Systematic analysis of NAC transcription factors in Gossypium barbadense uncovers their roles in response to Verticillium wilt
As one of the largest plant-specific gene families, the NAC transcription factor gene family plays important roles in various plant physiological processes that are related to plant development, hormone signaling, and biotic and abiotic stresses. However, systematic investigation of the NAC gene family in sea-island cotton (Gossypium babardense L.) has not been reported, to date. The recent release of the complete genome sequence of sea-island cotton allowed us to perform systematic analyses of G. babardense NAC GbNAC) genes. In this study, we performed a genome-wide survey and identified 270 GbNAC genes in the sea-island cotton genome. Genome mapping analysis showed that GbNAC genes were unevenly distributed on 26 chromosomes. Through phylogenetic analyses of GbNACs along with their Arabidopsis counterparts, these proteins were divided into 10 groups (I–X), and each contained a different number of GbNACs with a similar gene structure and conserved motifs. One hundred and fifty-four duplicated gene pairs were identified, and almost all of them exhibited strong purifying selection during evolution. In addition, various cis-acting regulatory elements in GbNAC genes were found to be related to major hormones, defense and stress responses. Notably, transcriptome data analyses unveiled the expression profiles of 62 GbNAC genes under Verticillium wilt (VW) stress. Furthermore, the expression profiles of 15 GbNAC genes tested by quantitative real-time PCR (qPCR) demonstrated that they were sensitive to methyl jasmonate (MeJA) and salicylic acid (SA) treatments and that they could be involved in pathogen-related hormone regulation. Taken together, the genome-wide identification and expression profiling pave new avenues for systematic functional analysis of GbNAC candidates, which may be useful for improving cotton defense against VW.
Liu et al. (2019) Systematic analysis of NAC transcription factors in Gossypium barbadense uncovers their roles in response to Verticillium wilt. PeerJ 7:e7995 https://doi.org/10.7717/peerj.7995
Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales
Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.
Näpflin et al. (2019) Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales. PeerJ 7:e8013 https://doi.org/10.7717/peerj.8013
A pilot study—genetic diversity and population structure of snow leopards of Gilgit-Baltistan, Pakistan, using molecular techniques
Background The Hindu Kush and Karakoram mountain ranges in Pakistan’s northern areas are a natural habitat of the snow leopard (Panthera uncia syn. Uncia uncia) but the ecological studies on this animal are scarce since it is human shy by nature and lives in difficult mountainous tracts. The pilot study is conducted to exploit the genetic diversity and population structure of the snow leopard in this selected natural habitat of the member of the wildcat family in Pakistan. Method About 50 putative scat samples of snow leopard from five localities of Gilgit-Baltistan (Pakistan) along with a control sample of zoo maintained male snow leopard were collected for comparison. Significant quality and quantity of genomic DNA was extracted from scat samples using combined Zhang–phenol–chloroform method and successful amplification of cytochrome c oxidase I gene (190 bp) using mini-barcode primers, seven simple sequence repeats (SSR) markers and Y-linked AMELY gene (200 bp) was done. Results Cytochrome c oxidase I gene sequencing suggested that 33/50 (66%) scat samples were of snow leopard. AMELY primer suggested that out of 33 amplified samples, 21 (63.63%) scats were from male and 12 (36.36%) from female leopards. Through successful amplification of DNA of 25 out of 33 (75.75%) scat samples using SSR markers, a total of 68 alleles on seven SSR loci were identified, showing low heterozygosity, while high gene flow between population. Discussion The low gene flow rate among the population results in low genetic diversity causing decreased diversification. This affects the adaptability to climatic changes, thus ultimately resulting in decreased population size of the species.
Aruge et al. (2019) A pilot study—genetic diversity and population structure of snow leopards of Gilgit-Baltistan, Pakistan, using molecular techniques. PeerJ 7:e7672 https://doi.org/10.7717/peerj.7672
Characterization of the acoustic community of vocal fishes in the Azores
Sounds produced by teleost fishes are an important component of marine soundscapes, making passive acoustic monitoring (PAM) an effective way to map the presence of vocal fishes with a minimal impact on ecosystems. Based on a literature review, we list the known soniferous fish species occurring in Azorean waters and compile their sounds. We also describe new fish sounds recorded in Azores seamounts. From the literature, we identified 20 vocal fish species present in Azores. We analysed long-term acoustic recordings carried out since 2008 in Condor and Princesa Alice seamounts and describe 20 new putative fish sound sequences. Although we propose candidates as the source of some vocalizations, this study puts into evidence the myriad of fish sounds lacking species identification. In addition to identifying new sound sequences, we provide the first marine fish sound library for Azores. Our acoustic library will allow to monitor soniferous fish species for conservation and management purposes.
Carriço et al. (2019) Characterization of the acoustic community of vocal fishes in the Azores. PeerJ 7:e7772 https://doi.org/10.7717/peerj.7772
MHC class I allele diversity in cynomolgus macaques of Vietnamese origin
Cynomolgus macaques (Macaca fascicularis, Mafa) have been used as important experimental animal models for carrying out biomedical researches. The results of biomedical experiments strongly depend on the immunogenetic background of animals, especially on the diversity of major histocompatibility complex (MHC) alleles. However, there is much less information available on the polymorphism of MHC class I genes in cynomolgus macaques, than is currently available for humans. In this study, we have identified 40 Mafa-A and 60 Mafa-B exons 2 and 3 sequences from 30 unrelated cynomolgus macaques of Vietnamese origin. Among these alleles, 28 are novel. As for the remaining 72 known alleles, 15 alleles are shared with other cynomolgus macaque populations and 32 are identical to alleles previously reported in other macaque species. A potential recombination event was observed between Mafa-A1*091:02 and Mafa-A1*057:01. In addition, the Mafa-A1 genes were found to be more diverse than human HLA-A and the functional residues for peptide binding sites (PBS) or TCR binding sites (TBS) in Mafa-A1 have greater variability than that for non-PBS or non-TBS regions. Overall, this study provides important information on the diversity of Mafa-A and Mafa-B alleles from Vietnamese origin, which may help researchers to choose the most appropriate animals for their studies.
Huang et al. (2019) MHC class I allele diversity in cynomolgus macaques of Vietnamese origin. PeerJ 7:e7941 https://doi.org/10.7717/peerj.7941
Allelic variant in SLC6A3 rs393795 affects cerebral regional homogeneity and gait dysfunction in patients with Parkinson’s disease
Aims We sought to explore the role of the SLC6A3 rs393795 allelic variant in cerebral spontaneous activity and clinical features in Parkinson’s disease (PD) via imaging genetic approach. Methods Our study recruited 50 PD and 45 healthy control (HC) participants to provide clinical, genetic, and resting state functional magnetic resonance imaging (rs-fMRI) data. All subjects were separated into 16 PD-AA, 34 PD-CA/CC, 14 HC-AA, and 31 HC-CA/CC four subgroups according to SLC6A3 rs393795 genotyping. Afterwards, main effects and interactions of groups (PD versus HC) and genotypes (AA versus CA/CC) on cerebral function reflected by regional homogeneity (ReHo) were explored using two-way analysis of covariance (ANCOVA) after controlling age and gender. Finally, Spearman’ s correlations were employed to investigate the relationships between significantly interactive brain regions and clinical manifestations in PD subgroups. Results Compared with HC subjects, PD patients exhibited increased ReHo signals in left middle temporal gyrus and decreased ReHo signals in left pallidum. Compared with CA/CC carriers, AA genotype individuals showed abnormal increased ReHo signals in right inferior frontal gyrus (IFG) and supplementary motor area (SMA). Moreover, significant interactions (affected by both disease factor and allelic variation) were detected in right inferior temporal gyrus (ITG). Furthermore, aberrant increased ReHo signals in right ITG were observed in PD-AA in comparison with PD-CA/CC. Notably, ReHo values in right ITG were negatively associated with Tinetti Mobility Test (TMT) gait subscale scores and positively related to Freezing of Gait Questionnaire (FOG-Q) scores in PD-AA subgroup. Conclusions Our findings suggested that SLC6A3 rs393795 allelic variation might have a trend to aggravate the severity of gait disorders in PD patients by altering right SMA and IFG function, and ultimately result in compensatory activation of right ITG. It could provide us with a new perspective for exploring deeply genetic mechanisms of gait disturbances in PD.
Wang et al. (2019) Allelic variant in SLC6A3 rs393795 affects cerebral regional homogeneity and gait dysfunction in patients with Parkinson’s disease. PeerJ 7:e7957 https://doi.org/10.7717/peerj.7957
Squirrel monkey responses to information from social demonstration and individual exploration using touchscreen and object choice tasks
We aimed to study whether a non-human primate species responded differently to information acquired socially compared with that acquired individually. To do so, we attempted to train squirrel monkeys to perform binary discriminations. These involved exposure to either social information (human or puppet demonstrator performs an initial ‘information trial’) or individual exploration (monkey performs information trial as well as subsequent test trials). In Experiment 1, we presented the task on a touchscreen tablet. Only one monkey appeared to learn the significance of the information trial, and across the group there was no improvement in performance over sessions. The proficient individual showed little evidence of successful transfer to three-way discrimination problems, suggesting limited representation of the task structure. In Experiment 2, we used a logically identical task, presented as a physical object choice (inverted cups concealing a food reward). No monkeys learned to use the information trial cues, and success again did not increase over sessions. We concluded that the monkeys’ poor performance in Experiment 1 was not attributable to the mode of presentation (touchscreen), but reflected real difficulties with mastering the task structure. For both experiments, we analysed the monkeys’ spontaneous responses to the different trial types (social-win, social-lose, individual-win, and individual-lose). We found that monkeys had a tendency to repeat selections made during the information trial, whether these were made by themselves or by a demonstrator. This tendency to repeat was observed even following lose trials (i.e. when incorrect). Apparent ‘success’ following win trials was probably largely an artefact of behavioural inertia (individual learning conditions) and stimulus enhancement (social learning conditions), rather than sensitivity to the reward cues associated with that stimulus. Although monkeys did respond somewhat differently (more repeats) following win trials, compared with lose trials, this was no more apparent in the object choice task than the touchscreen task, again suggesting that the less ecologically valid presentation medium did not actively disrupt potential for learning the discrimination rule. Both touchscreen and physical object choice tasks appear to be valid methods to study learning in squirrel monkeys, with neither method giving a clear performance advantage over the other. However, this population did not master the contingencies in these tasks.
Renner et al. (2019) Squirrel monkey responses to information from social demonstration and individual exploration using touchscreen and object choice tasks. PeerJ 7:e7960 https://doi.org/10.7717/peerj.7960
Correction of estimation bias of predictive equations of energy expenditure based on wrist/waist-mounted accelerometers
Background Using wearable inertial sensors to accurately estimate energy expenditure (EE) during an athletic training process is important. Due to the characteristics of inertial sensors, however, the positions in which they are worn can produce signals of different natures. To understand and solve this issue, this study used the heart rate reserve (HRR) as a compensation factor to modify the traditional empirical equation of the accelerometer EE sensor and examine the possibility of improving the estimation of energy expenditure for sensors worn in different positions. Methods Indirect calorimetry was used as the criterion measure (CM) to measure the EE of 90 healthy adults on a treadmill (five speeds: 4.8, 6.4, 8.0, 9.7, and 11.3 km/h). The measurement was simultaneously performed with the ActiGraph GT9X-Link (placed on the wrist and waist) with the Polar H10 Heart Rate Monitor. Results At the same exercise intensity, the EE measurements of the GT9X on the wrist and waist had significant differences from those of the CM (p < 0.05). By using multiple regression analysis—utilizing values from vector magnitudes (VM), body weight (BW) and HRR parameters—accuracy of EE estimation was greatly improved compared to traditional equation. Modified models explained a greater proportion of variance (R2) (wrist: 0.802; waist: 0.805) and demonstrated a good ICC (wrist: 0.863, waist: 0.889) compared to Freedson’s VM3 Combination equation (R2: wrist: 0.384, waist: 0.783; ICC: wrist: 0.073, waist: 0.868). Conclusions The EE estimation equation combining the VM of accelerometer measurements, BW and HRR greatly enhanced the accuracy of EE estimation based on data from accelerometers worn in different positions, particularly from those on the wrist.
Ho et al. (2019) Correction of estimation bias of predictive equations of energy expenditure based on wrist/waist-mounted accelerometers. PeerJ 7:e7973 https://doi.org/10.7717/peerj.7973
Geographic origin and timing of colonization of the Pacific Coast of North America by the rocky shore gastropod Littorina sitkana
The demographic history of a species can have a lasting impact on its contemporary population genetic structure. Northeastern Pacific (NEP) populations of the rocky shore gastropod Littorina sitkana have very little mitochondrial DNA (mtDNA) sequence diversity and show no significant population structure despite lacking dispersive planktonic larvae. A contrasting pattern of high mtDNA diversity in the northwestern Pacific (NWP) suggests that L. sitkana may have recently colonized the NEP from the NWP via stepping-stone colonization through the Aleutian-Commander Archipelago (ACA) following the end of the last glacial 20,000 years ago. Here, we use multi-locus sequence data to test that hypothesis using a combination of descriptive statistics and population divergence modeling aimed at resolving the timing and the geographic origin of NEP populations. Our results show that NEP populations share a common ancestor with a population of L. sitkana on the Kamchatka Peninsula ∼46,900 years ago and that NEP populations diverged from each other ∼21,400 years ago. A more recent population divergence between Kamchatka and NEP populations, than between Kamchatka and other populations in the NWP, suggests that the ACA was the most probable dispersal route. Taking into account the confidence intervals for the estimates, we conservatively estimate that L. sitkana arrived in the NEP between 107,400 and 4,100 years ago, a range of dates that is compatible with post-glacial colonization of the NEP. Unlike other congeners that are relatively abundant in the Pleistocene fossil record of the NEP, only one report of L. sitkana exists from the NEP fossil record. Although broadly consistent with the molecular data, the biogeographic significance of these fossils is difficult to evaluate, as the shells cannot be distinguished from the closely-related congener L. subrotundata.
Marko et al. (2019) Geographic origin and timing of colonization of the Pacific Coast of North America by the rocky shore gastropod Littorina sitkana. PeerJ 7:e7987 https://doi.org/10.7717/peerj.7987
The effect of social information from live demonstrators compared to video playback on blue tit foraging decisions
Video playback provides a promising method to study social interactions, and the number of video playback experiments has been growing in recent years. Using videos has advantages over live individuals as it increases the repeatability of demonstrations, and enables researchers to manipulate the features of the presented stimulus. How observers respond to video playback might, however, differ among species, and the efficacy of video playback should be validated by investigating if individuals’ responses to videos are comparable to their responses to live demonstrators. Here, we use a novel foraging task to compare blue tits’ (Cyanistes caeruleus) responses to social information from a live conspecific vs video playback. Birds first received social information about the location of food, and were then presented with a three-choice foraging task where they could search for food from locations marked with different symbols (cross, square, plain white). Two control groups saw only a foraging tray with similar symbols but no information about the location of food. We predicted that socially educated birds would prefer the same location where a demonstrator had foraged, but we found no evidence that birds copied a demonstrator’s choice, regardless of how social information was presented. Social information, however, had an influence on blue tits’ foraging choices, as socially educated birds seemed to form a stronger preference for a square symbol (against two other options, cross and plain white) than the control birds. Our results suggest that blue tits respond to video playback of a conspecific similarly as to a live bird, but how they use this social information in their foraging decisions, remains unclear.
Hämäläinen et al. (2019) The effect of social information from live demonstrators compared to video playback on blue tit foraging decisions. PeerJ 7:e7998 https://doi.org/10.7717/peerj.7998