The mechanism and detection of alternative splicing events in circular RNAs
Circular RNAs (circRNAs) are considered as functional biomolecules with tissue/development-specific expression patterns. Generally, a single gene may generate multiple circRNA variants by alternative splicing, which contain different combinations of exons and/or introns. Due to the low abundance of circRNAs as well as overlapped with their linear counterparts, circRNA enrichment protocol is needed prior to sequencing. Compared with numerous algorithms, which use back-splicing reads for detection and functional characterization of circRNAs, original bioinformatic analyzing tools have been developed to large-scale determination of full-length circRNAs and accurate quantification. This review provides insights into the complexity of circRNA biogenesis and surveys the recent progresses in the experimental and bioinformatic methodologies that focus on accurately full-length circRNAs identification.
Li et al. (2020) The mechanism and detection of alternative splicing events in circular RNAs. PeerJ 8:e10032 https://doi.org/10.7717/peerj.10032
Global gene expression analyses of the alkamide-producing plant Heliopsis longipes supports a polyketide synthase-mediated biosynthesis pathway
Background Alkamides are plant-specific bioactive molecules. They are low molecular weight N-substituted α-unsaturated acyl amides that display biological explicit activities in different organisms from bacteria, fungi, insects to mammals and plants. The acyl chain has been proposed to be biosynthesized from a fatty acid; however, this has not been demonstrated yet. Heliopsis longipes (Asteraceae) accumulates in root a C10 alkamide called affinin in its roots, but not in leaves. The closely related species Heliopsis annua does not produce alkamides. To elucidate the biosynthetic pathway of the alkamides acyl chain, a comparative global gene expression analysis contrasting roots and leaves of both species was performed. Methods Transcriptomics analysis allowed to identify genes highly expressed in H. longipes roots, but not in tissues and species that do not accumulate alkamides. The first domain searched was the Ketosynthase (KS) domain. The phylogenetic analysis using sequences of the KS domain of FAS and PKS from different organisms, revealed that KS domains of the differentially expressed transcripts in H. longipes roots and the KS domain found in transcripts of Echinacea purpurea, another alkamides producer species, were grouped together with a high bootstrap value of 100%, sharing great similarity. Among the annotated transcripts, we found some coding for the enzymatic domains KS, AT, ACP, DH, OR and TE, which presented higher expression in H. longipes roots than in leaves. The expression level of these genes was further evaluated by qRT-PCR. All unigenes tested showed higher expression in H. longipes roots than in any the other samples. Based on this and considering that the acyl chain of affinin presents unsaturated bonds at even C numbers, we propose a new putative biosynthesis pathway mediated by a four modules polyketide synthase (PKS). Results The global gene expression analysis led to the selection of a set of candidate genes involved in the biosynthesis of the acyl chain of affinin, suggesting that it may be performed by a non-iterative, partially reductive, four module type I PKS complex (PKS alk) previously thought to be absent from the plant kingdom.
Buitimea-Cantúa et al. (2020) Global gene expression analyses of the alkamide-producing plant Heliopsis longipes supports a polyketide synthase-mediated biosynthesis pathway. PeerJ 8:e10074 https://doi.org/10.7717/peerj.10074
Life history and habitat do not mediate temporal changes in body size due to climate warming in rodents
Temporal changes in body size have been documented in a number of vertebrate species, with different contested drivers being suggested to explain these changes. Among these are climate warming, resource availability, competition, predation risk, human population density, island effects and others. Both life history traits (intrinsic factors such as lifespan and reproductive rate) and habitat (extrinsic factors such as vegetation type, latitude and elevation) are expected to mediate the existence of a significant temporal response of body size to climate warming but neither have been widely investigated. Using examples of rodents, we predicted that both life history traits and habitat might explain the probability of temporal response using two tests of this hypothesis. Firstly, taking advantage of new data from museum collections spanning the last 106 years, we investigated geographical and temporal variation in cranial size (a proxy for body size) in six African rodent species of two murid subfamilies (Murinae and Gerbillinae) of varying life history, degree of commensality, range size, and habitat. Two species, the commensal Mastomys natalensis, and the non-commensal Otomys unisulcatus showed significant temporal changes in body size, with the former increasing and the latter decreasing, in relation with climate warming. Commensalism could explain the increase in size with time due to steadily increasing food availability through increased agricultural production. Apart from this, we found no general life history or habitat predictors of a temporal response in African rodents. Secondly, in order to further test this hypothesis, we incorporated our data into a meta-analysis based on published literature on temporal responses in rodents, resulting in a combined dataset for 50 species from seven families worldwide; among these, 29 species showed no significant change, eight showed a significant increase in size, and 13 showed a decline in size. Using a binomial logistic regression model for these metadata, we found that none of our chosen life history or habitat predictors could significantly explain the probability of a temporal response to climate warming, reinforcing our conclusion based on the more detailed data from the six African species.
Nengovhela et al. (2020) Life history and habitat do not mediate temporal changes in body size due to climate warming in rodents. PeerJ 8:e9792 https://doi.org/10.7717/peerj.9792
Forest before the trees in the aquatic world: global and local processing in teleost fishes
Background The study of illusory phenomena is important to understanding the similarities and differences between mammals and birds’ perceptual systems. In recent years, the analysis has been enlarged to include cold-blooded vertebrates, such as fish. However, evidence collected in the literature have drawn a contradictory picture, with some fish species exhibiting a human-like perception of visual illusions and others showing either a reversed perception or no susceptibility to visual illusions. The possibility exists that these mixed results relate to interspecific variability in perceptual grouping mechanisms. Therefore, we studied whether fish of five species exhibit a spontaneous tendency to prioritize a global analysis of the visual scene—also known as global-to-local precedence—instead of focusing on local details. Methods Using Navon-like stimuli (i.e., larger recognisable shapes composed of copies of smaller different shapes), we trained redtail splitfin, zebrafish, angelfish, Siamese fighting fish and three spot gourami to discriminate between two figures characterized by congruency between global and local information (a circle made by small circles and a cross made by small crosses). In the test phase, we put global and local cues (e.g., a circle made by small crosses) into contrast to see whether fish spontaneously rely on global or local information. Results Like humans, fish seem to have an overall global-to-local precedence, with no significant differences among the species. However, looking at the species-specific level, only four out of five species showed a significant global-to-local precedence, and at different degrees. Because these species are distantly related and occupy a broad spectrum of ecological adaptations, we suggest that the tendency to prioritize a global analysis of visual inputs may be more similar in fish than expected by the mixed results of visual illusion studies.
Santacà et al. (2020) Forest before the trees in the aquatic world: global and local processing in teleost fishes. PeerJ 8:e9871 https://doi.org/10.7717/peerj.9871
Distribution, habitat suitability, conservation state and natural history of endangered salamander Bolitoglossa pandi
Background Pandi’s mushroom-tongue salamander (Bolitoglossa pandi) is one of the threatened amphibians in South America, as well as a flagship species for the Colombian conservation agenda. This species is endemic to the Andean cloud forests of the western slope of the Cordillera Oriental of Colombia, occurring only in the department of Cundinamarca within a narrow elevational range. At night, B. pandi can be seen perching on the upper side of leaves at heights ranging from ground level to 2.5 m. During the day, it can be found under leaf litter or cover objects. Few studies have provided relevant information that can help the Colombian government to formulate lines of action for the conservation of this species; consequently, its threat assessments so far have been based on very limited information. Methods We conducted surveys for salamanders in four municipalities of Cundinamarca, Colombia, using two approaches: visual encounter surveys (Guaduas and Villeta) and the basic sampling protocol for single-species occupancy modeling (Supatá and Venecia). Multivariate analyses were employed to explore the correlation between habitat structure and natural history traits, abundance, and detection/non-detection of B. pandi. We evaluated the B. pandi activity pattern through kernel density curves for each sampling occasion and explored the variability of salamander abundance during their activity period by performing a nested ANOVA. Results We report the discovery of two new populations of B. pandi, which represent the most northwestern records known. A significant correlation between body length, body mass, and habitat structure was observed. Multivariate analyses indicated that leaf litter depth, mean temperature, percent vegetation cover, and altitude were the habitat variables that together explained 60.3% of the B. pandi abundance variability, as well as the main determinants of its optimal habitat. Bolitoglossa pandi exhibits an activity pattern characterized by two main activity peaks, in which niche time-partitioning was observed. Across the surveyed area, we found a healthy, stable, highly dense population of B. pandi (>1,300 individuals), with seasonal variability between development stages. Discussion Given the high habitat specificity of B. pandi, the species is highly vulnerable to local changes. Thus, we recommend that B. pandi be retained as Endangered (EN) on the IUCN Red List, based on the IUCN Criterion B, given its restricted extent of occurrence (ca. 2,500 km2) and the ongoing threats from agriculture, cattle ranching, logging, and urban development, which continue to reduce its suitable habitat.
Angarita-Sierra et al. (2020) Distribution, habitat suitability, conservation state and natural history of endangered salamander Bolitoglossa pandi. PeerJ 8:e9901 https://doi.org/10.7717/peerj.9901
Description of the unusual digestive tract of Platax orbicularis and the potential impact of Tenacibaculum maritimum infection
Background Ephippidae fish are characterized by a discoid shape with a very small visceral cavity. Among them Platax orbicularis has a high economic potential due to its flesh quality and flesh to carcass ratio. Nonetheless, the development of its aquaculture is limited by high mortality rates, especially due to Tenacibaculum maritimum infection, occurring one to three weeks after the transfer of fishes from bio-secure land-based aquaculture system to the lagoon cages for growth. Among the lines of defense against this microbial infection, the gastrointestinal tract (GIT) is less studied. The knowledge about the morphofunctional anatomy of this organ in P. orbicularis is still scarce. Therefore, the aims of this study are to characterize the GIT in non-infected P. orbicularis juveniles to then investigate the impact of T. maritimum on this multifunctional organ. Methods In the first place, the morpho-anatomy of the GIT in non-infected individuals was characterized using various histological techniques. Then, infected individuals, experimentally challenged by T. maritimum were analysed and compared to the previously established GIT reference. Results The overlapped shape of the GIT of P. orbicularis is probably due to its constrained compaction in a narrow visceral cavity. Firstly, the GIT was divided into 10 sections, from the esophagus to the rectum. For each section, the structure of the walls was characterized, with a focus on mucus secretions and the presence of the Na+/K+ ATPase pump. An identification key allowing the characterization of the GIT sections using in toto histology is given. Secondly, individuals challenged with T. maritimum exhibited differences in mucus type and proportion and, modifications in the mucosal and muscle layers. These changes could induce an imbalance in the trade-off between the GIT functions which may be in favour of protection and immunity to the disadvantage of nutrition capacities.
Alix et al. (2020) Description of the unusual digestive tract of Platax orbicularis and the potential impact of Tenacibaculum maritimum infection. PeerJ 8:e9966 https://doi.org/10.7717/peerj.9966
Characterization of a high-resolution breath acetone meter for ketosis monitoring
Background The ketone bodies beta-hydroxybutyrate (BHB) and acetone are endogenous products of fatty acid metabolism. Although ketone levels can be monitored by measuring either blood BHB or breath acetone, determining the precise correlation between these two measurement methods has been challenging. The purpose of this study is to characterize the performance of a novel portable breath acetone meter (PBAM) developed by Readout, Inc., to compare single versus multiple daily ketone measurements, and to compare breath acetone (BrAce) and blood BHB measurements. Methods We conducted a 14-day prospective observational cohort study of 21 subjects attempting to follow either a low-carbohydrate/ketogenic or a standard diet. Subjects were asked to concurrently measure both blood BHB and BrAce five times per day and report the results using an online data entry system. We evaluated the utility of multiple daily measurements by calculating the coefficient of variation (CV) for each daily group of measurements. We calculated the correlation between coincident BrAce and blood BHB measurements using linear ordinary least squares regression analysis. We assessed the ability of the BrAce measurement to accurately predict blood BHB states using receiver operating characteristic (ROC) analysis. Finally, we calculated a daily ketone exposure (DKE) using the area under the curve (AUC) of a ketone concentration versus time graph and compared the DKE of BrAce and blood BHB using linear ordinary least squares regression. Results BrAce and blood BHB varied throughout the day by an average of 44% and 46%, respectively. The BrAce measurement accurately predicted whether blood BHB was greater than or less than the following thresholds: 0.3 mM (AUC = 0.898), 0.5 mM (AUC = 0.854), 1.0 mM (AUC = 0.887), and 1.5 mM (AUC = 0.935). Coincident BrAce and blood BHB measurements were moderately correlated with R2 = 0.57 (P < 0.0001), similar to literature reported values. However, daily ketone exposures, or areas under the curve, for BrAce and blood BHB were highly correlated with R2 = 0.80 (P < 0.0001). Conclusions The results validated the performance of the PBAM. The BrAce/BHB correlation was similar to literature values where BrAce was measured using highly accurate lab instruments. Additionally, BrAce measurements using the PBAM can be used to predict blood BHB states. The relatively high daily variability of ketone levels indicate that single blood or breath ketone measurements are often not sufficient to assess daily ketone exposure for most users. Finally, although single coincident blood and breath ketone measurements show only a moderate correlation, possibly due to the temporal lag between BrAce and blood BHB, daily ketone exposures for blood and breath are highly correlated.
Suntrup III et al. (2020) Characterization of a high-resolution breath acetone meter for ketosis monitoring. PeerJ 8:e9969 https://doi.org/10.7717/peerj.9969
A new species of Scapholeberis Schoedler, 1858 (Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon basin highlighted by DNA barcodes and morphology
Background The Amazon basin is recognized as one of the most complex and species-rich freshwater environments globally. The diversity of zooplankton here remains unknown, with many species undescribed. Methods Here, we describe a new species of Scapholeberis Schoedler, 1858 (Cladocera: Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon Basin, collected with recently designed light traps. The description is based on detailed morphology (based on SEM and light microscopy) of parthenogenetic females, ephippial females, males, and molecular data based on the COI gene. Results Scapholeberis yahuarcaquensis n. sp. has a combination of characters present in Scapholeberis kingi Sars, 1888 and Scapholeberis armata freyi Dumont & Pensaert, 1983. These are a trilobate rostrum, with the middle lobe well developed with sides straight to relatively rounded, the presence of an elongated slit frontal head pore, a dorsal pore in the juncture of the cephalic shield and the valves, and a single denticulate membrane at the posterior rim of the valves, with stronger setae in the last third. The unique characters of the parthenogenetic females are ventral sucker with delicate triangles. Each has a filament-like projection in the lamellae’s inner side and an external section forming convex folds with denticle-like projections in the middle zone of the sucker-plate. There is a peculiar pitted sculpture in the ephippial females and a strong projection in the front of it. The male hook on the limb I with a blunt tip, a quirky lamella-like outgrow in the proximal side, and a paddle with well-developed spines scattered on its surface. The ventral sucker-lamellae in the male is much more developed than the female. The COI gene sequences showed an interspecific mean genetic divergence of 16.4% between S. yahuarcaquensis n. sp. and the closest species S. freyi from Mexico, supporting our results. A coalescence analysis and Barcode Index Number also support the new species based on the DNA sequences. New methods of collecting and integrative biology will give important support to recognize the fauna from the Amazon Basin, one of the most important sources of fresh water in the world that remains unknown in many respects.
Andrade-Sossa et al. (2020) A new species of Scapholeberis Schoedler, 1858 (Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon basin highlighted by DNA barcodes and morphology. PeerJ 8:e9989 https://doi.org/10.7717/peerj.9989
A model of twenty-three metabolic-related genes predicting overall survival for lung adenocarcinoma
Background The highest rate of cancer-related deaths worldwide is from lung adenocarcinoma (LUAD) annually. Metabolism was associated with tumorigenesis and cancer development. Metabolic-related genes may be important biomarkers and metabolic therapeutic targets for LUAD. Materials and Methods In this study, the gleaned cohort included LUAD RNA-SEQ data from the Cancer Genome Atlas (TCGA) and corresponding clinical data (n = 445). The training cohort was utilized to model construction, and data from the Gene Expression Omnibus (GEO, GSE30219 cohort, n = 83; GEO, GSE72094, n = 393) were regarded as a testing cohort and utilized for validation. First, we used a lasso-penalized Cox regression analysis to build a new metabolic-related signature for predicting the prognosis of LUAD patients. Next, we verified the metabolic gene model by survival analysis, C-index, receiver operating characteristic (ROC) analysis. Univariate and multivariate Cox regression analyses were utilized to verify the gene signature as an independent prognostic factor. Finally, we constructed a nomogram and performed gene set enrichment analysis to facilitate subsequent clinical applications and molecular mechanism analysis. Result Patients with higher risk scores showed significantly associated with poorer survival. We also verified the signature can work as an independent prognostic factor for LUAD survival. The nomogram showed better clinical application performance for LUAD patient prognostic prediction. Finally, KEGG and GO pathways enrichment analyses suggested several especially enriched pathways, which may be helpful for us investigative the underlying mechanisms.
Zhao et al. (2020) A model of twenty-three metabolic-related genes predicting overall survival for lung adenocarcinoma. PeerJ 8:e10008 https://doi.org/10.7717/peerj.10008
The lemur baseline: how lemurs compare to monkeys and apes in the Primate Cognition Test Battery
Primates have relatively larger brains than other mammals even though brain tissue is energetically costly. Comparative studies of variation in cognitive skills allow testing of evolutionary hypotheses addressing socioecological factors driving the evolution of primate brain size. However, data on cognitive abilities for meaningful interspecific comparisons are only available for haplorhine primates (great apes, Old- and New World monkeys) although strepsirrhine primates (lemurs and lorises) serve as the best living models of ancestral primate cognitive skills, linking primates to other mammals. To begin filling this gap, we tested members of three lemur species (Microcebus murinus, Varecia variegata, Lemur catta) with the Primate Cognition Test Battery, a comprehensive set of experiments addressing physical and social cognitive skills that has previously been used in studies of haplorhines. We found no significant differences in cognitive performance among lemur species and, surprisingly, their average performance was not different from that of haplorhines in many aspects. Specifically, lemurs’ overall performance was inferior in the physical domain but matched that of haplorhines in the social domain. These results question a clear-cut link between brain size and cognitive skills, suggesting a more domain-specific distribution of cognitive abilities in primates, and indicate more continuity in cognitive abilities across primate lineages than previously thought.
Fichtel et al. (2020) The lemur baseline: how lemurs compare to monkeys and apes in the Primate Cognition Test Battery. PeerJ 8:e10025 https://doi.org/10.7717/peerj.10025