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1.
  • Ababneh, Nidaa A., et al. (author)
  • Patterns of hepatitis B virus S gene escape mutants and reverse transcriptase mutations among genotype D isolates in Jordan
  • 2019
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 2019:3
  • Journal article (peer-reviewed)abstract
    • Background: Hepatitis B virus (HBV) is an important infectious cause of morbidity and mortality in Jordan. HBV genotype D is the most prevalent in the country. Virus escape mutants in the HBV S region is an important public health problem halting preventive efforts. The aim of the current study was to investigate patterns of HBV escape and resistance mutations and to assess domestic transmission of the virus. Methods: Patients infected with HBV were recruited at Jordan University Hospital (n ¼ 56) and were diagnosed during (1984-2012). A total of 37 partial HBV S sequences were generated using Sanger's method. Mutation analysis was done using the HIV grade HBV drug resistance interpretation online tool and Geno2pheno (HBV) online tools. Domestic transmission of HBV was assessed using maximum likelihood phylogenetic inference with similar GenBank sequences. Results: Genotyping revealed an exclusive presence of sub-genotype D1. Typical HBV escape mutants were identified in seven patients. These mutations included: L109R, Q129R, M133L, S143L and D144E with overall prevalence of 18.9% (95% CI [9.5-34.2]). Reverse transcriptase (RT) sequence analysis showed mutations in three patients with overall prevalence of 8.1% (95% CI [2.8-21.3]). RT mutations included: V173L, S202I, L180M, M204V and T184A. Transmission cluster analysis revealed a relatively high proportion of infections taking place as a result of domestic spread (29.7%). Conclusions: Based on our findings, RT mutation analysis appears to be of high value before the initiation of therapy in patients with chronic HBV infection in Jordan. Phylogenetic analyses revealed a considerable proportion of local spread in the country which should be considered in the preventive infection control efforts.
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2.
  • Addario, Barbara, et al. (author)
  • Characterisation of Schizosaccharomyces pombe alpha-actinin
  • 2016
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 4
  • Journal article (peer-reviewed)abstract
    • The actin cytoskeleton plays a fundamental role in eukaryotic cells. Its reorganization is regulated by a plethora of actin-modulating proteins, such as a-actinin. In higher organisms, alpha-actinin is characterized by the presence of three distinct structural domains: an N-terminal actin-binding domain and a C-terminal region with EF-hand motif separated by a central rod domain with four spectrin repeats. Sequence analysis has revealed that the central rod domain of alpha-actinin from the fission yeast Schizosaccharomyces pombe consists of only two spectrin repeats. To obtain a firmer understanding of the structure and function of this unconventional alpha-actinin, we have cloned and characterized each structural domain. Our results show that this alpha-actinin isoform is capable of forming dimers and that the rod domain is required for this. However, its actin-binding and cross-linking activity appears less efficient compared to conventional alpha-actinins. The solved crystal structure of the actin-binding domain indicates that the closed state is stabilised by hydrogen bonds and a salt bridge not present in other a-actinins, which may reduce the affinity for actin.
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3.
  • Ahi, Ehsan Pashay, et al. (author)
  • Appetite regulating genes may contribute to herbivory versus carnivory trophic divergence in haplochromine cichlids
  • 2020
  • In: PeerJ. - : PEERJ INC. - 2167-8359. ; 8
  • Journal article (peer-reviewed)abstract
    • Feeding is a complex behaviour comprised of satiety control, foraging, ingestion and subsequent digestion. Cichlids from the East African Great Lakes are renowned for their diverse trophic specializations, largely predicated on highly variable jaw morphologies. Thus, most research has focused on dissecting the genetic, morphological and regulatory basis of jaw and teeth development in these species. Here for the first time we explore another aspect of feeding, the regulation of appetite related genes that are expressed in the brain and control satiety in cichlid fishes. Using qPCR analysis, we first validate stably expressed reference genes in the brain of six haplochromine cichlid species at the end of larval development prior to foraging. We next evaluate the expression of 16 appetite related genes in herbivorous and carnivorous species from the parallel radiations of Lake Tanganyika, Malawi and Victoria. Interestingly, we find increased expression of two appetite-regulating genes (anorodgenic genes), cart and npy2r, in the brain of carnivorous species in all the three lakes. This supports the notion that appetite gene regulation might play a part in determining trophic niche specialization in divergent cichlid species, already prior to exposure to different diets. Our study contributes to the limited body of knowledge on the neurological circuitry that controls feeding transitions and adaptations in cichlids and other teleosts.
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4.
  • Ahmed, Mukhtar (author)
  • Growth and development of soybean under changing light environments in relay intercropping system
  • 2019
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 7
  • Journal article (peer-reviewed)abstract
    • Background: Maize-soybean relay-intercropping (MSR) is a famous system of crop production in developing countries. However, maize shading under this system directly affects the light quality and intensity of soybean canopy. This is a challenging scenario in which to implement the MSR system, in terms of varieties selection, planting pattern, and crop management since the duration of crop resource utilization clearly differs.Methods: Therefore, this experiment aimed to elucidate the effect of leaf excising treatments from maize top to fully clarify the needs and balance of light quality and intensity of intercrop-soybean under MSR in field conditions. The effects of different leaf excising treatments (T0, no removal of leaves; T2, removal of two topmost leaves; T4, removal of four topmost leaves; T6, removal of six topmost leaves from maize plants were applied at first-trifoliate stage (V-1) of soybean) on photosynthetically active radiation transmittance (PAR(T)), red to far-red ratio (R:FR), morphological and photosynthetic characteristics and total biomass production at second-trifoliate stage (V-2), fifth-trifoliate stage (V-5), and flowering-stage (R-1) of soybean were investigated through field experiments for 2-years under MSR.Results: As compared to T0, treatment T6 increased the PAR(T) and R:FR ratio at soybean canopy by 77% and 37% (V-2), 70% and 34% (V-5), and 41% and 36% (R-1), respectively. This improved light environment in T6 considerably enhanced the leaf area index, SPAD values and photosynthetic rate of soybean plants by 66%, 25% and 49% at R-1, respectively than T0. Similarly, relative to control, T6 also increased the stem diameter (by 29%) but decreased the plant height (by 23%) which in turn significantly increased stem breaking strength (by 87%) by reducing the lodging rate (by 59%) of soybean plants. Overall, under T6, relay-cropped soybean produced 78% of sole soybean seed-yield, and relay-cropped maize produced 81% of sole maize seed-yield. Our findings implied that by maintaining the optimum level of PAR(T) (from 60% to 80%) and R:FR ratio (0.9 to 1.1), we can improve morphological and photosynthetic characteristics of soybean plants in MSR. Therefore, more attention should be paid to the light environment when considering the sustainability of MSR via appropriate planting pattern selection.
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5.
  • Ahsan, Hajra, et al. (author)
  • Photocatalysis and adsorption kinetics of azo dyes by nanoparticles of nickel oxide and copper oxide and their nanocomposite in an aqueous medium
  • 2022
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 10
  • Journal article (peer-reviewed)abstract
    • Azo dyes are recalcitrant organic pollutants present in textile industry effluents. Conventional treatment methods to remove them come with a range of disadvantages. Nanoparticles and their nanocomposites offer more efficient, less expensive and easy to handle wastewater treatment alternative. Methods. In this study, nanoparticles of nickel oxide (NiO-NPs), copper oxide (CuO-NPs) and their nanocomposite (NiO/CuO-NC) were synthesized using co- precipitation method. The functional groups present on the surface of synthesized nanomaterials were verified using Fourier-transform infrared spectroscopy (FTIR). Surface morphology was assessed using scanning electron microscopy (SEM) whereas purity, shape and size of the crystallite were determined using X-ray diffraction (XRD) technique. The potential of these nanomaterials to degrade three dyes i.e., Reactive Red-2 (RR-2), Reactive Black-5 (RB-5) and Orange II sodium salt (OII) azo dyes, was determined in an aqueous medium under visible light (photocatalysis). The photodegradation effectiveness of all nanomaterials was evaluated under different factors like nanomaterial dose (0.02-0.1 g 10 mL-1), concentration of dyes (20-100 mg L-1), and irradiation time (60-120 min). They were also assessed for their potential to adsorb RR-2 and OII dyes. Results. Results revealed that at optimum concentration (60 mgL-1) of RR-2, RB-5, and OII dyes, NiO-NPs degraded 90, 82 and 83%, CuO-NPs degraded 49, 34, and 44%, whereas the nanocomposite NiO/CuO-NC degraded 92, 93, and 96% of the said dyes respectively. The nanomaterials were categorized as the efficient degraders of the dyes in the order: NiO/CuO-NC > NiO-NPs > CuO-NPs. The highest degradation potential shown by the nanocomposite was attributed to its large surface area, small particles size, and quick reactions which were proved by advance analytical techniques. The equilibrium and kinetic adsorption of RR-2 and OII on NiO-NPs, CuO-NPs, and NiO/CuO-NC were well explained with Langmuir and Pseudo second order model, respectively (R2 ≥0.96). The maximum RR-2 adsorption (103 mg/g) was obtained with NiO/CuO-NC. It is concluded that nanocomposites are more efficient and promising for the dyes degradation from industrial wastewater as compared with dyes adsorption onto individual NPs. Thus, the nanocomposite NiO/CuO-NC can be an excellent candidate for photodegradation as well as the adsorption of the dyes in aqueous media.
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6.
  • Alatalo, Juha M., et al. (author)
  • Dominance hierarchies, diversity and species richness of vascular plants in an alpine meadow: Contrasting short and medium termresponses to simulated global change
  • 2014
  • In: PeerJ. - : PeerJ Inc.. - 2167-8359. ; 2014:1
  • Journal article (peer-reviewed)abstract
    • We studied the impact of simulated global change on a high alpine meadow plant community. Specifically, we examined whether short-term (5 years) responses are good predictors for medium-term (7 years) changes in the system by applying a factorial warming and nutrient manipulation to 20 plots in Latnjajaure, subarctic Sweden. Seven years of experimental warming and nutrient enhancement caused dramatic shifts in dominance hierarchies in response to the nutrient and the combined warming and nutrient enhancement treatments. Dominance hierarchies in the meadow moved from a community being dominated by cushion plants, deciduous, and evergreen shrubs to a community being dominated by grasses, sedges, and forbs. Short-termresponses were shown to be inconsistent in their ability to predict medium-term responses for most functional groups, however, grasses showed a consistent and very substantial increase in response to nutrient addition over the seven years. The non-linear responses over time point out the importance of longer-term studies with repeated measurements to be able to better predict future changes. Forecasted changes to temperature and nutrient availability have implications for trophic interactions, and may ultimately influence the access to and palatability of the forage for grazers. Depending on what anthropogenic change will be most pronounced in the future (increase in nutrient deposits, warming, or a combination of them both), different shifts in community dominance hierarchies may occur. Generally, this study supports the productivity-diversity relationship found across arctic habitats, with community diversity peaking in mid-productivity systems and degrading as nutrient availability increases further. This is likely due the increasing competition in plant-plant interactions and the shifting dominance structure with grasses taking over the experimental plots, suggesting that global change could have high costs to biodiversity in the Arctic. © 2014 Alatalo et al.
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7.
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8.
  • Amato, Clara, et al. (author)
  • Modus Operandi and Affect in Sweden: The Swedish Version of the Regulatory Mode Questionnaire
  • 2017
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 5:e4092, s. 1-24
  • Journal article (peer-reviewed)abstract
    • Background: The Regulatory Mode Questionnaire (RMQ) is the most used and international well-known instrument for the measurement of individual differences in the two self-regulatory modes: locomotion (i.e., the aspect of self-regulation that is concerned with movement from state to state) and assessment (i.e., the comparative aspect of self-regulation). The aim of the present study was to verify the independence of the two regulatory modes, as postulated by the Regulatory Mode Theory (Kruglanski, Thompson, Higgins, Atash, Pierro, Shah & Spiegel, 2000), and the psychometric properties of the RMQ in the Swedish context. Furthermore, we investigated the relationship between regulatory modes (locomotion and assessment) and affective well-being (i.e., positive affect and negative affect). Method: A total of 655 university and high school students in the West of Sweden (males = 408 females = 242, and 5 participants who didn’t report their gender; agemean = 21.93±6.51) responded to the RMQ and the Positive Affect Negative Affect Schedule. We conducted two confirmatory factor analyses using structural equation modeling (SEM). A third SEM was conducted to test the relationship between locomotion and assessment to positive affect and negative affect. Results: The first analyses confirmed the unidimensional factor structure of locomotion and assessment and both scales showed good reliability. The assessment scale, however, was modified by dropping item 10 (“I don’t spend much time thinking about ways others could improve themselves.”) because it showed low loading (.07, p =.115). Furthermore, the effect of locomotion on positive affect was stronger than the effect of assessment on positive affect (Z = -15.16, p < .001), while the effect of assessment on negative affect was stronger than the effect of locomotion on negative affect (Z = 10.73, p < .001). Conclusion: The factor structure of the Swedish version of the RMQ is, as Regulatory Mode Theory suggests, unidimensional and it showed good reliability. The scales discriminated between the two affective well-being dimensions. We suggest that the Swedish version of the RMQ, with only minor modifications, is a useful instrument to tap individual differences in locomotion and assessment. Hence, the present study contributes to the validation of the RMQ in the Swedish culture and adds support to the theoretical framework of self-regulatory mode.
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9.
  • Andermann, Tobias, et al. (author)
  • SECAPR-a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments
  • 2018
  • In: Peerj. - : PeerJ. - 2167-8359. ; 6
  • Journal article (peer-reviewed)abstract
    • Evolutionary biology has entered an era of unprecedented amounts of DNA sequence data, as new sequencing technologies such as Massive Parallel Sequencing (MPS) can generate billions of nucleotides within less than a day. The current bottleneck is how to efficiently handle, process, and analyze such large amounts of data in an automated and reproducible way. To tackle these challenges we introduce the Sequence Capture Processor (SECAPR) pipeline for processing raw sequencing data into multiple sequence alignments for downstream phylogenetic and phylogeographic analyses. SECAPR is user-friendly and we provide an exhaustive empirical data tutorial intended for users with no prior experience with analyzing MPS output. SECAPR is particularly useful for the processing of sequence capture (synonyms: target or hybrid enrichment) datasets for non-model organisms, as we demonstrate using an empirical sequence capture dataset of the palm genus Geonoma (Arecaceae). Various quality control and plotting functions help the user to decide on the most suitable settings for even challenging datasets. SECAPR is an easy-to-use, free, and versatile pipeline, aimed to enable efficient and reproducible processing of MPS data for many samples in parallel.
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10.
  • Angell, IL, et al. (author)
  • De novo species identification using 16S rRNA gene nanopore sequencing
  • 2020
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 8, s. e10029-
  • Journal article (peer-reviewed)abstract
    • Nanopore sequencing is rapidly becoming more popular for use in various microbiota-based applications. Major limitations of current approaches are that they do not enable de novo species identification and that they cannot be used to verify species assignments. This severely limits applicability of the nanopore sequencing technology in taxonomic applications. Here, we demonstrate the possibility of de novo species identification and verification using hexamer frequencies in combination with k-means clustering for nanopore sequencing data. The approach was tested on the human infant gut microbiota of 3-month-old infants. Using the hexamer k-means approach we identified two new low abundant species associated with vaginal delivery. In addition, we confirmed both the vaginal delivery association for two previously identified species and the overall high levels of bifidobacteria. Taxonomic assignments were further verified by mock community analyses. Therefore, we believe our de novo species identification approach will have widespread application in analyzing microbial communities in the future.
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11.
  • Anikin, Andrey (author)
  • The honest sound of physical effort
  • 2023
  • In: PeerJ. - 2167-8359. ; 11:e14944
  • Journal article (peer-reviewed)abstract
    • Acoustic correlates of physical effort are still poorly understood, even though effort is vocally communicated in a variety of contexts with crucial fitness consequences, including both confrontational and reproductive social interactions. In this study 33 lay participants spoke during a brief, but intense isometric hold (L-sit), first without any voice-related instructions, and then asked either to conceal their effort or to imitate it without actually performing the exercise. Listeners in two perceptual experiments then rated 383 recordings on perceived level of effort (n = 39 listeners) or categorized them as relaxed speech, actual effort, pretended effort, or concealed effort (n = 102 listeners). As expected, vocal effort increased compared to baseline, but the accompanying acoustic changes (increased loudness, pitch, and tense voice quality) were under voluntary control, so that they could be largely suppressed or imitated at will. In contrast, vocal tremor at approximately 10 Hz was most pronounced under actual load, and its experimental addition to relaxed baseline recordings created the impression of concealed effort. In sum, a brief episode of intense physical effort causes pronounced vocal changes, some of which are difficult to control. Listeners can thus estimate the true level of exertion, whether to judge the condition of their opponent in a fight or to monitor a partner’s investment into cooperative physical activities.
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12.
  • Antonelli, Alexandre, 1978, et al. (author)
  • Conceptual and empirical advances in Neotropical biodiversity research
  • 2018
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 2018:10
  • Journal article (peer-reviewed)abstract
    • The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.
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13.
  • Antonelli, Alexandre, 1978, et al. (author)
  • Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics
  • 2019
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 2019:2
  • Journal article (peer-reviewed)abstract
    • Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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14.
  • Archer, Trevor, 1949, et al. (author)
  • Restoration of MPTP-induced deficits by Exercise and Milmed® Co-treatment
  • 2014
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 2:e531
  • Journal article (peer-reviewed)abstract
    • 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) induces permanent neurochemical and functional deficits. Following the administration of either two or four injections of the dopamine neurotoxin, MPTP, at a dose of 40 mg/kg, C57/BL6 mice were given access to running-wheels (30-min sessions, four times/week, Monday–Thursday) and treatment with the treated yeast, Milmed® (four times/week, Monday–Thursday), or simply running-wheel exercise by itself, over ten weeks. It was observed that the combination of physical exercise and Milmed® treatment, the MPTP + Exercise + Yeast (MC) group [MPTP + Ex- ercise + Milmed® (MC)], restored spontaneous motor activity markedly by test day 10, restored completely subthreshold L-Dopa-induced activity, and dopamine concentration to 76% of control values, in the condition wherein two adminis- trations of MPTP (2 × 40 mg/kg) were given prior to initiation of exercise and/or Milmed® treatment. Physical exercise by itself, MPTP + Exercise (MC) group, attenuated these deficits only partially. Administration of MPTP four times (i.e., 40 mg/kg, s.c., once weekly over four weeks for a total of 160 mg/kg, MPTP + Exer- cise + Yeast (MC) group [MPTP + Exercise + Milmed® (SC)] and MPTP + Exercise (SC), induced a lesioning effect that was far too severe for either exercise alone or the exercise + Milmed® combination to ameliorate. Nevertheless, these findings indicate a powerful effect of physical exercise reinforced by Milmed® treatment in restoring MPTP-induced deficits of motor function and dopamine neurochemistry in mice.
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15.
  • Backman, Lars, 1951- (author)
  • Alpha-actinin of the chlorarchiniophyte Bigelowiella natans
  • 2018
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 6
  • Journal article (peer-reviewed)abstract
    • The genome of the chlorarchiniophyte Bigelowiella natans codes for a protein annotated as an α-actinin-like protein. Analysis of the primary sequence indicate that this protein has the same domain structure as other α-actinins, a N-terminal actin-binding domain and a C-terminal calmodulin-like domain. These two domains are connected by a short rod domain, albeit long enough to form a single spectrin repeat. To analyse the functional properties of this protein, the full-length protein as well as the separate domains were cloned and isolated. Characerisation showed that the protein is capable of cross-linking actin filaments into dense bundles, probably due to dimer formation. Similar to human α-actinin, calcium-binding occurs to the most N-terminal EF-hand motif in the calmodulin-like C-terminal domain. The results indicate that this Bigelowiella protein is a proper α-actinin, with all common characteristics of a typical α-actinin.
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16.
  • Backman, Lars, 1951- (author)
  • Calcium affinity of human α-actinin1
  • 2015
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 3
  • Journal article (peer-reviewed)abstract
    • Due to alternative splicing, the human ACTN1 gene codes for three different transcripts of α-actinin; one isoform that is expressed only in the brain and two with a more general expression pattern. The sequence difference is located to the C-terminal domains and the EF-hand motifs. Therefore, any functional or structural distinction should involve this part of the protein. To investigate this further, the calcium affinities of these three isoforms of α-actinin 1 have been determined by isothermal calorimetry.
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17.
  • Bacon, Christine D., et al. (author)
  • Evolutionary persistence in Gunnera and the contribution of southern plant groups to the tropical Andes biodiversity hotspot
  • 2018
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 2018:3
  • Journal article (peer-reviewed)abstract
    • Several studies have demonstrated the contribution of northern immigrants to the flora of the tropical Andesthe world's richest and most diverse biodiversity hotspot. However, much less is known about the biogeographic history and diversification of Andean groups with southern origins, although it has been suggested that northern and southern groups have contributed roughly equally to the high Andean (i.e., páramo) flora. Here we infer the evolutionary history of the southern hemisphere plant genus Gunnera, a lineage with a rich fossil history and an important ecological role as an early colonising species characteristic of wet, montane environments. Our results show striking contrasts in species diversification, where some species may have persisted for some 90 million years, and whereas others date to less than 2 Ma since origination. The outstanding longevity of the group is likely linked to a high degree of niche conservatism across its highly disjunct range, whereby Gunnera tracks damp and boggy soils in cool habitats. Colonisation of the northern Andes is related to Quaternary climate change, with subsequent rapid diversification appearing to be driven by their ability to take advantage of environmental opportunities. This study demonstrates the composite origin of a mega-diverse biota.
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18.
  • Bailleul, Alida M., et al. (author)
  • Dinosaur paleohistology : Review, trends and new avenues of investigation
  • 2019
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 2019:9
  • Journal article (peer-reviewed)abstract
    • In the mid-19th century, the discovery that bone microstructure in fossils could be preserved with fidelity provided a new avenue for understanding the evolution, function, and physiology of long extinct organisms. This resulted in the establishment of paleohistology as a subdiscipline of vertebrate paleontology, which has contributed greatly to our current understanding of dinosaurs as living organisms. Dinosaurs are part of a larger group of reptiles, the Archosauria, of which there are only two surviving lineages, crocodilians and birds. The goal of this review is to document progress in the field of archosaur paleohistology, focusing in particular on the Dinosauria. We briefly review the "growth age" of dinosaur histology, which has encompassed new and varied directions since its emergence in the 1950s, resulting in a shift in the scientific perception of non-avian dinosaurs from "sluggish" reptiles to fast-growing animals with relatively high metabolic rates. However, fundamental changes in growth occurred within the sister clade Aves, and we discuss this major evolutionary transition as elucidated by histology. We then review recent innovations in the field, demonstrating how paleohistology has changed and expanded to address a diversity of non-growth related questions. For example, dinosaur skull histology has elucidated the formation of curious cranial tissues (e.g., "metaplastic" tissues), and helped to clarify the evolution and function of oral adaptations, such as the dental batteries of duck-billed dinosaurs. Lastly, we discuss the development of novel techniques with which to investigate not only the skeletal tissues of dinosaurs, but also less-studied soft-tissues, through molecular paleontology and paleohistochemistry-recently developed branches of paleohistology- and the future potential of these methods to further explore fossilized tissues. We suggest that the combination of histological and molecular methods holds great potential for examining the preserved tissues of dinosaurs, basal birds, and their extant relatives. This review demonstrates the importance of traditional bone paleohistology, but also highlights the need for innovation and new analytical directions to improve and broaden the utility of paleohistology, in the pursuit of more diverse, highly specific, and sensitive methods with which to further investigate important paleontological questions.
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19.
  • Bakker, F. T., et al. (author)
  • The Global Museum: natural history collections and the future of evolutionary science and public education
  • 2020
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 8
  • Journal article (peer-reviewed)abstract
    • Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the 'Global Museum') is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow's technologies and hence further increasing the relevance of natural history museums.
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20.
  • Baranowski, Bartosz, et al. (author)
  • Protein family neighborhood analyzer-ProFaNA
  • 2023
  • In: PeerJ. - 2167-8359. ; 11
  • Journal article (peer-reviewed)abstract
    • Background: Functionally related genes are well known to be often grouped in close vicinity in the genomes, particularly in prokaryotes. Notwithstanding the diverse evolutionary mechanisms leading to this phenomenon, it can be used to predict functions of uncharacterized genes. Methods: Here, we provide a simple but robust statistical approach that leverages the vast amounts of genomic data available today. Considering a protein domain as a functional unit, one can explore other functional units (domains) that significantly often occur within the genomic neighborhoods of the queried domain. This analysis can be performed across different taxonomic levels. Provisions can also be made to correct for the uneven sampling of the taxonomic space by genomic sequencing projects that often focus on large numbers of very closely related strains, e.g., pathogenic ones. To this end, an optional procedure for averaging occurrences within subtaxa is available. Results: Several examples show this approach can provide useful functional predictions for uncharacterized gene families, and how to combine this information with other approaches. The method is made available as a web server at http://bioinfo.sggw.edu.pl/neighborhood_analysis.
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21.
  • Barboutis, Christos, et al. (author)
  • Fuelling in front of the barrier-are there age based behavioral differences in Garden Warblers Sylvia borin?
  • 2014
  • In: PeerJ. - San Fransisco and London : PeerJ. - 2167-8359. ; 2
  • Journal article (peer-reviewed)abstract
    • Garden Warblers Sylvia borin were studied during autumn stopover in Crete before crossing the barrier of the Mediterranean Sea and the Sahara Desert. Birds followed with transmitters show extensive stopover periods, which were longer in first-year birds, 16 days, compared with adult birds, 14 days. The distribution of body masses from birds trapped in fig trees were used to estimate the departure body mass and the results found indicate that both age categories on average depart with a fuel load close to 100% of lean body mass. The movement of transmitter birds shows differences between first-year and adult birds. Adult birds move further away from the release site and many also left the study area. Several were found settled outside the study area, up to 17 km away, indicating that they regularly make longer stopover movements. It is suggested that this might be a result of that they return to a place where they stayed during an earlier migration. It was shown that stopover site fidelity exists and nine garden warblers were recaptured in the area during a following autumn. The results found highlights the importance of stopover areas close to the Sahara Desert.
  •  
22.
  • Bartomeus, Ignasi, et al. (author)
  • Contribution of insect pollinators to crop yield and quality varies with agricultural intensification
  • 2014
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 2
  • Journal article (peer-reviewed)abstract
    • Discussion. For the four crops in this study, there is clear benefit delivered by pollinators on yield quantity and/or quality, but it is not maximized under current agricultural intensification. Honeybees, the most abundant pollinator, might partially compensate the loss of wild pollinators in some areas, but our results suggest the need of landscape-scale actions to enhance wild pollinator populations.
  •  
23.
  • Beckmann, Lara Maleen, 1993, et al. (author)
  • Odd family reunion: DNA barcoding reveals unexpected relationship between three hydrozoan species
  • 2023
  • In: PeerJ. - 2167-8359. ; 11:e15118
  • Journal article (peer-reviewed)abstract
    • Knowledge of life histories is crucial for understanding ecological and evolutionary processes, but for many hydrozoan species only incomplete life cycles have been described due to challenges in linking hydromedusae with their polyp stages. Using a combination of DNA barcoding, morphology, and ecological information, we describe for the first time the polyp stage of Halopsis ocellata Agassiz, 1865 and re-describe that of Mitrocomella polydiademata (Romanes, 1876). Campanulinid hydroids referable to Lafoeina tenuis Sars, 1874 and collected in the same biogeographic region as the type locality of this species are shown to be the polyp stage of these two mitrocomid hydromedusae. The nominal species L. tenuis thus is a species complex that includes the polyp stage of medusae belonging to at least two genera currently placed in a different family. Consistent morphological and ecological differences were found between the polyps linked to each of these two hydromedusae, but molecular results suggest that yet other species may have morphologically similar hydroids. Polyps morphologically identified to L. tenuis are therefore better referred to as Lafoeina tenuis-type until further associations are resolved, particularly when occurring outside of the area of distribution of H. ocellata and M. polydiademata. Molecular identification integrated with traditional taxonomy is confirmed as an effective approach to link inconspicuous stages of marine invertebrates with hitherto unknown life cycles, especially in often-overlooked taxa. Disentangling the relationships between L. tenuis, H. ocellata, and M. polydiademata lays the ground for future research aimed at resolving the taxonomy and systematics of the enigmatic families Mitrocomidae and Campanulinidae.
  •  
24.
  • Belle, Simon (author)
  • Effects of changes in isotopic baselines on the evaluation of food web structure using isotopic functional indices
  • 2020
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 8
  • Journal article (peer-reviewed)abstract
    • Background. This study aimed to assess whether ecological inferences from isotopic functional indices (IFIs) are impacted by changes in isotopic baselines in aquatic food webs. We used sudden CO2-outgassing and associated shifts in DIC- delta C-13 brought by waterfalls as an excellent natural experimental set-up to quantify impacts of changes in algal isotopic baselines on ecological inferences from IFIs.Methods. Carbon (delta C-13) and nitrogen (delta N-15) stable isotopic ratios of invertebrate communities sharing similar structure were measured at above- and below-waterfall sampling sites from five rivers and streams in Southern Quebec (Canada). For each sampled invertebrate community, the six Laymans IFIs were then calculated in the delta-space (delta C-13 vs. delta N-15).Results. As expected, isotopic functional richness indices, measuring the overall extent of community trophic space, were strongly sensitive to changes in isotopic baselines unlike other IFIs. Indeed, other IFIs were calculated based on the distribution of species within delta-space and were not strongly impacted by changes in the vertical or horizontal distribution of specimens in the delta-space. Our results highlighted that IFIs exhibited different sensitivities to changes in isotopic baselines, leading to potential misinterpretations of IFIs in river studies where isotopic baselines generally show high temporal and spatial variabilities. The identification of isotopic baselines and their associated variability, and the use of independent trophic tracers to identify the actual energy pathways through food webs must be a prerequisite to IFIs-based studies to strengthen the reliability of ecological inferences of food web structural properties.
  •  
25.
  • Belton, Lydia E., et al. (author)
  • Spotted hyaena space use in relation to human infrastructure inside a protected area
  • 2016
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 4
  • Journal article (peer-reviewed)abstract
    • Increasing human population growth has led to elevated levels of human-carnivore conflict. However, some carnivore populations have adapted to urban environments and the resources they supply. Such associations may influence carnivore ecology, behaviour and life-history. Pockets of urbanisation sometimes occur within protected areas, so that anthropogenic influences on carnivore biology are not necessarily confined to unprotected areas. In this study we evaluated associations between human infrastructure and related activity and space use of spotted hyaenas within one of the largest protected areas in South Africa, the Kruger National Park. Home range size was smaller for the dominant female of a clan living in close proximity to humans than that of the dominant female of a clan without direct access to human infrastructure. The home range including human infrastructure was also used less evenly during the night, presumably when the animals were active. Within this home range, a village area was preferred during the night, when the least modified areas within the village were preferred and administration and highly modified areas were avoided. During the day, however, there were no preference or avoidance of the village area, but all habitats except unmodified habitats within the village area were avoided. We suggest that human infrastructure and associated activity influenced hyaena space use, primarily through alterations in the spatial distribution of food. However, these effects may have been indirectly caused by habitat modification that generated favourable hunting habitat rather than a direct effect caused by access to human food such as garbage. Because of the often pivotal effects of apex predators in terrestrial ecosystems, we encourage further work aimed to quantify how human presence influences large carnivores and associated ecosystem processes within protected areas.
  •  
26.
  • Benjamin, Bolduc, et al. (author)
  • The IsoGenie database : an interdisciplinary data management solution for ecosystems biology and environmental research
  • 2020
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 8
  • Journal article (peer-reviewed)abstract
    • Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project’s interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team’s modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB’s expandability and flexible architecture allow it to serve as an example ecosystems database.
  •  
27.
  • Bensch, Hanna, et al. (author)
  • Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples
  • 2022
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 10
  • Journal article (peer-reviewed)abstract
    • Background: The transport and storage of samples in temperatures of minus 80 °C is commonly considered as the gold standard for microbiome studies. However, studies conducting sample collection at remote sites without a reliable cold-chain would benefit from a sample preservation method that allows transport and storage at ambient temperature.Methods: In this study we compare alpha diversity and 16S microbiome composition of 20 fecal sample replicates from Damaraland mole-rats (Fukomys damarensis) preserved in a minus 80 °C freezer and transported on dry ice to freeze-dried samples that were stored and transported in ambient temperature until DNA extraction.Results: We found strong correlations between relative abundances of Amplicon Sequence Variants (ASVs) between preservation treatments of the sample, no differences in alpha diversity measures between the two preservation treatments and minor effects of the preservation treatment on beta diversity measures. Our results show that freeze-drying samples can be a useful method for cost-effective transportation and storage of microbiome samples that yields quantitatively almost indistinguishable results in 16S microbiome analyses as those stored in minus 80 °C.
  •  
28.
  • Bereketoglu, Ceyhun, et al. (author)
  • Transcriptomic analysis of nonylphenol effect on Saccharomyces cerevisiae
  • 2021
  • In: PeerJ. - : PeerJ Inc.. - 2167-8359. ; 9
  • Journal article (peer-reviewed)abstract
    • Nonylphenol (NP) is a bioaccumulative environmental estrogen that is widely used as a nonionic surfactant. We have previously examined short-term effects of NP on yeast cells using microarray technology. In the present study, we investigated the adaptive response of Saccharomyces cerevisiae BY4742 cells to NP exposure by analyzing genome-wide transcriptional profiles using RNA-sequencing. We used 2 mg/L NP concentration for 40 days of exposure. Gene expression analysis showed that a total of 948 genes were differentially expressed. Of these, 834 genes were downregulated, while 114 genes were significantly upregulated. GO enrichment analysis revealed that 369 GO terms were significantly affected by NP exposure. Further analysis showed that many of the differentially expressed genes were associated with oxidative phosphorylation, iron and copper acquisition, autophagy, pleiotropic drug resistance and cell cycle progression related processes such as DNA and mismatch repair, chromosome segregation, spindle checkpoint activity, and kinetochore organization. Overall, these results provide considerable information and a comprehensive understanding of the adaptive response to NP exposure at the gene expression level.
  •  
29.
  • Bomfleur, Benjamin, et al. (author)
  • The fossil Osmundales (Royal Ferns)—a phylogenetic network analysis, revised taxonomy, and evolutionary classification of anatomically preserved trunks and rhizomes
  • 2017
  • In: PeerJ. - Washington DC : Peer J Inc.. - 2167-8359. ; 5
  • Journal article (peer-reviewed)abstract
    • The Osmundales (Royal Fern order) originated in the late Paleozoic and is the most ancient surviving lineage of leptosporangiate ferns. In contrast to its low diversity today (less than 20 species in six genera), it has the richest fossil record of any extant group of ferns. The structurally preserved trunks and rhizomes alone are referable to more than 100 fossil species that are classified in up to 20 genera, four subfamilies, and two families. This diverse fossil record constitutes an exceptional source of information on the evolutionary history of the group from the Permian to the present. However, inconsistent terminology, varying formats of description, and the general lack of a uniform taxonomic concept renders this wealth of information poorly accessible. To this end, we provide a comprehensive review of the diversity of structural features of osmundalean axes under a standardized, descriptive terminology. A novel morphological character matrix with 45 anatomical characters scored for 15 extant species and for 114 fossil operational units (species or specimens) is analysed using networks in order to establish systematic relationships among fossil and extant Osmundales rooted in axis anatomy. The results lead us to propose an evolutionary classification for fossil Osmundales and a revised, standardized taxonomy for all taxa down to the rank of (sub)genus. We introduce several nomenclatural novelties: (1) a new subfamily Itopsidemoideae (Guaireaceae) is established to contain Itopsidema, Donwelliacaulis, and Tiania; (2) the thamnopteroid genera Zalesskya, Iegosigopteris, and Petcheropteris are all considered synonymous with Thamnopteris; (3) 12 species of Millerocaulis and Ashicaulis are assigned to modern genera (tribe Osmundeae); (4) the hitherto enigmatic Aurealcaulis is identified as an extinct subgenus of Plenasium; and (5) the poorly known Osmundites tuhajkulensis is assigned to Millerocaulis. In addition, we consider Millerocaulis stipabonettiorum a possible member of Palaeosmunda and Millerocaulis estipularis as probably constituting the earliest representative of the (Todea-)Leptopteris lineage (subtribe Todeinae) of modern Osmundoideae.
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30.
  • Borgström, Pernilla, et al. (author)
  • Aboveground insect herbivory increases plant competitive asymmetry, while belowground herbivory mitigates the effect
  • 2016
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 4
  • Journal article (peer-reviewed)abstract
    • Insect herbivores can shift the composition of a plant community, but the mechanism underlying such shifts remains largely unexplored. A possibility is that insects alter the competitive symmetry between plant species. The effect of herbivory on competition likely depends on whether the plants are subjected to aboveground or belowground herbivory or both, and also depends on soil nitrogen levels. It is unclear how these biotic and abiotic factors interactively affect competition. Ina greenhouse experiment, we measured competition between two coexisting grass species that respond differently to nitrogen deposition: Dactylis glomerata L., which is competitively favoured by nitrogen addition, and Festuca rubra L., which is competitively favoured on nitrogen-poor soils. We predicted: (1) that aboveground herbivory would reduce competitive asymmetry at high soil nitrogen by reducing the competitive advantage of D. glomerata; and (2), that belowground herbivory would relax competition at low soil nitrogen, by reducing the competitive advantage of F. rubra. Aboveground herbivory caused a 46 A) decrease in the competitive ability of F. rubra, and a 23% increase in that of D. glomerata, thus increasing competitive asymmetry, independently of soil nitrogen level. Belowground herbivory did not affect competitive symmetry, but the combined influence of above and belowground herbivory was weaker than predicted from their individual effects. Belowground herbivory thus mitigated the increased competitive asymmetry caused by aboveground herbivory. D. glomerata remained competitively dominant after the cessation of aboveground herbivory, showing that the influence of herbivory continued beyond the feeding period. We showed that insect herbivory can strongly influence plant competitive interactions. In our experimental plant community, aboveground insect herbivory increased the risk of competitive exclusion of F. rubra. Belowground herbivory appeared to mitigate the influence of aboveground herbivory, and this mechanism may play a role for plant species coexistence.
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31.
  • Brown, Nicholas, 1960-, et al. (author)
  • Does Twitter language reliably predict heart disease? : A commentary on Eichstaedt et al. (2015a)
  • 2018
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 6
  • Journal article (peer-reviewed)abstract
    • We comment on Eichstaedt et al.’s (2015a) claim to have shown that language patterns among Twitter users, aggregated at the level of US counties, predicted county-level mortality rates from atherosclerotic heart disease (AHD), with “negative” language being associated with higher rates of death from AHD and “positive” language associated with lower rates. First, we examine some of Eichstaedt et al.’s apparent assumptions about the nature of AHD, as well as some issues related to the secondary analysis of online data and to considering counties as communities. Next, using the data files supplied by Eichstaedt et al., we reproduce their regression- and correlation-based models, substituting mortality from an alternative cause of death—namely, suicide—as the outcome variable, and observe that the purported associations between “negative” and “positive” language and mortality are reversed when suicide is used as the outcome variable. We identify numerous other conceptual and methodological limitations that call into question the robustness and generalizability of Eichstaedt et al.’s claims, even when these are based on the results of their ridge regression/machine learning model. We conclude that there is no good evidence that analyzing Twitter data in bulk in this way can add anything useful to our ability to understand geographical variation in AHD mortality rates.
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32.
  • Bryant, Patrick, et al. (author)
  • Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries
  • 2020
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 8
  • Journal article (peer-reviewed)abstract
    • Background: As governments across Europe have issued non-pharmaceutical interventions (NPIs) such as social distancing and school closing, the mobility patterns in these countries have changed. Most states have implemented similar NPIs at similar time points. However, it is likely different countries and populations respond differently to the NPIs and that these differences cause mobility patterns and thereby the epidemic development to change.Methods: We build a Bayesian model that estimates the number of deaths on a given day dependent on changes in the basic reproductive number, R-0, due to differences in mobility patterns. We utilise mobility data from Google mobility reports using five different categories: retail and recreation, grocery and pharmacy, transit stations, workplace and residential. The importance of each mobility category for predicting changes in R-0 is estimated through the model.Findings: The changes in mobility have a considerable overlap with the introduction of governmental NPIs, highlighting the importance of government action for population behavioural change. The shift in mobility in all categories shows high correlations with the death rates 1 month later. Reduction of movement within the grocery and pharmacy sector is estimated to account for most of the decrease in R-0.Interpretation: Our model predicts 3-week epidemic forecasts, using real-time observations of changes in mobility patterns, which can provide governments with direct feedback on the effects of their NPIs. The model predicts the changes in a majority of the countries accurately but overestimates the impact of NPIs in Sweden and Denmark and underestimates them in France and Belgium. We also note that the exponential nature of all epidemiological models based on the basic reproductive number, R-0 cause small errors to have extensive effects on the predicted outcome.
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33.
  • Bukhari, Syed, et al. (author)
  • The behavior and welfare of neglected species: some examples from fish and mammals
  • 2024
  • In: PeerJ. - 2167-8359. ; 12
  • Journal article (peer-reviewed)abstract
    • Animal welfare is the state of an animal’s body and mind and the level to which its requirements are satisfied. Animal welfare is affected by human decisions and actions. Numerous decisions concerning animals are driven by human desires to enhance their own lives, and some of these decisions may be influenced by self-interest or a strong emphasis on economic factors. How to assess the welfare state of animals is a central issue in animal welfare science. Two critical questions can be used to address animal welfare: first, is the animal healthy, and second, does the animal have what it needs? Both of these questions can potentially be answered using the study of animal behavior. The development of behavioral methodologies is crucial for evaluating welfare in contexts where concern for animal welfare is often highest, such as on intensive modern farms and sites where working animals are used. Herein, we discuss animal welfare by focusing on some of its major concepts and explanations. Later, to illustrate key aspects of animal welfare, we chose to examine the information that is available for some ‘neglected’ livestock species, which are commercially important on a global basis and found in large numbers: buffaloes (Bubalus bubalis), camels (Camelus dromedarius), donkeys (Equus asinus), mules (Equus asinus × Equus caballus), and lumpfish (Cyclopterus lumpus). We chose these species because there are major ongoing concerns about their welfare, and more research is required to help solve the various problems. Overall, there are strong imbalances in terms of the species that are usually studied in terms of animal welfare research, and we call for greater attention to those that have traditionally been neglected.
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34.
  • Campennì, Marco, et al. (author)
  • Symmetry-based reciprocity : evolutionary constraints on a proximate mechanism
  • 2016
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 4
  • Journal article (peer-reviewed)abstract
    • Background. While the evolution of reciprocal cooperation has attracted an enormous attention, the proximate mechanisms underlying the ability of animals to cooperate reciprocally are comparatively neglected. Symmetry-based reciprocity is a hypothetical proximate mechanism that has been suggested to be widespread among cognitively unsophisticated animals. Methods. We developed two agent-baseds model of symmetry-based reciprocity (one relying on an arbitrary tag and the other on interindividual proximity) and tested their ability both to reproduce significant emergent features of cooperation in group living animals and to promote the evolution of cooperation. Results. Populations formed by', agents adopting symmetry-based reciprocity showed differentiated social relationships and a positive correlation between cooperation given and received: two common aspects of animal cooperation. However, when reproduction and selection across multiple generations were added to the models, agents adopting symmetry-based reciprocity were outcompeted by selfish agents that never cooperated. Discussion. In order to evolve, hypothetical proximate mechanisms must be able to from stand competition alternative strategies. While the results of our simulations require confirmation using analytical methods, we provisionally suggest symmetry based reciprocity is to be abandoned as a possible proximate mechanism underlying the ability of animals to reciprocate cooperative interactions.
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35.
  • Carrillo-Briceno, J. D., et al. (author)
  • Shark and ray diversity in the Tropical America (Neotropics)-an examination of environmental and historical factors affecting diversity
  • 2018
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 6
  • Journal article (peer-reviewed)abstract
    • We present the first comprehensive review of the present and past shark and ray diversity in marine waters of Tropical America, examining the patterns of distribution in the Eastern Central Pacific (EP) and Western Central Atlantic (WA) realms. We identified the major regions of diversity and of endemism, and explored the relations to physical variables. We found a strong relationship between shark and ray diversity with area and coastal length of each province. The Tropical Northwestern Atlantic Province is characterized by high diversity and greater occurrence of endemic species, suggesting this province as the hotspot of sharks and rays in Tropical America. The historical background for the current biogeography is explored and analyzed. Referential data from 67 geological units in 17 countries, from both shallow and deep-water habitats, across five time-clusters from the Miocene to the Pleistocene were studied. New data include 20 new assemblages from six countries. The most diverse Neogene and extant groups of shark and ray are Carcharhiniformes and Myliobatiformes, respectively. The differentiation between Pacific and Atlantic faunas goes to at least the middle Miocene, probably related with the increasing closure of the Central American Seaway acting as a barrier. The highest faunal similarity between the assemblages from the EP and the WA at the early Miocene could be related to the lack of a barrier back then, but increased sampling is needed to substantiate this hypothesis.
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36.
  • Carvalho, Francisca C., et al. (author)
  • Rock sponges (lithistid Demospongiae) of the Northeast Atlantic seamounts, with description of ten new species
  • 2020
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 8
  • Journal article (peer-reviewed)abstract
    • Background: Lithistid demosponges, also known as rock sponges, are a polyphyletic group of sponges which are widely distributed. In the Northeast Atlantic (NEA), 17 species are known and the current knowledge on their distribution is mainly restricted to the Macaronesian islands. In the Mediterranean Sea, 14 species are recorded and generally found in marine caves.Methods: Lithistids were sampled in nine NEA seamounts during the scientific expeditions Seamount 1 (1987) and Seamount 2 (1993) organized by the MNHN of Paris. Collected specimens were identified through the analyses of external and internal morphological characters using light and scanning electron microscopy, and compared with material from various museum collections as well as literature records.Results: A total of 68 specimens were analysed and attributed to 17 species across two orders, seven families, and seven genera, representing new records of distribution. Ten of these species are new to science, viz. Neoschrammeniella inaequalis sp. nov., N. piserai sp. nov., N. pomponiae sp. nov., Discodermia arbor sp. nov., D. kellyae sp. nov., Macandrewia schusterae sp. nov., M. minima sp. nov., Exsuperantia levii sp. nov., Leiodermatium tuba sp. nov. and Siphonidium elongatus sp. nov., and are here described and illustrated. New bathymetric records were also found for D. ramifera, D. verrucosa and M. robusta. The Meteor seamount group has a higher species richness (15 species) compared to the Lusitanian seamount group (six species). The majority of the species had their distribution restricted to one seamount, and ten are only known from a single locality, but this can be a result of sample bias.Discussion: The number of species shared between the seamounts and the Macaronesian islands is very reduced. The same pattern repeats between the NEA and Mediterranean Sea. This study demonstrates that NEA seamounts are ecosystems with a higher diversity of lithistids than previously thought, increasing the number of lithistids known to occur in the NEA and Mediterranean Sea from 26 to 36 species.
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37.
  • Cerca, José, et al. (author)
  • Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species
  • 2021
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 9, s. e10896-e10896
  • Journal article (peer-reviewed)abstract
    • Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.
  •  
38.
  • Chae, Han, et al. (author)
  • Cloninger’s TCI associations with adaptive and maladaptive emotion regulation strategies
  • 2019
  • In: PeerJ. - : PeerJ. - 2376-5992 .- 2167-8359. ; 7
  • Journal article (peer-reviewed)abstract
    • Background. Cognitive emotion regulation plays a crucial role in psychopathology, resilience and well-being by regulating response to stress situations. However, the relationship between personality and adaptive and maladaptive regulation has not been sufficiently examined. Methods. Adaptive and maladaptive cognitive emotion regulation strategies of 247 university students were measured using the Cognitive Emotion Regulation Questionnaire (CERQ) and their temperament and character characteristics were analyzed with the Temperament and Character Inventory – Revised Short (TCI-RS). Two-step hierarchical multiple regression analyses were used to analyze whether TCI-RS explains the use of adaptive and maladaptive cognitive emotion regulation strategies. The latent classes of cognitive emotion regulation strategies were extracted with Latent Class Analysis (LCA) and significant differences in the subscales of CERQ and TCI-RS were examined with Analysis of Covariance (ANCOVA) and Profile Analysis after controlling for sex and age. Results. The two-step hierarchical multiple regression model using the seven TCI-RS subscales explained 32.30% of the adaptive and 41.70% of the maladaptive CERQ subscale scores when sex and age were introduced in the first step as covariates. As for temperament, Novelty Seeking (NS) and Persistence (PS) were pivotal for adaptive and Harm Avoidance (HA) and PS for maladaptive CERQ total scores. In addition, the character traits Self-Directedness (SD) and Cooperativeness (CO) were critical for high adaptive and low maladaptive CERQ scores. Four latent emotion regulation classes were confirmed through LCA, and distinct TCI-RS profiles were found. The temperament trait HA and character trait SD were significantly different among the four latent emotion regulation classes. Discussion. This study demonstrated that SD and CO are related to cognitive emotion regulation strategies along with psychological health and well-being, and that PS exhibits dualistic effects when combined with NS or HA on response to stressful situations. The importance of developing mature character represented by higher SD and CO in regard to mental health and its clinical implementation was discussed.
  •  
39.
  • Cheng, Yirui, et al. (author)
  • Comparison of serum exosome isolation methods on co-precipitated free microRNAs.
  • 2020
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 8
  • Journal article (peer-reviewed)abstract
    • Background: Exosomes are nano-sized extracellular vesicles containing different biomolecules such as proteins and microRNAs (miRNAs) that mediate intercellular communication. Recently, numerous studies have reported the important functions of exosomal miRNAs in disease development and the potential clinical application as diagnostic biomarkers. Up to now, the most commonly used methods to extract exosomes are ultracentrifugation (UC) and precipitation-based commercial kit (e.g., ExoQuick). Generally, both UC and ExoQuick method could co-isolate contaminating proteins along with exosomes, with the UC method yielding even purer exosomes than ExoQuick. However, the comparison of these two methods on co-precipitated free miRNAs is still unknown.Methods: In this study, we isolated exosomes from the human serum with exogenously added cel-miR-39 by UC and ExoQuick and compared the proportion of cel-miR-39 co-precipitated with exosomes extracted by these two methods.Results: Using exogenous cel-miR-39 as free miRNAs in serum, we concluded that ExoQuick co-isolates a small proportion of free miRNAs while UC hardly precipitates any free miRNAs. We also found that incubation at 37 °C for 1 h could decrease the proportion of free miRNAs, and exosomal miRNAs like miR-126 and miR-152 also decreased when RNase A was used. In conclusion, our findings provide essential information about the details of serum exosome isolation methods for further research on exosomal miRNAs.
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40.
  • Clement, Alice M., et al. (author)
  • The cranial endocast of Dipnorhynchus sussmilchi (Sarcopterygii : Dipnoi) and the interrelationships of stem-group lungfishes
  • 2016
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 4
  • Journal article (peer-reviewed)abstract
    • The first virtual cranial endocast of a lungfish from the Early Devonian, Dipnorhynchus sussmilchi, is described. Dipnorhynchus, only the fourth Devonian lungfish for which a near complete cranial endocast is known, is a key taxon for clarifying primitive character states within the group. A ventrally-expanded telencephalic cavity is present in the endocast of Dipnorhynchus demonstrating that this is the primitive state for "true" Dipnoi. Dipnorhynchus also possesses a utricular recess differentiated from the sacculolagenar pouch like that seen in stratigraphically younger lungfish (Dipterus, Chirodipterus, Rhinodipterus), but absent from the dipnomorph Youngolepis. We do not find separate pineal and para-pineal canals in contrast to a reconstruction from previous authors. We conduct the first phylogenetic analysis of Dipnoi based purely on endocast characters, which supports a basal placement of Dipnorhynchus within the dipnoan stem group, in agreement with recent analyses. Our analysis demonstrates the value of endocast characters for inferring phylogenetic relationships.
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41.
  • de Abreu, Murilo S., et al. (author)
  • The variable monoaminergic outcomes of cleaner fish brains when facing different social and mutualistic contexts
  • 2018
  • In: PeerJ. - : PEERJ INC. - 2167-8359. ; 6
  • Journal article (peer-reviewed)abstract
    • The monoamines serotonin and dopamine are important neuromodulators present in the central nervous system, known to be active regulators of social behaviour in fish as in other vertebrates. Our aim was to investigate the region-specific brain monoaminergic differences arising when individual cleaners face a client (mutualistic context) compared to when they are introduced to another conspecific (conspecific context), and to understand the relevance of visual assessment compared to the impact of physical contact with any partner. We demonstrated that serotoninergic activity at the diencephalon responds mostly to the absence of physical contact with clients whereas cerebellar dopaminergic activity responds to actual cleaning engagement. We provide first insights on the brain's monoaminergic (region-specific) response variations, involved in the expression of cleaner fishes' mutualistic and conspecific behaviour. These results contribute to a better understanding of the monoaminergic activity in accordance to different socio-behavioural contexts.
  •  
42.
  • Derraik, Jose G. B., et al. (author)
  • Socioeconomic status is not associated with health-related quality of life in a group of overweight middle-aged men
  • 2018
  • In: PeerJ. - : PEERJ INC. - 2167-8359. ; 6
  • Journal article (peer-reviewed)abstract
    • Socioeconomic status is a known determinant of health. In secondary data analyses, we assessed whether socioeconomic status affected health-related quality of life in a group of overweight (body mass index 25-30 kg/m(2)) middle-aged (45.9 +/- 5.4 years) men, recruited in Auckland (New Zealand). Health-related quality of life was assessed with SF-36v2 three times: at baseline, and 12 and 30 weeks later. Socioeconomic status was determined by geo-coded deprivation scores derived from current address using the New Zealand Index of Deprivation 2006 (NZDep2006), as well as capital value of residence. Univariable and multivariable analyses showed no associations between measures of socioeconomic status and any mental or physical health domains. Our findings may reflect the fact that these men are not currently experiencing comorbidities associated with overweight.
  •  
43.
  • Dhaygude, Kishor, et al. (author)
  • Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta
  • 2017
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 5
  • Journal article (peer-reviewed)abstract
    • Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.
  •  
44.
  • Dhungel, Bidur, et al. (author)
  • Molecular systematics of the subfamily Limenitidinae (Lepidoptera : Nymphalidae)
  • 2018
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 2018:2
  • Journal article (peer-reviewed)abstract
    • We studied the systematics of the subfamily Limenitidinae (Lepidoptera: Nymphalidae) using molecular methods to reconstruct a robust phylogenetic hypothesis. The molecular data matrix comprised 205 Limenitidinae species, four outgroups, and 11,327 aligned nucleotide sites using up to 18 genes per species of which seven genes (CycY, Exp1, Nex9, PolII, ProSup, PSb and UDPG6DH) have not previously been used in phylogenetic studies. We recovered the monophyly of the subfamily Limenitidinae and seven higher clades corresponding to four traditional tribes Parthenini, Adoliadini, Neptini, Limenitidini as well as three additional independent lineages. One contains the genera Harma C Cymothoe and likely a third, Bhagadatta, and the other two independent lineages lead to Pseudoneptis and to Pseudacraea. These independent lineages are circumscribed as new tribes. Parthenini was recovered as sister to rest of Limenitidinae, but the relationships of the remaining six lineages were ambiguous. A number of genera were found to be non-monophyletic, with Pantoporia, Euthalia, Athyma, and Parasarpa being polyphyletic, whereas Limenitis, Neptis, Bebearia, Euryphura, and Adelpha were paraphyletic.
  •  
45.
  • Díaz, Julio A., et al. (author)
  • From caves to seamounts : the hidden diversity of tetractinellid sponges from the Balearic Islands, with the description of eight new species
  • 2024
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 12
  • Journal article (peer-reviewed)abstract
    • The sponge fauna of the Western Mediterranean stands as one of the most studied in the world. Yet sampling new habitats and a poorly studied region like the Balearic Islands highlights once again our limited knowledge of this group of animals. This work focused on demosponges of the order Tetractinellida collected in several research surveys (2016–2021) on a variety of ecosystems of the Balearic Islands, including shallow caves, seamounts and trawl fishing grounds, in a broad depth range (0–725 m). Tetractinellid material from the North Atlantic and more than twenty type specimens were also examined and, for some, re-described in this work. All species were barcoded with the traditional molecular markers COI (Folmer fragment) and 28S (C1-C2 or C1-D2 fragment). A total of 36 species were identified, mostly belonging to the family Geodiidae (15 species), thereby bringing the number of tetractinellids recorded in the Balearic Islands from 15 to 39. Eight species from this study are new: Stelletta mortarium sp. nov., Penares cavernensis sp. nov., Penares isabellae sp. nov., Geodia bibilonae sp. nov., Geodia microsphaera sp. nov. and Geodia matrix sp. nov. from the Balearic Islands; Geodia phlegraeioides sp. nov. and Caminus xavierae sp. nov. from the North East Atlantic. Stelletta dichoclada and Erylus corsicus are reported for the first time since their description in Corsica in 1983. Pachastrella ovisternata is documented for the first time in the Mediterranean Sea. Finally, after comparisons of type material, we propose new synonymies: Geodia anceps as a junior synonym of Geodia geodina, Erylus cantabricus as a junior synonym of Erylus discophorus and Spongosorites maximus as a junior synonym of Characella pachastrelloides.
  •  
46.
  • Dickel, Lisa, et al. (author)
  • Characterization of habitat requirements of European fishing spiders
  • 2022
  • In: PeerJ. - : PEERJ INC. - 2167-8359. ; 10
  • Journal article (peer-reviewed)abstract
    • Wetlands are among the most threatened habitats in the world, and so are their species, which suffer habitat loss due to climate and land use changes. Freshwater species, and especially arthropods, receive comparatively little attention in conservation plans, and the goals to stop and reverse the destruction of wetlands published 25 years ago in a manifesto by the Union of Concerned Scientists have not been reached. In this study, we investigated the occurrence and habitat requirements at two spatial scales of two species of European fishing spiders Dolomedes, which rely heavily on declining wetland habitats in Sweden and southern Norway. We collected occurrence data for Dolomedes plantarius and Dolomedes fimbriatus, using a live-determination method. We modelled the placement of nursery webs to describe fine-scale habitat requirements related to vegetation and micro-climate. Using a machine learning approach, we described the habitat features for each species and for co-occurrence sites, thus providing insight into variables relevant for the presence and detectability of Dolomedes. Nursery placement is mostly dependent on proximity to water, presence of Carex sp. (Sedges) and crossing vegetation structures, and on humidity, while detection can be affected by weather conditions. Furthermore, co-occurrence sites were more similar to D. plantarius sites than to D. fimbriatus sites, whereby surrounding forest, water type and velocity, elevation and latitude were of importance for explaining which species of Dolomedes was present. Overall, habitat requirements were narrower for D. plantarius compared to D. fimbiratus.
  •  
47.
  • Didion, John P., et al. (author)
  • Atropos : specific, sensitive, and speedy trimming of sequencing reads
  • 2017
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 5
  • Journal article (peer-reviewed)abstract
    • A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leadingedge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github. com/jdidion/atropos.
  •  
48.
  • Dittami, Simon M., et al. (author)
  • A community perspective on the concept of marine holobionts : current status, challenges, and future directions
  • 2021
  • In: PeerJ. - : PEERJ INC. - 2167-8359. ; 9
  • Journal article (peer-reviewed)abstract
    • Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.
  •  
49.
  • Donskov, A. O., et al. (author)
  • Oral function in patients with myasthenia gravis
  • 2021
  • In: PeerJ. - : PeerJ Inc.. - 2167-8359. ; 9
  • Journal article (peer-reviewed)abstract
    • Myasthenia Gravis (MG) is characterised by muscle weakness and increased fatigability. The aim of this pilot study was to investigate if patients with MG demonstrate different functional chewing patterns and report more complaints related to mastication as compared with healthy controls. Twelve patients (median 60 years Q1–Q3: 46–70) with generalised MG and nine healthy controls (median 57 years Q1–Q3: 55–63) participated. All participants underwent dental and oral examination and were asked to fill in a questionnaire concerning oral health. Static maximum bite force was measured with a bite force transducer, electromyography in the masseter, temporalis, and suprahyoid muscles were recorded, and jaw movement was tracked, during a 5-minute gum chewing test. The patients had more oral complaints (oral health impact profile total score 22.6 vs 7.5 P < 0.01) and had lower peak bite force than controls (18.8kgf (11.1;26.4) (95% CI) vs 29.5 kgf (21.6; 37.4) (P = 0.04)). In contrast, fatigability of the masticatory muscles, as defined by number of chewing cycles during the gum-chewing test, did not differ between patients and controls (P = 0.10). In conclusion, patients had more oral complaints and lower bite force than controls, but did not show significantly different functional chewing patterns. Future studies should aim at integrating measurement of peak force into functional tests. Attention should be given to oral complaints of patients with MG. © Copyright 2021 Donskov et al.
  •  
50.
  • Dudkiewicz, Malgorzata, et al. (author)
  • A novel conserved family of Macro-like domains—putative new players in ADP-ribosylation signaling
  • 2019
  • In: PeerJ. - : PeerJ. - 2167-8359. ; 2019:5
  • Journal article (peer-reviewed)abstract
    • The presence of many completely uncharacterized proteins, even in well-studied organisms such as humans, seriously hampers a full understanding of the functioning of living cells. One such example is the human protein C12ORF4, which belongs to the DUF2362 family, present in many eukaryotic lineages and conserved in metazoans. The only functional information available on C12ORF4 (Chromosome 12 Open Reading Frame 4) is its involvement in mast cell degranulation and its being a genetic cause of autosomal intellectual disability. Bioinformatics analysis of the DUF2362 family provides strong evidence that it is a novel member of the Macro clan/superfamily. Sequence similarity analysis versus other representatives of the Macro superfamily of ADP-ribose-binding proteins and mapping sequence conservation on predicted three-dimensional structure provides hypotheses regarding the molecular function for members of the DUF2362 family. For example, the available functional data suggest a possible role for C12ORF4 in ADP-ribosylation signaling in asthma and related inflammatory diseases. This novel family appears to be a likely novel ADP-ribosylation “reader” and “eraser,” a previously unnoticed putative new player in cell signaling by this emerging post-translational modification.
  •  
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