The pre-Pleistocene fossil thylacinids (Dasyuromorphia: Thylacinidae) and the evolutionary context of the modern thylacine
The thylacine is popularly used as a classic example of convergent evolution between placental and marsupial mammals. Despite having a fossil history spanning over 20 million years and known since the 1960s, the thylacine is often presented in both scientific literature and popular culture as an evolutionary singleton unique in its morphological and ecological adaptations within the Australian ecosystem. Here, we synthesise and critically evaluate the current state of published knowledge regarding the known fossil record of Thylacinidae prior to the appearance of the modern species. We also present phylogenetic analyses and body mass estimates of the thylacinids to reveal trends in the evolution of hypercarnivory and ecological shifts within the family. We find support that Mutpuracinus archibaldi occupies an uncertain position outside of Thylacinidae, and consider Nimbacinus richi to likely be synonymous with N. dicksoni. The Thylacinidae were small-bodied (< ~8 kg) unspecialised faunivores until after the ~15–14 Ma middle Miocene climatic transition (MMCT). After the MMCT they dramatically increase in size and develop adaptations to a hypercarnivorous diet, potentially in response to the aridification of the Australian environment and the concomitant radiation of dasyurids. This fossil history of the thylacinids provides a foundation for understanding the ecology of the modern thylacine. It provides a framework for future studies of the evolution of hypercarnivory, cursoriality, morphological and ecological disparity, and convergence within mammalian carnivores.
Rovinsky et al. (2019) The pre-Pleistocene fossil thylacinids (Dasyuromorphia: Thylacinidae) and the evolutionary context of the modern thylacine. PeerJ 7:e7457 https://doi.org/10.7717/peerj.7457
lnc-SAMD14-4 can regulate expression of the COL1A1 and COL1A2 in human chondrocytes
Osteoarthritis (OA) is the most common motor system disease in aging people, characterized by matrix degradation, chondrocyte death, and osteophyte formation. OA etiology is unclear, but long noncoding RNAs (lncRNAs) that participate in numerous pathological and physiological processes may be key regulators in the onset and development of OA. Because profiling of lncRNAs and their biological function in OA is not understood, we measured lncRNA and mRNA expression profiles using high-throughput microarray to study human knee OA. We identified 2,042 lncRNAs and 2,011 mRNAs that were significantly differentially expressed in OA compared to non-OA tissue (>2.0- or < − 2.0-fold change; p < 0.5), including 1,137 lncRNAs that were upregulated and 905 lncRNAs that were downregulated. Also, 1,386 mRNA were upregulated and 625 mRNAs were downregulated. QPCR was used to validate chip results. Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to study the biological function enrichment of differentially expressed mRNA. Additionally, coding-non-coding gene co-expression (CNC) network construction was performed to explore the relevance of dysregulated lncRNAs and mRNAs. Finally, the gain/loss of function experiments of lnc-SAMD14-4 was implemented in IL-1β-treated human chondrocytes. In general, this study provides a preliminary database for further exploring lncRNA-related mechnisms in OA.
Zhang et al. (2019) lnc-SAMD14-4 can regulate expression of the COL1A1 and COL1A2 in human chondrocytes. PeerJ 7:e7491 https://doi.org/10.7717/peerj.7491
Type I-like behavior of the type II α7 nicotinic acetylcholine receptor positive allosteric modulator A-867744
Cognitive impairment often involves the decreased expression or hypofunction of alpha 7-type nicotinic acetylcholine receptors (α7 nAChRs). Agonists or positive allosteric modulators (PAMs) of α7 nAChRs are known to be potential treatments for dementias, different neurodegenerative disorders, pain syndromes and conditions involving inflammation. In some of these conditions, it is desirable to maintain the temporal precision of fast cholinergic events, while in others, this temporal precision is unnecessary. For this reason, the optimal therapeutic effect for distinct indications may require PAMs with different mechanisms of action. The two major mechanisms are called “type I”, which are compounds that augment α7 nAChR-mediated currents but maintain their characteristic fast kinetics; and “type II”, which are compounds that produce augmented and prolonged currents. In this study, we performed a kinetic analysis of two type II PAMs of the α7 nAChR: PNU-120596 and A-867744, using a fast perfusion method that allowed high temporal resolution. We characterized the type of modulation produced by the two compounds, the state-dependence of the modulatory action, and the interaction between the two compounds. We found fundamental differences between the modulation mechanisms by PNU-120596 and A-867744. Most importantly, during brief agonist pulses, A-867744 caused a strikingly type I-like modulation, while PNU-120596 caused a type II-like prolonged activation. Our results demonstrate that specific compounds, even though all labeled as type II PAMs, can behave in completely different ways, including their onset and offset kinetics, state preference, and single channel open time. Our results emphasize that subtle details of the mechanism of action may be significant in assessing the therapeutic applicability of α7 nAChR PAM compounds.
Pesti et al. (2019) Type I-like behavior of the type II α7 nicotinic acetylcholine receptor positive allosteric modulator A-867744. PeerJ 7:e7542 https://doi.org/10.7717/peerj.7542
Revealing biases in the sampling of ecological interaction networks
The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases with respect to both the interactors (the nodes of the network) and interactions (the links between nodes), because the detectability of species and their interactions is highly heterogeneous. These ecological and statistical issues directly affect ecologists’ abilities to accurately construct ecological networks. However, statistical biases introduced by sampling are difficult to quantify in the absence of full knowledge of the underlying ecological network’s structure. To explore properties of large-scale ecological networks, we developed the software EcoNetGen, which constructs and samples networks with predetermined topologies. These networks may represent a wide variety of communities that vary in size and types of ecological interactions. We sampled these networks with different mathematical sampling designs that correspond to methods used in field observations. The observed networks generated by each sampling process were then analyzed with respect to the number of components, size of components and other network metrics. We show that the sampling effort needed to estimate underlying network properties depends strongly both on the sampling design and on the underlying network topology. In particular, networks with random or scale-free modules require more complete sampling to reveal their structure, compared to networks whose modules are nested or bipartite. Overall, modules with nested structure were the easiest to detect, regardless of the sampling design used. Sampling a network starting with any species that had a high degree (e.g., abundant generalist species) was consistently found to be the most accurate strategy to estimate network structure. Because high-degree species tend to be generalists, abundant in natural communities relative to specialists, and connected to each other, sampling by degree may therefore be common but unintentional in empirical sampling of networks. Conversely, sampling according to module (representing different interaction types or taxa) results in a rather complete view of certain modules, but fails to provide a complete picture of the underlying network. To reduce biases introduced by sampling methods, we recommend that these findings be incorporated into field design considerations for projects aiming to characterize large species interaction networks.
de Aguiar et al. (2019) Revealing biases in the sampling of ecological interaction networks. PeerJ 7:e7566 https://doi.org/10.7717/peerj.7566
Nutrient availability induces community shifts in seagrass meadows grazed by turtles
In the Caribbean, green turtles graze seagrass meadows dominated by Thalassia testudinum through rotational grazing, resulting in the creation of grazed and recovering (abandoned) patches surrounded by ungrazed seagrasses. We evaluated the seagrass community and its environment along a turtle grazing gradient; with the duration of (simulated) grazing as a proxy for the level of grazing pressure. The grazing levels consisted of Short-term (4 months clipping), Medium-term (8 months clipping), Long-term grazing (8 months of clipping in previously grazed areas), 8-months recovery of previously grazed patches, and ungrazed or unclipped patches as controls. We measured biomass and density of the seagrasses and rhizophytic algae, and changes in sediment parameters. Medium- and Long-term grazing promoted a shift in community species composition. At increasing grazing pressure, the total biomass of T. testudinum declined, whereas that of early-successional increased. Ammonium concentrations were highest in the patches of Medium-term (9.2 + 0.8 μM) and Long-term grazing levels (11.0 + 2.2 μM) and were lowest in the control areas (4.6 + 1.5 μM). T. testudinum is a late-successional species that maintains sediment nutrient concentrations at levels below the requirements of early-successional species when dominant. When the abundance of this species declines due to grazing, these resources become available, likely driving a shift in community composition toward a higher abundance of early-successional species.
Martínez López et al. (2019) Nutrient availability induces community shifts in seagrass meadows grazed by turtles. PeerJ 7:e7570 https://doi.org/10.7717/peerj.7570
The reproductive system of the male and oviparous female of a model organism—the pea aphid, Acyrthosiphon pisum (Hemiptera, Aphididae)
The structure of the reproductive system of the sexual generation—males and oviparous females—of the pea aphid Acyrthosiphon pisum (Harris) (Hemiptera, Aphididae), a serious pest of cultivated plants of Fabaceae, was investigated. For the first time we describe the morphology, histology and ultrastructure of the reproductive system in both morphs of the sexual generation of aphids within one species, using light and fluorescent microscopy, as well as transmission and scanning electron microscopy. The results revealed that males have testes composed of three follicles fused by the upper ends of the vasa efferentia, the vasa deferentia run independently, the accessory glands are asymmetric and the ejaculatory duct shortened. Oviparous females have ovaries composed of seven ovarioles each. The lateral oviducts join to a short common oviduct connected with the unpaired spermatheca and paired accessory glands. Yolky eggs with an aggregation of symbiotic bacteria at the posterior pole are produced. Histologically, the components of genital tracts are broadly similar: the epithelial cells of the walls of the vasa deferentia and accessory glands of the male and oviparous female have secretory functions which correlate with the age of the studied morphs. We also found symbiotic bacteria within the vasa deferentia epithelial cells in males and within the cells of the lateral oviducts of females. Because the pea aphid is listed among the 14 species that are of the greatest economic importance, our results will be useful for managing aphid populations, protecting plants and ensuring global food security.
Wieczorek et al. (2019) The reproductive system of the male and oviparous female of a model organism—the pea aphid, Acyrthosiphon pisum (Hemiptera, Aphididae). PeerJ 7:e7573 https://doi.org/10.7717/peerj.7573
Community composition of zooplankton exported from a shallow polymictic reservoir linked to wind conditions
Zooplankton exported from lentic systems provision lotic systems with easily captured, consumed, and assimilated prey items. Previous studies have demonstrated that the community composition of zooplankton exports (CCZE) vary over time, which introduces temporal differences in lotic resource availability (zooplankton prey) in downstream habitats. In the study presented here, we monitored variation in CCZE from a polymictic reservoir outfall in response to physical–chemical and atmospheric conditions bi-hourly over three different 24-h periods. Community composition of zooplankton export varied over the course of the day, and exports were most closely associated with wind directionality. Future studies of temporal variation in CCZE should incorporate wind conditions, especially in shallow systems where holomixis occurs frequently. Polymictic reservoirs are becoming increasingly common as the global pace of small dam construction quickens, making both the identification of factors influencing CCZE and the impact of zooplankton exports on local biodiversity and ecosystem function increasingly important to understand.
Ruhl et al. (2019) Community composition of zooplankton exported from a shallow polymictic reservoir linked to wind conditions. PeerJ 7:e7611 https://doi.org/10.7717/peerj.7611
Winter bird-window collisions: mitigation success, risk factors, and implementation challenges
Millions of birds die in bird-window collisions in the United States each year. In specialized test settings, researchers have developed methods to alter window designs to mitigate collisions. However, few published studies provide pretest and posttest evaluations of mitigation treatment areas and untreated control areas on existing buildings. We initially monitored bird-window collisions at a single building on the University of Utah campus in Salt Lake City, Utah, USA, during winter 1 (November 9, 2017–January 2, 2018). We found 15 bird-window collisions, most under a portion of the building with a mirrored façade. To test a mitigation treatment, we installed Feather Friendly® bird deterrent film on part of the mirrored façade after winter 1. The unmitigated areas of the same building served as a control area. We continued monitoring during the following winter 2 (November 15, 2018–January 12, 2019). The treated area collisions declined from seven before mitigation to two after mitigation, a 71% reduction. The control area had eight collisions at both times. Results of a generalized estimating equation yielded a significant area by season interaction effect (p = 0.03) and fewer collisions in the mitigated area than the control area at winter 2 (p = 0.03), supporting efficacy of the mitigation. In winter 2 we also expanded monitoring to eight total buildings to evaluate the risks of mirrored windows and proximity to fruiting pear trees (Prunus calleryana) and the benefits of bird-friendly glass. Bird-friendly glass, found on two buildings, included windows with permanent fritted dots or embedded ultraviolet patterns. We counted 22 collisions across the eight buildings. Mirrored windows and proximity to fruiting pear trees related to higher odds of bird-window collisions, based on separate generalized estimating equations. The best fit model included mirrored windows and pear trees. The two buildings with bird-friendly glass had only one collision, suggesting that these designs deter collisions, although the difference was not statistically significant. To publicize the study and to receive reports of additional bird collisions or fatalities on campus, we created a citizen science project on iNaturalist and engaged in additional outreach efforts that yielded 22 ad hoc reports. Many previous studies have documented Cedar Waxwing (Bombycilla cedrorum) collisions, but at relatively low numbers. Cedar Waxwings accounted for 31 of 34 identifiable collisions from the monitoring study and 4 of 21 identifiable collisions or fatalities from ad hoc reports.
Brown et al. (2019) Winter bird-window collisions: mitigation success, risk factors, and implementation challenges. PeerJ 7:e7620 https://doi.org/10.7717/peerj.7620
Serine protease inhibitors and human wellbeing interplay: new insights for old friends
Serine Protease Inhibitors (Serpins) control tightly regulated physiological processes and their dysfunction is associated to various diseases. Thus, increasing interest is given to these proteins as new therapeutic targets. Several studies provided functional and structural data about human serpins. By comparison, only little knowledge regarding bacterial serpins exists. Through the emergence of metagenomic studies, many bacterial serpins were identified from numerous ecological niches including the human gut microbiota. The origin, distribution and function of these proteins remain to be established. In this report, we shed light on the key role of human and bacterial serpins in health and disease. Moreover, we analyze their function, phylogeny and ecological distribution. This review highlights the potential use of bacterial serpins to set out new therapeutic approaches.
Mkaouar et al. (2019) Serine protease inhibitors and human wellbeing interplay: new insights for old friends. PeerJ 7:e7224 https://doi.org/10.7717/peerj.7224
Post-fledging habitat use in a declining songbird
Background Fledglings of many mature forest-dependent Neotropical songbirds move from mature forest habitats into areas of thick vegetation such as regenerating clearcuts. The Cerulean Warbler (Setophaga cerulea), a Neotropical migratory songbird, is a species of conservation concern across its range and it is listed as endangered in Indiana. This species has declined faster than any other species of wood-warbler in North America. Most prior research on Cerulean Warblers has examined the breeding biology, but there are no data on habitat use by fledgling Cerulean Warblers. Our research aimed to determine where fledgling Cerulean Warblers dispersed after they left their nest, but before they migrated to their wintering grounds. Methods Since 2007, Cerulean Warbler breeding populations have been monitored in Yellowwood and Morgan–Monroe state forests in southern Indiana as part of a 100-year study called the Hardwood Ecosystem Experiment. To identify habitats used by fledgling Cerulean Warblers, we captured by hand or mist-nets, adult and juvenile Cerulean Warblers once young had fledged from a nest. We attached radio-transmitters to individuals and tracked each bird daily using radio-telemetry. Radio-telemetry data were collected from May to July 2015–2017, and microhabitat data on fledgling locations and random locations were collected during the same years in the month of July. Results Fledgling presence, when compared to random non-use sites, was positively correlated to presence of grapevines, greater vertical vegetation density, and greater ground and canopy cover. Fledgling presence was negatively correlated with white oak abundance, aspect, basal area, and the abundance of mature trees that Cerulean Warbler adults use for nesting. Conclusions Our study is the first to demonstrate that Cerulean Warbler fledglings occupy habitats that are characterized by specific habitat components. Fledgling sites were located in areas with high vegetation density, such as clusters of grapevine, which provided cover from predators. Identifying Cerulean Warbler habitats throughout the breeding season can better inform natural resource personnel on how to manage forests to meet the habitat needs of this rapidly declining migratory songbird.
Delancey et al. (2019) Post-fledging habitat use in a declining songbird. PeerJ 7:e7358 https://doi.org/10.7717/peerj.7358