Identification and characterization of circRNAs as competing endogenous RNAs for miRNA-mRNA in colorectal cancer
Background Recent studies showed that circRNAs are involved in the biological process of some human cancers. However, little is known about their functions in colorectal cancer (CRC). Methods Here we first revealed the expression profiles of circRNAs in the CRC tissues and the adjacent non-tumorous tissues using high-throughput sequencing. The sequence feature, chromosome location, alternative splicing and other characteristics of the circRNAs were also explored. The miRNA and mRNA expression profiles were then obtained by analyzing relevant CRC data retrived from the TCGA database. We obtained and analyzed the competing endogenous RNA (ceRNA) network of the top three pairs of the largest up-regulated and down-regulated circRNAs. Results In this study, we obtained 50,410 circRNAs in the CRC tissue and the adjacent non-tumor tissues, of which 33.7% (16,975) were new, and revealed differential changes in circRNA expression during colorectal carcinogenesis. We have identified six potential key circRNAs (circPIEZO1-3, hsa_circ_0067163, hsa_circ_0140188, hsa_circ_0002632, hsa_circ_0001998 and hsa_circ_0023990) associated with CRC, which play important roles in carcinogenesis as ceRNA for regulation of miRNA-mRNA network. In the subsequent KEGG analysis, several CRC-related pathways were found. Conclusions Our findings advance the understanding of the pathogenesis of CRC from the perspective of circRNAs and provide some circRNAs as candidate diagnostic biomarkers or potential therapeutic targets.
Yuan et al. (2019) Identification and characterization of circRNAs as competing endogenous RNAs for miRNA-mRNA in colorectal cancer. PeerJ 7:e7602 https://doi.org/10.7717/peerj.7602
A new record of kelp Lessonia spicata (Suhr) Santelices in the Sub-Antarctic Channels: implications for the conservation of the “huiro negro” in the Chilean coast
The Katalalixar National Reserve (KNR) lies in an isolated marine protected area of Magellan Sub-Antarctic channels, which represent an important area for marine biodiversity and macroalgal conservation. The present study is the first report of the species Lessonia spicata, “huiro negro”, in the Magellan Sub-Antarctic channels. This finding has implications for macroalgal biogeography and conservation concerns in the Chilean coast. In the ecological assessments of the KNR in 2018 we found populations of L. spicata, specifically on rocky shores of Torpedo Island and Castillo Channel. The morphological identification and molecular phylogeny based on nuclear (ITS1) sequences revealed that these populations of Lessonia are within the lineage of L. spicata of central Chile. This report increases the species richness of kelps for the Magellan Sub-Antarctic Channels from two to three confirmed species (L. flavicans, L. searlesiana and L. spicata), and it also extends the southern distribution range of L. spicata. This species has high harvest demand and is moving towards southern Chile; thus, these populations should be considered as essential for macroalgal conservation in high latitudes of South America.
Rosenfeld et al. (2019) A new record of kelp Lessonia spicata (Suhr) Santelices in the Sub-Antarctic Channels: implications for the conservation of the “huiro negro” in the Chilean coast. PeerJ 7:e7610 https://doi.org/10.7717/peerj.7610
Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau
The rumen microbiota of ruminants plays a vital role in fiber digestion, and environmental factors affect its community structure. The yak (Bos grunniens) is the main livestock species that inhabits the Qinghai-Tibet Plateau (QTP) at regions located at high-altitude of 3,000–5,000 m. This work investigated the rumen bacterial community of yak that grazed on the QTP during the whole year to evaluate the relationship between the rumen bacterial community and the nutrient composition of forage plant at three stages. In this study, the diversity of the rumen prokaryotic community composition was monitored in 10 full-grazing yak in an alpine meadow of the QTP. The nutrient composition of three forage growth stages was determined: re-green stage (REGY), grassy stage (GY), and withered stage (WGY). High-throughput sequencing of bacterial 16S rRNA gene was used. The results showed that the nutritive composition of the alpine meadow changed with the seasons: crude protein (CP) (13.22%) was high in forage during REGY (spring), while neutral detergent fiber (NDF) (59.00%) was high during WGY (winter). Microbial diversity and richness were highest during REGY and the average number of operational taxonomic units from 30 samples was 4,470. The microbial composition was dominated by members of Bacteroidetes (51.82%), followed by Firmicutes (34.08%), and the relative microbial abundance changed in the three forage growth stages. Unweighted UniFrac distance PcoA showed that the bacterial community structure differed between REGY, GY, and WGY. Furthermore, taxonomic groups did not present differences regarding gender in these three stages. The rumen microbiota was enriched with functional potentials that were related to ABC transporters, the two-component system, Aminoacyl-tRNA biosynthesis, and metabolism of Purine, Pyrimidine, Starch and sucrose metabolism. Significant differences were found in the composition, diversity, and function of yak ruminal microorganisms during different forage growth stages. This indicates that microbial changes in the rumen depend on changes in the forage nutritional composition. These findings provide evidence on the rumen microbial diversity of yaks in the QTP.
Ma et al. (2019) Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau. PeerJ 7:e7645 https://doi.org/10.7717/peerj.7645
Nurhachius luei, a new istiodactylid pterosaur (Pterosauria, Pterodactyloidea) from the Early Cretaceous Jiufotang Formation of Chaoyang City, Liaoning Province (China) and comments on the Istiodactylidae
A new istiodactylid pterosaur, Nurhachius luei sp. nov., is here reported based on a complete skull with mandible and some cervical vertebrae from the lower part of the Jiufotang Formation of western Liaoning (China). This is the second species of Nurhachius, the type-species being N. ignaciobritoi from the upper part of the Jiufotang Formation. A revised diagnosis of the genus Nurhachius is provided, being this taxon characterized by the presence of a slight dorsal deflection of the palatal anterior tip, which is homoplastic with the Anhangueria and Cimoliopterus. N. luei sp. nov. shows an unusual pattern of tooth replacement, with respect to other pterodactyloid species. The relationships within the Istiodactylidae and with their closest taxa are investigated through a phylogenetic analysis by parsimony.
Zhou et al. (2019) Nurhachius luei, a new istiodactylid pterosaur (Pterosauria, Pterodactyloidea) from the Early Cretaceous Jiufotang Formation of Chaoyang City, Liaoning Province (China) and comments on the Istiodactylidae. PeerJ 7:e7688 https://doi.org/10.7717/peerj.7688
LC–MS/MS quantitative analysis of phylloquinone, menaquinone-4 and menaquinone-7 in the human serum of a healthy population
A novel application of the liquid chromatography method combined with the triple quadrupole tandem mass spectrometry method was developed for the quantification of vitamin K1 and two forms of vitamin K2 (menaquinone-4, menaquinone-7) in human serum. Total chromatography time for each run was 9 min. Time required for the sample pretreatment procedures was approximately 4 h. The coefficients of variation (CVs) of intra-assay were 10.4%, 3.2 % and 2.3% for vitamin K1 in three levels of quality control samples; were 14.3%, 3.2% and 6.7% for menaquinone-4; and were 11.1%, 6.0% and 7.0% for menaquinone-7. The inter-assay CVs were 12.8%, 11.3% and 7.4% for vitamin K1; were 15.2%, 9.2% and 8.7% for menaquinone-4; and were 13.2%,11.1% and 7.2% for menaquinone-7. No interference was found between K1, menaquinone-4 and menaquinone-7, nor any deuterated internal standards. This method was then used to determine reference values for Caucasian populations of central European origin. Samples were measured from 191 healthy volunteers (51.2 ± 16.2 years (mean ± SD)) and the values concerning K1 were 0.044–1.357 ng/mL for women and 0.030–1.214 ng/mL for men. The values for menaquinone-4 and menaquinone-7 did not exhibit any differences between women and men, and were 0.050–1.598 and 0.074–0.759 ng/mL, respectively.
Dunovska et al. (2019) LC–MS/MS quantitative analysis of phylloquinone, menaquinone-4 and menaquinone-7 in the human serum of a healthy population. PeerJ 7:e7695 https://doi.org/10.7717/peerj.7695
Phylogeny of Microphthalminae Hartmann-Schröder, 1971, and revision of Hesionella Hartman, 1939, and Struwela Hartmann-Schröder, 1959 (Annelida, Errantia)
Microphthalminae Hartmann-Schröder, 1971 was proposed in Hesionidae to include Microphthalmus and Hesionides; however, the affinities of these genera to other members of Hesionidae have been debated, and some authors have concluded they do not belong in Hesionidae. Herein, based on morphological characters, a phylogenetic analysis of the subfamily and some other similar poorly-known genera, with an uncertain position in Hesionidae was performed to clarify their affinities. Our results indicate that Microphthalminae, as currently delimited, is paraphyletic. The inclusion of Struwela, Uncopodarke, and Westheideius, a new genus, as well as the recognition of Fridericiella are proposed to meet the requirement of monophyly; and as result of this, the elevation in rank to the family level is herein presented. Furthermore, the type species for Hesionella and Struwela are redescribed, and a new species in the latter is described. A key to identify microphthalmid genera is also included.
Salazar-Vallejo et al. (2019) Phylogeny of Microphthalminae Hartmann-Schröder, 1971, and revision of Hesionella Hartman, 1939, and Struwela Hartmann-Schröder, 1959 (Annelida, Errantia). PeerJ 7:e7723 https://doi.org/10.7717/peerj.7723
The secret life of deep-sea shrimps: ecological and evolutionary clues from the larval description of Systellaspis debilis (Caridea: Oplophoridae)
Currently there are 21 shrimp species in the northeastern Atlantic and Mediterranean Sea which are considered to belong to the superfamily Oplophoroidea, but the larval development is unknown for most of them. The complete larval development of Systellaspis debilis (Milne-Edwards, 1881), here described and illustrated, is the first one to have been successfully reared in the laboratory, consisting of four zoeal and one decapodid stages. The zoeae were found to be fully lecithotrophic, which together with the females’ lower fecundity, are probably evolutionary consequences of the species mesopelagic habitat.
Bartilotti et al. (2019) The secret life of deep-sea shrimps: ecological and evolutionary clues from the larval description of Systellaspis debilis (Caridea: Oplophoridae). PeerJ 7:e7334 https://doi.org/10.7717/peerj.7334
Open ocean nocturnal insect migration in the Brazilian South Atlantic with comments on flight endurance
We observed a nocturnal insect swarm aboard the oceanographic ship Cruzeiro do Sul of the Brazilian Navy, while conducting a survey of the Montague guyot (seamount), 389 km distant from the nearest land in the South Atlantic. The insects came from open sea toward the ship from all directions, attracted by the powerful light of the deck. Most insects collided with the hull and fell into the ocean, but we managed to capture and determine 17 (13 Hemiptera of a single species, three Lepidoptera of three species and one Odonata). With one exception, we are certain that none of the specimens caught originated from the ship. The geographic origin, most likely the coast of Brazil, and flight endurance of these insects were inferred using data on wind speed and direction, provided by the crew of the ship, and were reconstructed using Hysplit modeling of air current trajectories.
Alves et al. (2019) Open ocean nocturnal insect migration in the Brazilian South Atlantic with comments on flight endurance. PeerJ 7:e7583 https://doi.org/10.7717/peerj.7583
Measuring body dimensions of leopards (Panthera pardus) from camera trap photographs
Measurement of body dimensions of carnivores usually requires the chemical immobilization of subjects. This process can be dangerous, costly and potentially harmful to the target individuals. Development of an alternative, inexpensive, and non-invasive method therefore warrants attention. The objective of this study was to test whether it is possible to obtain accurate measurements of body dimensions of leopards from camera trap photographs. A total of 10 leopards (Panthera pardus) were captured and collared at Malilangwe Wildlife Reserve, Zimbabwe from May 7 to June 20, 2017 and four body measurements namely shoulder height, head-to-tail, body, and tail length were recorded. The same measurements were taken from 101 scaled photographs of the leopards recorded during a baited-camera trapping (BCT) survey conducted from July 1 to October 22, 2017 and differences from the actual measurements calculated. Generalized Linear Mixed Effects Models were used to determine the effect of type of body measurement, photographic scale, posture, and sex on the accuracy of the photograph-based measurements. Type of body measurement and posture had a significant influence on accuracy. Least squares means of absolute differences between actual and photographic measurements showed that body length in the level back-straight forelimb-parallel tail posture was measured most accurately from photographs (2.0 cm, 95% CI [1.5–2.7 cm]), while head-to-tail dimensions in the arched back-bent forelimb-parallel tail posture were least accurate (8.3 cm, 95% CI [6.1–11.2 cm]). Using the BCT design, we conclude that it is possible to collect accurate morphometric data of leopards from camera trap photographs. Repeat measurements over time can provide researchers with vital body size and growth rate information which may help improve the monitoring and management of species of conservation concern, such as leopards.
Tarugara et al. (2019) Measuring body dimensions of leopards (Panthera pardus) from camera trap photographs. PeerJ 7:e7630 https://doi.org/10.7717/peerj.7630
13C values of glycolytic amino acids as indicators of carbohydrate utilization in carnivorous fish
Background Stable isotope analysis of single amino acids (AA) is usually applied in food web studies for tracing biosynthetic origins of AA carbon backbones and establishing trophic positions of consumers, but the method is also showing promise for characterizing quantity and quality of dietary lipids and carbohydrates. Methods To investigate whether changes in high- and low-digestible carbohydrates affect δ13C values of glycolytic AA, i.e., AA carbon backbones sourced from the glycolytic pathway, we compared Atlantic salmon (Salmo salar) from a feeding experiment with and without dietary inclusion of the red macroalga Palmaria palmata. The Control and experimental diets had similar relative proportions of macronutrients, but their ingredients differed; in the experimental treatment, 15% Palmaria inclusion substituted proteins from fishmeal and carbohydrates from corn starch. Results We found that 13C values of the glycolytic AA were highly sensitive to substitution of corn starch with Palmaria. The δ13C offsets of glycolytic AA between salmon and their diets were significantly greater in the Palmaria inclusion than Control treatment. This greater offset can be attributed to the different utilization of high- vs. low-digestible carbohydrate sources, i.e., corn starch vs. Palmaria, in the two treatments, and metabolic routing of dietary lipids. In addition, similar δ13C values of essential AA between treatments indicate similar nutrient assimilation efficiency for all terrestrial (pea protein concentrate and wheat gluten meal) and marine (fishmeal and red alga) derived protein sources. These results show that δ13CAA analysis is a promising tool for improving our understanding of how carnivorous fish utilize macronutrient and route metabolic intermediates to tissue.
Wang et al. (2019) 13C values of glycolytic amino acids as indicators of carbohydrate utilization in carnivorous fish. PeerJ 7:e7701 https://doi.org/10.7717/peerj.7701