped morph. Our study provides one of the first population genomic studies of a marine organism in New Zealand, and suggests that genotyping-by-sequencing can be a good alternative to more traditional investigations based on traditional markers such as microsatellites. Our study provides a foundation for further development of a highly tractable system for research on the evolutionary maintenance of CP.
Wells et al. (2018) Contrasting gene flow at different spatial scales revealed by genotyping-by-sequencing in Isocladus armatus, a massively colour polymorphic New Zealand marine isopod. PeerJ 6:e5462 https://doi.org/10.7717/peerj.5462
Global mapping of potential natural vegetation: an assessment of machine learning algorithms for estimating land potential
Potential natural vegetation (PNV) is the vegetation cover in equilibrium with climate, that would exist at a given location if not impacted by human activities. PNV is useful for raising public awareness about land degradation and for estimating land potential. This paper presents results of assessing machine learning algorithms—neural networks (nnet package), random forest (ranger), gradient boosting (gbm), K-nearest neighborhood (class) and Cubist—for operational mapping of PNV. Three case studies were considered: (1) global distribution of biomes based on the BIOME 6000 data set (8,057 modern pollen-based site reconstructions), (2) distribution of forest tree taxa in Europe based on detailed occurrence records (1,546,435 ground observations), and (3) global monthly fraction of absorbed photosynthetically active radiation (FAPAR) values (30,301 randomly-sampled points). A stack of 160 global maps representing biophysical conditions over land, including atmospheric, climatic, relief, and lithologic variables, were used as explanatory variables. The overall results indicate that random forest gives the overall best performance. The highest accuracy for predicting BIOME 6000 classes (20) was estimated to be between 33% (with spatial cross-validation) and 68% (simple random sub-setting), with the most important predictors being total annual precipitation, monthly temperatures, and bioclimatic layers. Predicting forest tree species (73) resulted in mapping accuracy of 25%, with the most important predictors being monthly cloud fraction, mean annual and monthly temperatures, and elevation. Regression models for FAPAR (monthly images) gave an R-square of 90% with the most important predictors being total annual precipitation, monthly cloud fraction, CHELSA bioclimatic layers, and month of the year, respectively. Further developments of PNV mapping could include using all GBIF records to map the global distribution of plant species at different taxonomic levels. This methodology could also be extended to dynamic modeling of PNV, so that future climate scenarios can be incorporated. Global maps of biomes, FAPAR and tree species at one km spatial resolution are available for download via http://dx.doi.org/10.7910/DVN/QQHCIK.
Spatial and Geographic Information Science
Hengl et al. (2018) Global mapping of potential natural vegetation: an assessment of machine learning algorithms for estimating land potential. PeerJ 6:e5457 https://doi.org/10.7717/peerj.5457
Paleoneuroanatomy of the aetosaur Neoaetosauroides engaeus (Archosauria: Pseudosuchia) and its paleobiological implications among archosauriforms
The paleoneuroanatomy of pseudosuchian archosaurs is poorly known, based on direct examination of the internal morphology of braincases and a few artificial endocasts. Among aetosaurs, only one endocast has been described almost a century ago by Case (1921) corresponding to Desmatosuchus spurensis from the Chinle Formation (Norian) of Texas, US, based on a resin cast. Here, we describe the first natural endocast of an aetosaur, Neoaetosauroides engaeus from the Los Colorados Formation (Norian) of NW Argentina, and also developed the first digital endocast of this taxon including the encephalon, cranial nerves, inner ear, and middle ear sinuses. The neuroanatomy of Neoaetosauroides engaeus exhibits several differences from that of Desmatosuchus spurensis despite their phylogenetic proximity, which may be a reflection of their different habits. The information provided by the endocasts of Neoaetosauroides engaeus about its olfactory region and the orientation of its head, based on the inclination of the inner ear, could support the proposal for an animalivorous diet, instead of an herbivorous one as in most aetosaurs. The new information here obtained contributes to the knowledge of the neuroanatomical diversity of archosauriforms and more specifically among pseudosuchians and their paleobiological roles in the Triassic continental communities.
von Baczko et al. (2018) Paleoneuroanatomy of the aetosaur Neoaetosauroides engaeus (Archosauria: Pseudosuchia) and its paleobiological implications among archosauriforms. PeerJ 6:e5456 https://doi.org/10.7717/peerj.5456
Eye movement control during visual pursuit in Parkinson’s disease
Background Prior studies of oculomotor function in Parkinson’s disease (PD) have either focused on saccades without considering smooth pursuit, or tested smooth pursuit while excluding saccades. The present study investigated the control of saccadic eye movements during pursuit tasksand assessed the quality of binocular coordinationas potential sensitive markers of PD. Methods Observers fixated on a central cross while a target moved toward it. Once the target reached the fixation cross, observers began to pursue the moving target. To further investigate binocular coordination, the moving target was presented on both eyes (binocular condition), or on one eye only (dichoptic condition). Results The PD group made more saccades than age-matched normal control adults (NC) both during fixation and pursuit. The difference between left and right gaze positions increased over time during the pursuit period for PD but not for NC. The findings were not related to age, as NC and young-adult control group (YC) performed similarly on most of the eye movement measures, and were not correlated with classical measures of PD severity (e.g., Unified Parkinson’s Disease Rating Scale (UPDRS) score). Discussion Our results suggest that PD may be associated with impairment not only in saccade inhibition, but also in binocular coordination during pursuit, and these aspects of dysfunction may be useful in PD diagnosis or tracking of disease course.
Wu et al. (2018) Eye movement control during visual pursuit in Parkinson’s disease. PeerJ 6:e5442 https://doi.org/10.7717/peerj.5442
Environmental stressors may cause equine herpesvirus reactivation in captive Grévy’s zebras (Equus grevyi)
Equine Herpesviruses (EHV) are common and often latent pathogens of equids which can cause fatalities when transmitted to non-equids. Stress and elevated glucocorticoids have been associated with EHV reactivation in domestic horses, but little is known about the correlation between stress and viral reactivation in wild equids. We investigated the effect of an environmental stressor (social group restructuring following a translocation event) on EHV reactivation in captive Grévy’s zebras (Equus grevyi). A mare was translocated by road transport from Zoo Mulhouse, France, to join a resident group of three mares in Tierpark Berlin, Germany. We used an indirect sampling method to assess the frequency of EHV shedding for 14 days immediately after the translocation event (termed the ‘experimental period’). The results were compared with those from two control periods, one preceding and one subsequent to the experimental period. In addition, we measured fecal glucocorticoid metabolite (fGCM) concentrations daily in all individuals from 6 days before, to 14 days after translocation. We found significantly higher EHV shedding frequencies during the experimental period, compared to each of the two control periods. All animals showed significantly elevated fGCM concentrations, compared to fGCM levels before translocation. Finally, we found that an increase in fGCM concentration was significantly associated with an increased likelihood of EHV shedding. Although the small number of animals in the study limits the conclusions that can be drawn from the study, taken together, our results support the hypothesis that environmental stressors induce viral reactivation in wild equids. Our results suggest that potentials stressors such as group restructuring and translocation should be considered in the management of zoological collections to reduce the risk of fatal EHV infections in novel hosts. Moreover, environmental stressors may play an important role in EHV reactivation and spread in wild equid populations.
Seeber et al. (2018) Environmental stressors may cause equine herpesvirus reactivation in captive Grévy’s zebras (Equus grevyi). PeerJ 6:e5422 https://doi.org/10.7717/peerj.5422
Expectancy effects in the Autonomous Sensory Meridian Response
The Autonomous Sensory Meridian Response (ASMR) is a tingling, almost euphoric, sensation often elicited following certain visual or auditory stimulations (Barratt & Davis, 2015). Despite considerable media attention, little empirical work has investigated the underlying mechanisms. In the present study, ASMR enthusiasts and naïve observers listened to audio clips with and without ASMR-eliciting characteristics. We also manipulated participants’ expectations of ASMR, providing a measure of “placebo effects.” Although naïve participants were susceptible to suggestive instructions, experienced users were not, suggesting that initial exposure to ASMR media may evoke somatosensory responses consistent with one’s expectations. Implications for at-home stress management techniques are discussed.
Cash et al. (2018) Expectancy effects in the Autonomous Sensory Meridian Response. PeerJ 6:e5229 https://doi.org/10.7717/peerj.5229