New mammalian and avian records from the late Eocene La Meseta and Submeseta formations of Seymour Island, Antarctica
The middle–late Eocene of Antarctica was characterized by dramatic change as the continent became isolated from the other southern landmasses and the Antarctic Circumpolar Current formed. These events were crucial to the formation of the permanent Antarctic ice cap, affecting both regional and global climate change. Our best insight into how life in the high latitudes responded to this climatic shift is provided by the fossil record from Seymour Island, near the eastern coast of the Antarctic Peninsula. While extensive collections have been made from the La Meseta and Submeseta formations of this island, few avian taxa other than penguins have been described and mammalian postcranial remains have been scarce. Here, we report new fossils from Seymour Island collected by the Antarctic Peninsula Paleontology Project. These include a mammalian metapodial referred to Xenarthra and avian material including a partial tarsometatarsus referred to Gruiformes (cranes, rails, and allies). Penguin fossils (Sphenisciformes) continue to be most abundant in new collections from these deposits. We report several penguin remains including a large spear-like mandible preserving the symphysis, a nearly complete tarsometatarsus with similarities to the large penguin clade Palaeeudyptes but possibly representing a new species, and two small partial tarsometatarsi belonging to the genus Delphinornis. These findings expand our view of Eocene vertebrate faunas on Antarctica. Specifically, the new remains referred to Gruiformes and Xenarthra provide support for previously proposed, but contentious, earliest occurrence records of these clades on the continent.
Davis et al. (2020) New mammalian and avian records from the late Eocene La Meseta and Submeseta formations of Seymour Island, Antarctica. PeerJ 8:e8268 https://doi.org/10.7717/peerj.8268
Analysis of the RNA virome of basal hexapods
The diversity and evolution of RNA viruses has been well studied in arthropods and especially in insects. However, the diversity of RNA viruses in the basal hexapods has not been analysed yet. To better understand their diversity, evolutionary histories and genome organizations, we searched for RNA viruses in transcriptome and genome databases of basal hexapods. We discovered 40 novel RNA viruses, some of which are also present as endogenous viral elements derived from RNA viruses. Here, we demonstrated that basal hexapods host 14 RNA viral clades that have been recently identified in invertebrates. The following RNA viral clades are associated with basal hexapods: Reo, Partiti-Picobirna, Toti-Chryso, Mono-Chu, Bunya-Arena, Orthomyxo, Qinvirus, Picorna-Calici, Hepe-Virga, Narna-Levi, Tombus-Noda, Luteo-Sobemo, Permutotetra and Flavi. We have found representatives of the nine RNA viral clades that are present as endogenous genomic copies in the genomes of Machilis (Monocondylia) and Catajapyx (Diplura). Our study provided a first insight into the diversity of RNA viruses in basal hexapods and demonstrated that the basal hexapods possess quite high diversity of RNA viral clades.
Ott Rutar et al. (2020) Analysis of the RNA virome of basal hexapods. PeerJ 8:e8336 https://doi.org/10.7717/peerj.8336
Temporal dynamics of the hummingbird-plant interaction network of a dry forest in Chamela, Mexico: a 30-year follow-up after two hurricanes
Background Interactions among species are a driving force of community structure. The species composition of animal-plant interaction networks can be highly dynamic on a temporal scale, even though the general network structure is usually not altered. However, few studies have examined how interaction networks change over long periods of time, particularly after extreme natural events. We analyzed herein the structure of the hummingbird-plant interaction network in a dry forest of Chamela, Mexico, comparing the structure in 1985–1986 with that in 2016–2017 following the passage of two hurricanes (category 2 Jova in 2011 and category 4 Patricia in 2015). Methods The fieldwork was carried out in the Chamela-Cuixmala Biosphere Reserve in Jalisco, Mexico. In the last 30 years, three severe drought events and two hurricanes have affected this region. Previously, from 1985–1986, hummingbird-plant interactions were recorded monthly for one year in the study area. Then, from 2016–2017, we replicated the sampling in the same localities. We compared the network parameters describing the plant-hummingbird interactions of each period using adjacency matrices. Results We found differences in the number and identity of interacting species, especially plants. The plant species missing in 2016–2017 were either the least connected in the original network (1985–1986) or belonged to groups such as cacti, epiphytes, or trees. The new plant species incorporated in the 2016–2017 network were herbs, vines, and shrubs, or other species barely connected. These changes in the composition are consistent with reports on vegetation damage after strong hurricanes at other study sites. Conversely, all hummingbird species remained in the network, with the exception of Heliomaster constantii, which was primarily connected to a plant species absent in the 2016–2017 network. Migratory and habitat generalist species (i.e., Archilochus spp.) showed higher abundances following the disturbance events. Conclusions Most of the parameters describing the hummingbird-plant network structure remained unchanged after 30 years, with the exception of an increase in plant robustness and hummingbird niche overlap. However, the network’s generalist core was affected by the loss of some species. Also, core plant species such as Ipomoea bracteata, Combretum farinosum, and Justicia candicans were found to be important for maintaining the hummingbird-plant interaction network. The temporal perspective of this study provides unique insights into the conservation of plant-hummingbird networks across time and extreme natural events.
Díaz Infante et al. (2020) Temporal dynamics of the hummingbird-plant interaction network of a dry forest in Chamela, Mexico: a 30-year follow-up after two hurricanes. PeerJ 8:e8338 https://doi.org/10.7717/peerj.8338
A multiomics comparison between endometrial cancer and serous ovarian cancer
Background Endometrial carcinoma (EC) and serous ovarian carcinoma (OvCa) are both among the common cancer types in women. EC can be divided into two subtypes, endometroid EC and serous-like EC, with distinct histological characterizations and molecular phenotypes. There is an increasing awareness that serous-like EC resembles serous OvCa in genetic landscape, but a clear relationship between them is still lacking. Methods Here, we took advantage of the large-scale molecular profiling of The Cancer Genome Atlas(TCGA) to compare the two EC subtypes and serous OvCa. We used bioinformatics data analytic methods to systematically examine the somatic mutation (SM) and copy number alteration (SCNA), gene expression, pathway activities, survival gene signatures and immune infiltration. Based on these quantifiable molecular characterizations, we asked whether serous-like EC should be grouped more closely to serous OvCa, based on the context of being serous-like; or if should be grouped more closely to endometroid EC, based on the same organ origin. Results We found that although serous-like EC and serous OvCa share some common genotypes, including mutation and copy number alteration, they differ in molecular phenotypes such as gene expression and signaling pathway activity. Moreover, no shared prognostic gene signature was found, indicating that they use unique genes governing tumor progression. Finally, although the endometrioid EC and serous OvCa are both highly immune infiltrated, the immune cell composition in serous OvCa is mostly immune suppressive, whereas endometrioid EC has a higher level of cytotoxic immune cells. Overall, our genetic aberration and molecular phenotype characterizations indicated that serous-like EC and serous OvCa cannot be simply treated as a simple “serous” cancer type. In particular, additional attention should be paid to their unique gene activities and tumor microenvironments for novel targeted therapy development.
Zhong et al. (2020) A multiomics comparison between endometrial cancer and serous ovarian cancer. PeerJ 8:e8347 https://doi.org/10.7717/peerj.8347
Age-related alterations in inhibitory control investigated using the minimally delayed oculomotor response task
Healthy, older adults are widely reported to experience cognitive decline, including impairments in inhibitory control. However, this general proposition has recently come under scrutiny because ageing effects are highly variable between individuals, are task dependent, and are sometimes not distinguished from general age-related slowing. We recently developed the minimally delayed oculomotor response (MDOR) task in which participants are presented with a simple visual target step, and instructed to saccade not to the target when it appears (a prosaccade response), but when it disappears (i.e. on target offset). Varying the target display duration (TDD) prevents offset timing being predictable from the time of target onset, and saccades prior to the offset are counted as errors. A comparison of MDOR task performance in a group of 22 older adults (mean age 62 years, range 50–72 years) with that in a group of 39 younger adults (22 years, range 19–27 years) demonstrated that MDOR latency was significantly increased in the older group by 34–68 ms depending on TDD. However, when MDOR latencies were corrected by subtracting the latency observed in a standard prosaccade task, the latency difference between groups was abolished. There was a larger latency modulation with TDD in the older group which was observed even when their generally longer latencies were taken into account. Error rates were significantly increased in the older group. An analysis of the timing distribution of errors demonstrated that most errors were failures to inhibit responses to target onsets. When error distributions were used to isolate clear inhibition failures from other types of error, the older group still exhibited significantly higher error rates as well as a higher residual error rate. Although MDOR latency in older participants may largely reflect a general slowing in the oculomotor system with age, both the latency modulation and error rate results are consistent with an age-related inhibitory control deficit. How this relates to performance on other inhibitory control tasks remains to be investigated.
Knox et al. (2020) Age-related alterations in inhibitory control investigated using the minimally delayed oculomotor response task. PeerJ 8:e8401 https://doi.org/10.7717/peerj.8401
Validity and reliability evidence of a point of care assessment of salivary cortisol and α-amylase: a pre-registered study
Purpose The iPro Cube is a small portable point-of-care device designed to analyse salivary markers of stress in a user-friendly manner (e.g., fast, convenient). Our aim was to test the reliability and validity of the iPro Cube to measure salivary cortisol and α-amylase as compared to the common laboratory standard method (ELISA immunoassay) prior to and after moderate intensity exercise. Methods The study was a repeated measures, pre-registered design, and statistical framework that incorporated prior knowledge directly into the estimation process. Twenty-nine individuals (age = 27.4 ± 6.6 y; body-mass = 70.8 ± 11.3 kg; height = 1.74 ± 0.92 m; 18 males) completed a single PWC75%HRmax, with repeated measures of salivary cortisol and -amylase pre, immediately post, and 30 min post-exercise. Results Correlation between the iPro Cube and laboratory-based assessments of salivary cortisol was moderate-to-large (0.53 > r < 0.81) across all three testing points. In contrast, correlation between the iPro Cube and laboratory-based assessments of -amylase was small-to-moderate (0.25 > r < 0.46). We found a large correlation between duplicate samples of iPro Cube cortisol assessment (0.75 > r < 0.82), and a moderate-to-large correlation for -amylase (0.51> r < 0.77). Conclusions The iPro Cube is capable of taking measures of salivary cortisol that are moderately correlated to values obtained via ELISA immunoassay, however the unit underestimates salivary cortisol and overestimates salivary -amylase at rest and post-moderate intensity exercise. It is recommended that researchers continue using standard laboratory techniques to assess these salivary stress markers.
Ducker et al. (2020) Validity and reliability evidence of a point of care assessment of salivary cortisol and α-amylase: a pre-registered study. PeerJ 8:e8366 https://doi.org/10.7717/peerj.8366
Quantification of the influence of drugs on zebrafish larvae swimming kinematics and energetics
The use of zebrafish larvae has aroused wide interest in the medical field for its potential role in the development of new therapies. The larvae grow extremely quickly and the embryos are nearly transparent which allows easy examination of its internal structures using fluorescent imaging techniques. Medical treatment of zebrafish larvae can directly influence its swimming behaviours. These behaviour changes are related to functional changes of central nervous system and transformations of the zebrafish body such as muscle mechanical power and force variation, which cannot be measured directly by pure experiment observation. To quantify the influence of drugs on zebrafish larvae swimming behaviours and energetics, we have developed a novel methodology to exploit intravital changes based on observed zebrafish locomotion. Specifically, by using an in-house MATLAB code to process the recorded live zebrafish swimming video, the kinematic locomotion equation of a 3D zebrafish larvae was obtained, and a customised Computational Fluid Dynamics tool was used to solve the fluid flow around the fish model which was geometrically the same as experimentally tested zebrafish. The developed methodology was firstly verified against experiment, and further applied to quantify the fish internal body force, torque and power consumption associated with a group of normal zebrafish larvae vs. those immersed in acetic acid and two neuroactive drugs. As indicated by our results, zebrafish larvae immersed in 0.01% acetic acid display approximately 30% higher hydrodynamic power and 10% higher cost of transport than control group. In addition, 500 μM diphenylhydantoin significantly decreases the locomotion activity for approximately 50% lower hydrodynamic power, whereas 100 mg/L yohimbine has not caused any significant influences on 5 dpf zebrafish larvae locomotion. The approach has potential to evaluate the influence of drugs on the aquatic animal’s behaviour changes and thus support the development of new analgesic and neuroactive drugs.
Zhao et al. (2020) Quantification of the influence of drugs on zebrafish larvae swimming kinematics and energetics. PeerJ 8:e8374 https://doi.org/10.7717/peerj.8374
DNA methylation profiling in recurrent miscarriage
Recurrent miscarriage (RM) is a complex clinical problem. However, specific diagnostic biomarkers and candidate regulatory targets have not yet been identified. To explore RM-related biological markers and processes, we performed a genome-wide DNA methylation analysis using the Illumina Infinium HumanMethylation450 array platform. Methylation variable positions and differentially methylated regions (DMRs) were selected using the Limma package in R language. Thereafter, gene ontology (GO) enrichment analysis and pathway enrichment analysis were performed on these DMRs. A total of 1,799 DMRs were filtered out between patients with RM and healthy pregnant women. The GO terms were mainly related to system development, plasma membrane part, and sequence-specific DNA binding, while the enriched pathways included cell adhesion molecules, type I diabetes mellitus, and ECM–receptor interactions. In addition, genes, including ABR, ALCAM, HLA-E, HLA-G, and ISG15, were obtained. These genes may be potential candidates for diagnostic biomarkers and possible regulatory targets in RM. We then detected the mRNA expression levels of the candidate genes. The mRNA expression levels of the candidate genes in the RM group were significantly higher than those in the control group. However, additional research is still required to confirm their potential roles in the occurrence of RM.
Pi et al. (2020) DNA methylation profiling in recurrent miscarriage. PeerJ 8:e8196 https://doi.org/10.7717/peerj.8196
Soil aggregate size influences the impact of inorganic nitrogen deposition on soil nitrification in an alpine meadow of the Qinghai–Tibet Plateau
Background Ammonium (NH4+) and nitrate (NO3−) are two inorganic forms of nitrogen (N) that are deposited from the atmosphere into soil systems. As the substrate and product of soil nitrification, these two forms of inorganic nitrogen will affect or be affected by the soil net nitrification rate (Nr). Our knowledge regarding soil nitrification is mainly derived from studies with bulk soil. However, soil is composed of different aggregate fractions, which may have an important impact on Nr. Methods In 2017, we collected soil samples from an alpine meadow of the Qinghai–Tibet Plateau and separated them into four soil aggregates (2–4, 1–2, 0.25–1, and <0.25 mm) using the dry sieving method. The four soil aggregate sizes amended with the 2 N deposition forms (NH4+-N and NO3−-N) were then incubated at 25 °C for 28 days, and the soil aggregates for each treatment were collected on day 0, 7, 14, 21, and 28 to determine the NO3−-N concentration. The soil Nr and contribution of soil aggregates to the nitrification rate in the bulk soil were calculated. Results There were differences in the physicochemical properties of the soil aggregates. The addition of N and aggregate size had strong effects on soil Nr, which were significantly increased under high levels of NH4+ addition across all soil aggregates. The Nr during the 4 week incubation period differed among aggregate sizes. Nr in the 2–4 mm aggregates was higher than in the other aggregates, which was correlated with the maximum values of the soil porosity observed in the 2–4 mm aggregates. Furthermore, almost half of the soil was composed of aggregates of <0.25 mm, indicating that the <0.25 mm aggregates made a higher contribution to the nitrification rate in the bulk soil than the other aggregates, even though these aggregates had a lower nitrification ability. Overall, our study revealed that the soil nitrification rate was influenced by both the N addition and soil aggregates, and that the 2–4 mm aggregates had a dominant effect on the response of soil N transformation processes to future nitrogen deposition in the alpine meadow.
Li et al. (2020) Soil aggregate size influences the impact of inorganic nitrogen deposition on soil nitrification in an alpine meadow of the Qinghai–Tibet Plateau. PeerJ 8:e8230 https://doi.org/10.7717/peerj.8230
A pilot study on searching for peri-nuclear NeuN-positive cells
The aim of this study was to find out neuron (-like) cells in peripheral organs by cell markers in rats. Adult male Sprague-Dawley rats were anaesthetized. Their organs including brain, heart, lung, liver, kidney, stomach, duodenum, and ileum were harvested. The mRNA and protein in these organs were extracted. RNA sequencing (RNA-Seq) was carried out, and NeuN, a “specific” marker for neuronal soma, was assayed with Western blotting. The sections of the aforementioned organs were obtained after a routine fixation (4% methanal)-dehydration (ethanol)-embedding (paraffin) process. NeuN in the sections and seven non-neuronal cell lines was analyzed by immunofluorescence (IF) or immunohistochemistry (IHC). Neuronal markers, such as Eno2, NeuN (Rbfox3), choline acetyltransferase (Chat), as well as tyrosine hydroxylase (Th), and neuronal-glial markers, e.g., glial fibrillary acidic protein (Gfap), S100b, 2′, 3′-cyclic nucleotide 3′-phosphodiesterase (Cnp), and other related markers, were positively expressed in all the organs at mRNA level. NeuN was further analyzed by Western blotting. The IF and IHC assays showed that NeuN-positive cells were distributed in all the peripheral tissues (mainly peri-nuclear NeuN-positive cells) though with different patterns from that in brain (nuclear NeuN-positive cells), and a NeuN-negative tissue could not be found. Especially, NeuN and Myl3 co-expressed in the cytoplasm of myocardial cells, suggesting that NeuN could possess other functions than neuronal differentiation. Also, the protein was positively expressed in seven non-neuronal cell lines. Our findings suggested that NeuN-positive cells exist widely, and without identification of its distribution pattern, the specificity of NeuN for neurons could be limited.
Yu et al. (2020) A pilot study on searching for peri-nuclear NeuN-positive cells. PeerJ 8:e8254 https://doi.org/10.7717/peerj.8254