Combined use of karyotyping and copy number variation sequencing technology in prenatal diagnosis
Background Karyotyping and genome copy number variation sequencing (CNV-seq) are two techniques frequently used in prenatal diagnosis. This study aimed to explore the diagnostic potential of using a combination of these two methods in order to provide a more accurate clinical basis for prenatal diagnosis. Methods We selected 822 pregnant women undergoing amniocentesis and separated them into six groups according to different risk indicators. Karyotyping and CNV-seq were performed simultaneously to compare the diagnostic performance of the two methods. Results Among the different amniocentesis indicators, abnormal fetal ultrasounds accounted for 39.29% of the total number of examinees and made up the largest group. The abnormal detection rate of non-invasive prenatal testing (NIPT) high risk was 37.93% and significantly higher than the other five groups (P < 0.05). The abnormal detection rate of mixed indicators was significantly higher than the history of the adverse reproductive outcomes group (P = 0.0151). The two methods combined found a total of 119 abnormal cases (14.48%). Karyotyping detected 57 cases (6.93%) of abnormal karyotypes, 30 numerical aberrations, and 27 structural aberrations. CNV-seq identified 99 cases (12.04%) with altered CNVs, 30 cases of chromosome aneuploidies, and 69 structural aberrations (28 pathogenic, eight that were likely pathogenic, and 33 microdeletion/duplication variants of uncertain significance (VUS)). Thirty-seven cases were found abnormal by both methods, 20 cases were detected abnormally by karyotyping (mainly mutual translocation and mostly balanced), and 62 cases of microdeletion/duplication were detected by CNV-seq. Steroid sulfatase gene (STS) deletion was identified at chromosome Xp22.31 in three cases. Postnatal follow-up confirmed that babies manifested skin abnormalities one week after birth. Six fetuses had Xp22.31 duplications ranging from 1.5 Kb to 1.7 Mb that were detected by CNV-seq. Follow-up showed that five babies presented no abnormalities during follow-up, except for one terminated pregnancy due to a history of adverse reproductive outcomes. Conclusion The combination of using CNV-seq and karyotyping significantly improved the detection rate of fetal pathogenic chromosomal abnormalities. CNV-seq is an effective complement to karyotyping and improves the accuracy of prenatal diagnosis.
Zhang et al. (2022) Combined use of karyotyping and copy number variation sequencing technology in prenatal diagnosis. PeerJ 10:e14400 https://doi.org/10.7717/peerj.14400
Upregulated TUBG1 expression is correlated with poor prognosis in hepatocellular carcinoma
Background Hepatocellular carcinoma (HCC) development is a complex pathological process. Tubulin gamma 1 (TUBG1) plays an oncogenic role in several human cancers; however, its functional role in HCC tumorigenesis remains unknown. Methods Herein we first evaluated the gene expression levels of TUBG1 in HCC using data from The Cancer Genome Atlas and Gene Expression Profiling Interactive Analysis databases. We then elucidated the association between TUBG1 gene expression levels and survival rates of patients with HCC. Cell cycle, proliferation, transwell migration, and matrigel invasion assays were used to study the effects of TUBG1 on the malignant phenotypes of HCC cells. Results Based on the data obtained from the aforementioned databases and our in vitro experiments, TUBG1 was found to be overexpressed in HCC and patients with high TUBG1 expression levels showed a remarkably poor overall survival rate. In addition, the expression of TUBG1 significantly promoted the malignant phenotypes of HCC cells in vitro. Gene ontology term enrichment analysis revealed that co-regulated genes were enriched in biological processes mainly involved in chromosome segregation, chromosomal region, and chromatin binding; moreover, Kyoto Encyclopedia of Genes and Genome pathway analysis showed that they were mainly involved in cell cycle, oocyte meiosis, platinum drug resistance, and the p53 signaling pathway. Conclusions We report that TUBG1 is an important oncogene in HCC. It promotes HCC progression and may serve as a potential prognostic biomarker for HCC. Future studies are warranted to unveil molecular biological mechanisms underlying TUBG1 carcinogenesis.
Zhang et al. (2022) Upregulated TUBG1 expression is correlated with poor prognosis in hepatocellular carcinoma. PeerJ 10:e14415 https://doi.org/10.7717/peerj.14415
Effects of saddle tilt and stirrup length on the kinetics of horseback riders
Background How the modification of saddle fitting parameters in horse riding affects rider’s kinetics is very uncertain. The aim of this study is to describe how manipulating the two main adjustments that an end-user is likely to perform (saddle tilt and stirrup length) affects the biomechanics of a horse rider on a living horse. Methods Eleven showjumpers volunteered to take part in this study. Each participant performed a 120-strides standardization trial at trot and canter, with 0° saddle tilt and stirrup length that would position the rider’s knee at 90°. Following the standardization trial, four interventions were performed, which consisted of 60 strides with 60 mm shorter stirrups, 60 mm longer stirrups, 4° forward tilted saddle and 4° backward tilted saddle. Stirrup and rein tension forces were measured with tension loadcells. A symmetry index was calculated. Acceleration was measured with inertial measuring units at the helmet and back of the rider and shock attenuation was calculated. Results Shortening the stirrups and adjusting saddle tilt significantly enhanced shock attenuation at canter and increased force on the stirrups at trot and canter (p < 0.05). Lowering the stirrups reduced rein tension forces (p = 0.01). At trot, adjusting saddle tilt and stirrup length enhanced symmetry index on the bit (p < 0.05). These results allowed for general guidelines to be proposed, although individualization became an evident part of any saddle setup design due to a high inter-subject variability.
Elmeua González et al. (2022) Effects of saddle tilt and stirrup length on the kinetics of horseback riders. PeerJ 10:e14438 https://doi.org/10.7717/peerj.14438
Prevalence, classification and dental treatment requirements of dens invaginatus by cone-beam computed tomography
Background This study aimed the evaluation of the prevalence, characteristics, types of dens invaginatus (DI) and co-observed dental anomalies to understand dental treatment requirements in anterior teeth that are susceptible to developmental anomalies by using cone-beam computed tomography (CBCT). Methods In this retrospective study, the anterior teeth of 958 patients were evaluated by using CBCT for the presence of DI. The demographic features, types of DI and treatment requirements were also recorded. The association between sex and the presence of DI was evaluated using chi-squared test. Results Seventy-three DI anomalies were detected in the anterior teeth of 49 patients (18 females, 31 males). The frequency of DI was 5.11% and the most frequently involved teeth were lateral (57.53%). Forty-six teeth were classified as Type I (63.01%), 24 as Type II (32.87%), and three as Type III (4.10%). Apical pathosis was found to be 20.54% in all DIs detected and accounted for all Type III and one-third of Type II. Conclusions CBCT imaging can be effective in the detection of dental anomalies such as DI and planning for root canal therapy and surgical treatments. Prophylactic interventions might be possible to prevent apical pathosis with the data obtained from CBCT images.
Yalcin et al. (2022) Prevalence, classification and dental treatment requirements of dens invaginatus by cone-beam computed tomography. PeerJ 10:e14450 https://doi.org/10.7717/peerj.14450
Genome-wide identification and expression pattern analysis of quinoa BBX family
BBX is a transcription factor encoding zinc finger protein that plays a key role in plant growth and development as well as in responding to abiotic stresses. However, in quinoa, which is known as a “super grain” and has extremely high nutritional value, this gene family has not yet been thoroughly studied. In this study, in order to fully understand the family function of the BBX in quinoa, a total of 31 BBX members were identified by bioinformatics methods. These BBX members were mainly acidic proteins, and most of their secondary structures were random coil s, 31 CqBBX members were unevenly distributed on 17 chromosomes, and the analysis of replication events found that quinoa BBX genes produced a total of 14 pairs of gene replication. The BBX genes were divided into five subfamilies according to phylogenetics, and its gene structure and conserved motif were basically consistent with the classification of its phylogenetic tree. In addition, a total of 43 light response elements, hormone response elements, tissue-specific expression response elements, and abiotic stress response elements were found in the promoter region, involving stress elements such as drought and low temperature. Finally, the expression patterns of CqBBX genes in different tissues and abiotic stresses were studied by combining transcriptome data and qRT-PCR , and all 13 genes responded to drought, salt, and low-temperature stress to varying degrees. This study is the first comprehensive study of the BBX family of quinoa, and its results provide important clues for further analysis of the function of the abiotic stress response.
Xuefen et al. (2022) Genome-wide identification and expression pattern analysis of quinoa BBX family. PeerJ 10:e14463 https://doi.org/10.7717/peerj.14463
Identification, classification, and expression profile analysis of heat shock transcription factor gene family in Salvia miltiorrhiza
In response to abiotic stresses, transcription factors are essential. Heat shock transcription factors (HSFs), which control gene expression, serve as essential regulators of plant growth, development, and stress response. As a model medicinal plant, Salvia miltiorrhiza is a crucial component in the treatment of cardiovascular illnesses. But throughout its growth cycle, S.miltiorrhiza is exposed to a series of abiotic challenges, including heat and drought. In this study, 35 HSF genes were identified based on genome sequencing of Salvia miltiorrhiza utilizing bioinformatics techniques. Additionally, 35 genes were classified into three groups by phylogeny and gene structural analysis, comprising 22 HSFA, 11 HSFB, and two HSFC. The distribution and sequence analysis of motif showed that SmHSFs were relatively conservative. In SmHSF genes, analysis of the promoter region revealed the presence of many cis-acting elements linked to stress, hormones, and growth and development, suggesting that these factors have regulatory roles. The majority of SmHSFs were expressed in response to heat and drought stress, according to combined transcriptome and real-time quantitative PCR (qRT-PCR) analyses. In conclusion, this study looked at the SmHSF gene family using genome-wide identification, evolutionary analysis, sequence characterization, and expression analysis. This research serves as a foundation for further investigations into the role of HSF genes and their molecular mechanisms in plant stress responses.
Liu et al. (2022) Identification, classification, and expression profile analysis of heat shock transcription factor gene family in Salvia miltiorrhiza. PeerJ 10:e14464 https://doi.org/10.7717/peerj.14464
Chemically mediated rheotaxis of endangered tri-spine horseshoe crab: potential dispersing mechanism to vegetated nursery habitats along the coast
Background An enhanced understanding of larval ecology is fundamental to improve the management of locally depleted horseshoe crab populations in Asia. Recent studies in the northern Beibu Gulf, China demonstrated that nesting sites of Asian horseshoe crabs are typically close to their nursery beaches with high-density juveniles distributed around mangrove, seagrass and other structured habitats. Methods A laboratory Y-maze chamber was used to test whether the dispersal of early-stage juvenile tri-spine horseshoe crab Tachypleus tridentatus is facilitated by chemical cues to approach suitable nursery habitats. The juvenile orientation to either side of the chamber containing controlled seawater or another with various vegetation cues, as well as their movement time, the largest distance and displacement were recorded. Results The juveniles preferred to orient toward seagrass Halophila beccarii cues when the concentration reached 0.5 g l−1, but ceased at 2 g l−1. The results can be interpreted as a shelter-seeking process to get closer to the preferred settlement habitats. However, the juveniles exhibited avoidance behaviors in the presence of mangrove Avicennia marina and invasive saltmarsh cordgrass Spartina alterniflora at 2 g l−1. The juveniles also spent less time moving in the presence of the A. marina cue, as well as reduced displacement in water containing the S. alterniflora cue at 1 and 2 g l−1. These results may explain the absence of juvenile T. tridentatus within densely vegetated areas, which have generally higher organic matter and hydrogen sulfide. Conclusion Early-stage juvenile T. tridentatus are capable of detecting and responding to habitat chemical cues, which can help guide them to high-quality settlement habitats. Preserving and restoring seagrass beds in the intertidal areas should be prioritized when formulating habitat conservation and management initiatives for the declining horseshoe crab populations.
Kwan et al. (2022) Chemically mediated rheotaxis of endangered tri-spine horseshoe crab: potential dispersing mechanism to vegetated nursery habitats along the coast. PeerJ 10:e14465 https://doi.org/10.7717/peerj.14465
Effects of cleaning sports mouthguards with ethylene-vinyl acetate on oral bacteria
Background Sports mouthguards, worn in the oral cavity to prevent sports injuries, are constantly exposed to various microorganisms that cause oral infections. Hence, the optimal cleaning methods for sports mouthguards have been thoroughly examined. In this study, we evaluated the efficiency of cleaning effects with a mouthguard cleaner (MC) on microbial biofilm formation in sports mouthguards in vitro and in vivo. Methods We evaluated the cleaning effects of the discs produced by ethylene-vinyl acetate (EVA) on bacterial biofilms formed by the commensal bacterium Streptococcus oralis, the cariogenic bacterium Streptococcus mutans, and the opportunistic pathogen Staphylococcus aureus in vitro. EVA discs with biofilm were subjected to sterile distilled water (CTRL) and ultrasonic washing (UW), followed by treatment with MC and sodium hypochlorite (NaClO) as positive controls. Thereafter, the viable bacterial cell counts were determined. The bacteria adhering to the sheets before and after the treatment were observed under an electron microscope. The degree of cleanliness and measurement of viable microbial cell counts for total bacteria, Streptococci and Candida, opportunistic fungi, were evaluated on the used experimental sports mouthguards with and without UW and MC treatment in vivo. Results The number of bacterial cells significantly decreased against all the tested biofilm bacteria upon treatment with MC, compared with CTRL and UW. Electron microscopy analysis revealed the biofilm formation by all bacteria on the EVA discs before cleaning. We observed fewer bacteria on the EVA discs treated with MC than those treated with CTRL and UW. Furthermore, the degree of cleanliness of the used experimental sports mouthguards cleaned using MC was significantly higher than that of the CTRL-treated mouthguards. Moreover, the viable microbial cell counts on the used experimental sports mouthguard were considerably lower than those on the CTRL ones. Conclusion The cleaning effect of MC against oral bacteria was more effective than that of UW. MC treatment might have a potential future application as a cleaning method for sports mouthguards to protect athletes from oral infection.
Hayashi et al. (2022) Effects of cleaning sports mouthguards with ethylene-vinyl acetate on oral bacteria. PeerJ 10:e14480 https://doi.org/10.7717/peerj.14480
Efficacy and indications of tonsillectomy in patients with IgA nephropathy: a retrospective study
Background The efficacy and indications of tonsillectomy in IgA nephropathy (IgAN) remain uncertain. Methods We performed a retrospective cohort study of 452 patients with primary IgAN, including 226 patients who received tonsillectomy and 226 controls selected by propensity score matching who had never undergone tonsillectomy. Study outcomes were clinical remission defined as negative hematuria and proteinuria on three consecutive visits over a 6-month period, the endpoint defined as end-stage renal disease or an irreversible 100% increase in serum creatinine from the baseline value. In addition, we further analyzed the critical level of proteinuria in the efficacy of tonsillectomy and the correlation between MEST-C score and tonsillectomy. Results Up to December 2019, the follow-up period lasted 46 ± 23 months (12–106 months). Kaplan–Meier and multivariate Cox regression analysis revealed that tonsillectomy was beneficial for clinical remission and renal survival. Whether proteinuria was ≤ 1 g/24h or >1 g/24h, the clinical remission and renal survival rates were greater in patients treated with tonsillectomy than without. When the pathological damage was mild or relatively severe, tonsillectomy may be beneficial to clinical remission or renal survival. Conclusions Tonsillectomy had a favorable effect on clinical remission and delayed renal deterioration in IgAN. In addition to patients with early stage IgAN, it may also be beneficial to IgAN patients with higher levels of proteinuria and relatively severe pathological damage.
Li et al. (2022) Efficacy and indications of tonsillectomy in patients with IgA nephropathy: a retrospective study. PeerJ 10:e14481 https://doi.org/10.7717/peerj.14481
Modeling the drying process of Masson pine needle fuel beds under different packing ratios based on two-phase models in the laboratory
Background When the moisture content of a fuel bed is higher than the fiber saturation moisture content (0.35 g g−1), the drying process is controlled by evaporation (>0.35 g g−1) and diffusion (>0.35 g g−1). Packing ratio has a significant effect on the drying process. Ignoring the impacts of packing ratio or the separate phases of the drying process is one main reason for inaccurate moisture content predictions. Method This study simulated the drying process in five Masson pine (Pinus massoniana Lamb.) needle beds with different packing ratios. Using the fiber saturation moisture content as the cut-off point, we divided the drying process into two phases. The drying mechanism of each phase was different and had its own drying equation. Using a model that does not distinguish the two phases of the drying process as a comparison, the prediction effect of the two-phase model was analyzed. The influence of the fuel bed packing ratio on the drying process was also analyzed. Results We found that, regardless of any changes in packing ratio, the two-phase model could better simulate the drying process, with a mean absolute error (MAE) and mean relative error (MRE) of the two-phase model 18.4% and 25.6% less than the one-phase model, respectively. The time-lag prediction model was established with the packing ratio, and the errors were all within the allowable range, but the prediction effect of the time-lag prediction model based on the two-phase model was larger. Conclusion It was further demonstrated that considering the packing ratio of the fuel bed and distinguishing the two separate phases of the drying process could both effectively improve the prediction accuracy of the moisture content of fuel beds based on the semi-physical method.
Zhang (2022) Modeling the drying process of Masson pine needle fuel beds under different packing ratios based on two-phase models in the laboratory. PeerJ 10:e14484 https://doi.org/10.7717/peerj.14484