Comparative transcriptome analysis of roots, stems, and leaves of Pueraria lobata (Willd.) Ohwi: identification of genes involved in isoflavonoid biosynthesis
Background Pueraria lobata (Willd.) Ohwi is a valuable herb used in traditional Chinese medicine. Isoflavonoids are the major bioactive compounds in P. lobata, namely puerarin, daidzin, glycitin, genistin, daidzein, and glycitein, which have pharmacological properties of anti-cardiovascular, anti-hypertension, anti-inflammatory, and anti-arrhythmic. Methods To characterize the corresponding genes of the compounds in the isoflavonoid pathway, RNA sequencing (RNA-Seq) analyses of roots, stems, and leaves of P. lobata were carried out on the BGISEQ-500 sequencing platform. Results We identified 140,905 unigenes in total, of which 109,687 were annotated in public databases, after assembling the transcripts from all three tissues. Multiple genes encoding key enzymes, such as IF7GT and transcription factors, associated with isoflavonoid biosynthesis were identified and then further analyzed. Quantitative real-time PCR (qRT-PCR) results of some genes encoding key enzymes were consistent with our RNA-Seq analysis. Differentially expressed genes (DEGs) were determined by analyzing the expression profiles of roots compared with other tissues (leaves and stems). This analysis revealed numerous DEGs that were either uniquely expressed or up-regulated in the roots. Finally, quantitative analyses of isoflavonoid metabolites occurring in the three P. lobata tissue types were done via high-performance liquid-chromatography and tandem mass spectrometry methodology (HPLC-MS/MS). Our comprehensive transcriptome investigation substantially expands the genomic resources of P. lobata and provides valuable knowledge on both gene expression regulation and promising candidate genes that are involved in plant isoflavonoid pathways.
Wang et al. (2021) Comparative transcriptome analysis of roots, stems, and leaves of Pueraria lobata (Willd.) Ohwi: identification of genes involved in isoflavonoid biosynthesis. PeerJ 9:e10885 https://doi.org/10.7717/peerj.10885
Higher bee abundance, but not pest abundance, in landscapes with more agriculture on a late-flowering legume crop in tropical smallholder farms
Background Landscape composition is known to affect both beneficial insect and pest communities on crop fields. Landscape composition therefore can impact ecosystem (dis)services provided by insects to crops. Though landscape effects on ecosystem service providers have been studied in large-scale agriculture in temperate regions, there is a lack of representation of tropical smallholder agriculture within this field of study, especially in sub-Sahara Africa. Legume crops can provide important food security and soil improvement benefits to vulnerable agriculturalists. However, legumes are dependent on pollinating insects, particularly bees (Hymenoptera: Apiformes) for production and are vulnerable to pests. We selected 10 pigeon pea (Fabaceae: Cajunus cajan (L.)) fields in Malawi with varying proportions of semi-natural habitat and agricultural area within a 1 km radius to study: (1) how the proportion of semi-natural habitat and agricultural area affects the abundance and richness of bees and abundance of florivorous blister beetles (Coleoptera: Melloidae), (2) if the proportion of flowers damaged and fruit set difference between open and bagged flowers are correlated with the proportion of semi-natural habitat or agricultural area and (3) if pigeon pea fruit set difference between open and bagged flowers in these landscapes was constrained by pest damage or improved by bee visitation. Methods We performed three, ten-minute, 15 m, transects per field to assess blister beetle abundance and bee abundance and richness. Bees were captured and identified to (morpho)species. We assessed the proportion of flowers damaged by beetles during the flowering period. We performed a pollinator and pest exclusion experiment on 15 plants per field to assess whether fruit set was pollinator limited or constrained by pests. Results In our study, bee abundance was higher in areas with proportionally more agricultural area surrounding the fields. This effect was mostly driven by an increase in honeybees. Bee richness and beetle abundances were not affected by landscape characteristics, nor was flower damage or fruit set difference between bagged and open flowers. We did not observe a positive effect of bee density or richness, nor a negative effect of florivory, on fruit set difference. Discussion In our study area, pigeon pea flowers relatively late—well into the dry season. This could explain why we observe higher densities of bees in areas dominated by agriculture rather than in areas with more semi-natural habitat where resources for bees during this time of the year are scarce. Therefore, late flowering legumes may be an important food resource for bees during a period of scarcity in the seasonal tropics. The differences in patterns between our study and those conducted in temperate regions highlight the need for landscape-scale studies in areas outside the temperate region.
Vogel et al. (2021) Higher bee abundance, but not pest abundance, in landscapes with more agriculture on a late-flowering legume crop in tropical smallholder farms. PeerJ 9:e10732 https://doi.org/10.7717/peerj.10732
Retinoic Acid Induced Protein 14 (Rai14) is dispensable for mouse spermatogenesis
Background Retinoic Acid Induced Protein 14 (Rai14) is an evolutionarily conserved gene that is highly expressed in the testis. Previous experiments have reported that small interfering RNA (siRNA)-mediated gene knockdown (KD) of Rai14 in rat testis disrupted spermatid polarity and transport. Of note, a gene knockout (KO) model is considered the “gold standard” for in vivo assessment of crucial gene functions. Herein, we used CRISPR/Cas9-based gene editing to investigate the in vivo role of Rai14 in mouse testis. Methods Sperm concentration and motility were assayed using a computer-assisted sperm analysis (CASA) system. Histological and immunofluorescence (IF) staining and transmission electron microscopy (TEM) were used to visualize the effects of Rai14 KO in the testes and epididymides. Terminal deoxynucleotidyl transferase-dUTP nick-end labeling (TUNEL) was used to determine apoptotic cells. Gene transcript levels were calculated by real-time quantitative PCR. Results Rai14 KO in mice depicted normal fertility and complete spermatogenesis, which is in sharp contrast with the results reported previously in a Rai14 KD rat model. Sperm parameters and cellular apoptosis did not appear to differ between wild-type (WT) and KO group. Mechanistically, in contrast to the well-known role of Rai14 in modulating the dynamics of F-actin at the ectoplasmic specialization (ES) junction in the testis, morphological changes of ES junction exhibited no differences between Rai14 KO and WT testes. Moreover, the F-actin surrounded at the ES junction was also comparable between the two groups. Conclusion In summary, our study demonstrates that Rai14 is dispensable for mouse spermatogenesis and fertility. Although the results of this study were negative, the phenotypic information obtained herein provide an enhanced understanding of the role of Rai14 in the testis, and researchers may refer to these results to avoid conducting redundant experiments.
Wu et al. (2021) Retinoic Acid Induced Protein 14 (Rai14) is dispensable for mouse spermatogenesis. PeerJ 9:e10847 https://doi.org/10.7717/peerj.10847
Regucalcin expression profiles in veal calf testis: validation of histological and molecular tests to detect sex steroids illicit administration
Background Sex steroids administration in meat producing animals is forbidden within the EU to preserve consumers’ safety, but continuous monitoring to identify resurgence of their misuse is needed. Among biomarkers related to sex steroids abuse in veal calves the regucalcin (RGN) mRNA perturbations in testis have been described in RNAlater samples. To setup novel diagnostic method, to update current tests available in National Residue Control Plans (NRCPs) and in legal dispute when illicit practices on farm animals are suspected, the reliability of RGN profiling was assessed by histological and molecular techniques. Methods Formalin fixed paraffin embedded (FFPE) testis samples, chosen being the most effective preservation strategy adopted by histological NRCPs and allowing easier retrospective analysis if required by legal disputes, were analyzed from veal calves treated with nandrolone, 17β-estradiol and a cocktail of the two hormones. RGN levels were determined by quantitative Real Time PCR and Immunohistochemistry assays. Test performances were assessed and compared by multiple ROC curves. Results Both tests resulted sensitive and specific, allowing to enrich, in future field investigation, novel integrated diagnostic protocols needed to unveil sex steroid abuse. Discussion Developed RT-qPCR and IHC methods confirmed RGN as a useful and robust biomarker to detect illegal administration of sex steroid hormones in veal calves. The developed methods, successfully applied to ten years old FFPE blocks, could allow both retrospective analysis, when supplementary investigations are requested by authorities, and future implementation of current NRCPs.
Benedetto et al. (2021) Regucalcin expression profiles in veal calf testis: validation of histological and molecular tests to detect sex steroids illicit administration. PeerJ 9:e10894 https://doi.org/10.7717/peerj.10894
Metasychis varicollaris sp. nov. and report of Metasychis gotoi (Maldanidae, Annelida) from the China Seas
Polychaete species are widely distributed throughout Indo-Pacific and European waters. We collected Metasychis specimens from the China Seas to report on Metasychis varicollaris sp. n. and Metasychis gotoi (Izuka, 1902) in greater detail. Geographic analysis of the potential distribution areas of M. gotoi indicates that it may be found in most coastal areas of China. The newly discovered species, M. varicollaris and M. gotoi, have an overlapping distribution in the northern South China Sea. Metasychis varicollaris sp. n. is characterized by a crenulated cephalic rim, complete collar on chaetiger 1, a packet-shaped anal funnel, and a spirally-fringed notochaetae with spiral pectinate bands imbricated over the main shaft. Our study provides a taxonomic key to all species of Metasychis.
Wang et al. (2021) Metasychis varicollaris sp. nov. and report of Metasychis gotoi (Maldanidae, Annelida) from the China Seas. PeerJ 9:e10608 https://doi.org/10.7717/peerj.10608
QTL mapping of agronomic traits in wheat using the UK Avalon × Cadenza reference mapping population grown in Kazakhstan
Background The success of wheat production is largely dependent on local breeding projects that focus on the development of high-yielding cultivars with the use of novel molecular tools. One strategy for improving wheat productivity involves the deployment of diverse germplasms with a high potential yield. An important factor for achieving success involves the dissection of quantitative trait loci (QTLs) for complex agronomic traits, such as grain yield components, in targeted environments for wheat growth. Methods In this study, we tested the United Kingdom (UK) spring set of the doubled haploid (DH) reference population derived from the cross between two British cultivars, Avalon (winter wheat) and Cadenza (spring wheat), in the Northern, Central, and Southern regions (Karabalyk, Karaganda, Kyzylorda) of Kazakhstan over three years (2013–2015). The DH population has previously been genotyped by UK scientists using 3647 polymorphic DNA markers. The list of tested traits includes the heading time, seed maturation time, plant height, spike length, productive tillering, number of kernels per spike, number of kernels per meter, thousand kernel weight, and yield per square meter. Windows QTL Cartographer was applied for QTL mapping using the composite interval mapping method. Results In total, 83 out of 232 QTLs were identified as stable QTLs from at least two environments. A literature survey suggests that 40 QTLs had previously been reported elsewhere, indicating that this study identified 43 QTLs that are presumably novel marker-trait associations (MTA) for these environments. Hence, the phenotyping of the DH population in new environments led to the discovery of novel MTAs. The identified SNP markers associated with agronomic traits in the DH population could be successfully used in local Kazakh breeding projects for the improvement of wheat productivity.
Amalova et al. (2021) QTL mapping of agronomic traits in wheat using the UK Avalon × Cadenza reference mapping population grown in Kazakhstan. PeerJ 9:e10733 https://doi.org/10.7717/peerj.10733
Effects of training frequency on muscular strength for trained men under volume matched conditions
Background In resistance training, the role of training frequency to increase maximal strength is often debated. However, the limited data available does not allow for clear training frequency “optimization” recommendations. The purpose of this study was to investigate the effects of training frequency on maximal muscular strength and rate of perceived exertion (RPE). The total weekly training volume was equally distributed between two and four sessions per muscle group. Methods Twenty-one experienced resistance-trained male subjects (height: 1.85 ± 0.06 m, body mass: 85.3 ± 12.3 kg, age: 27.6 ± 7.6 years) were tested prior to and after an 8-week training period in one-repetition maximum (1RM) barbell back squat and bench press. Subjects were randomly assigned to a SPLIT group (n = 10), in which there were two training sessions of squats and lower-body exercises and two training sessions of bench press and upper-body exercises, or a FULLBODY group (n = 11), in which four sessions with squats, bench press and supplementary exercises were conducted every session. In each session, the subjects rated their RPE after barbell back squat, bench press, and the full session. Results Both groups significantly increased 1RM strength in barbell back squat (SPLIT group: +13.25 kg; FULLBODY group: +14.31 kg) and bench press (SPLIT group: +7.75 kg; FULLBODY group: +8.86 kg) but training frequency did not affect this increase for squat (p = 0.640) or bench press (p = 0.431). Both groups showed a significant effect for time on RPE on all three measurements. The analyses showed only an interaction effect between groups on time for the RPE after the squat exercise (p = 0.002). Conclusion We conclude that there are no additional benefits of increasing the training frequency from two to four sessions under volume-equated conditions, but it could be favorable to spread the total training volume into several training bouts through the week to avoid potential increases in RPE, especially after the squat exercise.
Johnsen et al. (2021) Effects of training frequency on muscular strength for trained men under volume matched conditions. PeerJ 9:e10781 https://doi.org/10.7717/peerj.10781
Estimation of parameters for a humidity-dependent compartmental model of the COVID-19 outbreak
Building an effective and highly usable epidemiology model presents two main challenges: finding the appropriate, realistic enough model that takes into account complex biological, social and environmental parameters and efficiently estimating the parameter values with which the model can accurately match the available outbreak data, provide useful projections. The reproduction number of the novel coronavirus (SARS-CoV-2) has been found to vary over time, potentially being influenced by a multitude of factors such as varying control strategies, changes in public awareness and reaction or, as a recent study suggests, sensitivity to temperature or humidity changes. To take into consideration these constantly evolving factors, the paper introduces a time dynamic, humidity-dependent SEIR-type extended epidemiological model with range-defined parameters. Using primarily the historical data of the outbreak from Northern and Southern Italy and with the help of stochastic global optimization algorithms, we are able to determine a model parameter estimation that provides a high-quality fit to the data. The time-dependent contact rate showed a quick drop to a value slightly below 2. Applying the model for the COVID-19 outbreak in the northern region of Italy, we obtained parameters that suggest a slower shrinkage of the contact rate to a value slightly above 4. These findings indicate that model fitting and validation, even on a limited amount of available data, can provide useful insights and projections, uncover aspects that upon improvement might help mitigate the disease spreading.
Farkas et al. (2021) Estimation of parameters for a humidity-dependent compartmental model of the COVID-19 outbreak. PeerJ 9:e10790 https://doi.org/10.7717/peerj.10790
Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula
Rendzic Leptosols are intrazonal soils formed on limestone bedrock. The specialty of these soils is that parent rock material is more influential in shaping soil characteristics than zonal factors such as climate, especially during soil formation. Unlike fast evolving Podzols due to their leaching regime, Leptosols do not undergo rapid development due to the nature of the limestone. Little is known how microbiome reflects this process, so we assessed microbiome composition of Rendzic Leptosols of different ages, arising from disruption and subsequent reclamation. The mountains and foothills that cover much of the Crimean Peninsula are ideal for this type of study, as the soils were formed on limestone and have been subjected to anthropogenic impacts through much of human history. Microbiomes of four soil sites forming a chronosequence, including different soil horizons, were studied using sequencing of 16S rRNA gene libraries and quantitative PCR. Dominant phyla for all soil sites were Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Thaumarchaeota, Planctomycetes, Verrucomicrobia and Firmicutes. Alpha diversity was similar across sites and tended to be higher in topsoil. Beta diversity showed that microbiomes diverged according to the soil site and the soil horizon. The oldest and the youngest soils had the most similar microbiomes, which could have been caused by their geographic proximity. Oligotrophic bacteria from Chitinophagaceae, Blastocatellaceae and Rubrobacteriaceae dominated the microbiome of these soils. The microbiome of 700-year old soil was the most diverse. This soil was from the only study location with topsoil formed by plant litter, which provided additional nutrients and could have been the driving force of this differentiation. Consistent with this assumption, this soil was abundant in copiotrophic bacteria from Proteobacteria and Actinobacteria phyla. The microbiome of 50-year old Leptosol was more similar to the microbiome of benchmark soil than the microbiome of 700-year old soil, especially by weighted metrics. CCA analysis, in combination with PERMANOVA, linked differences in microbiomes to the joint change of all soil chemical parameters between soil horizons. Local factors, such as parent material and plant litter, more strongly influenced the microbiome composition in Rendzic Leptosols than soil age.
Kimeklis et al. (2021) Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula. PeerJ 9:e10871 https://doi.org/10.7717/peerj.10871
Pseudocnidae of ribbon worms (Nemertea): ultrastructure, maturation, and functional morphology
The fine structure of mature pseudocnidae of 32 species of nemerteans, representatives of 20 genera, six families, and two classes was investigated with scanning and transmission electron microscopy. Pseudocnidae are composed of four layers (cortex, medulla, precore layer, and core) in most species investigated, but the degree of development and position of each layer can vary between different species. The secretion products comprising immature pseudocnidae segregate into separate layers: a thin envelope, which subsequently separates into the cortex and medulla and an extensive internal layer. We distinguish two pseudocnida types: type I is characterized by a two-layered core and type II by a three-layered core. Type I pseudocnidae are present in archinemertean species, Carinoma mutabilis, and in all pilidiophoran species, except Heteronemertea sp. 5DS; type II pseudocnidae occur in all studied species of Tubulanidae and the basal Heteronemertea sp. 5DS. Based on the structure of the discharged pseudocnidae observed in eleven species of palaeonemerteans and in eight species of pilidiophorans, we distinguish three different mechanisms (1–3) of core extrusion/discharge with the following characteristics and distribution: (1) the outer core layer is everted simultaneously with the tube-like layer and occurs in type I pseudocnidae of most species; (2) the extruded core is formed by both eversion of the outer core layer and medullar layer, and occurs in type I pseudocnidae of Micrura cf. bella; (3) the eversion of the outer core layer begins together with the core rod and core rod lamina and occurs in type II pseudocnidae. Morpho-functional comparison with other extrusomes (cnidae, sagittocysts, rhabdtites, and paracnids) confirm that pseudocnidae are homologous structures that are unique to nemerteans.
Magarlamov et al. (2021) Pseudocnidae of ribbon worms (Nemertea): ultrastructure, maturation, and functional morphology. PeerJ 9:e10912 https://doi.org/10.7717/peerj.10912