How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships?
The Gastropoda contains 80% of existing mollusks and is the most diverse animal class second only to the Insecta. However, the deep phylogeny of gastropods has been controversial for a long time. Especially the position of Patellogastropoda is a major uncertainty. Morphology and some mitochondria studies concluded that Patellogastropoda is likely to be sister to all other gastropods (Orthogastropoda hypothesis), while transcriptomic and other mitogenomic studies indicated that Patellogastropoda and Vetigastropoda are sister taxa (Psilogastropoda). With the release of high-quality genomes, orthologous genes can be better identified and serve as powerful candidates for phylogenetic analysis. The question is, given the current limitations on the taxon sampling side, how many markers are needed to provide robust results. Here, we identified single-copy orthologous genes (SOGs) from 14 gastropods species with whole genomes available which cover five main gastropod subclasses. We generated different datasets from 395 to 1610 SOGs by allowing species missing in different levels. We constructed gene trees of each SOG, and inferred species trees from different collections of gene trees. We found as the number of SOGs increased, the inferred topology changed from Patellogastropoda being sister to all other gastropods to Patellogastropoda being sister to Vetigastropoda + Neomphalina (Psilogastropoda s.l.), with considerable support. Our study thus rejects the Orthogastropoda concept showing that the selection of the representative species and use of sufficient informative sites greatly influence the analysis of deep gastropod phylogeny.
Chen et al. (2022) How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships?. PeerJ 10:e13285 https://doi.org/10.7717/peerj.13285
Phenotypic variation of Chitala chitala (Hamilton, 1822) from Indian rivers using truss network and geometric morphometrics
Chitala chitala (Hamilton, 1822) is an economically important food fish species occurring throughout Indian rivers, which also has ornamental value. This study focuses on morphological variations in C. chitala from seven river basins across India namely; Son, Tons, Ken, Brahmaputra, Ganga, Gomti and Gandak. A truss network was constructed by interconnecting nine landmarks to generate 36 morphometric variables extracted from digital images of specimens sampled from the study locations. Transformed truss measurements were subjected to principal component analysis (PCA), canonical discriminant function analysis (CDFA) and discriminant analyses of principal components (DAPC). DAPC function coefficients performed much better in capturing the variation pattern and discrimination between the rivers which was not achieved using CDFA. Eight truss variables were identified with significant and highest loading for truss variables on principal components and coefficients on discriminant function from DAPC contributing to maximum variation between the rivers. Performance graph and functional distribution of identified truss variables clearly indicated distinction between the rivers. Thin plate spline analysis and procrustes shape analysis further showed the variation in morphology between specimens across the rivers. The significant parameters differentiating specimens from different rivers were linked to dorsal fin origin, the base of the pectoral fin and the perpendicular point on the anal fin from the dorsal fin origin. Variation in the hydrodynamics of the rivers studied might be possibly affecting the fin kinematics and consequently leading to adaption seen as phenotypic variation in C. chitala. The results showcased in the present study shall help in better understanding of intra-specific diversity which is significant for management and conservation of a species.
Chandran et al. (2022) Phenotypic variation of Chitala chitala (Hamilton, 1822) from Indian rivers using truss network and geometric morphometrics. PeerJ 10:e13290 https://doi.org/10.7717/peerj.13290
The sterile insect technique is protected from evolution of mate discrimination
Background The sterile insect technique (SIT) has been used to suppress and even extinguish pest insect populations. The method involves releasing artificially reared insects (usually males) that, when mating with wild individuals, sterilize the broods. If administered on a large enough scale, the sterility can collapse the population. Precedents from other forms of population suppression, especially chemicals, raise the possibility of resistance evolving against the SIT. Here, we consider resistance in the form of evolution of female discrimination to avoid mating with sterile males. Is resistance evolution expected? Methods We offer mathematical models to consider the dynamics of this process. Most of our models assume a constant-release protocol, in which the same density of males is released every generation, regardless of wild male density. A few models instead assume proportional release, in which sterile releases are adjusted to be a constant proportion of wild males. Results We generally find that the evolution of female discrimination, although favored by selection, will often be too slow to halt population collapse when a constant-release implementation of the SIT is applied appropriately and continually. The accelerating efficacy of sterile males in dominating matings as the population collapses works equally against discriminating females as against non-discriminating females, and rare genes for discrimination are too slow to ascend to prevent the loss of females that discriminate. Even when migration from source populations sustains the treated population, continued application of the SIT can prevent evolution of discrimination. However, periodic premature cessation of the SIT does allow discrimination to evolve. Likewise, use of a ‘proportional-release’ protocol is also prone to escape from extinction if discriminating genotypes exist in the population, even if those genotypes are initially rare. Overall, the SIT is robust against the evolution of mate discrimination provided care is taken to avoid some basic pitfalls. The models here provide insight for designing programs to avoid those pitfalls.
Bull et al. (2022) The sterile insect technique is protected from evolution of mate discrimination. PeerJ 10:e13301 https://doi.org/10.7717/peerj.13301
Differences in lower limb muscle activation between global and selective instability devices in single-leg stance in healthy active subjects
Background Balance and strength training are frequent strategies to address lower limb injuries, including ankle injuries, which are usually performed in single-leg stance on global instability devices, producing generalized muscular activation of the lower limb. In this context, new specific instability devices arise from the need to selectively work the ankle, specifically the peroneus longus. This study aimed to compare the EMG muscle activation of the peroneus longus, as well as other lower limbs muscles, in a single-leg stance on different balance training devices (BOSU, wobble board, power board, and Blackboard) in standing or squatting positions. Methods Twenty healthy recreationally trained subjects participated in the study. Subjects performed three repetitions of 15 s (one for familiarization and two for measurement) in standing and squatting positions on the floor, BOSU, wobble board, power board, and Blackboard. Surface electromyography (EMG) was used to record activity of the peroneus longus, soleus, gastrocnemius medialis, tibialis anterior, rectus femoris, and gluteus maximus. Results The main outcome was that no differences were found for the peroneus longus normalized EMG, neither between devices (p = 0.09) nor between conditions (p = 0.11), nor in the interaction between them (p = 0.16). For the normalized EMG of the other muscles, there were multiple differences between devices and conditions. Of the devices studied, the Blackboard was the one that implied a lower activation of the lower limb muscles and a lower degree of instability, activating the peroneus longus similarly to global instability devices. The BOSU and wobble board achieved high levels of EMG muscle activation for most muscles of the lower limbs. Therefore, they should be considered as potential devices for work in highly unstable conditions or when high activation levels are sought.
Sánchez-Barbadora et al. (2022) Differences in lower limb muscle activation between global and selective instability devices in single-leg stance in healthy active subjects. PeerJ 10:e13317 https://doi.org/10.7717/peerj.13317
miR-34a-5p inhibits the malignant progression of KSHV-infected SH-SY5Y cells by targeting c-fos
Background We aimed to investigate the effects of miR-34a-5p on c-fos regulation mediating the malignant behaviors of SH-SY5Y cells infected with Kaposi’s sarcoma-associated herpesvirus (KSHV). Methods The KSHV-infected (SK-RG) and uninfected SH-SY5Y parent cells were compared for differentially expressed miRNAs using transcriptome sequencing. Then miR-34a-5p was upregulated in SK-RG cells by the miRNA mimics transfection. Cell proliferation ability was determined by MTT and plate clone assays. The cell cycle was assessed by flow cytometry analysis, and CDK4, CDK6, cyclin D1 levels were determined by Western blot analysis. The migration behavior was detected by wound healing and transwell assays. The protein levels of MMP2 and MMP9 were measured by Western blot analysis. The regulation of c-fos by miR-34a-5p was detected by the dual-luciferase reporter gene assay. Rescue assays were carried out by upregulating c-fos in miR-34a-5p-overexpressing SK-RG cells. KSHV DNA copy numbers and relative virus gene expressions were detected. Xenograft tumor experiments and immunohistochemistry assays were further used to detect the effects of miR-34a-5p. Results miR-34a-5p was lower in SK-RG cells. Restoration of miR-34a-5p decreased cell proliferation and migration, leading to a G1 cell cycle arrest and down-regulation of CDK4/6, cyclin D1, MMP2, MMP9. KSHV copy number and expression of virus gene including latency-associated nuclear antigen (LANA), replication and transcription activator (RTA), open reading frame (K8.1), and KSHV G protein-coupled receptor (v-GPCR) were also reduced. Furthermore, c-fos is the target of miR-34a-5p, while enhanced c-fos weakened cellular behaviors of miR-34a-5p-overexpressing cells. Xenograft experiments and immunohistochemistry assays showed that miR-34a-5p inhibited tumor growth and virus gene expression. Conclusion Upregulated miR-34a-5p in KSHV-infected SH-SY5Y cells suppressed cell proliferation and migration through down-regulating c-fos. miR-34a-5p was a candidate molecular drug for KSHV-infected neuronal cells.
Wu et al. (2022) miR-34a-5p inhibits the malignant progression of KSHV-infected SH-SY5Y cells by targeting c-fos. PeerJ 10:e13233 https://doi.org/10.7717/peerj.13233
Genetic diversity and population structure of muscovy duck (Cairina moschata) from Nigeria
The domestic Muscovy duck (Cairina moschata) provide unique genetic resources patterned by both tropical environmental conditions and human activities, the evaluation of their genetic diversity and population structure will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the variation in mtDNA cytochrome b and nuclear DNA CYP2U1 sequences of 378 Nigerian Muscovy ducks (comprising of 287 de novo and 91 downloaded) plus 80 published sequences of Muscovy ducks from India. The results showed high haplotype diversity (0.800 ± 0.023) among Nigerian Muscovy duck populations with 91 distinct haplotypes for the nuclear DNA CYP2U1 gene but low (0.266 ± 0.033) for cytochrome b with 31 haplotypes. The median-joining networks of both markers grouped Nigerian Muscovy ducks into two; the first group consisting of only Nigerian Muscovy duck populations, and the second group Nigerian with Indian populations. Neutrality test results indicated that Nigerian populations experienced recent population expansion and/or genetic hitchhiking. A geographic signal was absent in line with previously studied poultry species in Nigeria. The most prominent haplotype dominated across all regions in Nigeria, which may be due to extensive genetic intermixing except for the Indian population (FST = 0.02550, P = 0.01075). This indicated low genetic differentiation between and within Nigerian Muscovy duck as revealed by the suitability of the nuclear DNA CYP2U1 gene.
Adeola et al. (2022) Genetic diversity and population structure of muscovy duck (Cairina moschata) from Nigeria. PeerJ 10:e13236 https://doi.org/10.7717/peerj.13236
Long forgotten: Eunice woodwardi Baird, 1869 (Annelida, Eunicidae) revisited, with an insight on internal anatomy
Eunice woodwardiBaird, 1869, originally described from the Ría de A Coruña (NW Iberian Peninsula), has been overlooked and never reported from the Atlantic coast of Spain after original description and the subsequent redescription of the holotype. In the present study, we revised comparatively the holotype, newly collected specimens of this species and specimens identified as Eunice vittata (Delle Chiaje, 1829) from western Mediterranean Sea. The validity of E. woodwardi is supported and previous descriptions are complemented after a throughout study of the external morphology by means of light compound microscopy and scanning electron microscopy, and that of the internal anatomy by histological sectioning and micro-computed tomography. The presence of eyes, nuchal organs, dorsal and ventral ciliary organs on parapodial cirri and paired nephridia in most segments is confirmed in E. woodwardi; the digestive tract is clearly regionalized and divided into pharynx, oesophagus, stomach, fore, mid- and hind intestine. The presence of E. woodwardi in the Ría de Ferrol is also reported, and we suggest that previous records of E. vittata in NW Iberian Peninsula should be reviewed. Eunice woodwardi is distinguished by a set of characters such as having non-articulated and non-constricted cephalic appendages, the maxillary formula, the range of branchial distribution, maximum number of branchial filaments, number of limbate and compound falciger chaetae per parapodium, the presence of an apical mucro in the guard of falciger chaetae blades and the number of teeth in pectinate chaetae. Epibiont Ciliophora on branchiae are also reported.
Barroso et al. (2022) Long forgotten: Eunice woodwardi Baird, 1869 (Annelida, Eunicidae) revisited, with an insight on internal anatomy. PeerJ 10:e13126 https://doi.org/10.7717/peerj.13126
Using a mechanistic framework to model the density of an aquatic parasite Ceratonova shasta
Ceratonova shasta is a myxozoan parasite endemic to the Pacific Northwest of North America that is linked to low survival rates of juvenile salmonids in some watersheds such as the Klamath River basin. The density of C. shasta actinospores in the water column is typically highest in the spring (March–June), and directly influences infection rates for outmigrating juvenile salmonids. Current management approaches require quantities of C. shasta density to assess disease risk and estimate survival of juvenile salmonids. Therefore, we developed a model to simulate the density of waterborne C. shasta actinospores using a mechanistic framework based on abiotic drivers and informed by empirical data. The model quantified factors that describe the key features of parasite abundance during the period of juvenile salmon outmigration, including the week of initial detection (onset), seasonal pattern of spore density, and peak density of C. shasta. Spore onset was simulated by a bio-physical degree-day model using the timing of adult salmon spawning and accumulation of thermal units for parasite development. Normalized spore density was simulated by a quadratic regression model based on a parabolic thermal response with river water temperature. Peak spore density was simulated based on retained explanatory variables in a generalized linear model that included the prevalence of infection in hatchery-origin Chinook juveniles the previous year and the occurrence of flushing flows (≥171 m3/s). The final model performed well, closely matched the initial detections (onset) of spores, and explained inter-annual variations for most water years. Our C. shasta model has direct applications as a management tool to assess the impact of proposed flow regimes on the parasite, and it can be used for projecting the effects of alternative water management scenarios on disease-induced mortality of juvenile salmonids such as with an altered water temperature regime or with dam removal.
Robinson et al. (2022) Using a mechanistic framework to model the density of an aquatic parasite Ceratonova shasta. PeerJ 10:e13183 https://doi.org/10.7717/peerj.13183
The potency of minerals to reduce oriental fruit fly infestation in chili fruits
Introductions In many areas, particularly in Asia, the oriental fruit fly Bactrocera dorsalis (Hendel) causes considerable fruit damage on various plants. The fruit fly causes significant economic losses every year due to reduced fruit quantity and quality as well as export restrictions. This study aimed to examine the potency of minerals in controlling the oriental fruit fly infestation in chili fruits. Methods Experiments were conducted under laboratory and semi-field conditions using randomized block design. Ten minerals (i.e. kaolin, talc, zinc oxide, bentonite, sulfur, dolomite, calcium oxide, calcium hydroxide, calcium carbonate, and zeolite) and an untreated control were tested under laboratory conditions. Twenty chili fruits at a green stage were soaked in each mineral suspension (2%, w/v), air-dried, and placed in a trial cage (23-L plastic container) containing 20 female oriental fruit flies. In a semi-field bioassay using a screen cage (100 cm × 70 cm × 120 cm), 20 female oriental fruit flies were exposed to a fruit-bearing chili plant sprayed with mineral suspension. Results Talc and calcium oxide significantly reduced the numbers of visiting fruit flies, oviposition holes, and eggs laid, as well as the percentage of infested chili fruits in a laboratory bioassay. Calcium hydroxide was substantially better than talc in controlling fruit fly infestation in a semi-field bioassay, although it was not significantly different from calcium oxide and calcium carbonate. Conclusion Overall, calcium oxide is a viable option for the long-term control of the oriental fruit fly on chili fruits. Calcium oxide could be utilized as the push component of a push-pull strategy to manage oriental fruit fly infestation in chili fruits because of its potential to inhibit the number of visiting fruit flies and oviposition.
Pangihutan et al. (2022) The potency of minerals to reduce oriental fruit fly infestation in chili fruits. PeerJ 10:e13198 https://doi.org/10.7717/peerj.13198
ELOVL2-AS1 inhibits migration of triple negative breast cancer
In this study, we identified a key enhancer RNA (eRNA) region in breast cancer (BRCA) by applying an integrated analysis method. Reported eRNA region and genes affected by them were selected as presumed target pairs. Kaplan–Meier (KM) survival and correlation analyses were performed to screen valuable eRNA region. Based on the KM value and its correlation with the paired target genes, we carefully selected ELOVL2-AS1 as a potential key eRNA region in BRCA. Subsequently, we analyzed the expression of ELOVL2-AS1 and ELOVL2 in four BRCA subtypes and in different BRCA cell lines. The expression of ELOVL2-AS1 and ELOVL2 in triple negative breast cancer (TNBC) was significantly lower than those in Luminal A. After that, we analyzed the function of genes that are positively correlated with ELOVL2-AS1. We found that the co-expression gene mainly related to cilia and cilia characteristics of TNBC is significantly weaker than that of Luminal A. Considering the stronger invasion and metastasis of TNBC (compared with Luminal A) and the close relationship between decreased cilia and metastasis, we overexpressed ELOVL2-AS1 in TNBC and observed its effect on cell migration. The results show that it can inhibit the migration of TNBC. Finally, we analyzed the assay for transposase-accessible chromatin sequencing data, chromatin interaction analysis with paired-end tag sequencing data, and chromatin immunoprecipitation sequencing data and identified the chromatin interaction between ELOVL2-AS1 and ELOVL2, suggesting a direct regulatory interaction.
Zhu et al. (2022) ELOVL2-AS1 inhibits migration of triple negative breast cancer. PeerJ 10:e13264 https://doi.org/10.7717/peerj.13264