title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1521
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: The mitochondrial genomes of two walnut pests, Gastrolina depressa depressa and G. depressa thoracica (Coleoptera: Chrysomelidae), and phylogenetic analyses
link: https://peerj.com/articles/4919
last-modified: 2018-06-05
description: In this study, the mitochondrial genomes (mitogenomes) of two walnut leaf insect pests, Gastrolina depressa depressa and G. depressa thoracica, were sequenced by Sanger sequencing technology. The mitogenome of G. depressa thoracica was complete at 16,109 bp in length, while the mitogenome of G. depressa depressa (14,277 bp) was partial. The genomic analyses indicated that both mitogenomes have the typical gene content and arrangement. The formerly identified elements, ‘TAGTA’ between trnSer(UCN) and nad2, and ‘ATGATAA’ between atp8 and atp6, were more conserved than that between nad4L and nad4, which was ‘ATGTTAA’ in Coleoptera excluding Polyphaga. Phylogenetic analyses of the 13 protein-coding genes from 36 coleopteran species well supported a close affinity between the subfamily Chrysomelinae including G. depressa thoracica and G. depressa depressa and Galerucinae, as well as a sister relationship of ((Eumolpinae + Cryptocephalinae) + Cassidinae) within Chrysomelidae.
creator: Qiqi Wang
creator: Guanghui Tang
uri: https://doi.org/10.7717/peerj.4919
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Wang and Tang

title: Shift in VEGFA isoform balance towards more angiogenic variants is associated with tumor stage and differentiation of human hepatocellular carcinoma
link: https://peerj.com/articles/4915
last-modified: 2018-06-05
description: BackgroundHepatocellular carcinoma (HCC) is the most common and aggressive type of malignant liver tumor. HCC progression depends significantly on its vascularization and formation of new blood vessels. Vascular endothelial growth factor A (VEGFA) is a crucial regulator of tumor vascularization and components of VEGF-induced cell signaling pathways are important targets of therapeutical drugs that demonstrated the highest efficiency in case of advanced HCC (sorafenib and regorafenib). VEGFA is expressed as a set of isoforms with different functional properties, thus VEGFA isoform expression pattern may affect tumor sensitivity to anti-angiogenic drugs. However, information about VEGFA isoforms expression in HCC is still incomplete and contradictory. The present study aims to quantitatively investigate VEGFA isoform expression aberrations in HCC tissue.MethodsA total of 50 pairs of HCC and non-tumor tissue samples were used to evaluate the VEGFA isoform spectrum using RT-PCR and quantitatively estimate changes in isoform expression using RT-qPCR. Correlations between these changes and tumor clinicopathological characteristics were analyzed.ResultsWe identified VEGFA-189, VEGFA-165, and VEGFA-121 as predominant isoforms in liver tissue. Anti-angiogenic VEGFA-xxxb variants constituted no more than 5% of all mature VEGFA transcripts detected and their expression was not changed significantly in HCC tissue. We demonstrated for the first time that the least active variant VEGFA-189 is frequently repressed in HCC (p < 0.001), while no uniform changes were detected for potent angiogenesis stimulators VEGFA-165 and VEGFA-121. Isoform balance in HCC shifts from VEGFA-189 towards VEGFA-165 or VEGFA-121 in the majority of cases (p < 0.001). Changes in fractions, but not expression levels, of VEGFA-189 (decrease) and VEGFA-121 (increase) correlated with advanced Tumor-Node-Metastasis (TNM) and Barcelona Clinic Liver Cancer (BCLC) tumor stages (p < 0.05), VEGFA-189 fraction reduction was also associated with poor tumor differentiation (p < 0.05).DiscussionA distinct shift in VEGFA isoform balance towards more pro-angiogenic variants occurs in HCC tissue and may modulate overall impact of VEGFA signaling. We suppose that the ratio between VEGFA isoforms is an important parameter governing HCC angiogenesis that may affect HCC progression and be used for optimizing the strategy of HCC therapy by predicting the response to anti-angiogenic drugs.
creator: Mikhail S. Chesnokov
creator: Polina A. Khesina
creator: Darya A. Shavochkina
creator: Inna F. Kustova
creator: Leonid M. Dyakov
creator: Olga V. Morozova
creator: Nikolai S. Mugue
creator: Nikolay E. Kudashkin
creator: Ekaterina A. Moroz
creator: Yuri I. Patyutko
creator: Natalia L. Lazarevich
uri: https://doi.org/10.7717/peerj.4915
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Chesnokov et al.

title: Discovery of digestive enzymes in carnivorous plants with focus on proteases
link: https://peerj.com/articles/4914
last-modified: 2018-06-05
description: BackgroundCarnivorous plants have been fascinating researchers with their unique characters and bioinspired applications. These include medicinal trait of some carnivorous plants with potentials for pharmaceutical industry.MethodsThis review will cover recent progress based on current studies on digestive enzymes secreted by different genera of carnivorous plants: Drosera (sundews), Dionaea (Venus flytrap), Nepenthes (tropical pitcher plants), Sarracenia (North American pitcher plants), Cephalotus (Australian pitcher plants), Genlisea (corkscrew plants), and Utricularia (bladderworts).ResultsSince the discovery of secreted protease nepenthesin in Nepenthes pitcher, digestive enzymes from carnivorous plants have been the focus of many studies. Recent genomics approaches have accelerated digestive enzyme discovery. Furthermore, the advancement in recombinant technology and protein purification helped in the identification and characterisation of enzymes in carnivorous plants.DiscussionThese different aspects will be described and discussed in this review with focus on the role of secreted plant proteases and their potential industrial applications.
creator: Rishiesvari Ravee
creator: Faris ‘Imadi Mohd Salleh
creator: Hoe-Han Goh
uri: https://doi.org/10.7717/peerj.4914
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Ravee et al.

title: Hindering the illegal trade in dog and cat furs through a DNA-based protocol for species identification
link: https://peerj.com/articles/4902
last-modified: 2018-06-05
description: In Western countries dogs and cats are the most popular pets, and people are increasingly opposed to their rearing for the fur industry. In 2007, a Regulation of the European Union (EU) banned the use and trade of dog and cat furs, but an official analytical protocol to identify them as source species was not provided, and violations of law are still frequent in all Member States. In this paper we report on the development and validation of a simple and affordable DNA method for species detection in furs to use as an effective tool to combat illegal trade in fur products. A set of mitochondrial primers was designed for amplification of partial cytochrome b, control region and ND1 gene in highly degraded samples, like furs and pelts. Our amplification workflow involved the use of a non-specific primer pair to perform a first test to identify the species through sequencing, then the application of species-specific primer pairs to use in singleplex end-point PCRs as confirmation tests. The advantage of this two-step procedure is twofold: on the one hand it minimises the possibility of negative test results from degraded samples, since failure of amplification with a first set of primers can be offset by successful amplification of the second, and on the other it adds confidence and reliability to final authentication of species. All designed primers were validated on a reference collection of tissue samples, obtaining solid results in terms of specificity, sensitivity, repeatability and reproducibility. Application of the protocol on real caseworks from seized furs yielded successful results also from old and dyed furs, suggesting that age and chemical staining do not necessarily affect positive amplifications. Major pros of this approach are: (1) sensitive and informative primer sets for detection of species; (2) short PCR amplicons for the analysis of poor quality DNA; (3) binding primers that avoid contamination from human DNA; (4) user-friendly protocol for any laboratory equipped for analysis of low-copy-number DNA. Our molecular procedure proved to be a good starting point for enforcing the EU Regulation against dog and cat fur trade in forensic contexts where source attribution is essential to the assignment of responsibilities.
creator: Luisa Garofalo
creator: Alessia Mariacher
creator: Rita Fanelli
creator: Rosario Fico
creator: Rita Lorenzini
uri: https://doi.org/10.7717/peerj.4902
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Garofalo et al.

title: In quest of contact: phylogeography of helmeted terrapins (Pelomedusa galeata, P. subrufa sensu stricto)
link: https://peerj.com/articles/4901
last-modified: 2018-06-05
description: Based on rangewide sampling and three mitochondrial and two nuclear markers (together up to 1,850 bp and 1,840 bp, respectively), we examine the phylogeography of two helmeted terrapin species (Pelomedusa galeata and P. subrufa sensu stricto) and infer shifts of climatically suitable spaces since the Last Glacial Maximum using a modeling approach. Whilst P. galeata displays significant phylogeographic structuring across its range and consists of two deeply divergent lineages that could represent distinct species, P. subrufa shows no obvious phylogeographic differentiation. This seems to be related to historically stable or fluctuating ranges. One of the lineages within P. galeata appears to be confined to the westernmost, winter-rainfall region of South Africa and deserves special conservational attention due to the scarcity of surface water. The other lineage is distributed further east and is differentiated in three weakly supported subclades with parapatric distribution; one occurring inland, and two along the south and east coasts, respectively. As far as is known, P. subrufa occurs in South Africa only in the northeast of the country (Limpopo, Mpumalanga) and we report the species for the first time from the Lapalala Wilderness Area in the Waterberg region (Limpopo), approximately 350 km further west than previously recorded. We confirmed the occurrence of P. galeata only 80 km south of Lapalala. Thus, a sympatric occurrence of P. galeata and P. subrufa is possible. Another putative contact zone, for the two lineages within P. galeata, must be located in the Western Cape region, and further contact zones are likely for the eastern subclades within P. galeata. The nuclear loci provided no evidence for gene flow across taxa or genetic clusters within taxa. Future investigations should use denser sampling from putative contact zones and more nuclear markers to re-examine this situation. Despite few phylogeographic studies published for southern African biota, it seems likely that differentiation follows general rules, and that climate and physiographic barriers (e.g., the Great Escarpment) have shaped phylogeographic patterns.
creator: Melita Vamberger
creator: Margaretha D. Hofmeyr
creator: Flora Ihlow
creator: Uwe Fritz
uri: https://doi.org/10.7717/peerj.4901
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Vamberger et al.

title: Growth, biochemical response and liver health of juvenile barramundi (Lates calcarifer) fed fermented and non-fermented tuna hydrolysate as fishmeal protein replacement ingredients
link: https://peerj.com/articles/4870
last-modified: 2018-06-05
description: Conventional aquaculture feed materials available in Australia are expensive, which has prompted the search for alternatives that would be cost-effective and locally available. The present study was undertaken in order to maximize the use of a tuna hydrolysate (TH), which was produced locally from the tuna-processing discards. The growth performance, biochemical status, antioxidant capacity and liver health of juvenile barramundi (Lates calcarifer) were assessed. Two series of isonitrogenous and isocaloric diets labelled as TH50, TH75 (non-fermented tuna hydrolysate) and FTH50, FTH75 (fermented tuna hydrolysate) were formulated to replace FM at 50% and 75%, respectively. A basal diet without the TH supplementation was used as a control. The experimental diets were fed to the triplicate groups of fish three times a day for 56 days. The results of the experiment revealed that fish fed on both fermented and non-fermented TH-containing diets significantly reduced (p < 0.05) the final body weight, weight gain and specific growth rate compared to the control. The highest apparent digestibility coefficients for dry matter, protein and lipid were obtained in the control group, and decreased with the increasing level of TH in the diets. However, the whole-body proximate compositions and the blood biochemical indices of fish were not affected by the TH inclusion in the diets. The fish fed on TH diets of TH50, FTH50 and TH75 exhibited reduced (p < 0.05) glutathione peroxidase (GPx) activity compared to the control; whereas the FTH75 exhibited no difference with the control. The excessive inclusion of TH in the diets of TH75 and FTH75 resulted in cytoplasmic vacuolization, with an increased amount of lipid accumulation, and necrosis in the liver tissue. These results indicated that the replacement of the FM protein with TH at 50% and 75% inclusion levels negatively affected the growth performance, feed utilization, and digestibility in juvenile barramundi; and it also increased the potential risk of hepatic failure in the fish. Further investigation is, therefore, required in order to optimize the TH levels in the fish diets which would be suitable for the growth of fish, as well as for maintaining the enhanced biochemical response in juvenile barramundi.
creator: Muhammad A.B. Siddik
creator: Janet Howieson
creator: Ilham Ilham
creator: Ravi Fotedar
uri: https://doi.org/10.7717/peerj.4870
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Siddik et al.

title: Biochemical and genetic analyses of the oomycete Pythium insidiosum provide new insights into clinical identification and urease-based evolution of metabolism-related traits
link: https://peerj.com/articles/4821
last-modified: 2018-06-05
description: The oomycete microorganism, Pythium insidiosum, causes the life-threatening infectious condition, pythiosis, in humans and animals worldwide. Affected individuals typically endure surgical removal of the infected organ(s). Detection of P. insidiosum by the established microbiological, immunological, or molecular methods is not feasible in non-reference laboratories, resulting in delayed diagnosis. Biochemical assays have been used to characterize P. insidiosum, some of which could aid in the clinical identification of this organism. Although hydrolysis of maltose and sucrose has been proposed as the key biochemical feature useful in discriminating P. insidiosum from other oomycetes and fungi, this technique requires a more rigorous evaluation involving a wider selection of P. insidiosum strains. Here, we evaluated 10 routinely available biochemical assays for characterization of 26 P. insidiosum strains, isolated from different hosts and geographic origins. Initial assessment revealed diverse biochemical characteristics across the P. insidiosum strains tested. Failure to hydrolyze sugars is observed, especially in slow-growing strains. Because hydrolysis of maltose and sucrose varied among different strains, use of the biochemical assays for identification of P. insidiosum should be cautioned. The ability of P. insidiosum to hydrolyze urea is our focus, because this metabolic process relies on the enzyme urease, an important virulence factor of other pathogens. The ability to hydrolyze urea varied among P. insidiosum strains and was not associated with growth rates. Genome analyses demonstrated that urease- and urease accessory protein-encoding genes are present in both urea-hydrolyzing and non-urea-hydrolyzing strains of P. insidiosum. Urease genes are phylogenetically conserved in P. insidiosum and related oomycetes, while the presence of urease accessory protein-encoding genes is markedly diverse in these organisms. In summary, we dissected biochemical characteristics and drew new insights into clinical identification and urease-related evolution of P. insidiosum.
creator: Theerapong Krajaejun
creator: Thidarat Rujirawat
creator: Teerat Kanpanleuk
creator: Pitak Santanirand
creator: Tassanee Lohnoo
creator: Wanta Yingyong
creator: Yothin Kumsang
creator: Pattarana Sae-Chew
creator: Weerayuth Kittichotirat
creator: Preecha Patumcharoenpol
uri: https://doi.org/10.7717/peerj.4821
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Krajaejun et al.

title: The energetic cost of mounting an immune response for Pallas’s long-tongued bat (Glossophaga soricina)
link: https://peerj.com/articles/4627
last-modified: 2018-06-05
description: The acute phase response (APR) is the first line of defense of the vertebrate immune system against pathogens. Mounting an immune response is believed to be energetically costly but direct measures of metabolic rate during immune challenges contradict this assumption. The energetic cost of APR for birds is higher than for rodents, suggesting that this response is less expensive for mammals. However, the particularly large increase in metabolic rate after APR activation for a piscivorous bat (Myotis vivesi) suggests that immune response might be unusually costly for bats. Here we quantified the energetic cost and body mass change associated with APR for the nectarivorous Pallas’s long-tongued bat (Glossophaga soricina). Activation of the APR resulted in a short-term decrease in body mass and an increase in resting metabolic rate (RMR) with a total energy cost of only 2% of the total energy expenditure estimated for G. soricina. This increase in RMR was far from the large increase measured for piscivorous bats; rather, it was similar to the highest values reported for birds. Overall, our results suggest that the costs of APR for bats may vary interspecifically. Measurement of the energy cost of vertebrate immune response is limited to a few species and further work is warranted to evaluate its significance for an animal’s energy budget.
creator: Lucia V. Cabrera-Martínez
creator: L. Gerardo Herrera M.
creator: Ariovaldo P. Cruz-Neto
uri: https://doi.org/10.7717/peerj.4627
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Cabrera-Martínez et al.

title: Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges
link: https://peerj.com/articles/4965
last-modified: 2018-06-04
description: Fungi play a critical role in a range of ecosystems; however, their interactions and functions in marine hosts, and particular sponges, is poorly understood. Here we assess the fungal community composition of three co-occurring sponges (Cymbastela concentrica, Scopalina sp., Tedania anhelans) and the surrounding seawater over two time points to help elucidate host-specificity, stability and potential core members, which may shed light into the ecological function of fungi in sponges. The results showed that ITS-amplicon-based community profiling likely provides a more realistic assessment of fungal diversity in sponges than cultivation-dependent approaches. The sponges studied here were found to contain phylogenetically diverse fungi (eight fungal classes were observed), including members of the family Togniniaceae and the genus Acrostalagmus, that have so far not been reported to be cultured from sponges. Fungal communities within any given sponge species were found to be highly variable compared to bacterial communities, and influenced in structure by the community of the surrounding seawater, especially considering temporal variation. Nevertheless, the sponge species studied here contained a few “variable/core” fungi that appeared in multiple biological replicates and were enriched in their relative abundance compared to seawater communities. These fungi were the same or highly similar to fungal species detected in sponges around the world, which suggests a prevalence of horizontal transmission where selectivity and enrichment of some fungi occur for those that can survive and/or exploit the sponge environment. Our current sparse knowledge about sponge-associated fungi thus indicate that fungal communities may perhaps not play as an important ecological role in the sponge holobiont compared to bacterial or archaeal symbionts.
creator: Mary T.H.D. Nguyen
creator: Torsten Thomas
uri: https://doi.org/10.7717/peerj.4965
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Nguyen and Thomas

title: D-GENIES: dot plot large genomes in an interactive, efficient and simple way
link: https://peerj.com/articles/4958
last-modified: 2018-06-04
description: Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited in the input sequence size. D-GENIES is a standalone and web application performing large genome alignments using minimap2 software package and generating interactive dot plots. It enables users to sort query sequences along the reference, zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy-to-install, open-source software package (GPL) developed in Python and JavaScript. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.
creator: Floréal Cabanettes
creator: Christophe Klopp
uri: https://doi.org/10.7717/peerj.4958
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Cabanettes and Klopp