Draft Aphaenogaster genomes expand our view of ant genome size variation across climate gradients
Given the abundance, broad distribution, and diversity of roles that ants play in many ecosystems, they are an ideal group to serve as ecosystem indicators of climatic change. At present, only a few whole-genome sequences of ants are available (19 of >16,000 species), mostly from tropical and sub-tropical species. To address this limited sampling, we sequenced genomes of temperate-latitude species from the genus Aphaenogaster, a genus with important seed dispersers. In total, we sampled seven colonies of six species: Aphaenogaster ashmeadi, Aphaenogaster floridana, Aphaenogaster fulva, Aphaenogaster miamiana, Aphaenogaster picea, and Aphaenogaster rudis. The geographic ranges of these species collectively span eastern North America from southern Florida to southern Canada, which encompasses a latitudinal gradient in which many climatic variables are changing rapidly. For the six genomes, we assembled an average of 271,039 contigs into 47,337 scaffolds. The Aphaenogaster genomes displayed high levels of completeness with 96.1% to 97.6% of Hymenoptera BUSCOs completely represented, relative to currently sequenced ant genomes which ranged from 88.2% to 98.5%. Additionally, the mean genome size was 370.5 Mb, ranging from 310.3 to 429.7, which is comparable to that of other sequenced ant genomes (212.8–396.0 Mb) and flow cytometry estimates (210.7–690.4 Mb). In an analysis of currently sequenced ant genomes and the new Aphaenogaster sequences, we found that after controlling for both spatial autocorrelation and phylogenetics ant genome size was marginally correlated with sample site climate similarity. Of all examined climate variables, minimum temperature, and annual precipitation had the strongest correlations with genome size, with ants from locations with colder minimum temperatures and higher levels of precipitation having larger genomes. These results suggest that climate extremes could be a selective force acting on ant genomes and point to the need for more extensive sequencing of ant genomes.
Lau et al. (2019) Draft Aphaenogaster genomes expand our view of ant genome size variation across climate gradients. PeerJ 7:e6447 https://doi.org/10.7717/peerj.6447
A systematic comparison of eight new plastome sequences from Ipomoea L
Background Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato’s close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798–30,910 bp each) separated by a large single copy (LSC) region (87,575–88,004 bp) and a small single copy (SSC) region (12,018–12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57–89 pairs of repetitive sequences and 39–64 simple sequence repeats were found. By conducting a sliding window analysis, we found six relatively high variable regions (ndhA intron, ndhH-ndhF, ndhF-rpl32, rpl32-trnL, rps16-trnQ, and ndhF) in the Ipomoea genus, eight (trnG, rpl32-trnL, ndhA intron, ndhF-rpl32, ndhH-ndhF, ccsA-ndhD, trnG-trnR, and pasA-ycf3) in the Batatas group, and eight (ndhA intron, petN-psbM, rpl32-trnL, trnG-trnR, trnK-rps16, ndhC-trnV, rps16-trnQ, and trnG) in the Quamoclit group. Our maximum-likelihood tree based on whole chloroplast genomes confirmed the phylogenetic topology reported in previous studies. Conclusions The chloroplast genome sequence and structure were highly conserved in the eight newly-sequenced Ipomoea species. Our comparative analysis included a broad range of Ipomoea chloroplast genomes, providing valuable information for Ipomoea species identification and enhancing the understanding of Ipomoea genetic resources.
Sun et al. (2019) A systematic comparison of eight new plastome sequences from Ipomoea L. PeerJ 7:e6563 https://doi.org/10.7717/peerj.6563
The distributive and structural characteristics of bronchus-associated lymphoid tissue (BALT) in Bactrian camels (Camelus bactrianus)
Background Bronchus-associated lymphoid tissue (BALT), distributed in the bronchial mucosa, plays a critical role in maintaining the mucosal immune homeostasis of the lower respiratory tract. The bronchial tree is a functional structure for gas exchange with the outside environment and maintains basic lung morphology. Methods To explore the structural and distributive characteristics of BALT in Bactrian camels, twelve healthy adult Bactrian camels were divided into two groups (six in each group). The lungs, bronchial tree and BALT were observed and analysed systematically through anatomical and histological methods. Results The results showed that Bactrian camel lungs were constituted by the left cranial lobe, left caudal lobe, right cranial lobe, right caudal lobe and accessory lobe, but lacked the middle lobe. The cranial lobe was narrow and small, the caudal lobe was extremely developed (almost four times the cranial lobe in size), and the accessory lobe was smaller than the cranial lobe; the bronchial tree, an unequal dichotomy with a tracheobronchial branch, was composed of dorsal, ventral, lateral and medial bronchiole systems. Isolated lymphoid follicles (the chief type) and aggregates of lymphoid follicles revealed two types of BALT, and germinal centres, follicle-associated epithelium and high endothelial venules could be observed in some well-developed BALT. Additionally, BALT was scattered along the bronchial tree in the entire lung, and the density increased from the trachea to the lower graded branches (densest in the bronchioles) and then decreased, with the occasional location around respiratory bronchioles or among the pulmonary mesenchyme. In the conducting portion, BALT was primarily located in the mucosa lamina propria but was also found in the submucosa, under the muscular layer, and around the submucosal glands and cartilage. Conclusion The results demonstrated that the lung morphology of Bactrian camels was similar to that of horses, but the bronchial branches were more closely related to those of ruminants. These characteristics were in accordance with the morphological and structural variation regularity of lungs with species evolution. BALT was mainly scattered in the conducting portion, and bronchioles, as the final “checkpoint” in the surveillance, capture and recognition of antigens before pulmonary exchange, were the pivotal locational position of BALT. However, BALT at different depths of the bronchial wall of the conducting portion might be at different developmental stages. Our study provided evidence for further insight into the mucosal immunomodulatory mechanism of BALT in the respiratory system of Bactrian camels.
He et al. (2019) The distributive and structural characteristics of bronchus-associated lymphoid tissue (BALT) in Bactrian camels (Camelus bactrianus). PeerJ 7:e6571 https://doi.org/10.7717/peerj.6571
Anatomical location of AICA loop in CPA as a prognostic factor for ISSNHL
The cerebellopontine angle (CPA) is a triangular-shaped space that lies at the junction of the pons and cerebellum. It contains cranial nerves and the anterior inferior cerebellar artery (AICA). The anatomical shape and location of the AICA is variable within the CPA and internal auditory canal (IAC). A possible etiology of idiopathic sudden sensorineural hearing loss (ISSNHL) is ischemia of the labyrinthine artery, which is a branch of the AICA. As such, the position of the AICA within the CPA and IAC may be related to the clinical development of ISSNHL. We adopted two methods to classify the anatomic position of the AICA, then analyzed whether these classifications affected the clinical features and prognosis of ISSNHL. We retrospectively reviewed patient data from January 2015 to March 2018. Two established classification methods designed by Cahvada and Gorrie et al. were used. Pure tone threshold at four different frequencies (0.5, 1, 4, and 8 kHz), at two different time points (at initial presentation and three months after treatment), were analyzed. We compared the affected and unaffected ears, and investigated whether there were any differences in hearing recovery and symptoms between the two classification types. There was no difference in AICA types between ears with and without ISSNHL. Patients who had combined symptoms such as tinnitus and vertigo did not show a different AICA distribution compared with patients who did not. There were differences in quantitative hearing improvement between AICA types, although without statistic significance (p = 0.09–0.13). At two frequencies, 1 and 4 kHz, there were differences in Chavda types between hearing improvement and no improvement (p < 0.05). Anatomical variances of the AICA loop position did not affect the incidence of ISSNHL or co-morbid symptoms including tinnitus and vertigo. In contrast, comparisons of hearing improvement based on Chavda type classification showed a statistical difference, with a higher proportion of Chavda type 1 showing improvements in hearing (AICA outside IAC).
Kim et al. (2019) Anatomical location of AICA loop in CPA as a prognostic factor for ISSNHL. PeerJ 7:e6582 https://doi.org/10.7717/peerj.6582
Numerical ability and improvement through interindividual cooperation varied between two cyprinid fish species, qingbo and crucian carp
We used qingbo (Spinibarbus sinensis) and Chinese crucian carp (Carassius auratus) to test whether numerical discrimination could be improved by the coexistence and possible cooperation of conspecies or heterospecies. We conducted a spontaneous shoal choice test of singletons, conspecific dyads and heterospecific dyads under different numerical comparisons (8 vs. 12, 9 vs. 12 and 10 vs. 12). Singletons of qingbo could discriminate only 8 vs. 12, whereas the dyads of qingbo showed better numerical acuity, as they could discriminate 10 vs. 12. Crucian carp may have poor numerical ability, as both singleton and dyads showed no significant preference for larger stimulus shoals, even at the ‘easier’ numerical discrimination, that is, 8 vs. 12. Furthermore, heterospecific dyads of crucian carp and qingbo did not show significant preference for larger shoals at any numerical comparison in the present study. It is suggested that both the numerical ability and the possibility for improvement by interindividual interaction and hence cooperation might vary among fish species, and the interaction between heterospecies in the present study showed negative effect on numerical ability possibly due to the different behavioural and cognitive traits which make the information transfer and consensus difficult to reach.
Xiong et al. (2019) Numerical ability and improvement through interindividual cooperation varied between two cyprinid fish species, qingbo and crucian carp. PeerJ 7:e6619 https://doi.org/10.7717/peerj.6619
Chronic fluoxetine treatment of juvenile zebrafish (Danio rerio) does not elicit changes in basal cortisol levels and anxiety-like behavior in adulthood
Exposure to selective serotonin reuptake inhibitors (SSRIs) during development may elicit long-term neuroadaptive changes that could alter the basal regulation of stress-associated physiological and behavioral processes later in life. Currently, the effects of juvenile fluoxetine exposure in rodent models appear to be dependent on the developmental window targeted as well as the duration of drug exposure. The zebrafish (Danio rerio) model is rapidly becoming a useful tool in pharmacological research and can be used to help elucidate some of the long-term effects of fluoxetine exposure prior to sexual maturation on neuroendocrine and behavioral stress markers. In the current study, juvenile zebrafish were chronically exposed to fluoxetine hydrochloride (0 or 100 μg/L) for 14 days (31–44 days post-fertilization (dpf)), then were left untreated until young adulthood. Starting at 90 dpf, basal neuroendocrine stress and behavioral responses of zebrafish were assessed. Cortisol was extracted from the young adult zebrafish body (trunk) and quantified via enzyme-linked immunosorbent assay (ELISA). Anxiety-like behaviors were assessed in response to introduction to the novel tank test. It was expected that juvenile exposure to fluoxetine would (1) reduce basal cortisol levels and (2) elicit anxiolytic effects in the novel tank test in adulthood. However, fluoxetine exposure during the juvenile period was not associated with alterations in basal levels of cortisol nor were there any significant changes in anxiety-like behavior in the young adult zebrafish. Thus, in zebrafish, it does not appear that SSRI exposure during the juvenile period has a long-term adverse or maladaptive impact on the basal expression of cortisol and anxiety-like behavior in adulthood. Further studies are needed to determine if SSRI exposure during this developmental window influences neuroendocrine and behavioral responses to acute stress.
Petrunich-Rutherford (2019) Chronic fluoxetine treatment of juvenile zebrafish (Danio rerio) does not elicit changes in basal cortisol levels and anxiety-like behavior in adulthood. PeerJ 7:e6407 https://doi.org/10.7717/peerj.6407
In vitro observation: the GFP-E. coli adhering to porcine erythrocytes can be removed by porcine alveolar macrophages
Although the activation of pathogen phagocytosis via complement system has been studied, erythrocyte-phagocyte interactions in pigs are not clearly understood. Therefore, we sought to investigate the ability of porcine erythrocytes to clear immune complexes (ICs) by using laser confocal microscopy and flow cytometry to observe the immune adhesion of porcine erythrocytes to fluorescent bacilli and the immune presentation process of transferring fluorescent bacilli to macrophages. Isolated porcine alveolar macrophages (PAMs) had uniform morphology and size, and a survival rate of 97.2%. The phagocytosis rate was 98.8%. After WT E. coli was labeled with Fluorescein Isothiocyanate (FITC), the bacteria showed a bright green fluorescence, and the labeling rate was 92.3%. When laser confocal microscopy was utilized to observe the co-incubation system of porcine erythrocytes, PAM, and fluorescent E. coli, the fluorescence intensity of bacilli decreased with increasing observation time and even disappeared. Flow Cytometry examination showed that the average fluorescence intensity of PAMs co-incubated with porcine erythrocytes adhered to WT-E. coli-FITC, was significantly higher than that of normal PAMs. Furthermore, when porcine erythrocytes adhered to WT E. coli were incubated with PAMs, the surface mean fluorescence intensity of porcine erythrocytes was significantly higher than that of the blank control group. This shows that PAMs can competitively bind to the oposinized E. coli adhered to the surface of porcine erythrocytes, and these oposinized pathogens can enter macrophages by the process of phagocytosis, which promoting the internalization of ICs or pathogens. During this process, the physical morphology of porcine erythrocytes was not damaged, but the levels of its main functional protein CR1-like were reduced.
Yin et al. (2019) In vitro observation: the GFP-E. coli adhering to porcine erythrocytes can be removed by porcine alveolar macrophages. PeerJ 7:e6439 https://doi.org/10.7717/peerj.6439
A multi-year experiment shows that lower precipitation predictability encourages plants’ early life stages and enhances population viability
Climate change is a key factor that may cause the extinction of species. The associated reduced weather predictability may alter the survival of plants, especially during their early life stages, when individuals are most fragile. While it is expected that extreme weather events will be highly detrimental for species, the effects of more subtle environmental changes have been little considered. In a four-year experiment on two herbaceous plants, Papaver rhoeas and Onobrychis viciifolia, we manipulated the predictability of precipitation by changing the temporal correlation of precipitation events while maintaining average precipitation constant, leading to more and less predictable treatments. We assessed the effect of predictability on plant viability in terms of seedling emergence, survival, seed production, and population growth rate. We found greater seedling emergence, survival, and population growth for plants experiencing lower intra-seasonal predictability, but more so during early compared to late life stages. Since predictability levels were maintained across four generations, we have also tested whether descendants exhibited transgenerational responses to previous predictability conditions. In P. rhoeas, descendants had increased the seedling emergence compared to ancestors under both treatments, but more so under lower precipitation predictability. However, higher predictability in the late treatment induced higher survival in descendants, showing that these conditions may benefit long-term survival. This experiment highlights the ability of some plants to rapidly exploit environmental resources and increase their survival under less predictable conditions, especially during early life stages. Therefore, this study provides relevant evidence of the survival capacity of some species under current and future short-term environmental alterations.
March-Salas et al. (2019) A multi-year experiment shows that lower precipitation predictability encourages plants’ early life stages and enhances population viability. PeerJ 7:e6443 https://doi.org/10.7717/peerj.6443
Modulating pain thresholds through classical conditioning
Background Classical conditioning has frequently been shown to be capable of evoking fear of pain and avoidance behavior in the context of chronic pain. However, whether pain itself can be conditioned has rarely been investigated and remains a matter of debate. Therefore, the present study investigated whether pain threshold ratings can be modified by the presence of conditioned non-nociceptive sensory stimuli in healthy participant. Methods In 51 healthy volunteers, pain threshold to electrocutaneous stimuli was determined prior to participation in a simultaneous conditioning paradigm. Participants underwent an acquisition phase in which one non-painful vibrotactile stimulus (CS+) was repeatedly paired with a painful electrocutaneous stimulus, whereas a second vibrotactile stimulus of the same quality and intensity (CS−) was paired with a non-painful electrocutaneous stimulus. Stimulation was provided on the lower back with close proximity between the conditioned stimulus and the unconditioned stimulus. In the test phase, electrocutaneous stimuli at the individually-set threshold intensity were simultaneously delivered together with either a CS+ or CS−. Pain intensity ratings were obtained after each trial; expectancy ratings were obtained after each block. The primary outcome was the percentage of test stimuli that were rated as painful. Results Test stimuli were more likely to be rated as painful when they were paired with the CS+ than when they were paired with the CS−. This effect was not influenced by contingency awareness, nor by expectancies or mood states. Discussion The findings support the notion that the judgement of an event being painful or non-painful can be influenced by classical conditioning and corroborate the possible role of associative learning in the development and maintenance of chronic pain.
Traxler et al. (2019) Modulating pain thresholds through classical conditioning. PeerJ 7:e6486 https://doi.org/10.7717/peerj.6486
Aboveground carbon of community-managed Chirpine (Pinus roxburghii Sarg.) forests of Nepal based on stand types and geographic aspects
On a global scale, about 15.5% of forests are administered through community-based forestry programs that offer the opportunity for enhanced carbon sequestration while maintaining the supply of more traditional goods and services such as cooking fuels, animal fodder and bedding. A challenge in community forest (CF) management is to realize their carbon value without compromising their role in the provision of these traditional goods and services. In this study of CF dominated by Pinus roxburghii in the Phalebas region of Nepal, the impacts of stand composition and geographic aspect on aboveground forest carbon is investigated as a means to optimize CF management for both traditional values and for emerging carbon market values. The aboveground carbon of mixed and monospecific stands of Pinus roxburghii was estimated using a combination of destructive sampling and species-specific allometric equations. On average, monospecific stands contained 106.2 Mg C ha−1 in aboveground tree biomass, significantly more than mixed stands at 73.1 Mg C ha−1 (p = 0.022). Similarly, stands growing on northern aspects (northeast 124.8 Mg C ha−1, northwest 100.9 Mg C ha−1) stored significantly more carbon (p = 0.002) than southern aspects (southeast 75.3 Mg C ha−1, southwest 57.6 Mg C ha−1), reflecting the more favorable growing conditions of northern aspects. These results suggest monospecific stands planted on northern aspects may be best suited for management to achieve carbon benefits, whilst mixed-species stands on southern aspects may be better suited for biodiversity conservation and supporting livelihoods. To maintain and increase carbon value, community forestry may need to implement nutrient return practices to limit the impact of sustained nutrient removals on stand productivity.
Pariyar et al. (2019) Aboveground carbon of community-managed Chirpine (Pinus roxburghii Sarg.) forests of Nepal based on stand types and geographic aspects. PeerJ 7:e6494 https://doi.org/10.7717/peerj.6494