title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=976 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effect of incubation temperature and substrate moisture on embryonic development, hatchling phenotypes and post-hatching growth in the Reeves’ Turtle, Mauremys reevesii link: https://peerj.com/articles/10553 last-modified: 2021-02-12 description: BackgroundReeves’ Turtles (Mauremys reevesii) are economically important in aquaculture in China. Understanding the effects of incubation temperature and substrate moisture on embryos and hatchlings is of great significance for improving the artificial culture of M. reevesii. However, available studies have not yet determined the thermal and hydric optima for M. reevesii eggs, and the potential interaction between the two factors.MethodsIn this study, eggs of M. reevesii were incubated at five temperature levels (23, 26, 29, 32 and 35 °C, fluctuation range ± 0.5 °C). In each temperature level, there were three substrate moisture levels (1:0.5, 1:0.9 and 1:1.2, weight ratio of vermiculite to water). Thus, a total of 15 combinations of temperature and moisture were used to examine the effects of incubation temperature and substrate moisture on incubation duration, hatching success, hatchling phenotypes, post-hatching growth and hatchling survival.ResultsSubstrate moisture did not significantly affect most development parameters (except incubation duration and carapace width of hatchlings). Eggs incubated at low moisture level (1:0.5) had a longer incubation duration and produced hatchlings with smaller carapace widths than those incubated at medium (1:0.9) or high (1:1.2) moisture levels. Incubation temperature had a significant effect on incubation duration, hatching success, hatchling phenotypes and hatchling survival. Incubation duration decreased as incubation temperature increased. Eggs incubated at 23, 26 and 29 °C showed higher hatching success than those incubated at 32 and 35 °C. Hatchlings incubated at 32 °C were smaller in body size and mass than those incubated at 23, 26 and 29 °C. At 12 months of age, incubation temperature had no long-lasting effect on body mass, but hatchlings incubated at 23 and 35 °C had lower survival rates than those incubated at 26, 29 and 32 °C. For the development of embryos and hatchlings, the interaction between incubation temperature and substrate moisture was not significant.ConclusionsOur results indicate that incubation temperature has a significant influence on the development of embryos and hatchlings of M. reevesii, while substrate moisture only significantly affects the incubation duration and carapace width of hatchlings. The combination of an incubation temperature of 29 ± 0.5 °C and a substrate moisture level of 1:1.2 represented optimal incubation conditions in this experiment. Such incubation conditions are helpful in obtaining higher hatching success, shorter incubation duration and higher survival rates for this aquaculture species. creator: Yufeng Wei creator: Yangchun Gao creator: Dainan Cao creator: Yan Ge creator: Haitao Shi creator: Shiping Gong uri: https://doi.org/10.7717/peerj.10553 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wei et al. title: COVID-19 incidence and mortality in Nigeria: gender based analysis link: https://peerj.com/articles/10613 last-modified: 2021-02-12 description: BackgroundCoronavirus Disease 2019 (COVID-19) has been surging globally. Risk strata in medical attention are of dynamic significance for apposite assessment and supply distribution. Presently, no known cultured contrivance is available to fill this gap of this pandemic. The aim of this study is to develop a predictive model based on vector autoregressive moving average (VARMA) model of various orders for gender based daily COVID-19 incidence in Nigeria. This study also aims to proffer empirical evidence that compares incidence between male and female for COVID-19 risk factors.MethodsWilcoxon signed-rank test is employed to investigate the significance of the difference in the gender distributions of the daily incidence. A VARMA model of various orders is formulated for the gender based daily COVID-19 incidence in Nigeria. The optimal VARMA model is identified using Bayesian information criterion. Also, a predictive model based on univariate autoregressive moving average model is formulated for the daily death cases in Nigeria. Fold change is estimated based on crude case-fatality risk to investigate whether there is massive underreporting and under-testing of COVID-19 cases in Nigeria.ResultsDaily incidence is higher in males on most days from 11 April 2020 to 12 September 2020. Result of Wilcoxon signed-rank test shows that incidence among male is significantly higher than female (p-value < 2.22 × 10−16). White neural network test shows that daily female incidence is not linear in mean (p-value = 0.00058746) while daily male incidence is linear in mean (p-value = 0.4257). McLeod-Li test shows that there is autoregressive conditional heteroscedasticity in the female incidence (Maximum p-value = 1.4277 × 10−5) and male incidence (Maximum p-value = 9.0816 × 10−14) at 5% level of significance. Ljung-Box test (Tsay, 2014) shows that the daily incidence cases are not random (p-value=0.0000). The optimal VARMA model for male and female daily incidence is VARMA (0,1). The optimal model for the Nigeria’s daily COVID-19 death cases is identified to be ARIMA (0,1,1). There is no evidence of massive underreporting and under-testing of COVID-19 cases in Nigeria.ConclusionsComparison of the observed incidence with fitted data by gender shows that the optimal VARMA and ARIMA models fit the data well. Findings highlight the significant roles of gender on daily COVID-19 incidence in Nigeria. creator: Olubukola O. Olusola-Makinde creator: Olusola S. Makinde uri: https://doi.org/10.7717/peerj.10613 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Olusola-Makinde and Makinde title: Gut bacterial communities in the freshwater snail Planorbella trivolvis and their modification by a non-herbivorous diet link: https://peerj.com/articles/10716 last-modified: 2021-02-12 description: The freshwater pulmonate snail Planorbella trivolvis is a common species in various bodies of water but is not native to China. Planorbella trivolvis usually live on diets with high fiber content, such as water grasses, algae and fallen leaves. These snails can attach to the wall of a water tank or to water grass and can be transported overseas to China through the ornamental fish trade. There are few studies investigating the intestinal microbiota of freshwater snails. In this study, using culture-independent molecular analysis, we assessed for the first time the complexity of bacterial communities in the intestines of reared snails. The intestinal microbiota in the snails fed different diets, that is, herbivorous feed (HV) with high cellulose and non-herbivorous feed (NHV) with low cellulose, were analyzed by Illumina sequencing. The results showed that the NHV-based diet significantly increased the body mass, shell diameter and specific growth rate of the snails after 60 days of rearing (P < 0.05). Histological experiments showed that the fat droplets in the epithelium columnar cells of the intestines of the NHV snails increased, and the cilia on these cells fell off. The sequencing results identified 486 and 195 OTUs in HV and NHV, respectively. Lots of bacteria were not reported previously in snails. The intestinal microbiota diversity index (Shannon, Simpson, Ace and Chao) in the NHV snails was significantly lower than that in the HV snails. The gut microbiota in the HV snails were predominantly Proteobacteria (52.97%) and Bacteroidetes (28.75%), while the gut microbiota in NHV snails were predominantly Proteobacteria (95.23%). At the genus level, Cloacibacterium (24.60%), Pseudomonas (4.47%), OM6ON (6.12%), and Rhodobacter (5.79%) were observed to be abundant in HV snails. However, Aeromonas (85.4%) was determined to be predominant in NHV snails. Functional prediction of the gut microbiome in snails by PICRUSt demonstrated a significant difference between the two groups, and the HV snails exhibited higher lignocellulose enzyme activity than did the NHV snails. This study represents a first step in characterizing the gut microbiota of the freshwater snail. Most of these microbes can process plant biomass and digest cellulose and lignocellulose, and the enzymes of these bacteria may have potential biotechnological applications in a variety of industrial processes. creator: Zongfu Hu creator: Qing Tong creator: Jie Chang creator: Jianhua Yu creator: Shuguo Li creator: Huaxin Niu creator: Deying Ma uri: https://doi.org/10.7717/peerj.10716 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Hu et al. title: Effects of dry-wet cycles on nitrous oxide emissions in freshwater sediments: a synthesis link: https://peerj.com/articles/10767 last-modified: 2021-02-12 description: BackgroundSediments frequently exposed to dry-wet cycles are potential biogeochemical hotspots for greenhouse gas (GHG) emissions during dry, wet and transitional phases. While the effects of drying and rewetting on carbon fluxes have been studied extensively in terrestrial and aquatic systems, less is known about the effects of dry-wet cycles on N2O emissions from aquatic systems. As a notable part of lotic systems are temporary, and small lentic systems can substantially contribute to GHG emissions, dry-wet cycles in these ecosystems can play a major role on N2O emissions.MethodologyThis study compiles literature focusing on the effects of drying, rewetting, flooding, and water level fluctuations on N2O emissions and related biogeochemical processes in sediments of lentic and lotic ecosystems.ResultsN2O pulses were observed following sediment drying and rewetting events. Moreover, exposed sediments during dry phases can be active spots for N2O emissions. The general mechanisms behind N2O emissions during dry-wet cycles are comparable to those of soils and are mainly related to physical mechanisms and enhanced microbial processing in lotic and lentic systems. Physical processes driving N2O emissions are mainly regulated by water fluctuations in the sediment. The period of enhanced microbial activity is driven by increased nutrient availability. Higher processing rates and N2O fluxes have been mainly observed when nitrification and denitrification are coupled, under conditions largely determined by O2 availability.ConclusionsThe studies evidence the driving role of dry-wet cycles leading to temporarily high N2O emissions in sediments from a wide array of aquatic habitats. Peak fluxes appear to be of short duration, however, their relevance for global emission estimates as well as N2O emissions from dry inland waters has not been quantified. Future research should address the temporal development during drying-rewetting phases in more detail, capturing rapid flux changes at early stages, and further explore the functional impacts of the frequency and intensity of dry-wet cycles. creator: Renata Pinto creator: Gabriele Weigelhofer creator: António Guerreiro Brito creator: Thomas Hein uri: https://doi.org/10.7717/peerj.10767 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Pinto et al. title: RNA sequencing-based exploration of the effects of far-red light on lncRNAs involved in the shade-avoidance response of D. officinale link: https://peerj.com/articles/10769 last-modified: 2021-02-12 description: Dendrobium officinale (D. officinale) is a valuable medicinal plant with a low natural survival rate, and its shade-avoidance response to far-red light is as an important strategy used by the plant to improve its production efficiency. However, the lncRNAs that play roles in the shade-avoidance response of D. officinale have not yet been investigated. This study found that an appropriate proportion of far-red light can have several effects, including increasing the leaf area and accelerating stem elongation, in D. officinale. The effects of different far-red light treatments on D. officinale were analysed by RNA sequencing technology, and a total of 69 and 78 lncRNAs were differentially expressed in experimental group 1 (FR1) versus the control group (CK) (FR1-CK) and in experimental group 4 (FR4) versus the CK (FR4-CK), respectively. According to GO and KEGG analyses, most of the differentially expressed lncRNA targets are involved in the membrane, some metabolic pathways, hormone signal transduction, and O-methyltransferase activity, among other functions. Physiological and biochemical analyses showed that far-red light promoted the accumulation of flavonoids, alkaloids, carotenoids and polysaccharides in D. officinale. The effect of far-red light on D. officinalemight be closely related to the cell membrane and Ca2+ transduction. Based on a Cytoscape analysis and previous research, this study also found that MSTRG.38867.1, MSTRG.69319.1, and MSTRG.66273.1, among other components, might participate in the far-red light signalling network through their targets and thus regulate the shade-avoidance response of D. officinale. These findings will provide new insights into the shade-avoidance response of D. officinale. creator: Hansheng Li creator: Wei Ye creator: Yaqian Wang creator: Xiaohui Chen creator: Yan Fang creator: Gang Sun uri: https://doi.org/10.7717/peerj.10769 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: The effect of ethanol concentration on the morphological and molecular preservation of insects for biodiversity studies link: https://peerj.com/articles/10799 last-modified: 2021-02-12 description: Traditionally, insects collected for scientific purposes have been dried and pinned, or preserved in 70% ethanol. Both methods preserve taxonomically informative exoskeletal structures well but are suboptimal for preserving DNA for molecular biology. Highly concentrated ethanol (95–100%), preferred as a DNA preservative, has generally been assumed to make specimens brittle and prone to breaking. However, systematic studies on the correlation between ethanol concentration and specimen preservation are lacking. Here, we tested how preservative ethanol concentration in combination with different sample handling regimes affect the integrity of seven insect species representing four orders, and differing substantially in the level of sclerotization. After preservation and treatments (various levels of disturbance), we counted the number of appendages (legs, wings, antennae, or heads) that each specimen had lost. Additionally, we assessed the preservation of DNA after long-term storage by comparing the ratio of PCR amplicon copy numbers to an added artificial standard. We found that high ethanol concentrations indeed induce brittleness in insects. However, the magnitude and nature of the effect varied strikingly among species. In general, ethanol concentrations at or above 90% made the insects more brittle, but for species with robust, thicker exoskeletons, this did not translate to an increased loss of appendages. Neither freezing the samples nor drying the insects after immersion in ethanol had a negative effect on the retention of appendages. However, the morphology of the insects was severely damaged if they were allowed to dry. We also found that DNA preserves less well at lower ethanol concentrations when stored at room temperature for an extended period. However, the magnitude of the effect varies among species; the concentrations at which the number of COI amplicon copies relative to the standard was significantly decreased compared to 95% ethanol ranged from 90% to as low as 50%. While higher ethanol concentrations positively affect long-term DNA preservation, there is a clear trade-off between preserving insects for morphological examination and genetic analysis. The optimal ethanol concentration for the latter is detrimental for the former, and vice versa. These trade-offs need to be considered in large insect biodiversity surveys and other projects aiming to combine molecular work with traditional morphology-based characterization of collected specimens. creator: Daniel Marquina creator: Mateusz Buczek creator: Fredrik Ronquist creator: Piotr Łukasik uri: https://doi.org/10.7717/peerj.10799 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Marquina et al. title: Prognostic implications of cell division cycle protein 45 expression in hepatocellular carcinoma link: https://peerj.com/articles/10824 last-modified: 2021-02-12 description: BackgroundThe overall prognosis of hepatocellular carcinoma (HCC) is poor and novel prognostic biomarkers might better monitor the progression of HCC. Cell division cycle protein 45 (CDC45) plays a key role in DNA replication and considered to be involved in tumorigenesis. This study investigated CDC45 expression in tumour tissues and defined its prognostic value in HCC patients.MethodsWe used immunohistochemistry (IHC) staining to examine the expression of CDC45 in tumour tissue specimens and compare them with adjacent normal tissue specimens using a constructed tissue microarray (TMA) and analyzed how clinical features are related to HCC prognosis. Functional enrichment analyses were used to describe significantly involved hallmark pathways of differentially expressed genes (DEGs, which were screened out according to the high or low expression of CDC45 in tumour tissues).ResultsOur findings showed that the proteome expression of CDC45 was evidently downregulated in HCC tissues compared with matched normal tissues (P < 0.0001). Although we did not find any differences in terms of vascular invasion, metastasis, lymphatic infiltration, or Edmondson grade between patients with high and low CDC45 expression, low CDC45 expression was significantly correlated with microvascular invasion (P = 0.046). Multivariate analysis indicated that CDC45 expression (P = 0.035) was an independent prognostic factor for the overall survival (OS) rate of HCC patients. Patients with CDC45 expression was positively correlated with OS rates among HCC patients (P < 0.05). Functional annotations indicated that CDC45 is involved in the most significant pathways, including the cell cycle, DNA replication, chemical carcinogenesis and drug metabolism–cytochrome P450 pathways.DiscussionOur findings showed that low proteomic level of CDC45 was associated with a poor prognosis in HCC patients, indicating that CDC45 might be a novel prognostic marker. creator: Chen Yang creator: shufang Xie creator: Yi Wu creator: Guoqing Ru creator: Xianglei He creator: Hong-yin Pan creator: Shibing Wang creator: Xiangmin Tong uri: https://doi.org/10.7717/peerj.10824 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: Effects of pharmaceutically active compounds (PhACs) on fish body and scale shape in natural waters link: https://peerj.com/articles/10642 last-modified: 2021-02-11 description: BackgroundIn recent years, there are growing concerns about pharmaceutically active compounds (PhACs) in natural ecosystems. These compounds have been found in natural waters and in fish tissues worldwide. Regarding their growing distribution and abundance, it is becoming clear that traditionally used risk assessment methodologies and ecotoxicological studies have limitations in several respects. In our study a new, combined approach of environmental impact assesment of PhACs has been used.MethodsIn this study, the constant watercourses of the suburban region of the Hungarian capital (Budapest) were sampled, and the body shape and scale shape of three fish species (roach Rutilus rutilus, chub Squalius cephalus, gibel carp Carassius gibelio) found in these waters were analyzed, based on landmark-based geometric morphometric methods. Possible connections were made between the differences in body shape and scale shape, and abiotic environmental variables (local- and landscape-scale) and measured PhACs.ResultsSignificant connections were found between shape and PhACs concentrations in several cases. Despite the relatively large number of compounds (54) detected, citalopram, propranolol, codeine and trimetazidine significantly affected only fish body and scale shape, based on their concentrations. These four PhACs were shown to be high (citalopram), medium (propranolol and codeine), and low (trimetazidine) risk levels during the environmental risk assessment, which were based on Risk Quotient calculation. Furthermore, seven PhACs (diclofenac, Estrone (E1), tramadol, caffeine 17α-Ethinylestradiol (EE2), 17α-Estradiol (aE2), Estriol (E3)) were also categorized with a high risk level. However, our morphological studies indicated that only citalopram was found to affect fish phenotype amongst the PhACs posing high risk. Therefore, our results revealed that the output of (traditional) environmental/ecological risk assessment based on ecotoxicological data of different aquatic organisms not necessarily show consistency with a “real-life” situation; furthermore, the morphological investigations may also be a good sub-lethal endpoint in ecotoxicological assessments. creator: Adam Staszny creator: Peter Dobosy creator: Gabor Maasz creator: Zoltan Szalai creator: Gergely Jakab creator: Zsolt Pirger creator: Jozsef Szeberenyi creator: Eva Molnar creator: Lilianna Olimpia Pap creator: Vera Juhasz creator: Andras Weiperth creator: Bela Urbanyi creator: Attila Csaba Kondor creator: Arpad Ferincz uri: https://doi.org/10.7717/peerj.10642 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Staszny et al. title: Freshwater sponge hosts and their green algae symbionts: a tractable model to understand intracellular symbiosis link: https://peerj.com/articles/10654 last-modified: 2021-02-11 description: In many freshwater habitats, green algae form intracellular symbioses with a variety of heterotrophic host taxa including several species of freshwater sponge. These sponges perform important ecological roles in their habitats, and the poriferan:green algae partnerships offers unique opportunities to study the evolutionary origins and ecological persistence of endosymbioses. We examined the association between Ephydatia muelleri and its chlorophyte partner to identify features of host cellular and genetic responses to the presence of intracellular algal partners. Chlorella-like green algal symbionts were isolated from field-collected adult E. muelleri tissue harboring algae. The sponge-derived algae were successfully cultured and subsequently used to reinfect aposymbiotic E. muelleri tissue. We used confocal microscopy to follow the fate of the sponge-derived algae after inoculating algae-free E. muelleri grown from gemmules to show temporal patterns of symbiont location within host tissue. We also infected aposymbiotic E. muelleri with sponge-derived algae, and performed RNASeq to study differential expression patterns in the host relative to symbiotic states. We compare and contrast our findings with work in other systems (e.g., endosymbiotic Hydra) to explore possible conserved evolutionary pathways that may lead to stable mutualistic endosymbioses. Our work demonstrates that freshwater sponges offer many tractable qualities to study features of intracellular occupancy and thus meet criteria desired for a model system. creator: Chelsea Hall creator: Sara Camilli creator: Henry Dwaah creator: Benjamin Kornegay creator: Christie Lacy creator: Malcolm S. Hill creator: April L. Hill uri: https://doi.org/10.7717/peerj.10654 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hall et al. title: Taxonomic revision of the threatened African genus Pseudohydrosme Engl. (Araceae), with P. ebo, a new, critically endangered species from Ebo, Cameroon link: https://peerj.com/articles/10689 last-modified: 2021-02-11 description: This is the first revision in more than 100 years of the African genus Pseudohydrosme, formerly considered endemic to Gabon. Closely related to Anchomanes, Pseudohydrosme is distinct from Anchomanes because of its 2-3-locular ovary (vs. unilocular), peduncle concealed by cataphylls at anthesis and far shorter than the spathe (vs. exposed, far exceeding the spathe), stipitate fruits and viviparous (asexually reproductive) roots (vs. sessile, roots non-viviparous), lack of laticifers (vs. laticifers present) and differences in spadix: spathe proportions and presentation. However, it is possible that a well sampled molecular phylogenetic analysis might show that one of these genera is nested inside the other. In this case the synonymisation of Pseudohydrosme will be required. Three species, one new to science, are recognised, in two sections. Although doubt has previously been cast on the value of recognising Pseudohydrosme buettneri, of Gabon, it is here accepted and maintained as a distinct species in the monotypic section, Zyganthera. However, it is considered to be probably globally extinct. Pseudohydrosme gabunensis, type species of the genus, also Gabonese but probably extending to Congo, is maintained in Sect. Pseudohydrosme together with Pseudohydrosme ebo sp.nov. of the Ebo Forest, Littoral Region, Cameroon, the first addition to the genus since the nineteenth century, and which extends the range of the genus 450 km north from Gabon, into the Cross-Sanaga biogeographic area. The discovery of Pseudohydrosme ebo resulted from a series of surveys for conservation management in Cameroon, and triggered this article. All three species are morphologically characterised, their habitat and biogeography discussed, and their extinction risks are respectively assessed as Critically Endangered (Possibly Extinct), Endangered and Critically Endangered using the IUCN standard. Clearance of forest habitat for logging, followed by agriculture or urbanisation are major threats. Pseudohydrosme gabunensis may occur in a formally protected area and is also cultivated widely but infrequently in Europe, Australia and the USA for its spectacular inflorescences. creator: Martin Cheek creator: Barthélemy Tchiengué creator: Xander van der Burgt uri: https://doi.org/10.7717/peerj.10689 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Cheek et al.