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Background: Brain magnetic resonance imaging voxel-based morphometry (VBM) and perfusion single-photon emission computed tomography (SPECT) are useful for differentiating dementia with Lewy bodies (DLB) from Alzheimer's disease (AD). Purpose: To determine whether combining multiple parameters of VBM and SPECT using a multiparametric scoring system (MSS) improves diagnostic accuracy in differentiating DLB from AD. Material and Methods: In total, 23 patients with DLB and 57 patients with AD underwent imaging using a voxel-based specific regional analysis system for AD (VSRAD), an easy Z-score imaging system, and a Z-Graph using three-dimensional stereotactic surface projection. The cutoff values were determined using the receiver operating characteristic curve to differentiate DLB from AD for all parameters. Patients were scored 1 (DLB) or 0 (AD) for each statistically significant parameter, according to a threshold. The total score was determined for each case to obtain a cutoff value for the MSS. Results: The mean Z-scores in the medial temporal lobes using the VSRAD were significantly lower in patients with DLB than in those with AD. Each Z-score of the summed Z-scores in all four segmented regions of the occipital lobes using the Z-Graph was significantly higher in patients with DLB than in those with AD. Among the five parameters, the highest accuracy was 80% for the Z-score of the summed Z-scores in the left medial occipital lobe. For the MSS, a cutoff value of four improved the diagnostic accuracy to 82%. Conclusion: MSS was more accurate than any single parameter of VBM or SPECT in differentiating DLB from AD. [ABSTRACT FROM AUTHOR]

Societal Impact Statement Advancements in science and technology enable us to address the challenges of the times: hunger, malnutrition, climate change, and dwindling natural resources. One of the most significant innovations in food and agriculture is the advent of genetic engineering, which may help us address the aforementioned challenges. Millions of people could benefit from the application of genetically engineered crops in agriculture and food. However, it is vital that biosafety assessments of unintended effects are carried out to identify any potential risks to humans, the environment, or society. Summary The study compared the extent of siRNA, transcriptomic and metabolomic changes in the leaves of four RNAi‐based genetically engineered rice lines to evaluate whether RNAi‐based genetically engineered rice that is resistant to black‐streaked dwarf virus experiences changes not seen in the non‐genetically engineered counterpart. siRNA, transcriptome, and metabolome profiling were conducted. siRNAs with different lengths and abundance were highly enriched in the transcript of rice; however, relative expression analysis of eight potential off‐target genes revealed that there was no decrease in gene expression in the RNAi‐based genetically engineered lines, meaning that no off‐target phenomena were caused as a result of siRNA derived from invert repeat sequences of rice black‐streaked dwarf virus in this study. This study identified some differentially expressed genes and differentially accumulated metabolites in the RNAi‐based genetically engineered lines; however, they were not enriched in pathways detrimental for humans, animals and the environment. Only 30 differentially expressed genes were significantly enriched in the plant hormone signal transduction pathway via a combined analysis using two‐way orthogonal partial least squares model. These genes belonging to salicylic acid, jasmonic acid, cytokinin, abscisic acid, and brassinosteroid pathway involved in pathways related to virus resistance or infection response were significantly changed. Taken together, there was no off‐target in RNAi‐based genetically engineered rice lines and may have a positive effect on virus resistance overall in this study.

Societal Impact Statement: Advancements in science and technology enable us to address the challenges of the times: hunger, malnutrition, climate change, and dwindling natural resources. One of the most significant innovations in food and agriculture is the advent of genetic engineering, which may help us address the aforementioned challenges. Millions of people could benefit from the application of genetically engineered crops in agriculture and food. However, it is vital that biosafety assessments of unintended effects are carried out to identify any potential risks to humans, the environment, or society. Summary: The study compared the extent of siRNA, transcriptomic and metabolomic changes in the leaves of four RNAi‐based genetically engineered rice lines to evaluate whether RNAi‐based genetically engineered rice that is resistant to black‐streaked dwarf virus experiences changes not seen in the non‐genetically engineered counterpart.siRNA, transcriptome, and metabolome profiling were conducted. siRNAs with different lengths and abundance were highly enriched in the transcript of rice; however, relative expression analysis of eight potential off‐target genes revealed that there was no decrease in gene expression in the RNAi‐based genetically engineered lines, meaning that no off‐target phenomena were caused as a result of siRNA derived from invert repeat sequences of rice black‐streaked dwarf virus in this study.This study identified some differentially expressed genes and differentially accumulated metabolites in the RNAi‐based genetically engineered lines; however, they were not enriched in pathways detrimental for humans, animals and the environment. Only 30 differentially expressed genes were significantly enriched in the plant hormone signal transduction pathway via a combined analysis using two‐way orthogonal partial least squares model. These genes belonging to salicylic acid, jasmonic acid, cytokinin, abscisic acid, and brassinosteroid pathway involved in pathways related to virus resistance or infection response were significantly changed.Taken together, there was no off‐target in RNAi‐based genetically engineered rice lines and may have a positive effect on virus resistance overall in this study. [ABSTRACT FROM AUTHOR]

Fractional vegetation cover (FVC) is a crucial indicator to estimate degradation and desertification for grasslands. However, traditional small-scale FVC analysis methods, such as visual estimation and point-sampling, are cumbersome and imprecise. Innovative methods like image-based FVC analysis methods, while accurate, face challenges such as complex analytical procedures and the necessary training for operations. Therefore, in this study, a combined application of ImageJ and Photoshop was employed to achieve a more effective analysis of FVC values in desertification areas. Our results showed that the FVC results obtained by combination of Photoshop and ImageJ were dependable and precise (R2 > 0.98), demonstrating equivalency to results obtained through either visual estimation or Photoshop-based methods. Furthermore, even in the face of background interference and varied shooting angles, the combination of ImageJ and Photoshop software was still able to maintain a low error rate when analyzing FVC values (average error rate = − 2.6%). In conclusion, the imaged-based combined FVC analysis method employed in our research was an effective, precise, and efficient technique for analyzing small-scale FVC, promising substantial improvement over conventional methods. [ABSTRACT FROM AUTHOR]

Lilium brownii var. viridulum, known as Longya lily, is a well-known medicinal and edible plant in China. Bulb rot is a common disease in Longya lily cultivation that severely affects the yield and quality of lilies. According field investigations, we found that different Longya lily plants in the same field had different degrees of resistance to root rot. To find the reasons leading to the difference, we performed metabolomic and transcriptomic analyses of Longya lily with different degrees of disease. The transcriptomic analyses showed that the number of differentially expressed genes increased in early and mid-stage infections (LYBH2 and LYBH3), while decreased in late-stage infection (LYBH4). A total of 2309 DEGs showed the same expression trend in diseased bulb compared healthy bulb (LYBH1). The transcription factors (TFs) analysis of DEGs showed that several common TFs, like WRKY, bHLH, AP2/ERF-ERF and MYB, were significantly activated in bulbs after decay. The metabolomic analyses showed that there were 794 differentially accumulated metabolites, and metabolites with significant changes in relative content largely were phenolic acids, followed by flavonoids and amino acids and derivatives. The combined analysis of transcriptome and metabolome indicated that phenylpropanoid biosynthesis pathway was crucial in Longya lily resistance to bulb rot. Therefore, we speculated that the different degree of resistance to bulb rot in Longya lily may be related to the transcript levels of gene and contents of metabolites in the phenylpropanoid biosynthesis pathway. Overall, these results elucidate the molecular responses of Longya lily to bulb rot and lay a theoretical foundation for breeding resistant varieties.

Experiments to evaluate the performance of 10 bread wheat genotypes with nitrogen deficiency and diagnose the optimal genotype for the appropriate environment commenced in the winter seasons, 2021-2022 and 2022-2023, in three locations of Iraq, i.e., Baghdad, Wasit, and Diwaniyah. All the experiments had a randomized complete block design (RCBD) with split-plot arrangement. Nitrogen levels (0, 50, and 100 kg N ha-1) occupied the prime plots, with 10 wheat genotypes (T2, T3, S1, S2, S148, IPA99, Adana99, Rasheed, Buhooth-10, and Buhooth-22) allocated to the subplots with three replications in each location. The interaction of wheat genotypes, nitrogen levels, and locations revealed that genotype S2 with 50 kg N ha-1 at Baghdad showed the highest mean nitrogen use efficiency at 105.00 and 96.00 for 2021-2022 and 2022- 2023, respectively. However, these values showed nonsignificant differences from the obtained values of wheat genotypes S148 and the IPA-99 during the second season, in the same location and fertilizer level, i.e., 92.87 and 90.00, respectively. Also, the genotype S2 gave the highest grain yield (6.53 t ha-1) with N2 fertilizer level in the Baghdad site, not differing significantly from two other wheat genotypes, S148 and IPA99 (6.13 and 5.85 t ha-1, respectively) in the second season. The presented study authenticated that some wheat genotypes provided good yield under nitrogen stress (50 kg N ha-1), as there were no significant increases in grain yield when doubling the nitrogen level (100 kg N ha-1). Therefore, the study suggested these genotypes' cultivation with nitrogen deficiency to preserve a healthy environment and promote sustainable agriculture. [ABSTRACT FROM AUTHOR]

Introduction: Bone metastasis (BoM) occurs when cancer cells spread from their primary sites to a bone. Currently, the mechanism underlying this metastasis process remains unclear. Methods: In this project, through an integrated analysis of bulk-sequencing and single-cell RNA transcriptomic data, we explored the BoM-related features in tumor microenvironments of different tumors. Results: We first identified 34 up-regulated genes during the BoM process in breast cancer, and further explored their expression status among different components in the tumor microenvironment (TME) of BoM samples. Enriched EMP1+ fibroblasts were found in BoM samples, and a COL3A1-ADGRG1 communication between these fibroblasts and cancer cells was identified which might facilitate the BoM process. Moreover, a significant correlation between EMP1 and COL3A1 was identified in these fibroblasts, confirming the potential connection of these genes during the BoM process. Furthermore, the existence of these EMP1+/COL3A1+ fibroblasts was also verified in prostate cancer and renal cancer BoM samples, suggesting the importance of these fibroblasts from a pan-cancer perspective. Discussion: This study is the first attempt to investigate the relationship between fibroblasts and BoM process across multi-tumor TMEs. Our findings contribute another perspective in the exploration of BoM mechanism while providing some potential targets for future treatments of tumor metastasis. [ABSTRACT FROM AUTHOR]

Castration-resistant prostate cancer (CRPC) represents one type of advanced prostate cancer (PCa) with a median survival time of 1–2 years. Currently, there is a lack of reliable gene panels in predicting hormone treatment (HT) responses due to limited knowledge of CRPC-specific tumor-microenvironment (TME) characteristics. In this study, we first screened for up-regulated genes in CRPC samples using bulk-sequencing data retrieved from TCGA online database, and further investigated the expression status of these genes in four sets of downloaded single-cell RNA sequencing (scRNAseq) data: GSE117403 containing 16 normal human prostate samples; GSE141445 containing 13 PCa samples; GSE176031 containing 11 PCa samples and GSE137829 containing 6 CRPC samples. We identified a series of CRPC-specific TME characteristics including an enriched number of PEG10+ neuroendocrine cells, elevated expression of PPIB/CCDC74A/GAPDH/AR genes in tumor cells, increased expression of FAP/TGFB1 in cancer-associated fibroblasts (CAFs), suppressed immune environment featured by enhanced M2 macrophage polarization, T cell exhaustion and increased number of regulatory B cells. We further established a 12-gene panel using these characteristics and showed that this panel could separate CRPC samples from PCa samples (AUC of 0.78), and CRPC patients with higher panel scores tended to have treatment failure or progression (R = −0.47, p = 0.019). Based on these unique TME characteristics of CRPC, we established a prediction tool for estimating the duration of HT responses in PCa treatment. Our results suggest mechanisms by which prostate cancer becomes castrate resistant. Further study of PEG10 (and/or others) to evaluate therapeutic efficacy should be considered. Increased number of PEG10+ neuroendocrine cells is associated with recurrence of HT PCa patients A 12-gene panel could be used to predict duration of HT responses in PCa treatment [ABSTRACT FROM AUTHOR]

Tomato spotted wilt virus (TSWV) is ranked among the top 10 most destructive viruses globally. It results in abnormal leaf growth, stunting, and even death, significantly affecting crop yield and quality. Phytohormones play a crucial role in regulating plant-virus interactions. However, there is still limited research on the effect of TSWV on phytohormone levels, particularly growth hormones and genes involved in the phytohormone pathway. In our study, we combined phytohormone metabolomics and transcriptomics to examine the impact of TSWV infection on phytohormone content and gene expression profile. Metabolomic results showed that 41 metabolites, including major phytohormones and their precursors and derivatives were significantly altered after 14 days of TSWV inoculation tobacco plants cvK326, with 31 being significantly increased and 10 significantly reduced. Specifically, the levels of abscisic acid (ABA) and jasmonoyl-isoleucine (JA-Ile) were significantly reduced. The levels of indole-3-acetic acid (IAA) have remained unchanged. However, the levels of cytokinin isopentenyladenine (iP) and salicylic acid (SA) significantly increased. The transcriptome analysis revealed 2,746 genes with significant changes in expression. Out of these, 1,072 genes were significantly downregulated, while 1,674 genes were significantly upregulated. Among them, genes involved in ABA synthesis and signaling pathways, such as 9-cis-epoxycarotenoid dioxygenase (NCED), protein phosphatase 2C (PP2C), serine/threonine-protein kinase (SnRK2), and abscisic acid responsive element binding factor (ABF), exhibited significant downregulation. Additionally, expression of the lipoxygenase gene LOX, Jasmonate ZIM domain-containing protein gene JAZ, and transcription factor gene MYC were significantly down-regulated. In the cytokinin pathway, while there were no significant changes in the expression of the cytokinin synthesis genes, a significant downregulation of transcriptionally active factor type-B response regulators (type-B RRs) was observed. In terms of SA synthesis and signaling pathways, the isochorismate synthase gene ICS1 and the pathogenesis-related gene PR1 were significantly upregulated. These results can strengthen the theoretical foundation for understanding the interaction between TSWV and tobacco and provide new insights for the future prevention and control of TSWV.

IntroductionBone metastasis (BoM) occurs when cancer cells spread from their primary sites to a bone. Currently, the mechanism underlying this metastasis process remains unclear.MethodsIn this project, through an integrated analysis of bulk-sequencing and single-cell RNA transcriptomic data, we explored the BoM-related features in tumor microenvironments of different tumors.ResultsWe first identified 34 up-regulated genes during the BoM process in breast cancer, and further explored their expression status among different components in the tumor microenvironment (TME) of BoM samples. Enriched EMP1+ fibroblasts were found in BoM samples, and a COL3A1-ADGRG1 communication between these fibroblasts and cancer cells was identified which might facilitate the BoM process. Moreover, a significant correlation between EMP1 and COL3A1 was identified in these fibroblasts, confirming the potential connection of these genes during the BoM process. Furthermore, the existence of these EMP1+/COL3A1+ fibroblasts was also verified in prostate cancer and renal cancer BoM samples, suggesting the importance of these fibroblasts from a pan-cancer perspective.DiscussionThis study is the first attempt to investigate the relationship between fibroblasts and BoM process across multi-tumor TMEs. Our findings contribute another perspective in the exploration of BoM mechanism while providing some potential targets for future treatments of tumor metastasis.

AbstractBackground Castration-resistant prostate cancer (CRPC) represents one type of advanced prostate cancer (PCa) with a median survival time of 1–2 years. Currently, there is a lack of reliable gene panels in predicting hormone treatment (HT) responses due to limited knowledge of CRPC-specific tumor-microenvironment (TME) characteristics.Methods In this study, we first screened for up-regulated genes in CRPC samples using bulk-sequencing data retrieved from TCGA online database, and further investigated the expression status of these genes in four sets of downloaded single-cell RNA sequencing (scRNAseq) data: GSE117403 containing 16 normal human prostate samples; GSE141445 containing 13 PCa samples; GSE176031 containing 11 PCa samples and GSE137829 containing 6 CRPC samples.Results We identified a series of CRPC-specific TME characteristics including an enriched number of PEG10+ neuroendocrine cells, elevated expression of PPIB/CCDC74A/GAPDH/AR genes in tumor cells, increased expression of FAP/TGFB1 in cancer-associated fibroblasts (CAFs), suppressed immune environment featured by enhanced M2 macrophage polarization, T cell exhaustion and increased number of regulatory B cells. We further established a 12-gene panel using these characteristics and showed that this panel could separate CRPC samples from PCa samples (AUC of 0.78), and CRPC patients with higher panel scores tended to have treatment failure or progression (R = −0.47, p = 0.019).Conclusions Based on these unique TME characteristics of CRPC, we established a prediction tool for estimating the duration of HT responses in PCa treatment. Our results suggest mechanisms by which prostate cancer becomes castrate resistant. Further study of PEG10 (and/or others) to evaluate therapeutic efficacy should be considered.

The Ta/Cr/Pt three‐layer system can be used as a planar x‐ray waveguide, that is to say it can guide an x‐ray beam inside its chromium layer. This property comes from the difference in density and hence in optical index between the two "heavy" or cladding tantalum and platinum layers and the "light" or guiding chromium layer. The waveguide will be efficient provided the layers are a few nanometers thick and that the interfaces are as sharp as possible. To control the quality of the stack, we combine grazing incidence x‐ray fluorescence (GIXRF) and x‐ray reflectivity (XRR) measurements on a series of Ta/Cr/Pt samples, whose only difference is the thickness of the Cr layer. The three considered samples have been deposited by magnetron sputtering and their designed structures are: Ta (8 nm)/Cr (5, 10, and 15 nm)/Pt (14 nm)/Si substrate. The combination of XRR and GIXRF tightens constraints on the parameters used to simulate the stack: thickness, roughness, composition, and density of the layers and their interlayers. For each sample we used six GIXRF curves obtained from three different characteristic x‐ray lines (Ta Lα, Cr Kα, and Pt Lβ2,15) excited at three different incident photons energies (6.25, 10, and 12 keV) as well as one XRR curve obtained at 6.25 keV. The XRR‐GIXRF combined analysis demonstrates that the Ta/Cr/Pt structure is too simplistic and that it is necessary to introduce some interlayers at the top and bottom of the stacks to obtain a reliable agreement between the experimental and simulated GIXRF and XRR curves. [ABSTRACT FROM AUTHOR]

Genotype by environment (Location) interaction (GEI) is essential for identifying environment-specific and widely adapted genotypes of wheat. The experiment was carried out across five locations (Shyampur and Godagari under Rajshahi district, Nachole at Chapainawabganj, Sapahar at Naogaon and Lalpur at Natore district in north-west Bangladesh) to assess GEI effects on grain yield and its components and to identify high yielding and stable genotypes of wheat for grain yield in the year of 2020-21. Combined analyses of variance for G and GEI were significant for almost all traits. Significant GEI suggested that the performance of genotypes was not consistent across locations, revealing strong influence of environments on the expression of phenotype for all traits. Average over five locations, genotypes G84 (3647 kg ha-1) and G76 (3576 kg ha-1) exhibited maximum values for grain yield and also produced similar tillers m-2 (SPM) and grains spike-1 (GPS) where difference between them was statistically insignificant thus appeared as leading genotypes for yield and production traits. Again, the genotypes G84 and G76 produced statistically insignificant maximum yield in all locations indicating that they are high yielding and wide adapted genotypes. The genotype G80 produced insignificant yield and other yield traits with G76 and G84 across the locations indicating its wide adaptability. However, G26, G69 and G77 with higher grain yield in Shyampur, G53 and G59 in Godagari ,G20 in Lalpur, G3 in Nachole and G8 in Sapahar proved their specific adaptability in particular locations. Among locations, Shyampur and Godagari were identified as highly productive locations in terms of grain yield and positive environmental index. Correlation analysis showed that grain yield had strong positive association with spikes m-2 (r = 0.92**), grains spike-1 (r = 0.72**) and TGW (r = 0.89**). On the basis of mean grain yield and higher positive phenotypic index for SPM, GPS, TGW and GY, G76, the genotypes G84,G76 and G80 were found as high yielding genotypes and thus could be recommended as important breeding materials in upcoming specific breeding program for drought prone north-west part of Bangladesh. [Fundam Appl Agric 2023; 8(1.000): 423-434]

New plant-type (NPT) rice can increase grain yield globally. Although many studies have shown the association between harvest and yield-related traits in rice, it remains obscure in the case of NPT rice. This study aimed to elucidate the relationship between agronomic and yield features in new plant-type rice based on a 12-years multi-experiment. A large dataset of 704 NPT rice lines of various generations (F4 to F10), derived from 24 different populations, underwent study. The analysis of variance showed a highly significant population effect (P < 0.01) on all traits studied. The NPT rice populations had groupings into four clusters, with a highly substantial cluster effect (P < 0.01) on the number of total tillers (NTT), number of total grains (NTG), number of filled grains (NFG), and thousand-grain weight (TGW). Standard best NPT lines from each experiment achieved an average of 1.67 t ha-1 or 26% higher yield than the Ciherang variety. Determining the yield advantage of NPT lines was by higher plant height (PH) (r = 0.37), panicle length (PL) (r = 0.15), NTG (r = 0.28), NFG (r = 0.28), TGW (r = 0.10), and lower days to harvest (DTH) (r = -0.10). The principal component analysis biplot revealed that NFG could better serve as a selection characteristic for enhancing grain yield in developing NPT rice adapted to irrigated tropical ecosystems. [ABSTRACT FROM AUTHOR]

The texture of fresh jujube fruit is related to its popularity and commercial value. The metabolic networks and essential genes that regulate the texture of jujube (Ziziphus jujuba) fruit are still unknown. In this study, two jujube cultivars with significantly different textures were selected by a texture analyzer. The four developmental stages of the exocarp and mesocarp of jujube fruit were studied separately using metabolomic and transcriptomic analyses. Differentially accumulated metabolites were enriched in several critical pathways related to cell wall substance synthesis and metabolism. Transcriptome analysis confirmed this by finding enriched differential expression genes in these pathways. Combined analysis showed that 'Galactose metabolism' was the most overlapping pathway in two omics. Genes such as β-Gal, MYB and DOF may affect fruit texture by regulating cell wall substances. Overall, this study provides an essential reference for the establishment of texture-related metabolic and gene networks of jujube fruit. [ABSTRACT FROM AUTHOR]

Knowledge about the extent of genotype in environment interaction is helpful for farmers and plant breeders. This is because it helps them choose the proper strategies for agricultural management and breeding new cultivars. The main contribution of this paper is to investigate genotype on environmental interaction using the GGE biplot method (Genotype and the Genotype-by-Environment) in ten canola cultivars. The experimental design was a randomized complete block design (RCBD) with three replications to assess the stability of grain yield of ten canola cultivars in five regions of Iran, including Birjand, Karaj, Kashmar, Sanandaj, and Shiraz, within two agricultural years of 2016 and 2017. The results of combined ANOVA illustrated that the effects of the environment, genotype × environment, and genotype were highly significant at 1%. Variance Analysis showed that three environmental impacts, genotype, and interaction of genotype in the environment effect, produced 68.44%, 18.63%, and 12.9% of the total variance. The GGE biplot graphs were constructed using PCA. The first principle component (PC1) explained 65.3%, and the second (PC2) explained 18.8% of the total variation. The research examined polygon diagrams to identify two top genotypes and four mega-environments. Also, the appropriate genotypes for each environment were diagnosed. Using the GGE biplot, it was possible to make visual comparisons and identify superior genotypes in canola. Accordingly,. The results obtained from graphical analysis indicated that Licord, Hyola 401 and Okapi genotypes showed the highest yield and were selected as the most stable genotypes. Also, Karaj region was chosen as a experimental region where the screening of genotypes was very suitable. Based on the ranking of the genotypes in the most suitable region (Karaj), Okapi genotype was selected as the desired genotype. In examining the heatmap drawn between the genotypes and the investigated environments, a lot of similarity between the genotypes of Sarigal, Hyola 401 and Okapi was observed in the investigated environments. The GGE biplot graphs enabled the detection of stable and superior environments and the grouping of cultivars and environments based on grain yield. The results of this research can be used both for extension and for future breeding programs. Our results provide helpful information about the canola genotypes and environments for future breeding programs. [ABSTRACT FROM AUTHOR]

Highlights: Water-bearing causes substantial reductions in the tensile strength of rocks under four-point bending. There is an obvious correlation between dominant frequency bands of acoustic emission waveform and failure modes. The water-bearing effect on rock tensile strength can be characterized by the failure components associated with it. Tensile strength degradation of rocks under four-point bending can be attributed to friction weakening and fracture energy reduction. [ABSTRACT FROM AUTHOR]

Powdery mildew is a serious problem in tomato production; therefore, the PM-resistant tomato inbred line, '63187', and the susceptible tomato variety, 'Moneymaker (MM)', were used as experimental materials for the combined analysis of transcriptome and widely targeted metabolome on tomato leaves at 0 h post inoculation (hpi), 12 hpi, and 48 hpi. The results indicated that 276 genes were expressed in all treatments, and the K-means cluster analysis showed that these genes were divided into eight classes in '63187' and ten classes in 'MM'. KEGG enrichment showed that amino acid metabolism, signal transduction, energy metabolism, and other secondary metabolites biosynthesis pathways were significantly enriched. Interestingly, the analysis of WRKY family transcription factors (TFs) showed that the expression of four TFs in '63187' increased with no obvious change in 'MM'; and the expression of one TF in 'MM' increased with no obvious change in '63187'. The combined analysis revealed that both phenylpropanoid biosynthesis and flavonoid biosynthesis pathways were enriched in '63187' and 'MM'. In '63187', six metabolites involved in this pathway were downregulated, and four genes were highly expressed, while in 'MM', three metabolites were upregulated, four metabolites were downregulated, and ten genes were highly expressed. These metabolites and genes might be candidates for PM resistance or susceptibility in subsequent studies. These results provide favorable molecular information for the study of the different resistances of tomatoes to PM, and they provide a basis for the breeding of tomato varieties resistant to PM. [ABSTRACT FROM AUTHOR]

Myostatin (MSTN), a growth and differentiation factor, plays an important role in regulating skeletal muscle growth and development. MSTN knockout (MSTN-KO) leads to skeletal muscle hypertrophy and regulates metabolic homeostasis. Moreover, MSTN is also detected in smooth muscle. However, the effect of MSTN-KO on smooth muscle has not yet been reported. In this study, combined metabolome and transcriptome analyses were performed to investigate the metabolic and transcriptional profiling in esophageal smooth muscles of MSTN-KO Chinese Luxi Yellow cattle (n = 5, 24 months, average body weight 608.5 ± 17.62 kg) and wild-type (WT) Chinese Luxi Yellow cattle (n = 5, 24 months, average body weight 528.25 ± 11.03 kg). The transcriptome was sequenced using the Illumina Novaseq™ 6000 sequence platform. In total, 337 significantly up- and 129 significantly down-regulated genes were detected in the MSTN-KO cattle compared with the WT Chinese Luxi Yellow cattle. Functional enrichment analysis indicated that the DEGs were mainly enriched in 67 signaling pathways, including cell adhesion molecules, tight junction, and the cGMP-PKG signaling pathway. Metabolomics analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) identified 130 differential metabolites between the groups, with 56 up-regulated and 74 down-regulated in MSTN knockout cattle compared with WT cattle. Differential metabolites were significantly enriched in 31 pathways, including glycerophospholipid metabolism, histidine metabolism, glutathione metabolism, and purine metabolism. Transcriptome and metabolome were combined to analyze the significant enrichment pathways, and there were three metabolically related pathways, including histidine metabolism, purine metabolism, and arginine and proline metabolism. These results provide important references for in-depth research on the effect of MSTN knockout on smooth muscle. [ABSTRACT FROM AUTHOR]

From bi-parental pure-inbred lines (PIL), immortalized backcross (i.e., IB1 and IB2, representing the two directions of backcrossing) and F2 (i.e., IF2) populations can be developed. These populations are suitable for genetic studies on heterosis, due to the present of both homozygous and heterozygous genotypes, and in the meantime allow repeated phenotyping trials across multiple locations and years. In this study, we developed a combined approach of quantitative trait locus (QTL) mapping, when some or all of the four immortalized populations (i.e., PIL, IB1, IB2, and IF2) are available. To estimate the additive and dominant effects simultaneously and accurately, suitable transformations are made on phenotypic values from different populations. When IB1 and IB2 are present, summation and subtraction are used. When IF2 and PIL are available, mid-parental values and mid-parental heterosis are used. One-dimensional genomic scanning is performed to detect the additive and dominant QTLs, based on the algorithm of inclusive composite interval mapping (ICIM). The proposed approach was applied to one IF2 population together with PIL in maize, and identified ten QTLs on ear length, showing varied degrees of dominance. Simulation studies indicated the proposed approach is similar to or better than individual population mapping by QTL detection power, false discovery rate (FDR), and estimated QTL position and effects. [ABSTRACT FROM AUTHOR]

Asparagus belongs to the Liliaceae family and has important economic and pharmacological value. Lignin plays a crucial role in cell wall structural integrity, stem strength, water transport, mechanical support and plant resistance to pathogens. In this study, various biological methods were used to study the mechanism of shading on the asparagus lignin accumulation pathway. The physiological results showed that shading significantly reduced stem diameter and cell wall lignin content. Microstructure observation showed that shading reduced the number of vascular bundles and xylem area, resulting in decreased lignin content, and thus reducing the lignification of asparagus. Cinnamic acid, caffeic acid, ferulic acid and sinapyl alcohol are crucial intermediate metabolites in the process of lignin synthesis. Metabolomic profiling showed that shading significantly reduced the contents of cinnamic acid, caffeic acid, ferulic acid and sinapyl alcohol. Transcriptome profiling identified 37 differentially expressed genes related to lignin, including PAL, C4H, 4CL, CAD, CCR, POD, CCoAOMT, and F5H related enzyme activity regulation genes. The expression levels of POD, CCoAOMT, and CCR genes were significantly decreased under shading treatment, while the expression levels of CAD and F5H genes exhibited no significant difference with increased shading. The downregulation of POD, CCoAOMT genes and the decrease in CCR gene expression levels inhibited the activities of the corresponding enzymes under shading treatment, resulting in decreased downstream content of caffeic acid, ferulic acid, sinaperol, chlorogenic acid and coniferin. A significant decrease in upstream cinnamic acid content was observed with shading, which also led to decreased downstream metabolites and reduced asparagus lignin content. In this study, transcriptomic and metabolomic analysis revealed the key regulatory genes and metabolites of asparagus lignin under shading treatment. This study provides a reference for further understanding the mechanism of lignin biosynthesis and the interaction of related genes. [ABSTRACT FROM AUTHOR]

Background: In this study, the impact of integrated nutrient management practice in cereal based cropping sequence has been examined. A detail study about the impact of INM in the above cropping system for last 8 years has been carried out. Methods: On-station research experiments were conducted at Karjat centre of district Raigad of Maharashtra, under the ICAR-Indian Institute of Farming Systems Research, Modipuram, Meerut of ICAR-All India Co-ordinated Research Project during the years 2010- 11 to 2017-18 on integrated nutrient supply (INM) system in rice-rice (Oryza sativa L.) cropping system at Karjat. Result: 100% recommended NPK dose through fertilizers was identified as the best INM practice at Karjat during kharif season. A detail study about the impact of INM in the above cropping system for last 8 years has been carried out and presented in tabular as well as graphical view both. [ABSTRACT FROM AUTHOR]

Rice breeding with genetic background of Iranian cultivars provides an opportunity to improve these cultivars that have high adaptability to the environment and favorable marketability. Therefore, seven promising lines, orginiated from cross combinations of Iranian and exotic rice genotypes, along with two check varieties including Tarom-Mahali and Shiroudi were evaluated in four experimental fields in Mazandaran provinces located in east zone (Behshahr), centre (Babol), west (Tonekabon) and Rice Research Instutute (Amol) in a randomized complete block design (RCBD) with three replicates during 2016-2017 (totally eight environments). Results of simple variance analysis showed that there were significant differences between genotypes for number of days to 50% of flowering, plant height, number of fertile tillers and grain yield. Combined analysis variance indicated that the effect of genotype and interaction effects of year and location and also year and location and genotype on grain yield were siginificant. G5 genotype had the highest yield in all environments and G1 genotype was in the second place in terms of yield. Stability analysis through AMMI method indicated that rice promising line G5 (DAH, originated from cross between Dasht and Ahlami-tarom) showed high of grain yield (5888.7 Kg/ha in average) and performed stable situation over environments, G1 genotype (AHS, a cross between Ahlami-tarom and Sepidroud) with 5312.1 Kg grain yield /ha in average, showed moderate stability in most of the environments. [ABSTRACT FROM AUTHOR]

To explore the molecular mechanisms of the antifungal compound phenazine1-carboxamide (PCN) inhibits Rhizoctonia solani and discover potential targets of action, we performed an integrated analysis of transcriptome and metabolome in R. solani mycelium by whether PCN treating or not. A total of 511 differentially expressed genes (DEGs) were identified between the PCN treatment and control groups. The fluorescence-based quantitative PCR (qPCR) got the accordant results of the gene expression trends for ten randomly selected DEGs. The Gene Ontology (GO) enrichment analysis revealed that fatty acid metabolic process, fatty acid oxidation, and lipid oxidation were among the most enriched in the biological process category, while integral component of membrane, plasma membrane, and extracellular region were among the most enriched in the cellular component category and oxidoreductase activity, cofactor binding, and coenzyme binding were among the most enriched in the molecular function category. KEGG enrichment analysis revealed the most prominently enriched metabolic pathways included ATP-binding cassette (ABC) transporters, nitrogen metabolism, aminobenzoate degradation. The DEGs related functions of cellular structures, cell membrane functions, cellular nutrition, vacuolemitochondrion membrane contact site and ATPase activity, pH, antioxidation, were downregulated. A total of 466 differential metabolites were found between the PCN treatment and control groups after PCN treatment. KEGG enrichment found purine, arachidonic acid, and phenylpropanoid biosynthesis pathways were mainly affected. Further results proved PCN decreased the mycelial biomass and protein content of R. solani, and superoxide dismutase (SOD) activity reduced while peroxidase (POD) and cytochrome P450 activities increased. The molecule docking indicted that NADPH nitrite reductase, ATP-binding cassette transporter, alpha/beta hydrolase family domain-containing protein, and NADPH-cytochrome P450 reductase maybe the particular target of PCN. In conclusion, the mechanisms via which PCN inhibits R. solani AG1IA may be related to cell wall damage, cell membrane impairment, intracellular nutrient imbalance, disturbed antioxidant system, and altered intracellular pH, which laid foundation for the further new compound designing to improve antifungal efficacy. [ABSTRACT FROM AUTHOR]

Physical attacks, including passive Side-Channel Analysis and active Fault Injection Analysis, are considered among the most powerful threats against physical cryptographic implementations. These attacks are well known and research provides many specialized countermeasures to protect cryptographic implementations against them. Still, only a limited number of combined countermeasures, i.e., countermeasures that protect implementations against multiple attacks simultaneously, were proposed in the past. Due to increasing complexity and reciprocal effects, design of efficient and reliable combined countermeasures requires longstanding expertise in hardware design and security. With the help of formal security specifications and adversary models, automated verification can streamline development cycles, increase quality, and facilitate development of robust cryptographic implementations. In this work, we revise and refine formal security notions for combined protection mechanisms and specifically embed them in the context of hardware implementations. Based on this, we present the first automated verification framework that can verify physical security properties of hardware circuits with respect to combined physical attacks. To this end, we conduct several case studies to demonstrate the capabilities and advantages of our framework, analyzing secure building blocks (gadgets), S-boxes build from Toffoli gates, and the ParTI scheme. For the first time, we reveal security flaws in analyzed structures due to reciprocal effects, highlighting the importance of continuously integrating security verification into modern design and development cycles.

The texture of fresh jujube fruit is related to its popularity and commercial value. The metabolic networks and essential genes that regulate the texture of jujube (Ziziphus jujuba) fruit are still unknown. In this study, two jujube cultivars with significantly different textures were selected by a texture analyzer. The four developmental stages of the exocarp and mesocarp of jujube fruit were studied separately using metabolomic and transcriptomic analyses. Differentially accumulated metabolites were enriched in several critical pathways related to cell wall substance synthesis and metabolism. Transcriptome analysis confirmed this by finding enriched differential expression genes in these pathways. Combined analysis showed that ‘Galactose metabolism’ was the most overlapping pathway in two omics. Genes such as β-Gal, MYB and DOF may affect fruit texture by regulating cell wall substances. Overall, this study provides an essential reference for the establishment of texture-related metabolic and gene networks of jujube fruit.

Myostatin (MSTN), a growth and differentiation factor, plays an important role in regulating skeletal muscle growth and development. MSTN knockout (MSTN-KO) leads to skeletal muscle hypertrophy and regulates metabolic homeostasis. Moreover, MSTN is also detected in smooth muscle. However, the effect of MSTN-KO on smooth muscle has not yet been reported. In this study, combined metabolome and transcriptome analyses were performed to investigate the metabolic and transcriptional profiling in esophageal smooth muscles of MSTN-KO Chinese Luxi Yellow cattle (n = 5, 24 months, average body weight 608.5 ± 17.62 kg) and wild-type (WT) Chinese Luxi Yellow cattle (n = 5, 24 months, average body weight 528.25 ± 11.03 kg). The transcriptome was sequenced using the Illumina Novaseq™ 6000 sequence platform. In total, 337 significantly up- and 129 significantly down-regulated genes were detected in the MSTN-KO cattle compared with the WT Chinese Luxi Yellow cattle. Functional enrichment analysis indicated that the DEGs were mainly enriched in 67 signaling pathways, including cell adhesion molecules, tight junction, and the cGMP-PKG signaling pathway. Metabolomics analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) identified 130 differential metabolites between the groups, with 56 up-regulated and 74 down-regulated in MSTN knockout cattle compared with WT cattle. Differential metabolites were significantly enriched in 31 pathways, including glycerophospholipid metabolism, histidine metabolism, glutathione metabolism, and purine metabolism. Transcriptome and metabolome were combined to analyze the significant enrichment pathways, and there were three metabolically related pathways, including histidine metabolism, purine metabolism, and arginine and proline metabolism. These results provide important references for in-depth research on the effect of MSTN knockout on smooth muscle.

Powdery mildew is a serious problem in tomato production; therefore, the PM-resistant tomato inbred line, ‘63187’, and the susceptible tomato variety, ‘Moneymaker (MM)’, were used as experimental materials for the combined analysis of transcriptome and widely targeted metabolome on tomato leaves at 0 h post inoculation (hpi), 12 hpi, and 48 hpi. The results indicated that 276 genes were expressed in all treatments, and the K-means cluster analysis showed that these genes were divided into eight classes in ‘63187’ and ten classes in ‘MM’. KEGG enrichment showed that amino acid metabolism, signal transduction, energy metabolism, and other secondary metabolites biosynthesis pathways were significantly enriched. Interestingly, the analysis of WRKY family transcription factors (TFs) showed that the expression of four TFs in ‘63187’ increased with no obvious change in ‘MM’; and the expression of one TF in ‘MM’ increased with no obvious change in ‘63187’. The combined analysis revealed that both phenylpropanoid biosynthesis and flavonoid biosynthesis pathways were enriched in ‘63187’ and ‘MM’. In ‘63187’, six metabolites involved in this pathway were downregulated, and four genes were highly expressed, while in ‘MM’, three metabolites were upregulated, four metabolites were downregulated, and ten genes were highly expressed. These metabolites and genes might be candidates for PM resistance or susceptibility in subsequent studies. These results provide favorable molecular information for the study of the different resistances of tomatoes to PM, and they provide a basis for the breeding of tomato varieties resistant to PM.

In nature, many different factors cause plants to develop variegated leaves. To explore the mechanism of variegated leaf formation in Pteroceltis tatarinowii, a mutant variety ('Jinyuyuan'), which was induced by ethylmethylsulfone, was selected, and its morphological structure, physiology, biochemistry, transcription and metabolism were analysed. According to differences in colour values, the colours were divided into two regions: a green region and a yellow-green region. The chlorophyll content of the two regions was significantly different. Moreover, the yellow-green regions of the leaves were significantly thinner than the green regions. The chloroplast ultrastructure in the yellow-green region revealed small chloroplasts, large vacuoles, small starch grains, obviously increased numbers of osmophilic grains, loose lamellae of the inner capsule and thin lamellae. Moreover, the yellow-green region was accompanied by oxidative stress, and the activity of the oxidative phosphorylation pathway related to oxidative activity in the transcriptome showed an upward trend. Vitamin B6 and proline contents also increased, indicating that the antioxidant activity of cells in the yellow-green region increased. Transcriptomic and metabolomic analysis showed that the differentially expressed genes (DEGs) related to chlorophyll synthesis and metabolism led to a decrease in the photosynthesis and then a decrease in the assimilation ability and contents of sucrose, starch and other assimilates. Amino acid synthesis and metabolism, lipid synthesis and the activity of metabolic pathways were obviously downregulated, and the contents of differentially accumulated metabolites associated with amino acids and lipids were also reduced. At the same time, 31 out of 32 DEGs involved in the flavonoid synthesis pathway were downregulated, which affected leaf colour. We hypothesized that the variegated leaves of P. tatarinowii 'Jinyuyuan' are caused by transcriptional and post-transcriptional regulation. Mutations in pigment and flavonoid synthesis pathway genes and transcription factor genes directly affect both pigment and flavonoid synthesis and degradation rate, which in turn affect carbon assimilation, carbon fixation, related protein synthesis and enzyme activity, lipid synthesis and degradation and the activity of other metabolic pathways, eventually leading to the formation of different colour regions. [ABSTRACT FROM AUTHOR]

Thyroid nodules are present in upto 50% of the population worldwide, and thyroid malignancy occurs in only 5–15% of nodules. Until now, fine-needle biopsy with cytologic evaluation remains the diagnostic choice to determine the risk of malignancy, yet it fails to discriminate as benign or malignant in one-third of cases. In order to improve the diagnostic accuracy and reliability, molecular testing based on transcriptomic data has developed rapidly. However, gene signatures of thyroid nodules identified in a plenty of transcriptomic studies are highly inconsistent and extremely difficult to be applied in clinical application. Therefore, it is highly necessary to identify consistent signatures to discriminate benign or malignant thyroid nodules. In this study, five independent transcriptomic studies were combined to discover the gene signature between benign and malignant thyroid nodules. This combined dataset comprises 150 malignant and 93 benign thyroid samples. Then, there were 279 differentially expressed genes (DEGs) discovered by the feature selection method (Student's t test and fold change). And the weighted gene co-expression network analysis (WGCNA) was performed to identify the modules of highly co-expressed genes, and 454 genes in the gray module were discovered as the hub genes. The intersection between DEGs by the feature selection method and hub genes in the WGCNA model was identified as the key genes for thyroid nodules. Finally, four key genes (ST3GAL5, NRCAM, MT1F, and PROS1) participated in the pathogenesis of malignant thyroid nodules were validated using an independent dataset. Moreover, a high-performance classification model for discriminating thyroid nodules was constructed using these key genes. All in all, this study might provide a new insight into the key differentiation of benign and malignant thyroid nodules. [ABSTRACT FROM AUTHOR]

Background: Teff is an important staple cereal crop in northwestern Ethiopia. However, the yield of the crop is very low due to, among others, lack of stable and high yielding varieties under varying environmental conditions because of genotype x environment interaction effect. Objective: The study was conducted to assess the effect of genotype by environment interaction, identify mega environments, and select high yielding and stable teff genotypes that interact less with the changing environment. Materials and Methods: Twenty improved teff varieties were evaluated using a randomized complete block design with three replications at Adet, Motta, Bichena, Debre-Tabor and Takussa districts for two consecutive years. Data were collected on days to heading and maturity, plant height, grain filling period, panicle and culm length, dry plant biomass and grain yield. The data were analyzed using a combined analysis of variance and genotype main effect plus genotype by environment interaction biplot. Results: The combined analysis of variance for grain yield revealed highly significant (P < 0.001) effects for genotype (16%), environment (54%) and genotype x environment interaction (23%). The effect of environment was three times higher than that of genotype, indicating significant and undesirable influence of the environment on genotype stability. The mean grain yield across the environments ranged from 1.65 to 2.77 tons ha-1 for Debre-Tabor and Takussa, respectively. The genotype mean yield ranged from 1.68 to 2.51 tons ha-1 for Simada and Hiber-1, respectively. Genotype by environment interaction biplot analysis grouped the ten test environments and twenty genotypes into three mega-environments and four genotype groups. Besides, Adet district and Bichena district had relatively the longest vector length and the smallest angles with the average environmental axis, thus being the most representative of all environments. Regarding genotypes, Hiber -1 followed by Kora, Etsub and Dukem were identified as the best yielding and relatively stable genotypes to increase teff productivity in the region. Conclusion: The biplot analysis of the genotype by environment interaction resulted in the identification of Adet and Bichena districts as the most favorable locations for teff production and as well as Hiber-1 as the most productive teff variety for cultivation in the study area. This implies that farmers in the two districts could be advised to take up this variety for enhancing yield of the crop and income from its production. [ABSTRACT FROM AUTHOR]

The relationship between urban economic growth and environmental quality is analyzed? which is significant to the high-quality and sustainable development of the city; Per capita GDP of Xi' an from 1999 to 2018 was selected as economic indicators, and industrial waste gas emissions, industrial waste water emissions, and industrial solid waste generation were selected as environmental quality indicators, performing the EKC compliance test and establishing analysis model on this basis, carrying out the EKC joint analysis of environmental pollution coefficient of industry "three wastes? and per capita GDP; In the past 20 years，with the increase of per capita GDP，environmental pollution indicators of Xi' an has shown a trend of turning from bad to good, taken as a whole, which is in line with the" inverted U・shaped" of EKC relationship ・ Xi' an is at the right end of the inflection point at present stage; With the high-quality continuous pushing of social and economic development in Xi' an，the environmental quality of Xi' an is continuously amelioratin and maintaining a trend of improving. [ABSTRACT FROM AUTHOR]

Abstract Background & Objective: This study was conducted to investigate the effect of moving averages, olive yield, elimination of Biennial bearing effect and data purification to study yield stability of some olive genotypes. Materials & Methods: For this purpose, 100 genotypes and cultivars during 6 years, from 1391 to 96, were planted at Tarom Research Station in Zanjan province. This experiment was performed based in a randomized complete block design (RCBD) with three replications. After collecting performance data based on kilogram / tree, in order to correct the data and eliminate the noise caused by the Biennial bearing effect of annoying, data analysis was performed based on the original and corrected data, respectively. Results: The results showed that the environmental component of the total variance for the corrected data decreased from 35.74% to 19.61%. Also, the heritability component increased from 15.02 to 38.51%. The paired t-test for the pair of corresponding years confirmed the significant difference between the mean and the corrected mean data. Using genotypic variation coefficient and mean yield, it was determined that at least three genotypes 'NO7', 'KHBA' and ' MANZANILLA' of state change are in stability. Also, with respect to eight other computational stability parameters, in most cases, genotypes were ranked with rank change Conclusion: Finally, it was determined that interfering with or eliminating the Biennial bearing effects can significantly affect the selection of stable genotypes. According the importance of eliminating the effects of Biennial bearing during the study period, it is necessary to apply the calculations on genetic material to the corrected data to determine the truth of the genetic potential of genotypes to show true and heritability compatibility.

Thyroid nodules are present in upto 50% of the population worldwide, and thyroid malignancy occurs in only 5–15% of nodules. Until now, fine-needle biopsy with cytologic evaluation remains the diagnostic choice to determine the risk of malignancy, yet it fails to discriminate as benign or malignant in one-third of cases. In order to improve the diagnostic accuracy and reliability, molecular testing based on transcriptomic data has developed rapidly. However, gene signatures of thyroid nodules identified in a plenty of transcriptomic studies are highly inconsistent and extremely difficult to be applied in clinical application. Therefore, it is highly necessary to identify consistent signatures to discriminate benign or malignant thyroid nodules. In this study, five independent transcriptomic studies were combined to discover the gene signature between benign and malignant thyroid nodules. This combined dataset comprises 150 malignant and 93 benign thyroid samples. Then, there were 279 differentially expressed genes (DEGs) discovered by the feature selection method (Student’s t test and fold change). And the weighted gene co-expression network analysis (WGCNA) was performed to identify the modules of highly co-expressed genes, and 454 genes in the gray module were discovered as the hub genes. The intersection between DEGs by the feature selection method and hub genes in the WGCNA model was identified as the key genes for thyroid nodules. Finally, four key genes (ST3GAL5, NRCAM, MT1F, and PROS1) participated in the pathogenesis of malignant thyroid nodules were validated using an independent dataset. Moreover, a high-performance classification model for discriminating thyroid nodules was constructed using these key genes. All in all, this study might provide a new insight into the key differentiation of benign and malignant thyroid nodules.

Asparagus belongs to the Liliaceae family and has important economic and pharmacological value. Lignin plays a crucial role in cell wall structural integrity, stem strength, water transport, mechanical support and plant resistance to pathogens. In this study, various biological methods were used to study the mechanism of shading on the asparagus lignin accumulation pathway. The physiological results showed that shading significantly reduced stem diameter and cell wall lignin content. Microstructure observation showed that shading reduced the number of vascular bundles and xylem area, resulting in decreased lignin content, and thus reducing the lignification of asparagus. Cinnamic acid, caffeic acid, ferulic acid and sinapyl alcohol are crucial intermediate metabolites in the process of lignin synthesis. Metabolomic profiling showed that shading significantly reduced the contents of cinnamic acid, caffeic acid, ferulic acid and sinapyl alcohol. Transcriptome profiling identified 37 differentially expressed genes related to lignin, including PAL, C4H, 4CL, CAD, CCR, POD, CCoAOMT, and F5H related enzyme activity regulation genes. The expression levels of POD, CCoAOMT, and CCR genes were significantly decreased under shading treatment, while the expression levels of CAD and F5H genes exhibited no significant difference with increased shading. The downregulation of POD, CCoAOMT genes and the decrease in CCR gene expression levels inhibited the activities of the corresponding enzymes under shading treatment, resulting in decreased downstream content of caffeic acid, ferulic acid, sinaperol, chlorogenic acid and coniferin. A significant decrease in upstream cinnamic acid content was observed with shading, which also led to decreased downstream metabolites and reduced asparagus lignin content. In this study, transcriptomic and metabolomic analysis revealed the key regulatory genes and metabolites of asparagus lignin under shading treatment. This study provides a reference for further understanding the mechanism of lignin biosynthesis and the interaction of related genes.

Abstract Background Flammulina velutipes has been recognized as a useful basidiomycete with nutritional and medicinal values. Ergosterol, one of the main sterols of F. velutipes is an important precursor of novel anticancer and anti-HIV drugs. Therefore, many studies have focused on the biosynthesis of ergosterol and have attempted to upregulate its content in multiple organisms. Great progress has been made in understanding the regulation of ergosterol biosynthesis in Saccharomyces cerevisiae. However, this molecular mechanism in F. velutipes remains largely uncharacterized. Results In this study, nine cDNA libraries, prepared from mycelia, young fruiting bodies and mature fruiting bodies of F. velutipes (three replicate sets for each stage), were sequenced using the Illumina HiSeq™ 4000 platform, resulting in at least 6.63 Gb of clean reads from each library. We studied the changes in genes and metabolites in the ergosterol biosynthesis pathway of F. velutipes during the development of fruiting bodies. A total of 13 genes (6 upregulated and 7 downregulated) were differentially expressed during the development from mycelia to young fruiting bodies (T1), while only 1 gene (1 downregulated) was differentially expressed during the development from young fruiting bodies to mature fruiting bodies (T2). A total of 7 metabolites (3 increased and 4 reduced) were found to have changed in content during T1, and 4 metabolites (4 increased) were found to be different during T2. A conjoint analysis of the genome-wide connection network revealed that the metabolites that were more likely to be regulated were primarily in the post-squalene pathway. Conclusions This study provides useful information for understanding the regulation of ergosterol biosynthesis and the regulatory relationship between metabolites and genes in the ergosterol biosynthesis pathway during the development of fruiting bodies in F. velutipes.

Lilium brownii var. viridulum , known as Longya lily, is a well-known medicinal and edible plant in China. Bulb rot is a common disease in Longya lily cultivation that severely affects the yield and quality of lilies. According field investigations, we found that different Longya lily plants in the same field had different degrees of resistance to root rot. To find the reasons leading to the difference, we performed metabolomic and transcriptomic analyses of Longya lily with different degrees of disease. The transcriptomic analyses showed that the number of differentially expressed genes increased in early and mid-stage infections (LYBH2 and LYBH3), while decreased in late-stage infection (LYBH4). A total of 2309 DEGs showed the same expression trend in diseased bulb compared healthy bulb (LYBH1). The transcription factors (TFs) analysis of DEGs showed that several common TFs, like WRKY, bHLH, AP2/ERF-ERF and MYB, were significantly activated in bulbs after decay. The metabolomic analyses showed that there were 794 differentially accumulated metabolites, and metabolites with significant changes in relative content largely were phenolic acids, followed by flavonoids and amino acids and derivatives. The combined analysis of transcriptome and metabolome indicated that phenylpropanoid biosynthesis pathway was crucial in Longya lily resistance to bulb rot. Therefore, we speculated that the different degree of resistance to bulb rot in Longya lily may be related to the transcript levels of gene and contents of metabolites in the phenylpropanoid biosynthesis pathway. Overall, these results elucidate the molecular responses of Longya lily to bulb rot and lay a theoretical foundation for breeding resistant varieties., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Chang, Zheng, Xu, Wang, Li and Wang.)

This study was aimed to evaluation the yield stability of twenty bread wheat genotypes that cultivated at two locations (fields of the College of Agricultural Engineering Sciences of Duhok and Zenawa district) during the 2019 - 2020 with two planting dates in each location using randomized complete block design with three replications. The results of the combined analysis of variance showed that the mean square for each of the environments, genotypes and their interactions were highly significant for all studied traits, and the variations due to the environments were greater than those of each of the genotypes and the interactions for most of the studied traits. The values of broad sense heritability ranged between 44.44% for spike length and 93.27% for grain weight per spike. The results of the stability parameters showed that the genotype Apst-12-85578 was highly stable for grains weight per spike and final grain yield followed by each of Adana, Bora, and Apst-6-85576 genotypes which showed high stability for the grain yield. [ABSTRACT FROM AUTHOR]

• Phytohormone-related metabolites were significantly altered after TSWV inoculation. • ABA and JA-Ile decreased significantly while isopentenyladenine and SA increased. • TSWV infection reduced expression of genes involved in ABA and JA pathways. • Expression of ICS1 and PR1 genes were significantly increased after TSWV infection. Tomato spotted wilt virus (TSWV) is ranked among the top 10 most destructive viruses globally. It results in abnormal leaf growth, stunting, and even death, significantly affecting crop yield and quality. Phytohormones play a crucial role in regulating plant-virus interactions. However, there is still limited research on the effect of TSWV on phytohormone levels, particularly growth hormones and genes involved in the phytohormone pathway. In our study, we combined phytohormone metabolomics and transcriptomics to examine the impact of TSWV infection on phytohormone content and gene expression profile. Metabolomic results showed that 41 metabolites, including major phytohormones and their precursors and derivatives were significantly altered after 14 days of TSWV inoculation tobacco plants cvK326, with 31 being significantly increased and 10 significantly reduced. Specifically, the levels of abscisic acid (ABA) and jasmonoyl-isoleucine (JA-Ile) were significantly reduced. The levels of indole-3-acetic acid (IAA) have remained unchanged. However, the levels of cytokinin isopentenyladenine (iP) and salicylic acid (SA) significantly increased. The transcriptome analysis revealed 2,746 genes with significant changes in expression. Out of these, 1,072 genes were significantly downregulated, while 1,674 genes were significantly upregulated. Among them, genes involved in ABA synthesis and signaling pathways, such as 9-cis-epoxycarotenoid dioxygenase (NCED), protein phosphatase 2C (PP2C), serine/threonine-protein kinase (SnRK2), and abscisic acid responsive element binding factor (ABF), exhibited significant downregulation. Additionally, expression of the lipoxygenase gene LOX , Jasmonate ZIM domain-containing protein gene JAZ , and transcription factor gene MYC were significantly down-regulated. In the cytokinin pathway, while there were no significant changes in the expression of the cytokinin synthesis genes, a significant downregulation of transcriptionally active factor type-B response regulators (type-B RRs) was observed. In terms of SA synthesis and signaling pathways, the isochorismate synthase gene ICS1 and the pathogenesis-related gene PR1 were significantly upregulated. These results can strengthen the theoretical foundation for understanding the interaction between TSWV and tobacco and provide new insights for the future prevention and control of TSWV. [ABSTRACT FROM AUTHOR]

In nature, many different factors cause plants to develop variegated leaves. To explore the mechanism of variegated leaf formation in Pteroceltis tatarinowii, a mutant variety (‘Jinyuyuan’), which was induced by ethylmethylsulfone, was selected, and its morphological structure, physiology, biochemistry, transcription and metabolism were analysed. According to differences in colour values, the colours were divided into two regions: a green region and a yellow-green region. The chlorophyll content of the two regions was significantly different. Moreover, the yellow-green regions of the leaves were significantly thinner than the green regions. The chloroplast ultrastructure in the yellow-green region revealed small chloroplasts, large vacuoles, small starch grains, obviously increased numbers of osmophilic grains, loose lamellae of the inner capsule and thin lamellae. Moreover, the yellow-green region was accompanied by oxidative stress, and the activity of the oxidative phosphorylation pathway related to oxidative activity in the transcriptome showed an upward trend. Vitamin B6 and proline contents also increased, indicating that the antioxidant activity of cells in the yellow-green region increased. Transcriptomic and metabolomic analysis showed that the differentially expressed genes (DEGs) related to chlorophyll synthesis and metabolism led to a decrease in the photosynthesis and then a decrease in the assimilation ability and contents of sucrose, starch and other assimilates. Amino acid synthesis and metabolism, lipid synthesis and the activity of metabolic pathways were obviously downregulated, and the contents of differentially accumulated metabolites associated with amino acids and lipids were also reduced. At the same time, 31 out of 32 DEGs involved in the flavonoid synthesis pathway were downregulated, which affected leaf colour. We hypothesized that the variegated leaves of P. tatarinowii ‘Jinyuyuan’ are caused by transcriptional and post-transcriptional regulation. Mutations in pigment and flavonoid synthesis pathway genes and transcription factor genes directly affect both pigment and flavonoid synthesis and degradation rate, which in turn affect carbon assimilation, carbon fixation, related protein synthesis and enzyme activity, lipid synthesis and degradation and the activity of other metabolic pathways, eventually leading to the formation of different colour regions.

The tectonic–geodynamic characteristics of the North African–Arabian region are complicated by the interaction of numerous factors. To study this interaction, we primarily used satellite gravimetric data (retracked to the Earth's surface), which has been acknowledged as a powerful tool for tectonic–geodynamic zoning. The applied polynomial averaging of gravity data indicated the presence of a giant, deep quasi-ring structure in the Eastern Mediterranean, the center of which is located under the island of Cyprus. Simultaneously, the geometrical center of the revealed structure coincides with the Earth's critical latitude of 35°. A quantitative analysis of the obtained gravitational anomaly made it possible to estimate the depth of the upper edge of the anomalous body as 1650‒1700 km. The GPS vector map coinciding with the gravitational trend indicates counterclockwise rotation of this structure. A review of paleomagnetic data on the projection of the discovered structure into the Earth's surface also confirms its counterclockwise rotation. Analysis of the geoid anomalies map and seismic tomography data commonly prove the presence of this deep anomaly. The structural and geodynamic characteristics of the region and paleobiogeographic data are consistent with the proposed physical–geological model. Comprehensive analysis of petrological, mineralogical, and tectonic data suggests a relationship between the discovered deep structure and near-surface processes. The deep structure also sheds light on specific anomalous effects in the upper layer of the crust, including the high-intensity Cyprus gravitational anomaly, counterclockwise rotation of the Mesozoic terrane belt, configuration of the Sinai Plate, and asymmetry of sedimentary basins along continental faults. [ABSTRACT FROM AUTHOR]

Tall festuca (Festuca arundinacea) is one of the most important crops and rangelands, with a high tolerance to different climatic conditions and its effective role in livestock feed and rangeland regeneration. In the present study, 36 populations of tall festuca from the Iranian Natural Resources Gene Bank were used that. Plant materials were evaluated in a randomized complete block design under two irrigation and rainfed conditions at Kheirabad Research Station, Zanjan, Iran, during 2005-2007. The results of the biplot method showed that the first component (as main effect of genotype or G) and second component (as genotype environment interaction effect or GE) were 49% and 28%, respectively, and totally explained 77% of the total variation, that is showing relatively good reliability in explanation of G+GE variations. Results of the graphical method indicated that in all environments, the population G15 (Tavankash), G31 (Australia), G11 (Borujen), G25 (Occupied Palestine) and G35 (Ireland) had relatively high yield and stability. Also, according to the ideal genotype, the G35 (Ireland) and G25 (Occupied Palestine) populations were identified as the nearest populations to ideal hypothetical genotype which are the most compatible populations suggested for the environments. [ABSTRACT FROM AUTHOR]

Abstract In Dual RNA-Seq experiments the simultaneous extraction of RNA and analysis of gene expression data from both interacting organisms could be a challenge. One alternative is separating the reads during in silico data analysis. There are two main mapping methods used: sequential and combined. Here we present a combined approach in which the libraries were aligned to a concatenated genome to sort the reads before mapping them to the respective annotated genomes. A comparison of this method with the sequential analysis was performed. Two RNA-Seq libraries available in public databases consisting of a eukaryotic (Zea mays) and a prokaryotic (Herbaspirillum seropediceae) organisms were mixed to simulate a Dual RNA-Seq experiment. Libraries from real Dual RNA-Seq experiments were also used. The sequential analysis consistently attributed more reads to the first reference genome used in the analysis (due to cross-mapping) than the combined approach. More importantly, the combined analysis resulted in lower numbers of cross-mapped reads. Our results highlight the necessity of combining the reference genomes to sort reads previously to the counting step to avoid losing information in Dual RNA-Seq experiments. Since most studies first map the RNA-Seq libraries to the eukaryotic genome, much prokaryotic information has probably been lost.

The etiology of schizophrenia (SCZ) is regarded as one of the most fundamental puzzles in current medical research, and its diagnosis is limited by the lack of objective molecular criteria. Although plenty of studies were conducted, SCZ gene signatures identified by these independent studies are found highly inconsistent. As one of the most important factors contributing to this inconsistency, the feature selection methods used currently do not fully consider the reproducibility among the signatures discovered from different datasets. Therefore, it is crucial to develop new bioinformatics tools of novel strategy for ensuring a stable discovery of gene signature for SCZ. In this study, a novel feature selection strategy (1) integrating repeated random sampling with consensus scoring and (2) evaluating the consistency of gene rank among different datasets was constructed. By systematically assessing the identified SCZ signature comprising 135 differentially expressed genes, this newly constructed strategy demonstrated significantly enhanced stability and better differentiating ability compared with the feature selection methods popular in current SCZ research. Based on a first-ever assessment on methods' reproducibility cross-validated by independent datasets from three representative studies, the new strategy stood out among the popular methods by showing superior stability and differentiating ability. Finally, 2 novel and 17 previously reported transcription factors were identified and showed great potential in revealing the etiology of SCZ. In sum, the SCZ signature identified in this study would provide valuable clues for discovering diagnostic molecules and potential targets for SCZ. [ABSTRACT FROM AUTHOR]

This study describes a combined method for rainfall-induced debris flow initiations (landslides) and propagations including a series of numerical analyses. In this study, the debris is assumed as a mixture of soils and water which is physically non-Newtonian fluid. The emphasis is placed on applying the effect of the combination of rainfall-induced landslides and debris flows to the numerical analysis. An analysis of rainfall-induced landslides is conducted to identify the thickness and location of the initial volume of debris flow. The movement of debris flow is subsequently simulated considering entrainments affected by the initial wetting condition (wetting front) estimated from the rainfall-infiltration analysis. The proposed method can simulate a sequential process from the initiation of the debris flows to the deposition based on the prediction of slope failure by rainfall, fluid dynamics based on Navier–Stokes equation, and the analysis of entrainments by considering the effect of the weight of debris and the wetting condition of soil beds. Based on the numerical results of this study, the proposed method could be applied to the analysis of regional-scale landslides and debris flows. [ABSTRACT FROM AUTHOR]

Background: Flammulina velutipes has been recognized as a useful basidiomycete with nutritional and medicinal values. Ergosterol, one of the main sterols of F. velutipes is an important precursor of novel anticancer and anti-HIV drugs. Therefore, many studies have focused on the biosynthesis of ergosterol and have attempted to upregulate its content in multiple organisms. Great progress has been made in understanding the regulation of ergosterol biosynthesis in Saccharomyces cerevisiae. However, this molecular mechanism in F. velutipes remains largely uncharacterized. Results: In this study, nine cDNA libraries, prepared from mycelia, young fruiting bodies and mature fruiting bodies of F. velutipes (three replicate sets for each stage), were sequenced using the Illumina HiSeq™ 4000 platform, resulting in at least 6.63 Gb of clean reads from each library. We studied the changes in genes and metabolites in the ergosterol biosynthesis pathway of F. velutipes during the development of fruiting bodies. A total of 13 genes (6 upregulated and 7 downregulated) were differentially expressed during the development from mycelia to young fruiting bodies (T1), while only 1 gene (1 downregulated) was differentially expressed during the development from young fruiting bodies to mature fruiting bodies (T2). A total of 7 metabolites (3 increased and 4 reduced) were found to have changed in content during T1, and 4 metabolites (4 increased) were found to be different during T2. A conjoint analysis of the genome-wide connection network revealed that the metabolites that were more likely to be regulated were primarily in the post-squalene pathway. Conclusions: This study provides useful information for understanding the regulation of ergosterol biosynthesis and the regulatory relationship between metabolites and genes in the ergosterol biosynthesis pathway during the development of fruiting bodies in F. velutipes. [ABSTRACT FROM AUTHOR]