DEVOUR: Deleterious Variants on Uncovered Regions in Whole-Exome Sequencing
The discovery of low-coverage (i.e. uncovered) regions containing clinically significant variants, especially when they are related to the patient’s clinical phenotype, is critical for whole-exome sequencing (WES) based clinical diagnosis. Therefore, it is essential to develop tools to identify the existence of clinically important variants in low-coverage regions. Here, we introduce a desktop application, namely DEVOUR (DEleterious Variants On Uncovered Regions), that analyzes read alignments for WES experiments, identifies genomic regions with no or low-coverage (read depth < 5) and then annotates known variants in the low-coverage regions using clinical variant annotation databases. As a proof of concept, DEVOUR was used to analyze a total of 28 samples from a publicly available Hirschsprung disease-related WES project (NCBI Bioproject: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB19327), revealing the potential existence of 98 disease-associated variants in low-coverage regions. DEVOUR is available from https://github.com/projectDevour/DEVOUR under the MIT license.
Türk et al. (2023) DEVOUR: Deleterious Variants on Uncovered Regions in Whole-Exome Sequencing. PeerJ 11:e16026 https://doi.org/10.7717/peerj.16026
Simulation of hearing loss can induce pitch shifts for complex tones
Background Most studies on pitch shift provoked by hearing loss have been conducted using pure tones. However, many sounds encountered in everyday life are harmonic complex tones. In the present study, psychoacoustic experiments using complex tones were performed on healthy participants, and the possible mechanisms that cause pitch shift due to hearing loss are discussed. Methods Two experiments were performed in this study. In experiment 1, two tones were presented, and the participants were asked to select the tone that was higher in pitch. Partials with frequencies less than 250, 500, 750, or 1,000 Hz were eliminated from the harmonic complex tones and used as test tones to simulate low-tone hearing loss. Each tone pair was constructed such that the tone with a lower fundamental frequency (F0) was higher in terms of the frequency of the lowest partial. Furthermore, partials whose frequencies were greater than 1,300 or 1,600 Hz were also eliminated from these test tones to simulate high-tone hearing loss or modified sounds that patients may hear in everyday life. When a tone with a lower F0 was perceived as higher in pitch, it was considered a pitch shift from the expected tone. In experiment 2, tonal sequences were constructed to create a passage of the song “Lightly Row.” Similar to experiment 1, partials of harmonic complex tones were eliminated from the tones. After listening to these tonal sequences, the participants were asked if the sequences sounded correct based on the melody or off-key. Results The results showed that pitch shifts and the melody sound off-key when lower partials are eliminated from complex tones, especially when a greater number of high-frequency components are eliminated. Conclusion Considering that these experiments were performed on healthy participants, the results suggest that the pitch shifts from the expected tone when patients with hearing loss hear certain complex tones, regardless of the underlying etiology of the hearing loss.
Ichimiya et al. (2023) Simulation of hearing loss can induce pitch shifts for complex tones. PeerJ 11:e16053 https://doi.org/10.7717/peerj.16053
Correlation analysis of lipid accumulation index, triglyceride-glucose index and H-type hypertension and coronary artery disease
Objective The current research was designed to explore the relationship between the lipid accumulation index (LAP), coronary artery disease (CAD), and the triglyceride-glucose (TyG) index in patient with H-type hypertension. Methods From June 2021 to January 2022, our hospital’s information management system collected data on 186 patients with essential hypertension. The participants were categorized into two groups (H-type hypertension (n = 113) and non-H-type hypertension (n = 73)) based on their homocysteine levels. Both groups’ general condition, lipid accumulation index, triglyceride-glucose index, and Gensini score were compared to determine the factors influencing the severity of CAD in H-type hypertension patients. Results There were statistically significant differences (P < 0.05) in homocysteine (Hcy, GLP-1 and SAA) level, LAP, and TyG indexes, but not in body mass index (BMI), smoking, sex, age, total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), fasting plasma glucose (FPG), diastolic blood pressure, and systolic blood pressure. Additionally, there were substantial variations between the two groups regarding the number of lesion branches, degree of stenosis, and Gensini score (P > 0.05). patient with grade III to IV lesions had substantially higher LAP and TyG indices than those with stage I to II (P < 0.05). TyG (OR = 2.687) and TyG-LAP (OR = 4.512) were the factors determining the incidence of coronary artery disease in H-type hypertension, according to multivariate logistic regression analysis. The lesion number, stenosis degree, and Gensini score (P < 0.05) varied among both groups. LAP and TyG indexes were substantially greater in patients with double and triple vessel lesions than in those without lesions or with single vessel lesions (P < 0.05); similarly, these two indexes were considerably higher in individuals with grade III to IV lesions than in patients with grade I to II lesions (P < 0.05). As per the Pearson correlation analysis, the LAP, TyG indices and SAAlevel were adversely connected to the Gensini score (r = 0.254, 0.262, 0.299, P < 0.05), the GLP-1 level was negatively correlated to the Gensini score (r = −0.291, P < 0.05). TyG (OR = 2.687) and TyG-LAP (OR = 4.512) were the factors determining the frequency of coronary artery disease in H-type hypertension, according to multivariate logistic regression analysis. Conclusion In conclusion, the LAP and TyG indexes were observed to be closely related to the degree of CAD in H-type individuals with hypertension, which can better understand the pathogenesis of coronary artery disease in patients with H-type hypertension and is of great significance for guiding clinical doctors to carry out personalized treatment and management.
Yuan et al. (2023) Correlation analysis of lipid accumulation index, triglyceride-glucose index and H-type hypertension and coronary artery disease. PeerJ 11:e16069 https://doi.org/10.7717/peerj.16069
Mycorrhizal inoculation enhanced tillering in field grown wheat, nutritional enrichment and soil properties
To meet food security, commercial fertilizers are available to boost wheat yield, but there are serious ill effects associated with these fertilizers. Amongst various organic alternatives, inoculating crop fields with mycorrhizal species is the most promising option. Although, mycorrhizae are known to enhance wheat yield, but how the mycorrhizae influence different yield and quality parameters of wheat, is not clear. Therefore, this study was undertaken to investigate the influence of indigenous mycorrhizal species on the growth of wheat, its nutritional status and soil properties, in repeated set of field experiments. In total 11 species of mycorrhizae were isolated from the experimental sites with Claroideoglomus, being the most dominant one. Five different treatments were employed during the present study, keeping plot size for each replicate as 6 × 2 m. Introduction of consortia of mycorrhizae displayed a significant increase in number of tillers/plant (49.5%), dry biomass (17.4%), grain yield (21.2%) and hay weight (16.7%). However, there was non-significant effect of mycorrhizal inoculation on 1,000 grains weight. Moreover, protein contents were increased to 24.2%. Zinc, iron, phosphorus and potassium concentrations were also increased to 24%, 21%, 30.9% and 14.8%, respectively, in wheat grains. Enhancement effects were also noted on soil fertility such as soil organic carbon % age, available phosphorus and potassium were increased up to 64.7%, 35.8% and 23.9%, respectively. Herein, we concluded that mycorrhizal introduction in wheat fields significantly increased tillering in wheat and this increased tillering resulted in overall increase in wheat biomass/yield. Mycorrhizae also enhanced nutritional attributes of wheat grains as well as soil fertility. The use of mycorrhizae will help to reduce our dependance on synthetic fertilizers in sustainable agriculture.
Akbar et al. (2023) Mycorrhizal inoculation enhanced tillering in field grown wheat, nutritional enrichment and soil properties. PeerJ 11:e15686 https://doi.org/10.7717/peerj.15686
Maintenance of xylem hydraulic function during winter in the woody bamboo Phyllostachys propinqua McClure
Background Frost is a common environmental stress for temperate plants. Xylem embolism occurs in many overwintering plants due to freeze-thaw cycles, so coping with freeze-thaw-induced embolisms is essential for the survival of temperate plants. Methods This study was conducted on Phyllostachys propinqua McClure, a woody bamboo species that was grown under natural frost conditions to explore its responses to winter embolisms. From autumn to the following spring, the following measurements were recorded: predawn branch and leaf embolism, branch and leaf relative water content (RWC), root pressure and soil temperature, xylem sap osmotic potential, branch and leaf electrolyte leakage (EL), branch nonstructural carbohydrate (NSC) content and leaf net photosynthetic rate. Results P. propinqua had a mean vessel diameter of 68.95 ±1.27 µm but did not suffer severe winter embolism, peaking around 60% in winter (January), with a distinct reduction in March when root pressure returned. Leaves had a more severe winter embolism, up to 90%. Leaf RWC was much lower in winter, and leaf EL was significantly higher than branch EL in all seasons. Root pressure remained until November when soil temperature reached 9 °C, then appeared again in March when soil temperatures increased from −6 °C (January) to 11 °C. Xylem sap osmotic potential decreased from autumn to winter, reaching a minimum in March, and then increasing again. Soluble sugar (SS) concentration increased throughout the winter, peaked in March, and then decreased. Conclusions These results suggest that (1) there is a hydraulic segmentation between the stem and leaf, which could prevent stem water loss and further embolization in winter; (2) maintenance of root pressure in early winter played an important role in reducing the effect of freeze-thaw cycles on the winter embolism; (3) the physiological process that resulted in a decrease in xylem sap osmotic potential and tissue water content, and an accumulation of SS associated with cold acclimation also aided in reducing the extent of freeze-thaw-induced embolism. All these strategies could be helpful for the maintenance of xylem hydraulic function of this bamboo species during winter.
Dai et al. (2023) Maintenance of xylem hydraulic function during winter in the woody bamboo Phyllostachys propinqua McClure. PeerJ 11:e15979 https://doi.org/10.7717/peerj.15979
Comparative expression analysis of sucrose phosphate synthase gene family in a low and high sucrose Pakistani sugarcane cultivars
Sugarcane is the world’s largest cultivated crop by biomass and is the main source of sugar and biofuel. Sucrose phosphate synthase (SPS) enzymes are directly involved in the synthesis of sucrose. Here, we analyzed and compared one of the important gene families involved in sucrose metabolism in a high and low sucrose sugarcane cultivar. A comprehensive in silico analysis of the SoSPS family displayed their phylogenetic relationship, gene and protein structure, miRNA targets, protein interaction network (PPI), gene ontology and collinearity. This was followed by a spatial expression analysis in two different sugarcane varieties. The phylogenetic reconstruction distributed AtSPS, ZmSPS, OsSPS, SoSPS and SbSPS into three main groups (A, B, C). The regulatory region of SoSPS genes carries ABRE, ARE, G-box, and MYC as the most dominant cis-regulatory elements. The PPI analysis predicted a total of 14 unique proteins interacting with SPS. The predominant expression of SPS in chloroplast clearly indicates that they are the most active in the organelle which is the hub of photosynthesis. Similarly, gene ontology attributed SPS to sucrose phosphate synthase and glucosyl transferase molecular functions, as well as sucrose biosynthetic and disaccharide biological processes. Overall, the expression of SPS in CPF252 (high sucrose variety) was higher in leaf and culm as compared to that of CPF 251 (low sucrose variety). In brief, this study adds to the present literature about sugarcane, sucrose metabolism and role of SPS in sucrose metabolism thereby opening up further avenues of research in crop improvement.
Niazi et al. (2023) Comparative expression analysis of sucrose phosphate synthase gene family in a low and high sucrose Pakistani sugarcane cultivars. PeerJ 11:e15832 https://doi.org/10.7717/peerj.15832
Bat activity is related to habitat structure and time since prescribed fire in managed pine barrens in New England
Background Several insectivorous bat species are found in New England, yet research on them is still scarce. Current research shows the ecological importance of bats due to their control of insect populations, but they are endangered by habitat loss and White Nose Syndrome, among other threats. Pine barrens are an uncommon ecosystem found in New England that supports other rare taxa and could be important for these bat species. Methods With hand-held audio recorders, we surveyed for bats in Montague Plains Wildlife Management Area in Massachusetts and Concord Pine Barrens in New Hampshire in June 2022. Our study objectives were to (1) describe the most common bat species and (2) compare bat activity across different habitat types at two managed pine barrens in New England. In particular, we examined bat activity related to habitat type (scrub oak, mature pitch pine, treated pitch pine, hardwood forest), habitat structure (i.e., canopy closure), time since prescribed fire, and path width. We analyzed our data through generalized linear modeling and logistic regression. Results Overall, we were able to measure the presence of five out of the nine total species found in the area, including the endangered Myotis lucifugus (little brown bat). We recorded 293 bat calls, with the majority of calls from big brown bats (71%). We found significant differences (p < 0.05) in bat activity in relation to time since prescribed fire and habitat structure. The index of bat activity was greatest in pitch pine and hardwood forests and lowest in scrub oak and treated pitch pine habitats. With preliminary data, we also found that silver-haired bat presence was influenced by habitat type, with more detections at survey points in hardwood forests. Discussion These findings demonstrate the importance of pine barrens as an ecosystem that supports bats in New England. According to the activity of bats in our study, closed canopy and mature pitch pine habitats may be prioritized in conservation efforts at managed barrens for bat species. Further research is recommended to better understand the relationship between prescribed fires, which are common in managed barrens, and bat activity.
Kay et al. (2023) Bat activity is related to habitat structure and time since prescribed fire in managed pine barrens in New England. PeerJ 11:e15888 https://doi.org/10.7717/peerj.15888
Probabilistic approaches for investigating species co-occurrence from presence-absence maps
Background In this research, we propose probabilistic approaches to identify pairwise patterns of species co-occurrence by using presence-absence maps only. In particular, the two-by-two contingency table constructed from a presence-absence map of two species would be sufficient to compute the test statistics and perform the statistical tests proposed in this article. Some previous studies have investigated species co-occurrence through incidence data of different survey sites. We focus on using presence-absence maps for a specific study plot instead. The proposed methods are assessed by a thorough simulation study. Methods A Chi-squared test is used to determine whether the distributions of two species are independent. If the null hypothesis of independence is rejected, the Chi-squared method can not distinguish positive or negative association between two species. We propose six different approaches based on either the binomial or Poisson distribution to obtain p-values for testing the positive (or negative) association between two species. When we test to investigate a positive (or negative) association, if the p-value is below the predetermined level of significance, then we have enough evidence to support that the two species are positively (or negatively) associated. Results A simulation study is conducted to demonstrate the type-I errors and the testing powers of our approaches. The probabilistic approach proposed by Veech (2013) is served as a benchmark for comparison. The results show that the type-I error of the Chi-squared test is close to the significance level when the presence rate is between 40% and 80%. For extremely low or high presence rate data, one of our approaches outperforms Veech (2013)’s in terms of the testing power and type-I error rate. The proposed methods are applied to a tree data of Barro Colorado Island in Panama and a tree data of Lansing Woods in USA. Both positive and negative associations are found among some species in these two real data.
Chang et al. (2023) Probabilistic approaches for investigating species co-occurrence from presence-absence maps. PeerJ 11:e15907 https://doi.org/10.7717/peerj.15907
Microbiome analysis of Spodoptera frugiperda (Lepidoptera, Noctuidae) larvae exposed to Bacillus thuringiensis (Bt) endotoxins
Background Spodoptera frugiperda (or fall armyworm, FAW) is a polyphagous pest native to Western Hemisphere and recently discovered in the Eastern Hemisphere. In Colombia, S. frugiperda is recognized as a pest of economic importance in corn. The species has genetically differentiated into two host populations named “corn” and “rice” strains. In 2012, a study made in central Colombia demonstrated that the corn strain is less susceptible to Bacillus thuringiensis (Bt) endotoxins (Cry1Ac and Cry 1Ab) than the rice strain. In this country, Bt transgenic corn has been extensively produced over the last 15 years. Since gut microbiota plays a role in the physiology and immunity of insects, and has been implicated in promoting the insecticidal activity of Bt, in this study an analysis of the interaction between Bt endotoxins and FAW gut microbiota was made. Also, the detection of endosymbionts was performed here, as they might have important implications in the biological control of a pest. Methods The composition and diversity of microbiomes associated with larval specimens of S. frugiperda(corn strain) was investigated in a bioassay based on six treatments in the presence/absence of Bt toxins and antibiotics (Ab) through bacterial isolate analyses and by high throughput sequencing of the bacterial 16S rRNA gene. Additionally, species specific primers were used, to detect endosymbionts from gonads in S. frugiperda corn strain. Results Firmicutes, Proteobacteria and Bacteroidota were the most dominant bacterial phyla found in S. frugiperda corn strain. No significant differences in bacteria species diversity and richness among the six treatments were found. Two species of Enterococcus spp., E. mundtii and E. casseliflavus were detected in treatments with Bt and antibiotics, suggesting that they are less susceptible to both of them. Additionally, the endosymbiont Arsenophonus was also identified on treatments in presence of Bt and antibiotics. The results obtained here are important since little knowledge exists about the gut microbiota on this pest and its interaction with Bt endotoxins. Previous studies made in Lepidoptera suggest that alteration of gut microbiota can be used to improve the management of pest populations, demonstrating the relevance of the results obtained in this work.
Castañeda-Molina et al. (2023) Microbiome analysis of Spodoptera frugiperda (Lepidoptera, Noctuidae) larvae exposed to Bacillus thuringiensis (Bt) endotoxins. PeerJ 11:e15916 https://doi.org/10.7717/peerj.15916
Risk factors for adverse pregnancy outcomes in Chinese women: a meta-analysis
Objective This study examined the associated risk factors of adverse pregnancy outcomes among Chinese females and furnished some fundamental principles and recommendations for enhanced prevention of adverse pregnancy and preservation of women’s well-being. Methods A systematic review was conducted by retrieving the MEDLINE (The National Library of Medicine), Embase, PubMed, and Cochrane databases. The relevant risk factors for adverse pregnancy in Chinese women were retrieved from May 2017 to April 2023. Use Review Manager for data analysis. Calculate the merge effect based on data attributes using mean difference (MD) or odds ratio (or) and 95% confidence interval (CI). The meta-analysis was registered at INPLASY (International Platform of Registered Systematic Review and Meta-analysis Protocols, 202340090). Results A total of 15 articles were included, with a total of 946,818 Chinese pregnant women. Moreover, all the literature was scored by the NOS (Newcastle-Ottawa Scale), and all literatures were ≥7 points, which were evaluated as high quality. There are seven risk factors related to adverse pregnancy in Chinese women: parity, pregnancy frequency, education level, smoking, gestational diabetes, gestational weeks, and age. Moreover, the main risk factors for adverse pregnancy are pregnancy frequency, education level, gestational diabetes mellitus, and age. Conclusion The pregnancy frequency, education level, gestational diabetes mellitus, and age were significantly associated with the adverse pregnancy in Chinese women, whereas gestational weeks, smoking, and parity had no significant effect on adverse pregnancy.
Huang et al. (2023) Risk factors for adverse pregnancy outcomes in Chinese women: a meta-analysis. PeerJ 11:e15965 https://doi.org/10.7717/peerj.15965