bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of single and combined applications of three root exudates of Sedum plumbizincicola on the phytoremediation efficiency of paddy soil contaminated with Cd
Authors: Xing Qianwen , Cao Xueying , Tan Changyin , Sun Lijuan , Deng Yueqiang , Yang Jia , Tu Chen
Published: January 2023

Root exudates are carriers for the transfer of material, energy and information between plant roots and soils. Plants encountering environmental stresses such as heavy metal pollution adapt to the environment by producing and secreting root exudates. In this study, laboratory soil culture experiment and pot experiment with Sedum plumbizincicola were used to study the effects of single and combined application of three root exudates, citric acid, glycine, and fructose, on the Cd-activation and phytoremediation of Cd-contaminated paddy soil. Results from the soil culture experiment showed that for the single application of root exudates, all three root exudates significantly activated the Cd in soil as presented by the increased content of diethylenetriamine pentaacetic acid extracted Cd (DTPA-Cd). In Particular, citric acid (SC) at a relatively low concentration (2 mmol/kg) exhibited the best Cd activation efficiency by increasing DTPA-Cd in the soil by 66.12%. For the combined application of root exudates, citric acid in combination with glycine (SC + G, 1:3) had the best activation effect on the Cd in the soil. In the phytoremediation pot experiment, both the single application of citric acid at a low concentrate (1 mmol/kg) and the combined application of citric acid and glycine (1:1) significantly reduced the total Cd and DTPA-Cd in the soil and increased the biomass and the content of Cd in S. plumbizincicola; thus, the phytoremediation efficiency of Cd-contaminated soil increased by 42.33% and 35.61%. The results from this study suggest that citric acid plays a crucial role in Cd activation and phytoremediation with single or combined applications with glycine. However, the mechanisms under the synergetic interaction between citric acid and glycine require further investigation.
A new method for classifying maize by combining the phenological information of multiple satellite-based spectral bands
Authors: Peng Qiongyan , Shen Ruoque , Dong Jie , Han Wei , Huang Jianxi , Ye Tao , Zhao Wenzhi , Yuan Wenping
Published: January 2023

Introduction: Using satellite data to identify the planting area of summer crops is difficult because of their similar phenological characteristics.

Methods: This study developed a new method for differentiating maize from other summer crops based on the revised time-weighted dynamic time warping (TWDTW) method, a phenology-based classification method, by combining the phenological information of multiple spectral bands and indexes instead of one single index. First, we compared the phenological characteristics of four main summer crops in Henan Province of China in terms of multiple spectral bands and indexes. The key phenological periods of each band and index were determined by comparing the identification accuracy based on the county-level statistical areas of maize. Second, we improved the TWDTW distance calculation for multiple bands and indexes by summing the rank maps of a single band or index. Third, we evaluated the performance of a multi-band and multi-period TWDTW method using Sentinel-2 time series of all spectral bands and some synthetic indexes for maize classification in Henan Province.

Results and Discussion: The results showed that the combination of red edge (740.2 nm) and short-wave infrared (2202.4 nm) outperformed all others and its overall accuracy of maize planting area was about 91.77% based on 2431 field samples. At the county level, the planting area of maize matched the statistical area closely. The results of this study demonstrate that the revised TWDTW makes effective use of crop phenological information and improves the extraction accuracy of summer crops’ planting areas over a large scale. Additionally, multiple band combinations are more effective for summer crops mapping than a single band or index input.
CO2 emissions from reed litter in the air and on the soil surface in the Yellow River Delta, China
Authors: Tao Baoxian , Wang Jingdong , Jiang Yuqing , Chen Qinghai , Zhang Baohua
Published: January 2023

The decay of litter in the air (that is, standing litter) and on the ground is an essential process of litter decomposition for many plant species. However, the contribution of standing litter to litter decomposition (e.g., CO2 emission) is still ambiguous, especially for non-leaf litter. In this study, we examined the CO2 emission from reed litter (Phragmites communis) in coastal wetlands in the Yellow River Delta (YRD), China. The results showed that the soil litter released more CO2 than the standing litter due to its rapid loss of labile organic carbon and high enzyme activities (that is, invertase and β-glucosidase). In contrast, cumulative CO2 emissions from standing litter were equivalent to 56%–70% of those on the soil surface, indicating that CO2 emissions from standing litter cannot be ignored. The sheath litter had the highest cumulative CO2 emission per unit of dry biomass among the three types of litter. Taking into account the biomass per unit area, the non-leaf litter (that is, culm and sheath) emitted more CO2 than leaf litter. On the daily scale, the litter released more CO2 at night than in the daytime, because low air temperature and high relative air humidity at night can help dew formation, accelerating CO2 emission at night. On the seasonal scale, air temperature and relative air humidity were positively related to CO2 emission, leading to rapid CO2 emission in summer and fall. The Q10 value of CO2 emission from standing litter (an average of 1.44) was lower than that of litter on the ground (an average of 2.16) due to a low residual rate of recalcitrant organic carbon in standing litter. Our findings highlight that standing litter decomposition should not be overlooked and suggest that more attention should be paid to the decay of non-leaf litter in the coastal wetland of the YRD.
Achieving carbon neutrality: How does the construction of national high-tech zones affect the green innovation of enterprises? Based on quasi-natural experiments in pilot areas in China
Authors: Liu Baoliu , Jin Xin , Zhao Pu , Li Zhou , Xia Jing
Published: January 2023

From the standpoint of green patents, verifying the influence of the construction of national high-tech zones on the degree of green innovation of enterprises is of enormous theoretical and practical importance. We construct a multi-period two-difference model to assess the influence of the national high-tech zone policy’s implementation on enterprises’ levels of green innovation. The outcomes of the study show that: first, the establishment of national high-tech zones greatly increases the level of green innovation among enterprises. While the effect on green and practical patents is average, the effect on green invention patents is more obvious. Second, how enterprises in national high-tech zones promote green innovation varies significantly. Promotional effects are more prominent in Tier 1 and Tier 2 regions, non-state firms, and high-tech industries with significant economic development. State-owned enterprises, non-high-tech industries, and third-tier and lower-tier regions, on the other hand, fared brilliantly. Third, additional action mechanisms show that the establishment of national high-tech zones can contribute to the institutional environmental effects of enterprises and the concentration of green innovation elements, thereby realizing regional green innovation development. Thus, our research provides an empirical foundation for stimulating the formation of national high-tech zones, increasing firms’ ability to innovate on their own, and nurturing the long-term growth of national high-tech zones and associated businesses.
Neurobehavioral characteristics of mice with SETD5 mutations as models of IDD23 and KBG syndromes
Authors: Nakagawa Tadashi , Hattori Satoko , Hosoi Toru , Nakayama Keiko
Published: January 2023

Genomic analysis has revealed that the genes for various chromatin regulators are mutated in many individuals with neurodevelopmental disorders (NDDs), emphasizing the important role of chromatin regulation in nervous system development and function. Chromatin regulation is mediated by writers, readers, and erasers of histone and DNA modifications, with such proteins being defined by specific domains. One of these domains is the SET domain, which is present in enzymes that catalyze histone methylation. Heterozygous loss-of-function mutations of the SETD5 (SET domain containing 5) gene have been identified in individuals with an NDD designated IDD23 (intellectual developmental disorder, autosomal dominant 23). KBG syndrome (named after the initials of the last names of the first three families identified with the condition) is characterized by features that either overlap with or are distinct from those of IDD23 and was initially thought to be caused only by mutations in the ANKRD11 (ankyrin repeat domain containing 11) gene. However, recent studies have identified SETD5 mutations in some KBG syndrome patients without ANKRD11 mutations. Here we summarize the neurobehavioral characterization of Setd5+/− mice performed by four independent research groups, compare IDD23 and KBG phenotypes, and address the utility and future development of mouse models for elucidation of the mechanisms underlying NDD pathogenesis, with a focus on SETD5 and its related proteins.
Epigenome-wide association studies of meat traits in Chinese Yorkshire pigs highlights several DNA methylation loci and genes
Authors: Wang Kai , Wang Shujie , Ji Xiang , Chen Dong , Shen Qi , Yu Yang , Wu Pingxian , Li Xuewei , Tang Guoqing
Published: January 2023

In this study, we aimed to identified CpG sites at which DNA methylation levels are associated with meat quality traits in 140 Yorkshire pigs, including pH at 45 min (pH45min), pH at 24 h (pH24h), drip loss (DL), meat redness value (a*), yellowness (b*) and lightness (L*). Genome-wide methylation levels were measured in muscular tissue using reduced representation bisulfite sequencing (RRBS). Associations between DNA methylation levels and meat quality traits were examined using linear mixed-effect models that were adjusted for gender, year, month and body weight. A Bonferroni-corrected p-value lower than 7.79×10−8 was considered statistically significant threshold. Eight CpG sites were associated with DL, including CpG sites annotated to RBM4 gene (cpg301054, cpg301055, cpg301058, cpg301059, cpg301066, cpg301072 and cpg301073) and NCAM1 gene (cpg1802985). Two CpG sites were associated with b*, including RNFT1 and MED13 (cpg2272837) and TRIM37 gene (cpg2270611). Five CpG sites were associated with L*, including GSDMA and LRRC3C gene (cpg2252750) and ENSSSCG00000043539 and IRX1 gene (cpg2820178, cpg2820179, cpg2820181 and cpg2820182). No significant associations were observed with pH45min, pH24h or a*. We reported associations of meat quality traits with DNA methylation and identified some candidate genes associated with these traits, such as NCAM1, MED13 and TRIM37 gene. These results provide new insight into the epigenetic molecular mechanisms of meat quality traits in pigs.
The prognosis difference between elderly and younger patients with adrenocortical carcinoma
Authors: He Shengyin , Huang Xuemei , Zhao Pan , Zhang Peng
Published: January 2023

Background and aim: Adrenocortical carcinoma (ACC) is uncommon in the elderly. This study aimed to compare the surgical prognosis and survival between senior and younger patients. We also explored the factors that were independently related to the survival of elderly patients.

Methods: We identified ACC patients between 2010 and 2019 in the Surveillance, Epidemiology, and End Results (SEER) database and applied Kaplan-Meier curves to evaluate the overall survival (OS) and cancer-specific survival (CSS) with log-rank tests. We also used Cox regression analysis to estimate the OS and CSS. The Fine and Gray model with the Gray test was used to measure the cumulative incidence function (CIF) of CSS and other mortality causes of patients in a competing-risks setting.

Results: Of 876 patients, 44.06% were elderly. A lower proportion of elderly patients underwent surgery, regional lymph node surgery, and chemotherapy than young patients. Elderly patients also had inferior OS and CSS than younger patients. The 1- and 5-year OS of elderly patients who underwent surgery were 68% [95% confidence interval (CI): 62%–74%] and 30% (95% CI: 24%–38%), and the 1- and 5-year CSS were 73% (95% CI: 67%–80%) and 40% (95% CI: 32%–47%). The factors independently related to worsened survival included age ≥60 [Hazard Ratio (HR): 1.47 (1.24–1.75)], metastatic disease [HR: 1.90 (1.49–2.51)], higher grade [HR: 1.94 (1.08–3.46)] and Network for the Study of Adrenal Tumors (ENSAT) stage [HR: 1.99 (1.48–2.66)].

Conclusion: Younger ACC patients had better survival than the elderly. Factors independently related to worsened survival in elderly patients included age ≥60, metastatic disease, higher grade, and European ENSAT stage.
Study of genetic variability, heritability, and genetic advance for yield-related traits in tomato (Solanum lycopersicon MILL.)
Authors: Rasheed Adnan , Ilyas Muhammad , Khan Taj Naseeb , Mahmood Athar , Riaz Usama , Chattha Muhammad Bilal , Al Kashgry Najla Amin T. , Binothman Najat , Hassan Muhammad Umair , Wu Ziming , Qari Sameer H.
Published: January 2023

Tomato is one of the most significant vegetable crops, which provides several important dietary components. Pakistan has a significant low tomato yield compared to other countries because of low genetic diversity and the absence of improved cultivars. The present study aimed to investigate the genetic variability, heritability, and genetic advance for yield and yield-related traits in tomato. For this purpose, eight tomato parents and their 15 crosses or hybrids were evaluated to study the relevant traits. Significant variation was observed for all studied traits. Higher values of the genotypic coefficient of variability (GCV) and phenotypic coefficient of variability (PCV) were recorded for yield per plant (YP) (kg) (37.62% and 37.79%), as well as the number of fruits per cluster (NFRC) (31.52% and 31.71%), number of flowers per cluster (24.63 and 24.67), and single fruit weight (g) (23.49 and 23.53), which indicated that the selection for these traits would be fruitful. Higher heritability (h2) estimates were observed for the number of flowers per cluster (NFC) (0.99%), single fruit weight (SFW) (g) (0.99%), and yield per plant (YP) (kg) (0.99%). Single fruit weight (SFW) (g) exhibited higher values for all components of variability. High genetic advance as a % of the mean (GAM) coupled with higher heritability (h2) was noted for the yield per plant (YP) (kg) (52.58%) and the number of fruits per cluster (NFRC) (43.91). NFRC and SFW (g) had a highly significant correlation with YP (kg), while FSPC had a significant positive association with YP (kg), and these traits can be selected to enhance YP (kg). Among the 15 hybrids, Nagina × Continental, Pakit × Continental, and Roma × BSX-935 were selected as high-yielding hybrids for further evaluation and analysis. These findings revealed that the best performing hybrids could be used to enhance seed production and to develop high-yielding varieties. The parents could be further tested to develop hybrids suitable for changing climatic conditions. The selection of YP (kg), SFW (g), NFC, and NFRC would be ideal for selecting the best hybrids.
Pan-cancer analyses reveal IGSF10 as an immunological and prognostic biomarker
Authors: Zhou Yongxia , Gao Manzhi , Jing Yaoyao , Wang Xiaofang
Published: January 2023

Background: IGSF10 is a member of the immunoglobulin superfamily. Over the previous decade, growing proof has validated definitive correlations between individuals of the immunoglobulin superfamily and human diseases. However, the function of IGSF10 in pan-cancer stays unclear. We aimed to analyze the immunological and prognostic value of IGSF10 in pan-cancer.

Methods: We utilized a vary of bioinformatic ways to inspect the function of IGSF10 in pan-cancer, including its correlation with prognosis, immune cell infiltration, tumor mutational burden (TMB), microsatellite instability (MSI), mismatch repair (MMR), DNA methyltransferases, genetic alteration, drug sensitivity, etc.

Results: We noticed low expression of IGSF10 in most cancer types. IGSF10 expression in tumor samples correlates with prognosis in most cancers. In most cancer types, IGSF10 expression was strongly related to immune cells infiltration, immune checkpoints, immune modulators, TMB, MSI, MMR, and DNA methyltransferases, among others. Functional enrichment analyses indicated that IGSF10 expression was involved in lymphocyte differentiation, cell molecules adhesion, etc. Furthermore, low IGSF10 expression could increase the drug sensitivity of many drugs.

Conclusion:IGSF10 could serve as a novel prognostic marker and attainable immunotherapy target for several malignancies.
Unravelling the instability of mutational signatures extraction via archetypal analysis
Authors: Pancotti Corrado , Rollo Cesare , Birolo Giovanni , Benevenuta Silvia , Fariselli Piero , Sanavia Tiziana
Published: January 2023

The high cosine similarity between some single-base substitution mutational signatures and their characteristic flat profiles could suggest the presence of overfitting and mathematical artefacts. The newest version (v3.3) of the signature database available in the Catalogue Of Somatic Mutations In Cancer (COSMIC) provides a collection of 79 mutational signatures, which has more than doubled with respect to previous version (30 profiles available in COSMIC signatures v2), making more critical the associations between signatures and specific mutagenic processes. This study both provides a systematic assessment of the de novo extraction task through simulation scenarios based on the latest version of the COSMIC signatures and highlights, through a novel approach using archetypal analysis, which COSMIC signatures are redundant and more likely to be considered as mathematical artefacts. 29 archetypes were able to reconstruct the profile of all the COSMIC signatures with cosine similarity >0.8. Interestingly, these archetypes tend to group similar original signatures sharing either the same aetiology or similar biological processes. We believe that these findings will be useful to encourage the development of new de novo extraction methods avoiding the redundancy of information among the signatures while preserving the biological interpretation.
Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus
Authors: Liu Dan , Qu Kai , Yuan Yangchen , Zhao Zhiheng , Chen Ying , Han Biao , Li Wei , El-Kassaby Yousry A. , Yin Yangyang , Xie Xiaoman , Tong Boqiang , Liu Hongshan
Published: January 2023

Clematis is one of the large worldwide genera of the Ranunculaceae Juss. Family, with high ornamental and medicinal value. China is the modern distribution centre of Clematis with abundant natural populations. Due to the complexity and high morphological diversity of Clematis, the genus is difficult to classify systematically, and in particular, the phylogenetic position of the endangered Clematis acerifolia is highly controversial. The use of the mitochondrial complete genome is a powerful molecular method that is frequently used for inferring plants phylogenies. However, studies on Clematis mitogenome are rare, thus limiting our full understanding of its phylogeny and genome evolution. Here, we sequenced and annotated the C. acerifolia mt genome using Illumina short- and Nanopore long-reads, characterized the species first complete mitogenome, and performed a comparative phylogenetic analysis with its close relatives. The total length of the C. acerifolia mitogenome is 698,247 bp and the main structure is multi-branched (linear molecule 1 and circular molecule 2). We annotated 55 genes, including 35 protein-coding, 17 tRNA, and 3 rRNA genes. The C. acerifolia mitogenome has extremely unconserved structurally, with extensive sequence transfer between the chloroplast and mitochondrial organelles, sequence repeats, and RNA editing. The phylogenetic position of C. acerifolia was determined by constructing the species mitogenome with 24 angiosperms. Further, our C. acerifolia mitogenome characteristics investigation included GC contents, codon usage, repeats and synteny analysis. Overall, our results are expected to provide fundamental information for C. acerifolia mitogenome evolution and confirm the validity of mitochondrial analysis in determining the phylogenetic positioning of Clematis plants.
Using whole genome sequence to compare variant callers and breed differences of US sheep
Authors: Stegemiller Morgan R. , Redden Reid R. , Notter David R. , Taylor Todd , Taylor J. Bret , Cockett Noelle E. , Heaton Michael P. , Kalbfleisch Theodore S. , Murdoch Brenda M.
Published: January 2023

As whole genome sequence (WGS) data sets have become abundant and widely available, so has the need for variant detection and scoring. The aim of this study was to compare the accuracy of commonly used variant calling programs, Freebayes and GATK HaplotypeCaller (GATK-HC), and to use U.S. sheep WGS data sets to identify novel breed-associated SNPs. Sequence data from 145 sheep consisting of 14 U.S. breeds were filtered and biallelic single nucleotide polymorphisms (SNPs) were retained for genotyping analyses. Genotypes from both programs were compared to each other and to genotypes from bead arrays. The SNPs from WGS were compared to the bead array data with breed heterozygosity, principal component analysis and identifying breed associated SNPs to analyze genetic diversity. The average sequence read depth was 2.78 reads greater with 6.11% more SNPs being identified in Freebayes compared to GATK-HC. The genotype concordance of the variant callers to bead array data was 96.0% and 95.5% for Freebayes and GATK-HC, respectively. Genotyping with WGS identified 10.5 million SNPs from all 145 sheep. This resulted in an 8% increase in measured heterozygosity and greater breed separation in the principal component analysis compared to the bead array analysis. There were 1,849 SNPs identified in only the Romanov sheep where all 10 rams were homozygous for one allele and the remaining 135 sheep from 13 breeds were homozygous for the opposite allele. Both variant calling programs had greater than 95% concordance of SNPs with bead array data, and either was suitably accurate for ovine WGS data sets. The use of WGS SNPs improved the resolution of PCA analysis and was critical for identifying Romanov breed-associated SNPs. Subsets of such SNPs could be used to estimate germplasm composition in animals without pedigree information.
An immune and epithelial–mesenchymal transition-related risk model and immunotherapy strategy for grade II and III gliomas
Authors: Luo Wei , Quan Qi , Jiang Jiaxin , Peng Roujun
Published: January 2023

Grade II and III gliomas are heterogeneous and aggressive diseases. More efficient prognosis models and treatment methods are needed. This study aims to construct a new risk model and propose a new strategy for grade II and III gliomas. The data were downloaded from The Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO), gene set enrichment analysis (GSEA), and the EMTome website for analysis. The Human Cell Landscape website and the Genomics of Drug Sensitivity in Cancer website were used for single-cell analysis and drug susceptibility analysis. Gene set enrichment analysis, gene function enrichment analysis, univariate and multivariate Cox regression analyses, Pearson’s correlation analysis, log-rank test, Kaplan–Meier survival analysis, and ROC analysis were performed. We constructed an immune-related prognostic model associated with the isocitrate dehydrogenase 1 (IDH1) mutation status. By analyzing the immune microenvironment of patients with different risk scores, we found that high-risk patients were more likely to have an inflammatory immune microenvironment and a higher programmed death ligand-1 (PD-L1) expression level. Epithelial–mesenchymal transition (EMT)-related gene sets were significantly enriched in the high-risk group, and the epithelial–mesenchymal transition phenotype was associated with a decrease in CD8+ T cells and an increase in M2 macrophages. Transforming growth factor-β (TGF-β) signaling was the most important signaling in inducing epithelial–mesenchymal transition, and TGFB1/TGFBR1 was correlated with an increase in CD8+ T cytopenia and M2 macrophages. Survival analysis showed that simultaneous low expression of TGFBR1 and PD-L1 had better survival results. Through single-cell analysis, we found that TGFB1 is closely related to microglia and macrophages, especially M2 macrophages. Finally, we discussed the sensitivity of TGFB1 inhibitors in gliomas using cell line susceptibility data. These results demonstrated a potential immunotherapy strategy in combination with the TGFB1/TGFBR1 inhibitor and PD-1/PD-L1 inhibitor for grade II and III gliomas.
Sweetpotato cultivars responses to interactive effects of warming, drought, and elevated carbon dioxide
Authors: Taduri Shasthree , Bheemanahalli Raju , Wijewardana Chathurika , Lone Ajaz A. , Meyers Stephen L. , Shankle Mark , Gao Wei , Reddy K. Raja
Published: January 2023

Plants are sensitive to changes projected in climates, such as elevated carbon dioxide (eCO2), high temperature (T), and drought stress (DS), which affect crop growth, development, and yield. These stresses, either alone or in combination, affect all aspects of sweetpotato plant growth and development, including storage root development and yield. We tested three sweetpotato cultivars (Beauregard, Hatteras, and LA1188) responses to eight treatments (Control, DS, T, eCO2, DS + T, T + eCO2,DS + eCO2,DS + T + eCO2). All treatments were imposed 36 days after transplanting (DAP) and continued for 47 days. Treatments substantially affected gas exchange, photosynthetic pigments, growth, and storage root components. Cultivars differed considerably for many of the measured parameters. The most significant negative impact of DS was recorded for the shoot and root weights. The combination of DS + T had a significant negative effect on storage root parameters. eCO2alleviated some of the damaging effects of DS and high T in sweetpotato. For instance, eCO2alone or combined with DS increased the storage root weights by 22% or 42% across all three cultivars, respectively. Based on the stress response index, cultivar “Hatteras” was most tolerant to individual and interactive stresses, and “LA 1188” was sensitive. Our findings suggest that eCO2negates the negative impact of T or DS on the growth and yield of sweetpotato. We identified a set of individual and interactive stress-tolerant traits that can help select stress cultivars or breed new lines for future environments.
Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfish Pangasianodon hypophthalmus
Authors: Vu Nguyen Thanh , Phuc Tran Huu , Nguyen Nguyen Hong , Van Sang Nguyen
Published: January 2023

Common full-sib families (c2) make up a substantial proportion of total phenotypic variation in traits of commercial importance in aquaculture species and omission or inclusion of the c2 resulted in possible changes in genetic parameter estimates and re-ranking of estimated breeding values. However, the impacts of common full-sib families on accuracy of genomic prediction for commercial traits of economic importance are not well known in many species, including aquatic animals. This research explored the impacts of common full-sib families on accuracy of genomic prediction for tagging weight in a population of striped catfish comprising 11,918 fish traced back to the base population (four generations), in which 560 individuals had genotype records of 14,154 SNPs. Our single step genomic best linear unbiased prediction (ssGLBUP) showed that the accuracy of genomic prediction for tagging weight was reduced by 96.5%–130.3% when the common full-sib families were included in statistical models. The reduction in the prediction accuracy was to a smaller extent in multivariate analysis than in univariate models. Imputation of missing genotypes somewhat reduced the upward biases in the prediction accuracy for tagging weight. It is therefore suggested that genomic evaluation models for traits recorded during the early phase of growth development should account for the common full-sib families to minimise possible biases in the accuracy of genomic prediction and hence, selection response.
Full-length transcriptome of in Medicago sativa L. roots in response to drought stress
Authors: Fang Zhihong , Liu Jianning , Wu Xinming , Zhang Yan , Jia Huili , Shi Yonghong
Published: January 2023

Background: Alfalfa (Medicago sativa L.), serves as a legume with high drought tolerance, is a major forage crop with a high biomass of production. However, the molecular mechanism of Alfalfa in response to drought stress are still unclear.

Results: We constructed the first full-length transcriptome for Alfalfa root. 21.53Gb clean data were obtained by further data filtering, in which incorporate 566,076 reads of Insert (ROI), and 409,291 full length reads non-Chimeric (FLNC) sequences. Combined with second-generation sequencing (SGS), there were 2615, 6011, and 4617 differentially expressed genes (DEGs) in three comparisons. KEGG pathway analysis showed enrichment of ribosome, glutathione metabolism, and biosynthesis of amino acids are among the DEGs. The majority of transcription factors (TFs) from DEGs were AP2/ERF-ERF (37), C2H2 (32), and bHLH (22) bZIP (22), followed by C3H (19), MYB (18), WRKY (18), GRAS (16), and NAC (15). 32 C2H2 genes were differentially expressed in three groups. In addition, TFs annotated as C3H (19), MYB (18), GRAS (16), and NAC (15) also changed significantly in expression in the three comparisons. We found 24 genes participate in the abscisic acid (ABA) and auxin hormone signaling pathway in response to drought stress, and monitored the expression patterns of these related genes.

Conclusion: The present study enhanced our understanding of the genetic diversity and complexity, and provides greater insight into the fundamental transcriptome reprogramming of Alfalfa under drought.
Improper preanalytical processes on peripheral blood compromise RNA quality and skew the transcriptional readouts of mRNA and LncRNA
Authors: He Yinli , Dong Lele , Yi Hongyang , Zhang Linpei , Shi Xue , Su Lin , Gan Baoyu , Guo Ruirui , Wang Yawen , Luo Qinying , Li Xiaojiao
Published: January 2023

Genetic and epigenetic reprogramming caused by disease states in other tissues is always systemically reflected in peripheral blood leukocytes (PBLs). Accurate transcriptional readouts of Messenger RNA (mRNA) and Long non-coding RNA (lncRNA) in peripheral blood leukocytes are fundamental for disease-related study, diagnosis and treatment. However, little is known about the impact of preanalytical variables on RNA quality and downstream messenger RNA and Long non-coding RNA readouts. In this study, we explored the impact of RNA extraction kits and timing of blood placement on peripheral blood leukocyte-derived RNA quality. A novel enhanced evaluation system including RNA yields, purity, RNA integrity number (RIN) values and β-actin copies was employed to more sensitively identify RNA quality differences. The expression levels of informative mRNAs and Long non-coding RNAs in patients with chronic obstructive pulmonary disease (COPD) or triple-negative breast cancer (TNBC) were measured by Quantitative reverse transcription polymerase chain reaction (qRT–PCR) to investigate the impact of RNA quality on transcriptional readouts. Our results showed that the quality of RNA extracted by different kits varies greatly, and commercial kits should be evaluated and managed before batch RNA extraction. In addition, the quality of extracted RNA was highly correlated with the timing of blood placement, and the copy number of β-actin was significantly decreased after leaving blood at RT over 12 h. More importantly, compromised RNA leads to skewed transcriptional readouts of informative mRNAs and Long non-coding RNAs in patients with chronic obstructive pulmonary disease or triple-negative breast cancer. These findings have significant implications for peripheral blood leukocyte-derived RNA quality management and suggest that quality control is necessary prior to the analysis of patient messenger RNA and Long non-coding RNA expression.
Developing a pyroptosis-related gene signature to better predict the prognosis and immune status of patients with head and neck squamous cell carcinoma
Authors: Liu Dan , Zhou Liu-Qing , Cheng Qing , Wang Jun , Kong Wei-Jia , Zhang Su-Lin
Published: January 2023

Chronic inflammation may promote the incidence and development of neoplasms. As a pro-inflammatory death pathway, pyroptosis could induce normal cells to transform into cancerous cells, but the potential effect of pyroptosis in head and neck squamous cell carcinoma (HNSCC) remains unclear. This study developed and evaluated a pyroptosis-related gene signature to predict the prognosis and immune status of patients with HNSCC. The gene expression, mutation information, and clinical characteristics of HNSCC were extracted from TCGA to establish a comprehensive genome database (GEO). Based on LASSO Cox regression model, nine pyroptosis-related genes (TTLL1, TRIML2, DYNC1I1, KLHL35, CAMK2N1, TNFRSF18, GLDC, SPINK5, and DKK1) were used to construct a pyroptosis-related gene signature, which had good ability to predict the prognosis of HNSCC. Furthermore, the expression of nine pyroptosis-related genes in HNSCC and paracancerous tissues was detected by quantitative real-time PCR (qRT-PCR). The potential immunotherapeutic features and drug sensitivity prediction of this signature were also explored. Because pyroptosis regulators play an important role in HNSCC development and prognoses, further exploration might assist in identifying new biomarkers and predictors of prognosis to benefit clinical identification and management.
Screening and identifying a novel M-MDSCs-related gene signature for predicting prognostic risk and immunotherapeutic responses in patients with lung adenocarcinoma
Authors: Wang Geng-Chong , Zhou Mi , Zhang Yan , Cai Hua-Man , Chiang Seok-Theng , Chen Qi , Han Tian-Zhen , Li Rong-Xiu
Published: January 2023

Background: Lung adenocarcinoma (LUAD) shows intratumoral heterogeneity, a highly complex phenomenon that known to be a challenge during cancer therapy. Considering the key role of monocytic myeloid-derived suppressor cells (M-MDSCs) in the tumor microenvironment (TME), we aimed to build a prognostic risk model using M-MDSCs-related genes.

Methods: M-MDSCs-related genes were extracted from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Utilized univariate survival analysis and random forest algorithm to screen candidate genes. A least absolute shrinkage and selection operator (LASSO) Cox regression analysis was selected to build the risk model. Patients were scored and classified into high- and low-risk groups based on the median risk scores. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis along with R packages “estimate” and “ssGSEA” were performed to reveal the mechanism of risk difference. Prognostic biomarkers and tumor mutation burden (TMB) were combined to predict the prognosis. Nomogram was carried out to predict the survival probability of patients in 1, 3, and 5 years.

Results: 8 genes (VPREB3, TPBG, LRFN4, CD83, GIMAP6, PRMT8, WASF1, and F12) were identified as prognostic biomarkers. The GEO validation dataset demonstrated the risk model had good generalization effect. Significantly enrichment level of cell cycle-related pathway and lower content of CD8+ T cells infiltration in the high-risk group when compared to low-risk group. Morever, the patients were from the intersection of high-TMB and low-risk groups showed the best prognosis. The nomogram demonstrated good consistency with practical outcomes in predicting the survival rate over 1, 3, and 5 years.

Conclusion: The risk model demonstrate good prognostic predictive ability. The patients from the intersection of low-risk and high-TMB groups are not only more sensitive response to but also more likely to benefit from immune-checkpoint-inhibitors (ICIs) treatment.
Identification of oxidative stress-related genes and potential mechanisms in atherosclerosis
Authors: Tang Chao , Deng Lingchen , Luo Qiang , He Guijun
Published: January 2023

Atherosclerosis (AS) is the main cause of death in individuals with cardiovascular and cerebrovascular diseases. A growing body of evidence suggests that oxidative stress plays an essential role in Atherosclerosis pathology. The aim of this study was to determine genetic mechanisms associated with Atherosclerosis and oxidative stress, as well as to construct a diagnostic model and to investigate its immune microenvironment. Seventeen oxidative stress-related genes were identified. A four-gene diagnostic model was constructed using the least absolute shrinkage and selection operator (LASSO) algorithm based on these 17 genes. The area under the Receiver Operating Characteristic (ROC) curve (AUC) was 0.967. Based on the GO analysis, cell-substrate adherens junction and focal adhesion were the most enriched terms. KEGG analysis revealed that these overlapping genes were enriched in pathways associated with Alzheimer’s disease and Parkinson’s disease, as well as with prion disease pathways and ribosomes. Immune cell infiltration correlation analysis showed that the immune cells with significant differences were CD4 memory activated T cells and follicular helper T cells in the GSE43292 dataset and CD4 naïve T cells and CD4 memory resting T cells in the GSE57691 dataset. We identified 17 hub genes that were closely associated with oxidative stress in AS and constructed a four-gene (aldehyde dehydrogenase six family member A1 (ALDH6A1), eukaryotic elongation factor 2 kinase (EEF2K), glutaredoxin (GLRX) and l-lactate dehydrogenase B (LDHB)) diagnostic model with good accuracy. The four-gene diagnostic model was also found to have good discriminatory efficacy for the immune cell infiltration microenvironment of AS. Overall, these findings provide valuable information and directions for future research into Atherosclerosis diagnosis and aid in the discovery of biological mechanisms underlying AS with oxidative stress.
Feasibility and acceptability of an adapted environmental enrichment intervention for endometriosis: A pilot study
Authors: Nieves-Vázquez Cristina I. , Detrés-Marquéz Amanda C. , Torres-Reverón Annelyn , Appleyard Caroline B. , Llorens-De Jesús Astrid P. , Resto Ivana N. , López-Rodríguez Verónica , Ramos-Echevarría Paola M. , Castro Eida M. , Flores Idhaliz
Published: January 2023

Introduction

We have previously shown that Environmental Enrichment (EE)-consisting of social support, novelty, and open spaces—decreased disease progression and anxiety in a rat model of endometriosis. We developed a novel EE intervention to be tested in a pilot randomized clinical trial (RCT) in patients with endometriosis, a painful, stressful disease.

Objective

To translate and evaluate the feasibility and acceptability of an adapted EE intervention as an adjuvant to standard-of-care for endometriosis patients.

Methods

Feasibility was assessed through recruitment, enrollment, and adherence rates. Acceptability was evaluated through a post-intervention survey and focus group discussion 3-months after the end of the intervention.

Results

Of the 103 subjects recruited, 64 were randomized to the intervention group and 39 to the control group. At the start of the intervention, the study groups consisted of 29 (intervention) and 27 (control) subjects. Enrollment rates were 45.3% and 69.2%, and adherence rates were 41.4% and 100% for the intervention and control groups, respectively. Delays resulting from natural events (earthquakes, the COVID-19 pandemic) impacted enrollment and adherence rates. The most common reasons for missing an intervention were period pain (39.1%) and work-study (34.8%). There was high acceptability (>80%) of the intervention's logistics. The majority (82.4%) of subjects would continue participating in support groups regularly, and 95.7% would recommend the intervention to other patients.

Conclusions

We showed that EE could be translated into an acceptable integrative multi-modal therapy perceived as valuable among participants who completed the intervention. High attrition/low adherence indicates that additional refinements would be needed to improve feasibility. Acceptability data indicate that EE has the potential to be integrated into the clinical management of patients with endometriosis and other inflammatory, painful disorders. Studies are ongoing to assess the efficacy of EE in improving pain symptoms, mental health, and quality of life (QoL).
Transfer factors peptides (Imuno TF®) modulate the lung inflammation and airway remodeling in allergic asthma
Authors: Oliveira Carlos Rocha , Carvalho Jessica , Olímpio Fabiana , Vieira Rodolfo , Aimbire Flavio , Polonini Hudson
Published: January 2023

Background

Allergic asthma is a chronic lung disease in which the lung inflammation and airway remodeling are orchestrated by both the inflammatory and the immune cells that creates a lung millieu that favors the perpetuation of clinical symptoms. The cell signaling in asthma involves the mast cells activation during initial contact with the allergen and, principally, the participation of eosinophils as well as Th2 cells which determine increased levels of IgE, exaggerated secretion of mucus and collagen, and bronchial hyperreactivity. Moreover, allergic asthma presents lower level of cytokines associated to the both Th1 and Treg cells response, and it implies in deficiency of anti-inflammatory response to counterregulate the exaggerated inflammation against allergen. Therefore, the equilibrium between cytokines as well as transcription factors associated to Th2, Th1, and Treg cells is compromised in allergic asthma. Imuno TF® is a food supplement with ability to interfere in immune system pathways. It has been previously demonstrated that Imuno TF® upregulated Th1 cell response whilst downregulated Th2 cell response in human lymphocytes.

Objective

For this reason, we hypothesized that the Imuno TF effect could be restore the balance between Th1/Th2 CD4 T cells response in murine allergic asthma.

Methods

Initially, animals were sensitized with OVA via i.p. and challenged with OVA i.n. on days 14, 15 and 16. Treatment with Imuno TF once a day was performed via orogastric from day 17 to day 20. Mice were euthanized on day 21.

Results

The Imuno TF reduced eosinophilia, mucus production, and airway remodeling (collagen deposition) in asthma mice. Imuno TF influenced cellular signaling associated to allergic asthma once downregulated STAT6 expression as well as decreased IL-4, IL-5, and IL-13 in lung and serum. In addition, Imuno TF restored T-bet and Foxp3 expression as well as increased IL-12, IFN-ɣ, and IL-10.

Conclusion

Ultimately, Imuno TF mitigated the allergic asthma due to the restoration of balance between the responses of Th1/Th2 as well as Treg cells, and their respective transcription factors the T-bet/STAT6 and Foxp3.
Comprehensive autoantibody profiles in systemic sclerosis: Clinical cluster analysis
Authors: Höppner Jakob , Tabeling Christoph , Casteleyn Vincent , Kedor Claudia , Windisch Wolfram , Burmester Gerd Rüdiger , Huscher Dörte , Siegert Elise
Published: January 2023

Background

Systemic sclerosis (SSc) belongs to the group of connective tissue diseases and is associated with the occurrence of disease-specific autoantibodies. Although it is still controversial whether these antibodies contribute to pathogenesis, there are new insights into the development of these specific antibodies and their possible pathophysiological properties. Interestingly, they are associated with specific clinical manifestations, but for some rarer antibodies this association is not fully clarified. The aim of this study is a comprehensive analysis of the serum autoantibody status in patients with SSc followed by correlation analyses of autoantibodies with the clinical course of the disease.

Methods

Serum from SSc patients was analyzed using a line blot (EUROLINE, EUROIMMUN AG) for SSc-related autoantibodies. Autoantibodies to centromere, Topo-1, antimitochondrial antibodies (AMA) M2 subunit, angiotensin II type 1 receptors (AT1R) and endothelin-1 type-A-receptors (ETAR) were also determined by ELISA. We formed immunological clusters and used principal components analysis (PCA) to assign specific clinical characteristics to these clusters.

Results

A total of 372 SSc patients were included. 95.3% of the patients were antinuclear antibody positive and in 333 patients at least one SSc specific antibody could be detected. Four immunological clusters could be found by PCA. Centromere, Topo-1 and RP3 all formed own clusters, which are associated with distinct clinical phenotypes. We found that patients with an inverted phenotype, such as limited cutaneous SSc patients within the Topo-1 cluster show an increased risk for interstital lung disease compared to ACA positive patients. Anti-AT1R and anti-ETAR autoantibodies were measured in 176 SSc patients; no association with SSc disease manifestation was found. SSc patients with AMA-M2 antibodies showed an increased risk of cardiovascular events.

Conclusion

In our in large cluster analysis, which included an extended autoantibody profile, we were able to show that serologic status of SSc patients provides important clues to disease manifestation, co-morbidities and complications. Line blot was a reliable technique to detect autoantibodies in SSc and detected rarer autoantibodies in 42% of our patients.