Evaluation of leaf rust resistance in the Chinese wheat cultivar ‘Een1’
Wheat cultivar Een1, 34 near isogenic lines (NILs), and two cultivars were used as plant materials to evaluate the resistance of Een1 to leaf rust disease. Infection type identification and gene postulation were carried out by inoculation of 12 Chinese Puccinia triticina (Pt) pathotypes. Based on the unique phenotype of Een1, we speculated that Een1 might carry Lr gene(s) different from the tested ones. The chromosomal locations for resistance gene to leaf rust disease was employed using SSR primers mapping the populations derived from the cross between Een1 and susceptible Thatcher. A total of 285 plants in the F2 population were tested by inoculating Pt pathotype FHNQ during the seedling stage. Results from the segregation analysis fits a ratio of 3:1 ( ${\chi }_{3:1}^{2}=2.37$ χ 3 : 1 2 = 2 . 37 , P = 0.12), indicating the presence of a single dominant gene in Een1 conferring resistance to FHNQ. A total of 1,255 simple sequence repeat (SSR) primers were first used to identify the likely linked markers based on bulk segregation analysis (BSA), and then those likely linked markers were further genotyped in the F2 population for linkage analysis. Our linkage analysis found that the resistance gene (LrE1) was distal to seven SSR loci on the long arm of chromosome 7B, with distances from 2.6 cM (Xgwm344) to 27.1 cM (Xgwm131). The closest marker Xgwm344 was further verified with F3 lines.
Zhang et al. (2020) Evaluation of leaf rust resistance in the Chinese wheat cultivar ‘Een1’. PeerJ 8:e8993 https://doi.org/10.7717/peerj.8993
Ancient genetic divergence in bumblebee catfish of the genus Pseudopimelodus (Pseudopimelodidae: Siluriformes) from northwestern South America
Pseudopimelodus is a Neotropical genus of bumblebee catfish, composed of four valid species occurring in both trans- and cis-Andean rivers of South America. The orogeny of the Andes has led to diversification in the genus Pseudopimelodus in Colombia. This study analyzed partial sequences of mitochondrial cox1 and nuclear rag2 genes to test the hypothesis that the species, nominally recognized as P. schultzi and P. bufonius in Colombia, correspond to more than two different evolutionary lineages. Results indicate high levels of genetic divergence among individuals of nominal P. schultzi and P. bufonius, from trans- and cis-Andean basins in Colombia. In addition, five divergent lineages of Pseudopimelodus were confidently delimited by using a single-locus species-discovery approach and confirmed by species tree analyses. Additionally, molecular-clock dating showed that most diversification processes in Pseudopimelodus took place during the Miocene, when Andean tectonic evolution was occurring in northwestern South America. The present study provides, for the first time, phylogeographic insight into this Neotropical genus.
Rangel-Medrano et al. (2020) Ancient genetic divergence in bumblebee catfish of the genus Pseudopimelodus (Pseudopimelodidae: Siluriformes) from northwestern South America. PeerJ 8:e9028 https://doi.org/10.7717/peerj.9028
Meiofaunal communities and nematode diversity characterizing the Secca delle Fumose shallow vent area (Gulf of Naples, Italy)
Hydrothermal venting is rather prevalent in many marine areas around the world, and marine shallow vents are relatively abundant in the Mediterranean Sea, especially around Italy. However, investigations focusing on the characterization of meiofaunal organisms inhabiting shallow vent sediments are still scant compared to that on macrofauna. In the present study, we investigated the meiobenthic assemblages and nematode diversity inhabiting the Secca delle Fumose (SdF), a shallow water vent area located in the Gulf of Naples (Italy). In this area, characterized by a rapid change in the environmental conditions on a relative small spatial scale (i.e., 100 m), we selected four sampling sites: one diffusive emission site (H); one geyser site (G) and two inactive sites (CN, CS). Total meiofauna abundance did not vary significantly between active and inactive sites and between surface and deeper sediment layers due to a high inter-replicate variability, suggesting a pronounced spatial-scale patchiness in distribution of meiofauna. Nematofauna at site H presented the typical features of deep-sea vents with low structural and functional diversity, high biomass and dominance of few genera (i.e., Oncholaimus; Daptonema) while from site G we reported diversity values comparable to that of the inactive sites. We hypothesized that site G presented a condition of “intermediate disturbance” that could maintain a high nematode diversity. Environmental features such as sediment temperature, pH, total organic carbon and interstitial waters ions were found to be key factors influencing patterns of meiofauna and nematofauna assemblages at SdF. Even though the general theory is that nematodes inhabiting shallow vent areas include a subset of species that live in background sediments, this was not the case for SdF vent area. Due to a marked change in nematode composition between all sites and to the presence of many exclusive species, every single investigated site was characterized by a distinct nematofauna reflecting the high spatial heterogeneity of SdF.
Baldrighi et al. (2020) Meiofaunal communities and nematode diversity characterizing the Secca delle Fumose shallow vent area (Gulf of Naples, Italy). PeerJ 8:e9058 https://doi.org/10.7717/peerj.9058
Mountain goat survival and mortality during a period of increased puma abundance in the Black Hills, South Dakota
We investigated survival and cause-specific mortality for a mountain goat (Oreamnos americanus) population during a period when the puma (Puma concolor) population was growing in the Black Hills, South Dakota, 2006–2018. We obtained survival data from 47 adult goats (n = 33 females, n = 14 males). Annual survival varied from 0.538 (95% CI [0.285–0.773]) to 1.00 (95% CI [1.00–1.00]) and puma predation was the primary cause-specific mortality factor over a 12-year period. Cumulative hectares of mountain pine beetle (Dendroctonus ponderosae) disturbance was a covariate of importance (wi = 0.972; β = 0.580, 95% CI [0.302–0.859]) influencing survival. To our knowledge, this is the first account of puma being the primary mortality factor of mountain goats over a long-term study. The Black Hills system is unique because we could examine the expanded realized niche of puma in the absence of other large carnivores and their influence on mountain goats. We hypothesize that puma were being sustained at higher densities due to alternate prey sources (e.g., white-tailed deer; Odocoileous virginianus) and this small population of mountain goats was susceptible to predation by one or several specialized puma in the Black Hills. However, we also hypothesize a changing landscape with increased tree mortality due to insect infestation provided conditions for better predator detection by goats and increased survival. Alternatively, open canopy conditions may have increased understory forage production potentially increasing mountain goat survival but we did not evaluate this relationship. Survival and mortality rates of mountain goats should continue to be monitored as this small population may be highly susceptible to population declines due to slow growth rates.
Lehman et al. (2020) Mountain goat survival and mortality during a period of increased puma abundance in the Black Hills, South Dakota. PeerJ 8:e9143 https://doi.org/10.7717/peerj.9143
Proliferating activity in a bryozoan lophophore
Bryozoans are small benthic colonial animals; their colonies consist of zooids which are composed of a cystid and polypide. According to morphological and molecular data, three classes of bryozoans are recognized: Phylactolaemata, Gymnolaemata and Stenolaemata. Bryozoans are active suspension feeders and their feeding apparatus, the lophophore, is fringed with a single row of ciliated tentacles. In gymnolaemates, the lophophore is bell-shaped and its tentacles may be equal in length (equitentacled lophophores) or some tentacles may be longer than others (obliquely truncated lophophores). In encrusting colonies, polypides with obliquely truncated lophophores usually border specific sites of excurrent water outlets (colony periphery and chimneys) where depleted water has to be removed. It is known that during colony astogeny, colony-wide water currents rearrange: new chimneys are formed and/or location of the chimneys within a given colony changes with time. Such rearrangement requires remodeling of the lophophore shape and lengthening of some tentacles in polypides surrounding water outlets. However, proliferating activity has not been described for bryozoans. Here, we compared the distribution of S-phase and mitotic cells in young and adult polypides in three species of Gymnolaemata. We tested the hypothesis that tentacle growth/elongation is intercalary and cell proliferation takes place somewhere at the lophophore base because such pattern does not interfere with the feeding process. We also present a detailed description of ultrastructure of two parts of the lophophore base: the oral region and ciliated pits, and uncover the possible function of the latter. The presence of stem cells within the ciliated pits and the oral region of polypides provide evidence that both sites participate in tentacle elongation. This confirms the suggested hypothesis about intercalary tentacle growth which provides a potential to alter a lophophore shape in adult polypides according to rearrangement of colony wide water currents during colony astogeny. For the first time deuterosome-like structures were revealed during kinetosome biogenesis in the prospective multiciliated epithelial cells in invertebrates. Tentacle regeneration experiments in Electra pilosa demonstrated that among all epidermal cell types, only non-ciliated cells at the abfrontal tentacle surface are responsible for wound healing. Ciliated cells on the frontal and lateral tentacle surfaces are specialized and unable to proliferate, not even under wound healing. Tentacle regeneration in E. pilosa is very slow and similar to the morphallaxis type. We suggest that damaged tentacles recover their length by a mechanism similar to normal growth, powered by proliferation of cells both within ciliated pits and the oral region.
Shunatova et al. (2020) Proliferating activity in a bryozoan lophophore. PeerJ 8:e9179 https://doi.org/10.7717/peerj.9179
Future sea-level rise drives rocky intertidal habitat loss and benthic community change
The impacts of sea-level rise (SLR) are likely to be the greatest for ecosystems that exist at the land-sea interface, where small changes in sea-level could result in drastic changes in habitat availability. Rocky intertidal ecosystems possess a number of characteristics which make them highly vulnerable to changes in sea-level, yet our understanding of potential community-scale responses to future SLR scenarios is limited. Combining remote-sensing with in-situ large-area imaging, we quantified habitat extent and characterized the biological community at two rocky intertidal study locations in California, USA. We then used a model-based approach to estimate how a range of SLR scenarios would affect total habitat area, areal extent of dominant benthic space occupiers, and numerical abundance of invertebrates. Our results suggest that SLR will reduce total available rocky intertidal habitat area at our study locations, leading to an overall decrease in areal extent of dominant benthic space occupiers, and a reduction in invertebrate abundances. As large-scale environmental changes, such as SLR, accelerate in the next century, more extensive spatially explicit monitoring at ecologically relevant scales will be needed to visualize and quantify their impacts to biological systems.
Spatial and Geographic Information Science
Kaplanis et al. (2020) Future sea-level rise drives rocky intertidal habitat loss and benthic community change. PeerJ 8:e9186 https://doi.org/10.7717/peerj.9186
Recent advances in the contribution of noncoding RNAs to cisplatin resistance in cervical cancer
Cervical cancer (CC) remains a major disease burden on the female population worldwide. Chemotherapy with cisplatin (cis-diamminedichloroplatinum (II); CDDP) and related drugs are the main treatment option for CC; however, their efficacy is limited by the development of drug resistance. Noncoding RNAs (ncRNAs) have been found to play critical roles in numerous physiological and pathological cellular processes, including drug resistance of cancer cells. In this review, we describe some of the ncRNAs, including miRNAs, lncRNAs and circRNAs, that are involved in the sensitivity/resistance of CC to CDDP-based chemotherapy and discuss their mechanisms of action. We also describe some ncRNAs that could be therapeutic targets to improve the sensitivity of CC to CDDP-based chemotherapy.
Wen et al. (2020) Recent advances in the contribution of noncoding RNAs to cisplatin resistance in cervical cancer. PeerJ 8:e9234 https://doi.org/10.7717/peerj.9234
Decreased inhibitory control after partial sleep deprivation in individuals reporting binge eating: preliminary findings
Background Poor executive functions are associated with dysregulated eating and greater caloric intake in healthy samples. In parallel, findings suggested that sleep deprivation impairs executive functions. Methods We investigated whether partial sleep deprivation impairs executive functions in individuals reporting binge eating (BE, N = 14) and healthy controls (C, N = 13). Switch cost and backward inhibition were measured using the Task Switching Paradigm after a habitual night of sleep and after a night of partial sleep deprivation. Results Results showed a Night by Group interaction on the backward inhibition. The two groups differed in the habitual night, evidencing higher inhibitory control in BE compared to C. Additionally, after partial sleep deprivation, compared to the habitual night, backward inhibition decreased in BE group. This preliminary study was the first to explore the impact of sleep deprivation on executive functions in participants reporting binge eating and healthy controls, thus highlighting their potential role in influencing eating behavior.
Cerolini et al. (2020) Decreased inhibitory control after partial sleep deprivation in individuals reporting binge eating: preliminary findings. PeerJ 8:e9252 https://doi.org/10.7717/peerj.9252
Uncovering the species diversity of subterranean rodents at the end of the World: three new species of Patagonian tuco-tucos (Rodentia, Hystricomorpha, Ctenomys)
Ctenomys Blainville 1826 is one of the most diverse genera of South American caviomorph rodents. Currently, six species of this genus are reported from Patagonia, south of 42°S. In this contribution, we assessed the taxonomic status of several populations from eastern and central Chubut province, northern Patagonia. Based on phylogenetic analyses of DNA sequences, morphology assessment (qualitative and quantitative), and previously published karyological data, we describe three new species of this genus, one formed by two subspecies, endemic to northern Patagonia. In addition, we include C. coyhaiquensis Kelt and Gallardo 1994 into the synonymy of C. sericeus J.A. Allen 1903. Finally, we discussed the need for additional integrative approaches, including field collection of specimens, to better understand the diversity of this highly speciose rodent genus.
Teta et al. (2020) Uncovering the species diversity of subterranean rodents at the end of the World: three new species of Patagonian tuco-tucos (Rodentia, Hystricomorpha, Ctenomys). PeerJ 8:e9259 https://doi.org/10.7717/peerj.9259
Isotopic biomonitoring of anthropic carbon emissions in a megalopolis
Atmospheric pollution has become a serious threat for human health and the environment. However, the deployment, operation and maintenance of monitoring networks can represent a high cost for local governments. In certain locations, the use of naturally occurring plants for monitoring pollution can be a useful supplement of existing monitoring networks, and even provide information when other types of monitoring are lacking. In this work, we (i) determined the tissue carbon content and the δ13C values for the epiphytic CAM bromeliad Tillandsia recurvata and the relationship of both parameters with the existing CO concentrations in the Valley of Mexico basin and (ii) mapped the spatial distribution of such elemental and isotopic composition for this plant within the basin, in order to assess its potential as an atmospheric biomonitor of carbon monoxide, a pollutant with important repercussions on public health. The CO concentrations in the basin ranged from 0.41 ppm at rural locations to 0.81 ppm at urban sites. The carbon content of T. recurvata, which averaged 42.9 ± 0.34% (dry weight), was not influenced by the surrounding CO concentration. In contrast, the δ13C depended on the sites where the plants were collected. For example, the values were −13.2‰ in rural areas and as low as –17.5‰ in an urban site. Indeed, the isotopic values had a positive linear relationship with the atmospheric CO concentrations. Given the close relationship observed between the isotopic composition of T. recurvata with the CO concentrations in the Valley of Mexico, the δ13C values can be useful for the detection of atmospheric carbonaceous emissions.
Environmental Contamination and Remediation
Díaz-Álvarez et al. (2020) Isotopic biomonitoring of anthropic carbon emissions in a megalopolis. PeerJ 8:e9283 https://doi.org/10.7717/peerj.9283