title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1771 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Assessing pollinators’ use of floral resource subsidies in agri-environment schemes: An illustration using Phacelia tanacetifolia and honeybees link: https://peerj.com/articles/2677 last-modified: 2016-11-15 description: BackgroundHoneybees (Apis mellifera L.) are frequently used in agriculture for pollination services because of their abundance, generalist floral preferences, ease of management and hive transport. However, their populations are declining in many countries. Agri-Environment Schemes (AES) are being implemented in agricultural systems to combat the decline in populations of pollinators and other insects. Despite AES being increasingly embedded in policy and budgets, scientific assessments of many of these schemes still are lacking, and only a few studies have examined the extent to which insect pollinators use the floral enhancements that are part of AES and on which floral components they feed (i.e., pollen and/or nectar).MethodsIn the present work, we used a combination of observations on honeybee foraging for nectar/pollen from the Californian annual plant Phacelia tanacetifolia in the field, collection of pollen pellets from hives, and pollen identification, to assess the value of adding phacelia to an agro-ecosystem to benefit honeybees.ResultsIt was found that phacelia pollen was almost never taken by honeybees. The work here demonstrates that honeybees may not use the floral enhancements added to a landscape as expected and points to the need for more careful assessments of what resources are used by honeybees in AES and understanding the role, if any, which AES play in enhancing pollinator fitness.DiscussionWe recommend using the methodology in this paper to explore the efficacy of AES before particular flowering species are adopted more widely to give a more complete illustration of the actual efficacy of AES. creator: Rowan Sprague creator: Stéphane Boyer creator: Georgia M. Stevenson creator: Steve D. Wratten uri: https://doi.org/10.7717/peerj.2677 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Sprague et al. title: Zebra mussel beds: an effective feeding ground for Ponto-Caspian gobies or suitable shelter for their prey? link: https://peerj.com/articles/2672 last-modified: 2016-11-15 description: Aggregations of the Ponto-Caspian invasive zebra mussel (Dreissena polymorpha) constitute a suitable habitat for macroinvertebrates, considerably increasing their abundance and providing effective antipredator protection. Thus, the overall effect of a mussel bed on particular predator species may vary from positive to negative, depending on both prey density increase and predator ability to prey in a structurally complex habitat. Alien Ponto-Caspian goby fish are likely to be facilitated when introduced into new areas by zebra mussels, provided that they are capable of utilizing mussel beds as habitat and feeding grounds. We ran laboratory experiments to find which prey (chironomid larvae) densities (from ca. 500 to 2,000 individuals m−2) in a mussel bed make it a more beneficial feeding ground for the racer goby Babka gymnotrachelus (RG) and western tubenose goby Proterorhinus semilunaris (WTG) compared to sandy and stone substrata (containing the basic prey density of 500 ind. m−2). Moreover, we checked how food availability affects habitat selection by fish. Mussel beds became more suitable for fish than alternative mineral substrata when food abundance was at least two times higher (1,000 vs. 500 ind. m−2), regardless of fish size and species. WTG was associated with mussel beds regardless of its size and prey density, whereas RG switched to this habitat when it became a better feeding ground than alternative substrata. Larger RG exhibited a stronger affinity for mussels than small individuals. WTG fed more efficiently from a mussel bed at high food abundances than RG. A literature review has shown that increasing chironomid density, which in our study was sufficient to make a mussel habitat an attractive feeding ground for the gobies, is commonly observed in mussel beds in the field. Therefore, we conclude that zebra mussels may positively affect the alien goby species and are likely to facilitate their establishment in novel areas, contributing to an invasional meltdown in the Ponto-Caspian invasive community. creator: Jarosław Kobak creator: Małgorzata Poznańska creator: Łukasz Jermacz creator: Tomasz Kakareko creator: Daniel Prądzynski creator: Małgorzata Łodygowska creator: Karolina Montowska creator: Karolina Bącela-Spychalska uri: https://doi.org/10.7717/peerj.2672 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Kobak et al. title: Lithocholic acid induces endoplasmic reticulum stress, autophagy and mitochondrial dysfunction in human prostate cancer cells link: https://peerj.com/articles/2445 last-modified: 2016-11-15 description: Lithocholic acid (LCA) is a secondary bile acid that is selectively toxic to human neuroblastoma, breast and prostate cancer cells, whilst sparing normal cells. We previously reported that LCA inhibited cell viability and proliferation and induced apoptosis and necrosis of androgen-dependent LNCaP and androgen-independent PC-3 human prostate cancer cells. In the present study, we investigated the roles of endoplasmic reticulum (ER) stress, autophagy and mitochondrial dysfunction in the toxicity of LCA in PC-3 and autophagy deficient, androgen-independent DU-145 cells. LCA induced ER stress-related proteins, such as CCAAT-enhancer-binding protein homologous protein (CHOP), and the phosphorylation of eukaryotic initiation factor 2-alpha (p-eIF2α) and c-Jun N-terminal kinases (p-JNK) in both cancer cell-types. The p53 upregulated modulator of apoptosis (PUMA) and B cell lymphoma-like protein 11 (BIM) levels were decreased at overtly toxic LCA concentrations, although PUMA levels increased at lower LCA concentrations in both cell lines. LCA induced autophagy-related conversion of microtubule-associated proteins 1A/1B light chain 3B (LC3BI–LC3BII), and autophagy-related protein ATG5 in PC-3 cells, but not in autophagy-deficient DU-145 cells. LCA (>10 µM) increased levels of reactive oxygen species (ROS) concentration-dependently in PC-3 cells, whereas ROS levels were not affected in DU-145 cells. Salubrinal, an inhibitor of eIF2α dephosphorylation and ER stress, reduced LCA-induced CHOP levels slightly in PC-3, but not DU-145 cells. Salubrinal pre-treatment increased the cytotoxicity of LCA in PC-3 and DU-145 cells and resulted in a statistically significant loss of cell viability at normally non-toxic concentrations of LCA. The late-stage autophagy inhibitor bafilomycin A1 exacerbated LCA toxicity at subtoxic LCA concentrations in PC-3 cells. The antioxidant α-tocotrienol strongly inhibited the toxicity of LCA in PC-3 cells, but not in DU-145 cells. Collectively, although LCA induces autophagy and ER stress in PC-3 cells, these processes appear to be initially of protective nature and subsequently consequential to, but not critical for the ROS-mediated mitochondrial dysfunction and cytotoxicity of LCA. The full mechanism of LCA-induced mitochondrial dysfunction and cytotoxicity in the similarly sensitive DU-145 cells remains to be elucidated. creator: Ahmed A. Gafar creator: Hossam M. Draz creator: Alexander A. Goldberg creator: Mohamed A. Bashandy creator: Sayed Bakry creator: Mahmoud A. Khalifa creator: Walid AbuShair creator: Vladimir I. Titorenko creator: J. Thomas Sanderson uri: https://doi.org/10.7717/peerj.2445 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gafar et al. title: Identification of phenolic secondary metabolites from Schotia brachypetala Sond. (Fabaceae) and demonstration of their antioxidant activities in Caenorhabditis elegans link: https://peerj.com/articles/2404 last-modified: 2016-11-15 description: BackgroundSchotia brachypetala Sond. (Fabaceae) is an endemic tree of Southern Africa whose phytochemistry and pharmacology were slightly studied. The present work aimed at profiling the major phenolics compounds present in the hydro-alcohol extract from S. brachypetala leaves (SBE) using LC/HRESI/MS/MS and NMR and prove their antioxidant capabilities using novel methods.MethodsIn vitro assays; DPPH, TEAC persulfate decolorizing kinetic and FRAP assays, and in vivo assays: Caenorhabditis elegans strains maintenance, Intracellular ROS in C. elegans, Survival assay, GFP expression and Subcellular DAF-16 localization were employed to evaluate the antioxidant activity.ResultsMore than forty polyphenols, including flavonoid glycosides, galloylated flavonoid glycosides, isoflavones, dihydrochalcones, procyanidins, anthocyanins, hydroxy benzoic acid derivatives, hydrolysable tannins, and traces of methylated and acetylated flavonoid derivatives were identified. Three compounds were isolated and identified from the genus Schotia for the first time, namely gallic acid, myricetin-3-O-α-L-1C4-rhamnoside and quercetin-3-O-L-1C4-rhamnoside. The total phenolics content of SBE was (376 mg CAE/g), followed by flavonoids (67.87 QE/g). In vitro antioxidant activity of SBE was evidenced by DPPH radical scavenging activity (IC50 of 9 µg/mL), FRAP ferric reducing activity (5,000 mol Fe2+ E/mg) and ABTS peroxide inhibiting activity (1,054 mM Trolox E/mg). The tested extract was able to protect the worms against juglone induced oxidative stress, an increased survival rate (up to 41%) was recorded, when compared with the control group (11%) and attenuate the reactive oxygen species (ROS) accumulation in dose-dependent and reached up to 72% for the highest tested concentration. SBE was also able to attenuate the levels of heat shock protein (HSP) expression in dose-dependent up to 60% in the 150 µg SBE/mL group. In DAF-16 Subcellular localization SBE treated worms showed nuclear localization pattern up to 78%, while it was only 5% in the untreated control group.DiscussionA pronounced antioxidant activity in vivo, which can be attributed to its ability to promote the nuclear translocation of DAF-16/FOXO, the main transcription factor regulating the expression of stress response genes. The remarkable antioxidant activity in vitro and in vivo correlates to SBE rich phenolic profile. creator: Mansour Sobeh creator: Esraa ElHawary creator: Herbenya Peixoto creator: Rola M. Labib creator: Heba Handoussa creator: Noha Swilam creator: Ahmed H. El-Khatib creator: Farukh Sharapov creator: Tamer Mohamed creator: Sonja Krstin creator: Michael W. Linscheid creator: Abdel Nasser Singab creator: Michael Wink creator: Nahla Ayoub uri: https://doi.org/10.7717/peerj.2404 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sobeh et al. title: Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae) link: https://peerj.com/articles/2699 last-modified: 2016-11-10 description: The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes of Haloxylon ammodendron (HA) and Haloxylon persicum (HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species. Similar to other higher plants, we found that the Haloxylon cp genome is a quadripartite, double-stranded, circular DNA molecule of 151,570 bp in HA and 151,586 bp in HP. It contains a pair of inverted repeats (24,171 bp in HA and 24,177 bp in HP) that separate the genome into a large single copy region of 84,214 bp in HA and 84,217 bp in HP, and a small single copy region of 19,014 bp in HA and 19,015 bp in HP. Each Haloxylon cp genome contains 112 genes, including 78 coding, 30 tRNA, and four ribosomal RNA genes. We detected 59 different simple sequence repeat loci, including 44 mono-nucleotide, three di-nucleotide, one tri-nucleotide, and 11 tetra-nucleotide repeats. Comparative analysis revealed only 67 mutations between the two species, including 44 substitutions, 23 insertions/deletions, and two micro-inversions. The two inversions, with lengths of 14 and 3 bp, occur in the petA-psbJ intergenic region and rpl16 intron, respectively, and are predicted to form hairpin structures with repeat sequences of 27 and 19 bp, respectively, at the two ends. The ratio of transitions to transversions was 0.76. These results are valuable for future studies on Haloxylon genetic diversity and will enhance our understanding of the phylogenetic evolution of Amaranthaceae. creator: Wenpan Dong creator: Chao Xu creator: Delu Li creator: Xiaobai Jin creator: Ruili Li creator: Qi Lu creator: Zhili Suo uri: https://doi.org/10.7717/peerj.2699 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Dong et al. title: Soymilk residue (okara) as a natural immobilization carrier for Lactobacillus plantarum cells enhances soymilk fermentation, glucosidic isoflavone bioconversion, and cell survival under simulated gastric and intestinal conditions link: https://peerj.com/articles/2701 last-modified: 2016-11-10 description: Cell immobilization is an alternative to microencapsulation for the maintenance of cells in a liquid medium. However, artificial immobilization carriers are expensive and pose a high safety risk. Okara, a food-grade byproduct from soymilk production, is rich in prebiotics. Lactobacilli could provide health enhancing effects to the host. This study aimed to evaluate the potential of okara as a natural immobilizer for L. plantarum 70810 cells. The study also aimed to evaluate the effects of okara-immobilized L. plantarum 70810 cells (IL) on soymilk fermentation, glucosidic isoflavone bioconversion, and cell resistance to simulated gastric and intestinal stresses. Scanning electron microscopy (SEM) was used to show cells adherence to the surface of okara. Lactic acid, acetic acid and isoflavone analyses in unfermented and fermented soymilk were performed by HPLC with UV detection. Viability and growth kinetics of immobilized and free L. plantarum 70810 cells (FL) were followed during soymilk fermentation. Moreover, changes in pH, titrable acidity and viscosity were measured by conventional methods. For in vitro testing of simulated gastrointestinal resistance, fermented soymilk was inoculated with FL or IL and an aliquot incubated into acidic MRS broth which was conveniently prepared to simulate gastric, pancreatic juices and bile salts. Survival to simulated gastric and intestinal stresses was evaluated by plate count of colony forming units on MRS agar. SEM revealed that the lactobacilli cells attached and bound to the surface of okara. Compared with FL, IL exhibited a significantly higher specific growth rate, shorter lag phase of growth, higher productions of lactic and acetic acids, a faster decrease in pH and increase in titrable acidity, and a higher soymilk viscosity. Similarly, IL in soymilk showed higher productions of daizein and genistein compared with the control. Compared with FL, IL showed reinforced resistance to simulatedgastric and intestinal stresses in vitro that included low pH, low pH plus pepsin, pancreatin, and bile salt. Our results indicate that okara is a new potential immobilization carrier to enhance the growth and glucosidic isoflavone bioconversion activities of L. plantarum in soymilk and improve cell survivability following simulated gastric and intestinal conditions. creator: Xia Xiudong creator: Wang Ying creator: Liu Xiaoli creator: Li Ying creator: Zhou Jianzhong uri: https://doi.org/10.7717/peerj.2701 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Xiudong et al. title: Induced pluripotent stem cells from human hair follicle keratinocytes as a potential source for in vitro hair follicle cloning link: https://peerj.com/articles/2695 last-modified: 2016-11-10 description: BackgroundHuman hair follicles are important for the renewal of new hairs and their development. The generation of induced pluripotent stem cells (iPSCs) from hair follicles is easy due to its accessibility and availability. The pluripotent cells derived from hair follicles not only have a higher tendency to re-differentiate into hair follicles, but are also more suited for growth in hair scalp tissue microenvironment.MethodsIn this study, human hair follicular keratinocytes were used to generate iPSCs, which were then further differentiated in vitro into keratinocytes. The derived iPSCs were characterised by using immunofluorescence staining, flow cytometry, and reverse-transcription PCR to check for its pluripotency markers expression.ResultsThe iPSC clones expressed pluripotency markers such as TRA-1-60, TRA-1-81, SSEA4, OCT4, SOX2, NANOG, LEFTY, and GABRB. The well-formed three germ layers were observed during differentiation using iPSCs derived from hair follicles. The successful formation of keratioctyes from iPSCs was confirmed by the expression of cytokeratin 14 marker.DiscussionHair follicles represent a valuable keratinocytes source for in vitro hair cloning for use in treating hair balding or grafting in burn patients. Our significant findings in this report proved that hair follicles could be used to produce pluripotent stem cells and suggested that the genetic and micro-environmental elements of hair follicles might trigger higher and more efficient hair follicles re-differentiation. creator: Sheng Jye Lim creator: Shu Cheow Ho creator: Pooi Ling Mok creator: Kian Lee Tan creator: Alan H.K. Ong creator: Seng Chiew Gan uri: https://doi.org/10.7717/peerj.2695 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lim et al. title: Reanalysis of the anthrax epidemic in Rhodesia, 1978–1984 link: https://peerj.com/articles/2686 last-modified: 2016-11-10 description: In the mid-1980s, the largest epidemic of anthrax of the last 200 years was documented in a little known series of studies by Davies in The Central African Journal of Medicine. This epidemic involved thousands of cattle and 10,738 human cases with 200 fatalities in Rhodesia during the Counterinsurgency. Grossly unusual epidemiological features were noted that, to this day, have not been definitively explained. This study performed a historical reanalysis of the data to reveal an estimated geographic involvement of 245,750 km2, with 171,990 cattle and 17,199 human cases. Here we present the first documented geotemporal visualization of the human anthrax epidemic. creator: James M. Wilson creator: Walter Brediger creator: Thomas P. Albright creator: Julie Smith-Gagen uri: https://doi.org/10.7717/peerj.2686 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Wilson et al. title: Sexual reproduction in the Caribbean coral genus Isophyllia (Scleractinia: Mussidae) link: https://peerj.com/articles/2665 last-modified: 2016-11-10 description: The sexual pattern, reproductive mode, and timing of reproduction of Isophyllia sinuosa and Isophyllia rigida, two Caribbean Mussids, were assessed by histological analysis of specimens collected monthly during 2000–2001. Both species are simultaneous hermaphroditic brooders characterized by a single annual gametogenetic cycle. Spermatocytes and oocytes of different stages were found to develop within the same mesentery indicating sequential maturation for extended planulation. Oogenesis took place during May through April in I. sinuosa and from August through June in I. rigida. Oocytes began development 7–8 months prior to spermaries but both sexes matured simultaneously. Zooxanthellate planulae were observed in I. sinuosa during April and in I. rigida from June through September. Higher polyp and mesenterial fecundity were found in I. rigida compared to I. sinuosa. Larger oocyte sizes were found in I. sinuosa than in I. rigida, however larger planula sizes were found in I. rigida. Hermaphroditism is the exclusive sexual pattern within the Mussidae while brooding has been documented within the related genera Mussa, Scolymia and Mycetophyllia. This study represents the first description of the sexual characteristics of I. rigida and provides an updated description of I. sinuosa. creator: Derek Soto creator: Ernesto Weil uri: https://doi.org/10.7717/peerj.2665 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Soto and Weil title: Hyainailourine and teratodontine cranial material from the late Eocene of Egypt and the application of parsimony and Bayesian methods to the phylogeny and biogeography of Hyaenodonta (Placentalia, Mammalia) link: https://peerj.com/articles/2639 last-modified: 2016-11-10 description: Hyaenodonta is a diverse, extinct group of carnivorous mammals that included weasel- to rhinoceros-sized species. The oldest-known hyaenodont fossils are from the middle Paleocene of North Africa and the antiquity of the group in Afro-Arabia led to the hypothesis that it originated there and dispersed to Asia, Europe, and North America. Here we describe two new hyaenodont species based on the oldest hyaenodont cranial specimens known from Afro-Arabia. The material was collected from the latest Eocene Locality 41 (L-41, ∼34 Ma) in the Fayum Depression, Egypt. Akhnatenavus nefertiticyon sp. nov. has specialized, hypercarnivorous molars and an elongate cranial vault. In A. nefertiticyon the tallest, piercing cusp on M1–M2 is the paracone. Brychotherium ephalmos gen. et sp. nov. has more generalized molars that retain the metacone and complex talonids. In B. ephalmos the tallest, piercing cusp on M1–M2 is the metacone. We incorporate this new material into a series of phylogenetic analyses using a character-taxon matrix that includes novel dental, cranial, and postcranial characters, and samples extensively from the global record of the group. The phylogenetic analysis includes the first application of Bayesian methods to hyaenodont relationships. B. ephalmos is consistently placed within Teratodontinae, an Afro-Arabian clade with several generalist and hypercarnivorous forms, and Akhnatenavus is consistently recovered in Hyainailourinae as part of an Afro-Arabian radiation. The phylogenetic results suggest that hypercarnivory evolved independently three times within Hyaenodonta: in Teratodontinae, in Hyainailourinae, and in Hyaenodontinae. Teratodontines are consistently placed in a close relationship with Hyainailouridae (Hyainailourinae + Apterodontinae) to the exclusion of “proviverrines,” hyaenodontines, and several North American clades, and we propose that the superfamily Hyainailouroidea be used to describe this relationship. Using the topologies recovered from each phylogenetic method, we reconstructed the biogeographic history of Hyaenodonta using parsimony optimization (PO), likelihood optimization (LO), and Bayesian Binary Markov chain Monte Carlo (MCMC) to examine support for the Afro-Arabian origin of Hyaenodonta. Across all analyses, we found that Hyaenodonta most likely originated in Europe, rather than Afro-Arabia. The clade is estimated by tip-dating analysis to have undergone a rapid radiation in the Late Cretaceous and Paleocene; a radiation currently not documented by fossil evidence. During the Paleocene, lineages are reconstructed as dispersing to Asia, Afro-Arabia, and North America. The place of origin of Hyainailouroidea is likely Afro-Arabia according to the Bayesian topologies but it is ambiguous using parsimony. All topologies support the constituent clades–Hyainailourinae, Apterodontinae, and Teratodontinae–as Afro-Arabian and tip-dating estimates that each clade is established in Afro-Arabia by the middle Eocene. creator: Matthew R. Borths creator: Patricia A. Holroyd creator: Erik R. Seiffert uri: https://doi.org/10.7717/peerj.2639 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Borths et al.