title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1460 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Elaborate plumage patterning in a Cretaceous bird link: https://peerj.com/articles/5831 last-modified: 2018-11-02 description: Integumentary patterns and colors can differentiate species, sexes, and life changes and can inform on habitat and ecology. However, they are rarely preserved in the fossil record. Here, we report on an extremely well-preserved specimen of the Cretaceous bird Confuciusornis with unprecedented complexity, including small spots on the wings, crest, and throat. Morphological and chemical evidence suggest that these patterns are produced by melanin, but unusual preservation prevents assignment of specific colors. Based on comparisons with extant birds, these patterns were likely used for camouflage, although other functions including sexual signaling cannot be ruled out. Our data show that even more elaborate plumage patterns than the spangles in Anchiornis and stripes in Sinosauropteryx were present at a relatively early stage of avian evolution, showing the significance of coloration and patterning to feather evolution. creator: Quanguo Li creator: Julia A. Clarke creator: Ke-Qin Gao creator: Jennifer A. Peteya creator: Matthew D. Shawkey uri: https://doi.org/10.7717/peerj.5831 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Li et al. title: Structure, dynamics and predicted functional role of the gut microbiota of the blue (Haliotis fulgens) and yellow (H. corrugata) abalone from Baja California Sur, Mexico link: https://peerj.com/articles/5830 last-modified: 2018-11-02 description: The GI microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities of abalone species characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their abalone host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA gene pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our findings revealed that Mycoplasma dominated the GI microbiome in both species. However, the structure of the bacterial communities differed significantly in spite of considerable intraspecific variation. This resulted from changes in predominant species composition in each GI microbiota, suggesting host-specific adaptation of bacterial lineages to these sympatric abalone. We hypothesize that the presence of exclusive OTUs in each microbiota may relate to host-specific differences in competitive pressure. Significant differences in bacterial diversity were found between species for the explored metabolic pathways despite their functional overlap. A more diverse array of bacteria contributed to each function in HC, whereas a single or much fewer OTUs were generally observed in HF. The structural and functional analyses allowed us to describe a significant taxonomic split and functional overlap between the microbiota of HF and HC abalone. creator: Francesco Cicala creator: José Alejandro Cisterna-Céliz creator: James D. Moore creator: Axayácatl Rocha-Olivares uri: https://doi.org/10.7717/peerj.5830 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cicala et al. title: Home sick: impacts of migratory beekeeping on honey bee (Apis mellifera) pests, pathogens, and colony size link: https://peerj.com/articles/5812 last-modified: 2018-11-02 description: Honey bees are important pollinators of agricultural crops and the dramatic losses of honey bee colonies have risen to a level of international concern. Potential contributors to such losses include pesticide exposure, lack of floral resources and parasites and pathogens. The damaging effects of all of these may be exacerbated by apicultural practices. To meet the pollination demand of US crops, bees are transported to areas of high pollination demand throughout the year. Compared to stationary colonies, risk of parasitism and infectious disease may be greater for migratory bees than those that remain in a single location, although this has not been experimentally established. Here, we conducted a manipulative experiment to test whether viral pathogen and parasite loads increase as a result of colonies being transported for pollination of a major US crop, California almonds. We also tested if they subsequently transmit those diseases to stationary colonies upon return to their home apiaries. Colonies started with equivalent numbers of bees, however migratory colonies returned with fewer bees compared to stationary colonies and this difference remained one month later. Migratory colonies returned with higher black queen cell virus loads than stationary colonies, but loads were similar between groups one month later. Colonies exposed to migratory bees experienced a greater increase of deformed wing virus prevalence and load compared to the isolated group. The three groups had similar infestations of Varroa mites upon return of the migratory colonies. However, one month later, mite loads in migratory colonies were significantly lower compared to the other groups, possibly because of lower number of host bees. Our study demonstrates that migratory pollination practices has varying health effects for honey bee colonies. Further research is necessary to clarify how migratory pollination practices influence the disease dynamics of honey bee diseases we describe here. creator: Samantha A. Alger creator: P. Alexander Burnham creator: Zachary S. Lamas creator: Alison K. Brody creator: Leif L. Richardson uri: https://doi.org/10.7717/peerj.5812 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Alger et al. title: Assessment of a mouse xenograft model of primary colorectal cancer with special reference to perfluorooctane sulfonate link: https://peerj.com/articles/5602 last-modified: 2018-11-02 description: Colorectal cancer ranks third among the most commonly diagnosed cancers in the United States. Current therapies have a range of side effects, and the development of a reliable animal model to speed the discovery of safe effective preventative therapies would be of great value. A cross-sectional study in a large Appalachian population recently showed an association between low circulating levels of perfluorooctane sulfonate (PFOS) and a reduced prevalence of colorectal cancer. A study using APCmin (C57BL/6J-ApcMin/J) mice prone to familial adenomatous polyposis found PFOS was protective when exposure occurred during tumor development. To test the possible benefit of PFOS on spontaneous colorectal cancer, we developed a mouse model utilizing primary patient colorectal cancer implants into NSG (NOD.Cg-PrkdcscidIl2rgtm1Wjl/Sz) mice. Study goals included: (1) to assess potential factors supporting the successful use of colorectal cancer from heterogeneous tumors for PDX studies; and, (2) evaluate PFOS as a therapy in tumor matched pairs of mice randomized to receive PFOS or vehicle. The time in days for mice to grow primary tumors to 5 mm took almost 2 months (mean = 53.3, se = 5.7, range = 17–136). Age of mice at implantation, patient age, gender and race appeared to have no discernable effect on engraftment rates. Engraftment rates for low and high-grade patient tumors were similar. PFOS appeared to reduce tumor size dramatically in one group of tumors, those from the right ascending colon. That is, by 5 weeks of treatment in two mice, PFOS had eliminated their 52.4 mm3 and 124.6 mm3 masses completely, an effect that was sustained for 10 weeks of treatment; in contrast, their corresponding matched vehicle control mice had tumors that grew to 472.7 mm3 and 340.1 mm3 in size respectively during the same period. In a third xenograft mouse, the tumor growth was dramatically blunted although not eliminated, and compared favorably to their matched vehicle controls over the same period. These preliminary findings suggested that this mouse model may be advantageous for testing compounds of potential value in the treatment of colorectal cancer, and PFOS may have utility in selected cases. creator: Jeffrey H. Wimsatt creator: Caitlin Montgomery creator: Laurel S. Thomas creator: Charity Savard creator: Rachel Tallman creator: Kim Innes creator: Nezar Jrebi uri: https://doi.org/10.7717/peerj.5602 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wimsatt et al. title: Plant defense elicitors: plant fitness versus wheat stem sawfly link: https://peerj.com/articles/5892 last-modified: 2018-11-01 description: The wheat stem sawfly (WSS), Cephus cinctus Norton, is an important wheat pest in the Northern Great Plains of the USA. No single control measure effectively suppresses WSS damage. This study provides information on the effects on the WSS adult settling preference behavior on wheat plants under laboratory conditions from treatment with both synthetic plant defense elicitors (Actigard® and cis-jasmone) and a botanical insecticide (Azadirachtin®). In addition, field experiments were performed to determine whether these chemicals impact the WSS fitness (larval mortality and larval body weight), winter wheat plant fitness (infestation, stem lodging, yield, and quality), adult population of WSS and Bracon spp., and larval parasitism levels. Our lab results showed that there were no significant differences in adult settling behavior on plants exposed separately to each chemical and control. In contrast, when adults were exposed simultaneously to treated and untreated plants, there was a significant reduction in the percentage of adults settling on Actigard® and Azadirachtin® treated plants compared to plants sprayed with water in the same cage. However, in field situations, regardless of application timing and field location, none of the chemicals significantly reduced adult population or stems damage. The exception was two times applications of Actigard® had significantly lower WSS infested stem damage levels at 30 days after initial treatment applications at Knees and 50 days at Choteau locations compared to control, but without effect at the Conrad location. The field study indicated that two times applications of Actigard® significantly increased diapausing larval mortality percentages and lowered stem lodging levels compared to untreated controls at Knees and Choteau locations, while no effects at Conrad location. Larval body weight was significantly lower in plots treated with Actigard® at Knees and Conrad, but no effects at Choteau. No significant differences were found in wheat yield and quality in plots treated with chemicals and controls at any location. Bracon spp. adult population and parasitism levels were not negatively affected by the use of chemicals. In conclusion, this study offers insights on what treatments should be emphasized in more detail despite variable findings. creator: Govinda Shrestha creator: Shabeg S. Briar creator: Gadi V.P. Reddy uri: https://doi.org/10.7717/peerj.5892 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Shrestha et al. title: Prionochelys matutina Zangerl, 1953 (Testudines: Pan-Cheloniidae) from the Late Cretaceous of the United States and the evolution of epithecal ossifications in marine turtles link: https://peerj.com/articles/5876 last-modified: 2018-11-01 description: BackgroundMany neritic to nearshore species of marine adapted turtle from the Late Cretaceous of North America are thought to represent the stem lineage of Cheloniidae but due to fragmentary holotypes, low total specimen counts, and resultantly incomplete morphological character suites, are routinely placed either within or outside of crown group Chelonioidea leaving their precise cladistic affinities uncertain. Despite this systematic ambiguity, the referral of these species to either the stem of Cheloniidae or Chelonioidea belies the critical importance of these taxa in any investigation into the origins of extant marine turtles. The adequate incorporation of these species into phylogenetic studies requires the formal description of relatively complete specimens, particularly those possessing associated cranial and post-cranial material.MethodsRemarkably complete fossil specimens of several adult and juvenile marine turtles from the Mooreville Chalk and Eutaw Formations (Alabama, USA) are formally described and assigned to Prionochelys matutina. This material provides new information into the anatomy, ontogeny, and cladistic affinities of the species. A phylogenetic hypothesis for Late Cretaceous marine turtles is then generated through the consilience of stratigraphic, morphological, and molecular data.ResultsPhylogenetic analysis places Prionochelys matutina on the stem of Cheloniidae as a member of a monophyletic clade with other putative pan-cheloniids, including Ctenochelys stenoporus, Ctenochelys acris, Peritresius martini, and Peritresius ornatus. The members of this clade possess incipient secondary palates, pronounced carapacial and plastral fontanelles at all stages of development, and are characterized by the presence of superficial ossifications at the apices of the neural keel elevations along the dorsal midline of the carapace.DiscussionThe epithecal osteoderms dorsal to the neural series (epineurals) found in Ctenochelyidae are unique among turtles. The presence of epineurals in ctenochelyid turtles shows that epithecal ossifications arose independently in both leatherback (Dermochelyidae) and hard-shelled (Cheloniidae) marine turtles. Whether or not the epineurals of Ctenochelyidae are homologous with the dermal ossicles comprising the carapace of Dermochelys coriacea remains untested however, histological thin sectioning of dermochelyid and ctenochelyd epithecal elements may reveal meaningful information in future studies. creator: Andrew D. Gentry uri: https://doi.org/10.7717/peerj.5876 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gentry title: Effect of seasonality on chemical profile and antifungal activity of essential oil isolated from leaves Psidium salutare (Kunth) O. Berg link: https://peerj.com/articles/5476 last-modified: 2018-11-01 description: Medicinal plants play a crucial role in the search for components that are capable of neutralizing the multiple mechanisms of fungal resistance. Psidium salutare (Kunth) O. Berg is a plant native to Brazil used as both food and traditional medicine to treat diseases and symptoms such as stomach ache and diarrhea, whose symptoms could be related to fungal infections from the genus Candida. The objective of this study was to investigate the influence of seasonal variability on the chemical composition of the Psidium salutare essential oil, its antifungal potential and its effect on the Candida albicans morphogenesis. The essential oils were collected in three different seasonal collection periods and isolated by the hydrodistillation process in a modified Clevenger apparatus with identification of the chemical composition determined by gas chromatography coupled to mass spectrometry (GC/MS). The antifungal assays were performed against Candida strains through the broth microdilution method to determine the minimum fungicidal concentration (MFC). Fungal growth was assessed by optical density reading and the Candida albicans dimorphic effect was evaluated by optical microscopy in microculture chambers. The chemical profile of the essential oils identified 40 substances in the different collection periods with γ-terpinene being the predominant constituent. The antifungal activity revealed an action against the C. albicans, C. krusei and C. tropicalis strains with an IC50 ranging from 345.5 to 2,754.2 µg/mL and a MFC higher than 1,024 µg/mL. When combined with essential oils at sub-inhibitory concentrations (MIC/16), fluconazole had its potentiated effect, i.e. a synergistic effect was observed in the combination of fluconazole with P.salutare oil against all Candida strains; however, for C. albicans, its effect was reinforced by the natural product in all the collection periods. The results show that the Psidium salutare oil affected the dimorphic transition capacity, significantly reducing the formation of hyphae and pseudohyphae in increasing concentrations. The results show that P. salutare oil exhibits a significant antifungal activity against three Candida species and that it can act in synergy with fluconazole. These results support the notion that this plant may have a potential use in pharmaceutical and preservative products. creator: Delmacia G. de Macêdo creator: Marta Maria A. Souza creator: Maria Flaviana B. Morais-Braga creator: Henrique Douglas M. Coutinho creator: Antonia Thassya L. dos Santos creator: Rafael P. da Cruz creator: José Galberto M. da Costa creator: Fábio Fernandes G. Rodrigues creator: Lucindo J. Quintans-junior creator: Jackson Roberto G. da Silva Almeida creator: Irwin Rose A. de Menezes uri: https://doi.org/10.7717/peerj.5476 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 de Macêdo et al. title: A large-scale survey on finger counting routines, their temporal stability and flexibility in educated adults link: https://peerj.com/articles/5878 last-modified: 2018-10-31 description: A strong link between bodily activity and number processing has been established in recent years. Although numerous observations indicate that adults use finger counting (FC) in various contexts of everyday life for different purposes, existing knowledge of FC routines and their use is still limited. In particular, it remains unknown how stable the (default) FC habits are over time and how flexible they can be. To investigate these questions, 380 Polish participants completed a questionnaire on their FC routines, the stability of these routines, and the context of FC usage, preceded by the request to count on their fingers from 1 to 10. Next, the test–retest stability of FC habits was examined in 84 participants 2 months following the first session. To the best of our knowledge, such a study design has been adopted for the first time. The results indicate that default FC routines of the majority of participants (75%) are relatively stable over time. At the same time, FC routines can flexibly adapt according to the situation (e.g., when holding an object). As regards prevalence, almost all participants, in line with previous findings on Western individuals, declared starting from the closed palm and extending consecutive fingers. Furthermore, we observed relations between FC preferences and handedness (more left-handers start from the left hand) and that actual finger use is still widespread in healthy adults for a variety of activities (the most prevalent uses of FC are listing elements, presenting arguments and plans, and calendar calculations). In sum, the results show the practical relevance of FC in adulthood, the relative stability of preferences over time along with flexible adaptation to a current situation, as well as an association of FC routines with handedness. Taken together our results suggest that FC is the phenomenon, which is moderated or mediated by multiple embodied factors. creator: Mateusz Hohol creator: Kinga Wołoszyn creator: Hans-Christoph Nuerk creator: Krzysztof Cipora uri: https://doi.org/10.7717/peerj.5878 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Hohol et al. title: Heterologous expression of a Glyoxalase I gene from sugarcane confers tolerance to several environmental stresses in bacteria link: https://peerj.com/articles/5873 last-modified: 2018-10-31 description: Glyoxalase I belongs to the glyoxalase system that detoxifies methylglyoxal (MG), a cytotoxic by-product produced mainly from triose phosphates. The concentration of MG increases rapidly under stress conditions. In this study, a novel glyoxalase I gene, designated as SoGloI was identified from sugarcane. SoGloI had a size of 1,091 bp with one open reading frame (ORF) of 885 bp encoding a protein of 294 amino acids. SoGloI was predicted as a Ni2+-dependent GLOI protein with two typical glyoxalase domains at positions 28–149 and 159–283, respectively. SoGloI was cloned into an expression plasmid vector, and the Trx-His-S-tag SoGloI protein produced in Escherichia coli was about 51 kDa. The recombinant E. coli cells expressing SoGloI compared to the control grew faster and tolerated higher concentrations of NaCl, CuCl2, CdCl2, or ZnSO4. SoGloI ubiquitously expressed in various sugarcane tissues. The expression was up-regulated under the treatments of NaCl, CuCl2, CdCl2, ZnSO4 and abscisic acid (ABA), or under simulated biotic stress conditions upon exposure to salicylic acid (SA) and methyl jasmonate (MeJA). SoGloI activity steadily increased when sugarcane was subjected to NaCl, CuCl2, CdCl2, or ZnSO4 treatments. Sub-cellular observations indicated that the SoGloI protein was located in both cytosol and nucleus. These results suggest that the SoGloI gene may play an important role in sugarcane’s response to various biotic and abiotic stresses. creator: Qibin Wu creator: Shiwu Gao creator: Yong-Bao Pan creator: Yachun Su creator: Michael P. Grisham creator: Jinlong Guo creator: Liping Xu creator: Youxiong Que uri: https://doi.org/10.7717/peerj.5873 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wu et al. title: High-level expression and molecular characterization of a recombinant prolidase from Escherichia coli NovaBlue link: https://peerj.com/articles/5863 last-modified: 2018-10-31 description: Long-term use of organophosphorus (OP) compounds has become an increasing global problem and a major threat to sustainability and human health. Prolidase is a proline-specific metallopeptidase that can offer an efficient option for the degradation of OP compounds. In this study, a full-length gene from Escherichia coli NovaBlue encoding a prolidase (EcPepQ) was amplified and cloned into the commercially-available vector pQE-30 to yield pQE-EcPepQ. The overexpressed enzyme was purified from the cell-free extract of isopropyl thio-β-D-galactoside IPTG-induced E. coli M15 (pQE-EcPepQ) cells by nickel-chelate chromatography. The molecular mass of EcPepQ was determined to be about 57 kDa by 12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis and the result of size-exclusion chromatography demonstrated that the enzyme was mainly present in 25 mM Tris–HCl buffer (pH 8.0) as a dimeric form. The optimal conditions for EcPepQ activity were 60 °C, pH 8.0, and 0.1 mM Mn2+ ion. Kinetic analysis with Ala-Pro as the substrate showed that the Km and kcat values of EcPepQ were 8.8 mM and 926.5 ± 2.0 s−1, respectively. The thermal unfolding of EcPepQ followed a two-state process with one well-defined unfolding transition of 64.2 °C. Analysis of guanidine hydrochloride (GdnHCl)-induced denaturation by tryptophan emission fluorescence spectroscopy revealed that the enzyme had a [GdnHCl]0.5,N-U value of 1.98 M. The purified enzyme also exhibited some degree of tolerance to various water/organic co-solvents. Isopropanol and tetrahydrofuran were very detrimental to the enzymatic activity of EcPepQ; however, other more hydrophilic co-solvents, such as formamide, methanol, and ethylene glycol, were better tolerated. Eventually, the non-negative influence of some co-solvents on both catalytic activity and structural stability of EcPepQ allows to adjust the reaction conditions more suitable for EcPepQ-catalyzed bioprocess. creator: Tzu-Fan Wang creator: Meng-Chun Chi creator: Kuan-Ling Lai creator: Min-Guan Lin creator: Yi-Yu Chen creator: Huei-Fen Lo creator: Long-Liu Lin uri: https://doi.org/10.7717/peerj.5863 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Wang et al.