Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia
Breeding practices adopted at different farms are aimed at maximizing the profitability of pig farming. In this work, we have analyzed the genetic diversity of Large White pigs in Russia. We compared genomes of historic and modern Large White Russian breeds using 271 pig samples. We have identified 120 candidate regions associated with the differentiation of modern and historic pigs and analyzed genomic differences between the modern farms. The identified genes were associated with height, fitness, conformation, reproductive performance, and meat quality.
Bakoev et al. (2021) Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia. PeerJ 9:e11595 https://doi.org/10.7717/peerj.11595
Repression of ZCT1, ZCT2 and ZCT3 affects expression of terpenoid indole alkaloid biosynthetic and regulatory genes
Terpenoid indole alkaloids (TIAs) include several valuable pharmaceuticals. As Catharanthus roseus remains the primary source of these TIA pharmaceuticals, several research groups have devoted substantial efforts to increase production of these compounds by C. roseus. Efforts to increase TIA production by overexpressing positive regulators of TIA biosynthetic genes have met with limited success. This limited success might be due to the fact that overexpression of several positive TIA regulators turns on expression of negative regulators of TIA biosynthetic genes. Consequently, a more effective approach for increasing expression of TIA biosynthetic genes might be to decrease expression of negative regulators of TIA biosynthetic genes. Towards this end, an RNAi construct was generated that expresses a hairpin RNA carrying nucleotide fragments from three negative transcriptional regulators of TIA genes, ZCT1, ZCT2 and ZCT3, under the control of a beta-estradiol inducible promoter. Transgenic C. roseus hairy root lines carrying this ZCT RNAi construct exhibit significant reductions in transcript levels of all three ZCT genes. Surprisingly, out of eight TIA biosynthetic genes analyzed, seven (CPR, LAMT, TDC, STR, 16OMT, D4H and DAT) exhibited decreased rather than increased transcript levels in response to reductions in ZCT transcript levels. The lone exception was T19H, which exhibited the expected negative correlation in transcript levels with transcript levels of all three ZCT genes. A possible explanation for the T19H expression pattern being the opposite of the expression patterns of the other TIA biosynthetic genes tested is that T19H shunts metabolites away from vindoline production whereas the products of the other genes tested shunt metabolites towards vindoline metabolism. Consequently, both increased expression of T19H and decreased expression of one or more of the other seven genes tested would be expected to have similar effects on flux through the TIA pathway. As T19H expression is lower in the ZCT RNAi hairy root lines than in the control hairy root line, the ZCTs could act directly to inhibit expression of T19H. In contrast, ZCT regulation of the other seven TIA biosynthetic genes tested is likely to occur indirectly, possibly by the ZCTs turning off expression of a negative transcriptional regulator of some TIA genes. In fact, transcript levels of a negative TIA transcriptional regulator, GBF1, exhibited a strong, and statistically significant, negative correlation with transcript levels of ZCT1, ZCT2 and ZCT3. Together, these findings suggest that the ZCTs repress expression of some TIA biosynthetic genes, but increase expression of other TIA biosynthetic genes, possibly by turning down expression of GBF1.
Li et al. (2021) Repression of ZCT1, ZCT2 and ZCT3 affects expression of terpenoid indole alkaloid biosynthetic and regulatory genes. PeerJ 9:e11624 https://doi.org/10.7717/peerj.11624
First record of entomopathogenic nematodes from Yucatán State, México and their infectivity capacity against Aedes aegypti
Background Biological control using entomopathogenic nematodes (EPN) has demonstrated good potential to contribute to the integral control of mosquito larvae, which as adults are vectors of diseases such as Dengue fever, Zika and Chikungunya. However, until now there are no records of the presence of EPN or their killing capacity in Yucatán state, southern México. The objectives of the current study were: (1) to report the entomopathogenic nematodes present in Yucatán soils and (2) to determine the killing capacity of the most frequent and abundant EPN against Aedes aegypti mosquito larvae and the microbial community developed by Ae. Aegypti exposed to this EPN. Methods The nematodes were collected by the insect trap technique using the great wax moth Galleria mellonella. Internal transcribed spacer (ITS), 28S gene of ribosomal DNA and phylogenetic analyses were performed to identify the EPN. For the bioassay, four concentrations of the most frequent and abundant EPN were tested: 1,260:1 infective juveniles (IJs) per mosquito larvae, 2,520 IJs:1, 3,780 IJs:1 and 5,040 IJs:1. High-throughput sequencing of the 16S rRNA gene was used to identify bacterial amplicon sequences in the mosquito larvae infected with EPN. Results Six isolates of Heterorhabditis were recovered from 144 soil samples. Heterorhabditis indica (four isolates) was the most frequent and abundant EPN, followed by Heterorhabditis n. sp. (two isolates). Both nematodes are reported for the first time for Yucatán state, Mexico. The concentration of 2,520 IJs:1 produced 80% of mosquito larvae mortality in 48 h. Representative members of Photorhabdus genus were numerically dominant (74%) in mosquito larvae infected by H. indica. It is most likely that these bacteria produce secondary toxic metabolites that enhance the mortality of these mosquito larvae.
Ávila-López et al. (2021) First record of entomopathogenic nematodes from Yucatán State, México and their infectivity capacity against Aedes aegypti. PeerJ 9:e11633 https://doi.org/10.7717/peerj.11633
Application of different building representation techniques in HEC-RAS 2-D for urban flood modeling using the Toce River experimental case
This paper presents the impact of the choice of building representation techniques and hydrodynamic models on urban flood simulations using HEC-RAS 2-D for the Toce River physical model. To this end, eight numerical models based on previous laboratory experiments were prepared to simulate unsteady urban flooding on each side of building units. Two simplified building layouts (aligned and staggered) were examined, where models were prepared for two different building representation techniques: Building Block (BB) and Building Resistance (BR). Water depth variation computations using the BR and BB techniques were compared to the laboratory measurements and previous studies in the literature. A statistical analysis was performed using both the Root Mean Square Error (RMSE) and the Pearson Product-Moment Correlation Coefficient (PPMCC) in order to evaluate the performance of the models. A sensitivity analysis showed that the proper mesh resolution and model parameter values were obtained. As far as the BR technique is concerned, it is well-suited for representing building units in numerical simulations using high Manning coefficients. Furthermore, this study confirms the importance of the BR technique, which should help researchers in using low-resolution Digital Elevation Models (DEMs) along with open-source programs. Moreover, the study aims to produce a deeper comprehension of numerical modeling and urban flooding.
Mustafa et al. (2021) Application of different building representation techniques in HEC-RAS 2-D for urban flood modeling using the Toce River experimental case. PeerJ 9:e11667 https://doi.org/10.7717/peerj.11667
Confidence intervals for the difference between the coefficients of variation of Weibull distributions for analyzing wind speed dispersion
Wind energy is an important renewable energy source for generating electricity that has the potential to replace fossil fuels. Herein, we propose confidence intervals for the difference between the coefficients of variation of Weibull distributions constructed using the concepts of the generalized confidence interval (GCI), Bayesian methods, the method of variance estimates recovery (MOVER) based on Hendricks and Robey’s confidence interval, a percentile bootstrap method, and a bootstrap method with standard errors. To analyze their performances, their coverage probabilities and expected lengths were evaluated via Monte Carlo simulation. The simulation results indicate that the coverage probabilities of GCI were greater than or sometimes close to the nominal confidence level. However, when the Weibull shape parameter was small, the Bayesian- highest posterior density interval was preferable. All of the proposed confidence intervals were applied to wind speed data measured at 90-meter wind energy potential stations at various regions in Thailand.
La-ongkaew et al. (2021) Confidence intervals for the difference between the coefficients of variation of Weibull distributions for analyzing wind speed dispersion. PeerJ 9:e11676 https://doi.org/10.7717/peerj.11676
CGRP overexpression does not alter depression-like behavior in mice
Background The calcitonin gene-related peptide (CGRP) is a neuropeptide that is released from capsaicin-sensitive nerves as a potent vasodilator involved in nociceptive transmission. While CGRP has been rigorously studied for its role in migraines owing to its vasodilation and inflammation activities, the effects of CGRP overexpression on depressive-like behaviors remain insufficiently understood. Methods In the present study, we performed a battery of behavioral tests, including the social interaction test, open field test, and sucrose preference test, to evaluate social defeat stress using male C57BL6J or CGRP overexpression in transgenic (Tg) mice (CGRP Tg). We performed mRNA and protein analyses on the brain-derived neurotrophic factor (BDNF), phosphorylated Akt, mTOR, and p70S6K in the hippocampi. Results CGRP Tg mice showed increased levels of Bdnf mRNAs, low locomotor activity, and no deficits in social interaction, which indicate that CGRP Tg mice exhibit stress resistance and not depression. However, the open field test significantly decreased after 15-day social defeat stress exposure. We also evaluated depressive-like behavior using the sucrose preference and social interaction tests. Our data indicate that defeated CGRP Tg mice exhibited a depressive-like phenotype, which was inferred from increased social avoidance and reduced sucrose preference compared with non-defeated controls. Although stress exposure did not change the BDNF levels in CGRP Tg mice, it significantly decreased the expression levels of p-Akt, p-mTOR and p-p70S6K in the mice hippocampi. We conclude that CGRP-overexpressing Tg mice have normal sensitivity to stress and down-regulated hippocampal Akt/mTOR/p70S6K pathways.
Hashikawa-Hobara et al. (2021) CGRP overexpression does not alter depression-like behavior in mice. PeerJ 9:e11720 https://doi.org/10.7717/peerj.11720
Cytological analysis of tracheal wash and bronchoalveolar lavage fluid in health and respiratory disease in dromedary camels
Background Tracheal wash (TW) and bronchoalveolar lavage (BAL) have proven to be useful tools for the identification of disease-associated changes in the respiratory tract in human and different animal species. In the dromedary camel, little is known about cytological analysis of TW and BAL in health and disease. The aim of the present study was to evaluate the cytological composition of TW and BAL in health and respiratory disease in dromedary camels. Methods TW and BAL samples were collected from dromedary camels and cytological analysis was performed by microscopic examination of prepared smears. Camels with clinical respiratory disease (n = 18) were compared with apparently healthy (control) camels (n = 9). Results In the apparently healthy camels, differential cytological analysis of TW samples identified macrophages and neutrophils as the main cell populations with lesser proportions of lymphocytes and epithelial cells and very rare abundance of eosinophils and mast cells. In the TW of camels with respiratory disease, neutrophils were the most abundant cells followed by macrophages and lymphocytes. In the BAL of healthy camels, macrophages represented the main cell type followed by lymphocytes and neutrophils. In respiratory-diseased camels, BAL samples contained higher percentages of neutrophils with reduced percentages of macrophages and lymphocytes in comparison to camels from the control group. Collectively, the results of the current study revealed higher abundance of neutrophils in the TW and BAL from dromedary camels than many other veterinary species. The cytological patterns of TW and BAL from camels with respiratory diseases were characterized by increased proportion of neutrophils and decreased proportion of macrophages in comparison to healthy camels. The proportion of lymphocytes was also decreased in TW samples from diseased camels.
Shawaf et al. (2021) Cytological analysis of tracheal wash and bronchoalveolar lavage fluid in health and respiratory disease in dromedary camels. PeerJ 9:e11723 https://doi.org/10.7717/peerj.11723
Metabolism and transcriptome profiling provides insight into the genes and transcription factors involved in monoterpene biosynthesis of borneol chemotype of Cinnamomum camphora induced by mechanical damage
Background The borneol chemotype of Cinnamomum camphora (BCC), a monoterpene-rich woody plant species, is the sole source prescribed by the Chinese Pharmacopoeia for the production of natural D-borneol, a major monoterpene in BCC used for millennia as a topical analgesic in China. Nevertheless, the possible gene-regulatory roles of transcription factors (TFs) in BCC’s monoterpenoid biosynthesis remained unknown. Here, a joint analysis of the transcriptome and terpenoid metabolome of BCC induced by mechanical damage (MD) was used to comprehensively explore the interaction between TFs and terpene synthase (TPS) unigenes that might participate in monoterpene biosynthesis in BCC. Results Gas chromatography–mass spectrometry analysis detected 14 monoterpenes and seven sesquiterpenes. All but two monoterpenes underwent a significantly increased accumulation after the MD treatment. RNA sequencing data revealed that 10 TPS, 82 MYB, 70 AP2/ERF, 38 BHLH, 31 WRKY, and 29 bZIP unigenes responded to the MD treatment. A correlation analysis revealed that three monoterpene synthase genes (CcTPS1, CcTPS3, CcTPS4) highly correlated with multiple monoterpenes, namely D-borneol, camphor, and bornyl acetate, which could be responsible for monoterpenoid biosynthesis in BCC. Furthermore, five WRKY, 15 MYB, 10 ERF/AP2, five bZIP, and two BHLH genes had strong, positive correlations with CcTPS1 or CcTPS4, judging by their high coefficient values (R2 > 0.8). The bioinformatics results were verified by quantitative real-time PCR. Conclusion This study provides insight into the genes involved in the biosynthesis and regulation of monoterpene in BCC and thus provides a pool of candidate genes for future mechanistic analyses of how monoterpenes accumulate in BCC.
Yang et al. (2021) Metabolism and transcriptome profiling provides insight into the genes and transcription factors involved in monoterpene biosynthesis of borneol chemotype of Cinnamomum camphora induced by mechanical damage. PeerJ 9:e11465 https://doi.org/10.7717/peerj.11465
Dumpster diving for diatom plastid 16S rRNA genes
High throughput sequencing is improving the efficiency of monitoring diatoms, which inhabit and support aquatic ecosystems across the globe. In this study, we explored the potential of a standard V4 515F-806RB primer pair in recovering diatom plastid 16S rRNA sequences. We used PhytoREF to classify the 16S reads from our freshwater biofilm field sampling from three stream segments across two streams in south-eastern Australia and retrieved diatom community data from other, publicly deposited, Australian 16S amplicon datasets. When these diatom operational taxonomic units (OTUs) were traced using the default RDPII and NCBI databases, 68% were characterized as uncultured cyanobacteria. We analysed the 16S rRNA sequences from 72 stream biofilm samples, separated the chloroplast OTUs, and classified them using the PhytoREF database. After filtering the reads attributed to Bacillariophyta (relative abundance >1%), 71 diatom OTUs comprising more than 90% of the diatom reads in each stream biofilm sample were identified. Beta-diversity analyses demonstrated significantly different diatom assemblages and discrimination among river segments. To further test the approach, the diatom OTUs from our biofilm sampling were used as reference sequences to identify diatom reads from other Australian 16S rRNA datasets in the NCBI-SRA database. Across the three selected public datasets, 67 of our 71 diatom OTUs were detected in other Australian ecosystems. Our results show that diatom plastid 16S rRNA genes are readily amplified with existing 515F-806RB primer sets. Therefore, the volume of existing 16S rRNA amplicon datasets initially generated for microbial community profiling can also be used to detect, characterize, and map diatom distribution to inform phylogeny and ecological health assessments, and can be extended into a range of ecological and industrial applications. To our knowledge, this study represents the first attempt to classify freshwater samples using this approach and the first application of PhytoREF in Australia.
Bonfantine et al. (2021) Dumpster diving for diatom plastid 16S rRNA genes. PeerJ 9:e11576 https://doi.org/10.7717/peerj.11576
Analysis of ceRNA network of differentially expressed genes in FaDu cell line and a cisplatin-resistant line derived from it
Background Hypopharyngeal cancer accounts for 2% in head and neck cancers and has a poor prognosis. Cisplatin is a widely used chemotherapeutic drug in kinds of carcinomas, concluding hypopharyngeal cancer. However, the resistance of cisplatin appeared in recent years. Cisplatin-resistance has been partly explored before, but rarely in hypopharyngeal cancer. Methods We cultured the hypopharyngeal cancer cell (FaDu) and induced its cisplatin-resistant cell (FaDu/DDP4). Then we tested the differentially expressed genes (DEGs) between FaDu and FaDu/DDP4. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted on the DEGs, and we drew the ceRNA networks of DEGs. Finally, we chose eight miRNAs and six mRNAs for qRT-PCR to verify our microarray. Results We induced cisplatin-resistant FaDu/DDP4 and proved its chemoresistance. The resistance index (RI) of FaDu/DDP4 was 2.828. DEGs contain 2,388 lncRNAs, 1,932 circRNAs, 745 mRNAs and 202 miRNAs. These 745 mRNAs were classified into three domains and 47 secondary GO terms. In KEGG pathway enrichment, the “TNF signaling pathway”, “IL-17 signaling pathway” and “JAK-STAT signaling pathway” were potentially significant signaling pathways. Then, 52 lncRNAs, 148 circRNAs, 155 mRNAs and 18 miRNAs were selected to draw the network. We noticed several potential targets (as miR-197-5p, miR-6808-5p, APOE, MMP1, S100A9 and CYP24A1). At last, the eight miRNAs and six mRNAs that are critical RNAs in ceRNA network were verified by qRT-PCR. Conclusion The microarray helped to find DEGs in cisplatin-resistant hypopharyngeal cancer. TNF, IL-17 and JAK-STAT signaling pathways might be more significant for cisplatin-resistance. MiR-197-5p, miR-6808-5p, APOE, MMP1, S100A9 and CYP24A1 might be potential genes inducing resistance.
Zhang et al. (2021) Analysis of ceRNA network of differentially expressed genes in FaDu cell line and a cisplatin-resistant line derived from it. PeerJ 9:e11645 https://doi.org/10.7717/peerj.11645