Comparison of the clinical value of MRI and plasma markers for cognitive impairment in patients aged ≥75 years: a retrospective study
Background Dementia has become the main cause of disability in older adults aged ≥75 years. Cerebral small vessel disease (CSVD) is involved in cognitive impairment (CI) and dementia and is a cause of vascular CI (VCI), which is manageable and its onset and progression can be delayed. Simple and effective markers will be beneficial to the early detection and intervention of CI. The aim of this study is to investigate the clinical application value of plasma amyloid β1-42 (Aβ42), phosphorylated tau 181 (p-tau181) and conventional structural magnetic resonance imaging (MRI) parameters for cognitive impairment (CI) in patients aged ≥75 years. Methods We retrospectively selected patients who visited the Affiliated Hospital of Xuzhou Medical University and were clinically diagnosed with or without cognitive dysfunction between May 2018 and November 2021. Plasma indicators (Aβ42 and p-tau181) and conventional structural MRI parameters were collected and analyzed. Multivariate logistic regression and receiver operator characteristic (ROC) curve were used to evaluate the diagnostic value. Results One hundred and eighty-four subjects were included, including 54 cases in CI group and 130 cases in noncognitive impairment (NCI) groups, respectively. Univariate logistic regression analysis revealed that the percentages of Aβ42+, P-tau 181+, and Aβ42+/P-tau181+ showed no significant difference between the groups of CI and NCI (all P > 0.05). Multivariate logistic regression analysis showed that moderate/severe periventricular WMH (PVWMH) (OR 2.857, (1.365–5.983), P = 0.005), lateral ventricle body index (LVBI) (OR 0.413, (0.243–0.700), P = 0.001), and cortical atrophy (OR 1.304, (1.079−1.575), P = 0.006) were factors associated with CI. The combined model including PVWMH, LVBI, and cortical atrophy to detect CI and NCI showed an area under the ROC curve (AUROC) is 0.782, with the sensitivity and specificity 68.5% and 78.5%, respectively. Conclusion For individuals ≥75 years, plasma Aβ42 and P-tau181 might not be associated with cognitive impairment, and MRI parameters, including PVWMH, LVBI and cortical atrophy, are related to CI. The cognitive statuses of people over 75 years old were used as the endpoint event in this study. Therefore, it can be considered that these MRI markers might have more important clinical significance for early assessment and dynamic observation, but more studies are still needed to verify this hypothesis.
Wang et al. (2023) Comparison of the clinical value of MRI and plasma markers for cognitive impairment in patients aged ≥75 years: a retrospective study. PeerJ 11:e15581 https://doi.org/10.7717/peerj.15581
Investigating the sequence landscape in the Drosophila initiator core promoter element using an enhanced MARZ algorithm
The core promoter elements are important DNA sequences for the regulation of RNA polymerase II transcription in eukaryotic cells. Despite the broad evolutionary conservation of these elements, there is extensive variation in the nucleotide composition of the actual sequences. In this study, we aim to improve our understanding of the complexity of this sequence variation in the TATA box and initiator core promoter elements in Drosophila melanogaster. Using computational approaches, including an enhanced version of our previously developed MARZ algorithm that utilizes gapped nucleotide matrices, several sequence landscape features are uncovered, including an interdependency between the nucleotides in position 2 and 5 in the initiator. Incorporating this information in an expanded MARZ algorithm improves predictive performance for the identification of the initiator element. Overall our results demonstrate the need to carefully consider detailed sequence composition features in core promoter elements in order to make more robust and accurate bioinformatic predictions.
Dresch et al. (2023) Investigating the sequence landscape in the Drosophila initiator core promoter element using an enhanced MARZ algorithm. PeerJ 11:e15597 https://doi.org/10.7717/peerj.15597
Concordance of microbial and visual health indicators of white-band disease in nursery reared Caribbean coral Acropora cervicornis
Background Coral diseases are one of the leading causes of declines in coral populations. In the Caribbean, white band disease (WBD) has led to a substantial loss of Acropora corals. Although the etiologies of this disease have not been well described, characterizing the coral microbiome during the transition from a healthy to diseased state is critical for understanding disease progression. Coral nurseries provide unique opportunities to further understand the microbial changes associated with diseased and healthy corals, because corals are monitored over time. We characterized the microbiomes before and during an outbreak of WBD in Acropora cervicornis reared in an ocean nursery in Little Cayman, CI. We asked (1) do healthy corals show the same microbiome over time (before and during a disease outbreak) and (2) are there disease signatures on both lesioned and apparently healthy tissues on diseased coral colonies? Methods Microbial mucus-tissue slurries were collected from healthy coral colonies in 2017 (before the disease) and 2019 (during the disease onset). Diseased colonies were sampled at two separate locations on an individual coral colony: at the interface of Disease and ∼10 cm away on Apparently Healthy coral tissue. We sequenced the V4 region of the 16S rRNA gene to characterize bacterial and archaeal community composition in nursery-reared A. cervicornis. We assessed alpha diversity, beta diversity, and compositional differences to determine differences in microbial assemblages across health states (2019) and healthy corals between years (2017 and 2019). Results Microbial communities from healthy A. cervicornis from 2017 (before disease) and 2019 (after disease) did not differ significantly. Additionally, microbial communities from Apparently Healthy samples on an otherwise diseased coral colony were more similar to Healthy colonies than to the diseased portion on the same colony for both alpha diversity and community composition. Microbial communities from Diseased tissues had significantly higher alpha diversity than both Healthy and Apparently Healthy tissues but showed no significant difference in beta-diversity dispersion. Our results show that at the population scale, Healthy and Apparently Healthy coral tissues are distinct from microbial communities associated with Diseased tissues. Furthermore, our results suggest stability in Little Cayman nursery coral microbiomes over time. We show healthy Caymanian nursery corals had a stable microbiome over a two-year period, an important benchmark for evaluating coral health via their microbiome.
Schul et al. (2023) Concordance of microbial and visual health indicators of white-band disease in nursery reared Caribbean coral Acropora cervicornis. PeerJ 11:e15170 https://doi.org/10.7717/peerj.15170
Microbial community in buckwheat rhizosphere with different nitrogen application rates
Microorganism plays a pivotal role in regulating sustainable development of agriculture. The excessive application of nitrogen fertilizer is considered to affect the microbial structure in many agricultural systems. The present study aimed to assess the impacts of nitrogen application rate on microbial diversity, community and functionality in rhizosphere of Tartary buckwheat in short-time. The nitrogen fertilizer was applied at rates of 90 kg (N90), 120 kg (N120) and 150 kg (N150) urea per hectare, respectively. The soil properties were measured chemical analysis and displayed no difference among treatments. Metagenome analysis results showed that the microbial diversity was not affected, but the microbial community and functionality were affected by the nitrogen application rate. According to the Linear discriminant analysis effect size (LEfSe) analysis, 15 taxa were significantly enriched in the N120 and N150 groups, no taxon was enriched in the N90 group. Kyoto Encyclopaedia of Genes and Genomes (KEGG) annotation results revealed that the genes related to butanoate and beta alanine metabolism were significantly enriched in the N90 group, the genes related to thiamine metabolism, lipopolysaccharide biosynthesis and biofilm formation were significantly enriched in the N120 group, and the genes related to neurodegenerative disease was significantly enriched in the N150 group. In conclusion, short-time nitrogen fertilizer application shifted the microbial community structure and functionality.
Wang et al. (2023) Microbial community in buckwheat rhizosphere with different nitrogen application rates. PeerJ 11:e15514 https://doi.org/10.7717/peerj.15514
Micrococcal nuclease sequencing of porcine sperm suggests enriched co-location between retained histones and genomic regions related to semen quality and early embryo development
The mammalian spermatozoon has a unique chromatin structure in which the majority of histones are replaced by protamines during spermatogenesis and a small fraction of nucleosomes are retained at specific locations of the genome. The sperm’s chromatin structure remains unresolved in most animal species, including the pig. However, mapping the genomic locations of retained nucleosomes in sperm could help understanding the molecular basis of both sperm development and function as well as embryo development. This information could then be useful to identify molecular markers for sperm quality and fertility traits. Here, micrococcal nuclease digestion coupled with high throughput sequencing was performed on pig sperm to map the genomic location of mono- and sub-nucleosomal chromatin fractions in relation to a set of diverse functional elements of the genome, some of which were related to semen quality and early embryogenesis. In particular, the investigated elements were promoters, the different sections of the gene body, coding and non-coding RNAs present in the pig sperm, potential transcription factor binding sites, genomic regions associated to semen quality traits and repeat elements. The analysis yielded 25,293 and 4,239 peaks in the mono- and sub-nucleosomal fractions, covering 0.3% and 0.02% of the porcine genome, respectively. A cross-species comparison revealed positional conservation of the nucleosome retention in sperm between the pig data and a human dataset that found nucleosome enrichment in genomic regions of importance in development. Both gene ontology analysis of the genes mapping nearby the mono-nucleosomal peaks and the identification of putative transcription factor binding motifs within the mono- and the sub- nucleosomal peaks showed enrichment for processes related to sperm function and embryo development. There was significant motif enrichment for Znf263, which in humans was suggested to be a key regulator of genes with paternal preferential expression during early embryogenesis. Moreover, enriched positional intersection was found in the genome between the mono-nucleosomal peaks and both the RNAs present in pig sperm and the RNAs related to sperm quality. There was no co-location between GWAS hits for semen quality in swine and the nucleosomal sites. Finally, the data evidenced depletion of mono-nucleosomes in long interspersed nuclear elements and enrichment of sub-nucleosomes in short interspersed repeat elements.These results suggest that retained nucleosomes in sperm could both mark regulatory elements or genes expressed during spermatogenesis linked to semen quality and fertility and act as transcriptional guides during early embryogenesis. The results of this study support the undertaking of ambitious research using a larger number of samples to robustly assess the positional relationship between histone retention in sperm and the reproductive ability of boars.
Gòdia et al. (2023) Micrococcal nuclease sequencing of porcine sperm suggests enriched co-location between retained histones and genomic regions related to semen quality and early embryo development. PeerJ 11:e15520 https://doi.org/10.7717/peerj.15520
Genetic polymorphism of the Dab2 gene and its association with Type 2 Diabetes Mellitus in the Chinese Uyghur population
Objective The human Disabled-2 (Dab2) protein is an endocytic adaptor protein, which plays an essential role in endocytosis of transmembrane cargo, including low-density lipoprotein cholesterol (LDL-C). As a candidate gene for dyslipidemia, Dab2 is also involved in the development of type 2 diabetes mellitus(T2DM). The aim of this study was to investigate the effects of genetic variants of the Dab2 gene on the related risk of T2DM in the Uygur and Han populations of Xinjiang, China. Methods A total of 2,157 age- and sex-matched individuals (528 T2DM patients and 1,629 controls) were included in this case-control study. Four high frequency SNPs (rs1050903, rs2255280, rs2855512 and rs11959928) of the Dab2 gene were genotyped using an improved multiplex ligation detection reaction (iMLDR) genotyping assay, and the forecast value of the SNP for T2DM was assessed by statistical analysis of clinical data profiles and gene frequencies. Results We found that in the Uygur population studied, for both rs2255280 and rs2855512, there were significant differences in the distribution of genotypes (AA/CA/CC), and the recessive model (CC vs. CA + AA) between T2DM patients and the controls (P < 0.05). After adjusting for confounders, the recessive model (CC vs. CA + AA) of both rs2255280 and rs2855512 remained significantly associated with T2DM in this population (rs2255280: OR = 5.303, 95% CI [1.236 to −22.755], P = 0.025; rs2855512: OR = 4.892, 95% CI [1.136 to −21.013], P = 0.033). The genotypes (AA/CA/CC) and recessive models (CC vs. CA + AA) of rs2855512 and rs2255280 were also associated with the plasma glucose and HbA1c levels (all P < 0.05) in this population. There were no significant differences in genotypes, all genetic models, or allele frequencies between the T2DM and control group in the Han population group (all P > 0.05). Conclusions The present study suggests that the variation of the Dab2 gene loci rs2255280 and rs2855512 is related to the incidence of T2DM in the Uygur population, but not in the Han population. In this study, these variations in Dab2 were an independent predictor for T2DM in the Uygur population of Xinjiang, China.
Li et al. (2023) Genetic polymorphism of the Dab2 gene and its association with Type 2 Diabetes Mellitus in the Chinese Uyghur population. PeerJ 11:e15536 https://doi.org/10.7717/peerj.15536
Direct, indirect, and vicarious nature experiences collectively predict preadolescents’ self-reported nature connectedness and conservation behaviors
Background The quantity and context of children’s nature experiences are undergoing significant changes, exacerbating a pervasive negative cycle that could impact future conservation efforts. Therefore, it is essential to conduct further studies on the potential impacts of these changes on children’s willingness to engage in conservation practices. Methods We surveyed 2,175 preadolescents (aged 9–12) from rural and city schools in Hangzhou, Kunming, and Xishuangbanna, China, regarding their nature experiences (direct, indirect, and vicarious) and self-reported nature connectedness and conservation behaviors. Results We found that children in urban areas have higher frequencies of indirect and vicarious experiences than those in rural areas, with some direct nature experiences seldom reported among city respondents. Direct, indirect, and vicarious nature experiences significantly predicted children’s conservation behavior and collectively provided the highest predictive power for conservation behavior. Direct and vicarious experiences were strongly correlated with pro-nature behavior, and the latter with pro-environmental behavior. Emotional and cognitive connection with nature positively predicted conservation behavior, influenced by location and residence type. Discussion This study reveals that different types of nature experiences shape children’s current conservation behaviors in China.
Yue et al. (2023) Direct, indirect, and vicarious nature experiences collectively predict preadolescents’ self-reported nature connectedness and conservation behaviors. PeerJ 11:e15542 https://doi.org/10.7717/peerj.15542
Cnidom in Ceriantharia (Cnidaria, Anthozoa): new findings in the composition and micrometric variations of cnidocysts
Background Like all cnidarians, the subclass Ceriantharia (Cnidaria, Anthozoa) is known for producing cnidocysts, which mainly serve for prey immobilization, predator defense, and locomotion. Aim The present study aimed to understand the variability of the cnidom, i.e., the inventory of all cnidocyst types, in the ceriantharians (tube anemones) Ceriantheomorphe brasiliensis (10 individuals) and Cerianthus sp. (seven individuals). Methods In each individual, 30 intact cnidocysts of each identified type were measured in the following parts of tube anemones: marginal tentacles (four from each individual), labial tentacles (four from each individual), column, actinopharynx and metamesenteries. Each of these structures was divided into three levels (high, middle, and low) and the cnidom was analyzed. Statistical descriptive parameters (mean, standard deviation, minimum and maximum) of the sizes of all types of cnidocysts were calculated. The normality of the data for cnidocyst length was assessed using a Shapiro-Wilk test (α = 0.05). Based on the acceptance or rejection of the normality, either linear models or generalized linear models were used to evaluate variations in cnidocyst lengths. The normality of the cnidocyst length was tested by Shapiro-Wilk, and due to its rejection, generalized linear mixed models were applied to test the cnidocyst lengths variations. Results The analysis of Ceriantheomorphe brasiliensis revealed 23 categories of cnidocysts, thereby expanding the understanding of its cnidome. The cnidoms of Ceriantheomorphe brasiliensis and Cerianthus sp. presented intraspecific variations, both qualitatively and in the lengths of cnidocysts. The cnidoms of the two species studied also showed qualitative intra-individual variations between different levels (high, middle, low) within each structure of the tube anemone (tentacles, actinopharynx, column and metamesenteries). Some cnidocyst types, such as atrichs from the column of C. brasiliensis, presented a length gradient along the column, from larger lengths at the “low” level to smaller lengths at the “high” level. Conclusions The cnidom of a tube anemone could be better described if samples are taken at different levels of the structures, as observed in C. brasiliensis. In addition, we can conclude that the cnidocyst lengths of both C. brasiliensis and Cerianthus sp. present intraspecific variation, which is coincident with that observed in actiniarian sea anemones. Moreover, as main conclusion, this work also proved that individuals of tube anemone species could present qualitative intra-structure variations in both the cnidom and cnidocyst lengths. This characteristic appears as an exception in cnidom variations, and has so far not been recorded even in the most studied actiniarian sea anemones. Finally, the intra-structure cnidocyst variations could reveal different functions of the different levels of a particular body part of the organisms.
Garese et al. (2023) Cnidom in Ceriantharia (Cnidaria, Anthozoa): new findings in the composition and micrometric variations of cnidocysts. PeerJ 11:e15549 https://doi.org/10.7717/peerj.15549
Response of in situ root phenotypes to potassium stress in cotton
Potassium plays a significant role in the basic functions of plant growth and development. Potassium uptake is closely associated with morphological characteristics of the roots. However, the dynamic characteristics of phenotype and lifespan of cotton (Gossypium hirsutum L.) lateral roots and root hairs under low and high potassium stress remain unclear. In this study, potassium stress experiments (low and high potassium, medium potassium as control) were conducted using RhizoPot (an in situ root observation device) to determine the response characteristics of lateral roots and root hairs in cotton under potassium stress. The plant morphology, photosynthetic characteristics, root phenotypic changes, and lifespan of lateral roots and root hairs were measured. Potassium accumulation, aboveground phenotype, photosynthetic capacity, root length density, root dry weight, root diameter, lateral root lifespan, and root hair lifespan under low potassium stress were significantly decreased compared to medium potassium treatment. However, the root hair length of the former was significantly increased than that of the latter. Potassium accumulation and the lateral root lifespan were significantly increased under high potassium treatment, while root length density, root dry weight, root diameter, root hair length, and root hair lifespan were significantly decreased compared to the medium potassium treatment. Notably, there were no significant differences in aboveground morphology and photosynthetic characters. Principal component analysis revealed that lateral root lifespan, root hair lifespan of the first lateral root, and root hair length significantly correlated with potassium accumulation. The root had similar regularity responses to low and high potassium stress except for lifespan and root hair length. The findings of this study enhance the understanding of the phenotype and lifespan of cotton’s lateral roots and root hairs under low and high potassium stress.
Tian et al. (2023) Response of in situ root phenotypes to potassium stress in cotton. PeerJ 11:e15587 https://doi.org/10.7717/peerj.15587
Identification of iron metabolism-related genes as prognostic indicators for papillary thyroid carcinoma: a retrospective study
Background The thyroid cancer subtype that occurs more frequently is papillary thyroid carcinoma (PTC). Despite a good surgical outcome, treatment with traditional antitumor therapy does not offer ideal results for patients with radioiodine resistance, recurrence, and metastasis. The evidence for the connection between iron metabolism imbalance and cancer development and oncogenesis is growing. Nevertheless, the iron metabolism impact on PTC prognosis is still indefinite. Methods Herein, we acquired the medical data and gene expression of individuals with PTC from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database. Typically, three predictive iron metabolism-related genes (IMRGs) were examined and employed to build a risk score (RS) model via the least absolute shrinkage and selection operator (LASSO) regression, univariate Cox, and differential gene expression analyses. Then we analyzed somatic mutation and immune cell infiltration among RS groups. We also validated the prognostic value of two IMRGs (SFXN3 and TFR2) by verifying their biological function through in vitro experiments. Results Based on RS, all patients with PTC were stratified into low- and high-risk groups, where Kaplan-Meier analysis indicated that disease-free survival (DFS) in the high-risk group was much lower than in the low-risk group (P < 0.0001). According to ROC analysis, the RS model successfully predicted the 1-, 3-, and 5-year DFS of individuals with PTC. Additionally, in the TCGA cohort, a nomogram model with RS was developed and exhibited a strong capability to anticipate PTC patients’ DFS. In the high-risk group, the enriched pathological processes and signaling mechanisms were detected utilizing the gene set enrichment analysis (GSEA). Moreover, the high-risk group had a significantly higher level of BRAF mutation frequency, tumor mutation burden, and immune cell infiltration than the low-risk group. In vitro experiments found that silencing SFXN3 or TFR2 significantly reduced cell viability. Conclusion Collectively, our predictive model depended on IMRGs in PTC, which could be potentially utilized to predict the PTC patients’ prognosis, schedule follow-up plans, and provide potential targets against PTC.
Jin et al. (2023) Identification of iron metabolism-related genes as prognostic indicators for papillary thyroid carcinoma: a retrospective study. PeerJ 11:e15592 https://doi.org/10.7717/peerj.15592