Functional Classification Analysis Research Articles

Proteomic and metabolomic insights into the mechanisms of calcium-mediated salt stress tolerance in hemp.

Industrial hemp (Cannabis sativa L.) is a multifaced crop that has the potential to be exploited for many industrial applications, and making use of salt lands is considered to be a sustainable development strategy for the hemp industry. However, no elite salt-tolerant hemp varieties have been developed, and therefore supplementing appropriate exogenous substances to saline soil is one possible solution. Calcium-containing compounds are well-known for their salt tolerance enhancing effects, but the underlying molecular mechanisms remain largely unclear. Here, we first assessed the ameliorative effects of calcium amendments on salt-stressed hemp plants and then investigated these mechanisms on hemp using integrative analysis of proteomics and metabolomics. The stress phenotypes could be lessened by Ca2+ treatment. Certain concentrations of Ca2+ maintained relative electrical conductivity and the contents of malondialdehyde and chlorophyll. Ca2+ treatment also generally led to greater accumulations of soluble proteins, soluble carbohydrates and proline, and enhanced the activities of superoxide dismutase and peroxidase. Through functional classification, pathway enrichment, and network analysis, our data reveal that accumulation of dipeptides is a prominent metabolic signature upon exogenous Ca2+ treatment, and that changes in mitochondrial properties may play an important role in enhancing the salt tolerance. Our results outline the complex metabolic alternations involved in calcium-mediated salt stress resistance, and these data and analyses would be useful for future functional studies.

Abstract 4124828: The Methylation Landscape Of Human Aortic And Mitral Valvular Interstitial Cells

Valvular interstitial cells (VICs), the valves’ predominant cell type, are crucial in ensuring proper valve function, structural integrity, tissue repair and valve homeostasis. DNA methylation regulates gene expression profiles and a matched aortic to mitral human VIC methylation analysis will further our understanding of aortic- and mitral-specific VIC biology and pathobiology. This is the first study analyzing methylation profiles of non-diseased, matched human aortic and mitral VICs. We analyzed the differential methylation fingerprint of 12 non-diseased aortic and mitral VICs (10 males:2 females; 42–64 years) extracted from de-endothelialized leaflets using reduced representation bisulfite sequencing (RRBS) on HiSeq2500. Analysis of methylation levels of 12,676 genome-wide promoters revealed 651 differentially methylated (DM) promoters. The top 3 DM promoters were linked to TBX4 (meth diff = -28.9%, P = 5.2E-135) essential for valve morphogenesis, to EXOC3L2 (meth diff = 25.7%, P = 1.3E-92) and NT5DC2 (meth diff = -20.3%, P = 7.1E-69) potentially implicated in ECM remodeling, the former via vesicle trafficking and the latter through nucleotide metabolism. Functional classification and network analysis showed that the genes associated with the DM promoters were enriched for WNT-, TGFβ-, FGF-, EGF- and PDGF- pathways involved in physiological processes such as valve development, repair and VIC regulation, as well as pathological processes such as calcification. Additional enrichment was detected for integrin- and cadherin- pathways involved in cell-cell-ECM interactions and endothelin- and VEGF pathways involved in hemodynamic regulation. This work provides the first insight into the differential methylation regulation patterns of human aortic and mitral VICs. Understanding how aortic and mitral VICs are differentially epigenetically regulated will extend our understanding of their role in aortic- and mitral-specific leaflet homeostasis, susceptibility to disease processes and will contribute to dynamic innovative experimental setup designs, animal-free human-based modeling frameworks, tissue engineering and drug identification approaches.

A Functional Classification Analysis of Government Spending Multipliers

A Functional Classification Analysis of Government Spending Multipliers

Characterization of the Regulatory Network under Waterlogging Stress in Soybean Roots via Transcriptome Analysis.

Flooding stress caused by climate change is a serious threat to crop productivity. To enhance our understanding of flooding stress in soybean, we analyzed the transcriptome of the roots of soybean plants after waterlogging treatment for 10 days at the V2 growth stage. Through RNA sequencing analysis, 870 upregulated and 1129 downregulated differentially expressed genes (DEGs) were identified and characterized using Gene Ontology (GO) and MapMan software (version 3.6.0RC1). In the functional classification analysis, "alcohol biosynthetic process" was the most significantly enriched GO term in downregulated DEGs, and phytohormone-related genes such as ABA, cytokinin, and gibberellin were upregulated. Among the transcription factors (TFs) in DEGs, AP2/ERFs were the most abundant. Furthermore, our DEGs encompassed eight soybean orthologs from Arabidopsis and rice, such as 1-aminocyclopropane-1-carboxylate oxidase. Along with a co-functional network consisting of the TF and orthologs, the expression changes of those genes were tested in a waterlogging-resistant cultivar, PI567343. These findings contribute to the identification of candidate genes for waterlogging tolerance in soybean, which can enhance our understanding of waterlogging tolerance.

Identification of rare genetic variants in the PCDH genetic family in a cohort of transgender women

ObjectiveTo study the identification of rare genetic variants in the PCDH genetic family in a cohort of transgender women and their potential role in gender identity. DesignExome sequencing and functional ontology analysis. SettingAugusta University, including the Equality Clinic of Augusta and the Reproductive Medicine and Infertility Associates Clinic. Patients24 transgender women and 22 cisgender men. InterventionsExome sequencing followed by variant confirmation through Sanger sequencing and functional classification analysis using the Database for Annotation, Visualization and Integrated Discovery (DAVID) tool. Main Outcome MeasuresIdentification of rare, functionally significant genetic variants in the PCDH gene family and their prevalence in transgender women compared to cisgender men. ResultsExome sequencing revealed 38,524 genetic variants, of which 2441 were rare and predicted to be functionally significant. DAVID analysis demonstrated a statistically enriched functional group, “homophilic cell adhesion via plasma membrane adhesion molecules” (Benjamini corrected p-value 1.5 x 10-11), containing 55 genes, including 18 PCDH gene family members. A total of 37 rare variants in 21 PCDH genes were identified, with 36 confirmed by Sanger sequencing. A statistically significant increase in these variants was observed in transgender women compared to cisgender men (Z = 2.08905, p= 0.037). ConclusionsTransgender women exhibited a greater than 3-fold increase in functionally significant PCDH gene variants compared to cisgender men. These findings suggest that the PCDH family may play a role in the genetic pathways associated with gender identity in transgender women.

Comparative proteomic and metabolomic analyses reveal stress responses of hemp to salinity.

Integrated omics analyses outline the cellular and metabolic events of hemp plants in response to salt stress and highlight several photosynthesis and energy metabolism related pathways as key regulatory points. Soil salinity affects many physiological processes of plants and leads to crop yield losses worldwide. For hemp, a crop that is valued for multiple aspects, such as its medical compounds, fibre, and seed, a comprehensive understanding of its salt stress responses is a prerequisite for resistance breeding and tailoring its agronomic performance to suit certain industrial applications. Here, we first observed the phenotype of salt-stressed hemp plants and found that under NaCl treatment, hemp plants displayed pronounced growth defects, as indicated by the significantly reduced average height, number of leaves, and chlorophyll content. Next, we conducted comparative proteomics and metabolomics to dissect the complex salt-stress response mechanisms. A total of 314 proteins and 649 metabolites were identified to be differentially behaving upon NaCl treatment. Functional classification and enrichment analysis unravelled that many differential proteins were proteases associated with photosynthesis. Through metabolic pathway enrichment, several energy-related pathways were found to be altered, such as the biosynthesis and degradation of branched-chain amino acids, and our network analysis showed that many ribosomal proteins were involved in these metabolic adaptations. Taken together, for hemp plants, influences on chloroplast function probably represent a major toxic effect of salinity, and modulating several energy-producing pathways possibly through translational regulation is presumably a key protective mechanism against the negative impacts. Our data and analyses provide insights into our understanding of hemp's stress biology and may lay a foundation for future functional genomics studies.

Study of the Physic-Mechanical Properties of a Typha Concrete Composites: A Possible New Material for Sustainable Construction

Natural fibers have garnered considerable attention from researchers and academics alike due to their eco-friendly nature and sustainability. These fibers are being explored for their potential use in polymer composites. The use of natural fiber-reinforced polymer composite materials is rapidly increasing in both industrial and fundamental research applications due to their renewable, low, and biodegradable properties. In order to reduce the CO2 emissions, the building energy consumption and preserve the natural sand. The present study involved conducting an analysis of the results obtained from the experimental investigation where five mixtures of typha fiber sand, and cement (MHC0, MHC5, MHC10, MHC15 and MHC20)) were utilized to make Typha-concrete. The experimental mixtures being examined and the results indicate that the density of the samples diminishes in proportion to the incorporation of typha fiber, while the thermal conductivity is enhanced. In addition, the characteristics of lightweight structures can be attributed to the generated specimens, which have been determined by their documented compressive strength. Based on the results of RILEM's functional classification analysis, it can be concluded that Typha-concrete meets the mechanical and thermal requirements of construction materials, making it a feasible option for both structural and insulating concrete applications.

Long-term study of phytoplankton dynamics in a supply reservoir reveals signs of trophic state shift linked to changes in hydrodynamics associated with flow management and extreme events

This study analyses over a decade (2009–2022) of monitoring data to understand the impact of hydrological characteristics on water quality and phytoplankton dynamics in Prospect Reservoir, a critical water supply for Greater Sydney, Australia, known for its excellent water quality. Water quality and phytoplankton dynamics were related to hydrodynamics, linked to flow management and the water quality of inflows. Phytoplankton biovolume increased after a prolonged drawdown and subsequent refill event, mainly driven by dinoflagellates, and corresponded to increases in total phosphorus and water temperature. The hydrological period following the 2019/2020 summer bushfires (post-bushfire) that impacted connected reservoirs, was marked by increased flow activity and nutrient loading, leading to significant shifts in the phytoplankton community. Functional group classification and ordination analysis indicated a transition from taxa typically dominant in oligotrophic conditions to meso‑eutrophic. This transition correlated with elevated nutrient levels and chlorophyll-a (Chl-a), and reduced Secchi depth and dissolved oxygen, providing evidence of eutrophication. Q index indicated good water quality post-bushfire, contrasting with a eutrophic status assessment using Chl-a. Our findings highlight the importance of analysing long-term datasets encompassing varied hydroclimatological conditions for a deeper understanding of reservoir behaviour. A comprehensive approach to water quality assessment is recommended, combining functional group classification, Q index and Chl-a measurements for effective reservoir health assessment. This research provides novel insights into the effects of disturbances such as bushfires, on water quality and phytoplankton dynamics in an underrepresented geographic region, offering valuable knowledge for managing water resources amidst growing climate variability.

Isolation, identification and transcriptome analysis of triadimefon-degrading strain Enterobacter hormaechei TY18.

Triadimefon, a type of triazole systemic fungicide, has been extensively used to control various fungal diseases. However, triadimefon could lead to severe environmental pollution, and even threatens human health. To eliminate triadimefon residues, a triadimefon-degrading bacterial strain TY18 was isolated from a long-term polluted site and was identified as Enterobacter hormaechei. Strain TY18 could grow well in a carbon salt medium with triadimefon as the sole nitrogen source, and could efficiently degrade triadimefon. Under triadimefon stress, a total of 430 differentially expressed genes (DEGs), including 197 up-regulated and 233 down-regulated DEGs, were identified in strain TY18 using transcriptome sequencing (RNA-Seq). Functional classification and enrichment analysis revealed that these DEGs were mainly related to amino acid transport and metabolism, carbohydrate transport and metabolism, small molecule and pyrimidine metabolism. Interestingly, the DEGs encoding monooxygenase and hydrolase activity acting on carbon-nitrogen were highly up-regulated, might be mainly responsible for the metabolism in triadimefon. Our findings in this work suggest that strain E. hormaechei TY18 could efficiently degrade triadimefon for the first time. They provide a great potential to manage triadimefon biodegradation in the environment successfully.

Вводные слова в ливвиковском наречии карельского языка: семантика, этимология и функционирование

the presented article is a comprehensive study of parenthetical words in the Livvik dialect of the newly written Karelian language. Within the framework of the study, the authors turn to the consideration of semantics, etymology and functioning of modal words in the newly written Livvik dialect of the Karelian language. Objective: to study the semantic groups and etymology of the subjective modal components of a sentence functioning in the Livvik dialect of the Karelian language. Research materials: textbooks and dictionaries of the Livvik dialect of the newly written Karelian language. Results and novelty of the research: the article proposes a functional and semantic classification and etymological analysis of Karelian parenthetical modal words. In the Livvik dialect of the Karelian language about 40 parenthetical elements collected in newly written Karelian dictionaries are recorded. The data obtained in the process of studying dictionary materials on the Livvik dialect make it possible to distinguish 5 categories of parenthetical words by their meaning, of which the richest in composition of lexemes is the class intended to express varying degrees of reliability of a statement; other semantic subgroups (expressing a link to the source of a message, a call to an interlocutor, logical connections in a text, the emotional state of a speaker) demonstrate a much more modest segment of the field of subjective-modal collocations in the Livvik dialect of the Karelian language in terms of the number of units recorded in the dictionaries. The etymological analysis of parenthetical modal words showed that parentheses expressing the speaker’s assessment of his statement are in the process of their formation, replenishment with new lexemes; the formation of parenthetical modal phraseology is largely accomplished through syntactic derivation as the transition of notional words (names and verbs) into the class of parenthetical modal ones. The scientific novelty of the study lies in the fact that a semantic classification of parenthetical constructions of the Livvik dialect is proposed based on data from newly written dictionary sources, as well as observations in the field of etymology of parenthetical modal words.

Comparative proteomic analysis of vancomycin-sensitive and vancomycin-intermediate resistant Staphylococcus aureus.

The extensive use of vancomycin has led to the development of Staphylococcus aureus strains with varying degrees of resistance to vancomycin. The present study aimed to explore the molecular causes of vancomycin resistance by conducting a proteomics analysis of subcellular fractions isolated from vancomycin-intermediate resistant S. aureus (VISA) and vancomycin-sensitive S. aureus (VSSA) strains. We conducted proteomics analysis of subcellular fractions isolated from 2 isogenic S. aureus strains: strain 11 (VSSA) and strain 11Y (VISA). We used an integrated quantitative proteomics approach assisted by bioinformatics analysis, and comprehensively investigated the proteome profile. Intensive bioinformatics analysis, including protein annotation, functional classification, functional enrichment, and functional enrichment-based cluster analysis, was used to annotate quantifiable targets. We identified 128 upregulated proteins and 21 downregulated proteins in strain 11Y as compared to strain 11. The largest group of differentially expressed proteins was composed of enzymatic proteins associated with metabolic and catalytic activity, which accounted for 32.1% and 50% of the total proteins, respectively. Some proteins were indispensable parts of the regulatory networks of S. aureus that were altered with vancomycin treatment, and these proteins were related to cell wall metabolism, cell adhesion, proteolysis, and pressure response. Our proteomics study revealed regulatory proteins associated with vancomycin resistance in S. aureus. Some of these proteins were involved in the regulation of cell metabolism and function, which provides potential targets for the development of strategies to manage vancomycin resistance in S. aureus.

Prenatal Alcohol Exposure Impairs the Placenta-Cortex Transcriptomic Signature, Leading to Dysregulation of Angiogenic Pathways.

Although alcohol consumption during pregnancy is a major cause of behavioral and learning disabilities, most FASD infants are late- or even misdiagnosed due to clinician's difficulties achieving early detection of alcohol-induced neurodevelopmental impairments. Neuroplacentology has emerged as a new field of research focusing on the role of the placenta in fetal brain development. Several studies have reported that prenatal alcohol exposure (PAE) dysregulates a functional placenta-cortex axis, which is involved in the control of angiogenesis and leads to neurovascular-related defects. However, these studies were focused on PlGF, a pro-angiogenic factor. The aim of the present study is to provide the first transcriptomic "placenta-cortex" signature of the effects of PAE on fetal angiogenesis. Whole mouse genome microarrays of paired placentas and cortices were performed to establish the transcriptomic inter-organ "placenta-cortex" signature in control and PAE groups at gestational day 20. Genespring comparison of the control and PAE signatures revealed that 895 and 1501 genes were only detected in one of two placenta-cortex expression profiles, respectively. Gene ontology analysis indicated that 107 of these genes were associated with vascular development, and String protein-protein interaction analysis showed that they were associated with three functional clusters. PANTHER functional classification analysis indicated that "intercellular communication" was a significantly enriched biological process, and 27 genes were encoded for neuroactive ligand/receptors interactors. Protein validation experiments involving Western blot for one ligand-receptor couple (Agt/AGTR1/2) confirmed the transcriptomic data, and Pearson statistical analysis of paired placentas and fetal cortices revealed a negative correlation between placental Atg and cortical AGTR1, which was significantly impacted by PAE. In humans, a comparison of a 38WG control placenta with a 36WG alcohol-exposed placenta revealed low Agt immunolabeling in the syncytiotrophoblast layer of the alcohol case. In conclusion, this study establishes the first transcriptomic placenta-cortex signature of a developing mouse. The data show that PAE markedly unbalances this inter-organ signature; in particular, several ligands and/or receptors involved in the control of angiogenesis. These data support that PAE modifies the existing communication between the two organs and opens new research avenues regarding the impact of placental dysfunction on the neurovascular development of fetuses. Such a signature would present a clinical value for early diagnosis of brain defects in FASD.

The Phosphoproteomic Response of Pepper (Capsicum annuum L.) Seedlings to Selenium Stress

Excessive selenium has gradually become a potential environmentally hazardous element for all organisms. Limited knowledge is available regarding the toxic mechanism of selenium in pepper, so the quantitative proteomics of phosphorylation was studied by Tandem Mass Tag approaches. A total of 4434 phosphorylation sites were identified on 2058 proteins, of which 3749 sites of 1919 proteins contained quantitative information. In the Se/mock (seedlings without Se treatment) comparison group, the number of upregulated phosphoproteins (658) was significantly higher than that of the downregulated ones (61). Systematic bioinformatics analysis, including protein annotation, functional classification, subcellular localization, and cluster analysis was performed. A total of 33 over-represented motifs were found in serine phosphorylation, and the most frequent motif was ‘sP’ (308 occurrences). According to KEGG enrichment analysis, the upregulated phosphorylated proteins (DPPs) were most strongly associated with the ’phenylpropanoid biosynthesis’ and ’nicotinate and nicotinamide metabolism’ pathways, while those that were downregulated were associated with the ’ABC transporters’ and ‘plant hormone signal transduction’ pathways. Our data can provide new insights for evaluating the response mechanism of plants to selenium pollution and improving their resistance to selenium.

The anti-inflammatory effect of electroacupuncture in mice with spinal cord injury and molecular mechanism based on transcriptome sequencing technology

To observe the effect of electroacupuncture(EA) on neural function and spinal cord pathological morphology in spinal cord injury(SCI) mice and investigate the anti-inflammatory molecular mechanism of EA on SCI mice from the aspects of gene by using bioinformatics. Seventy-two female C57BL/6 mice were randomized into sham operation, model and EA groups, with 24 mice in each group. The SCI model was established by clamping the spinal cord with a serrefine after laminectomy at the 1st lumbar vertebra(L1). EA(1.5 Hz/7.5 Hz, 1.0 mA) was applied to bilateral "Jiaji"(EX-B2) and "Zusanli"(ST36) for 10 min, once a day for 14 consecutive days. Basso Mouse Scale(BMS) score was used to assess the hindlimb locomotor function of mice. Histopathological changes of the injured area of the spinal cord were determined by HE staining. The spinal cord RNA was sequenced by using RNA-Seq technology. The bioinformatic analysis was then performed to detect the diffe-rential genes between groups, and the function classification and the involved pathways were enriched. The mRNA and protein expressions of differential genes were detected and verified by using qRT-PCR and Western blot. Compared with the sham operation group, BMS score of the model group was significantly decreased(P<0.05), while that of EA group was increased relevant to the model group (P<0.05). HE staining showed loose and disordered structure and arrangement, cavitation, more inflammatory infiltration, nucleus pycnosis, and neuronal necrosis in the model group, which was alleviated in the EA group. Compared with the sham operation group, 565 differential genes were detected in the model group, including 545 up-regulated and 20 down-regulated, while 41 were detected between the EA and the model group, including 2 up-regulated and 39 down-regulated in the EA group. Fifteen genes that were all up-regulated after modeling and down-regulated after EA intervention were detected by using Venn plot, which are Retn, Adipoq, Myh1, Actn2, Pck1, Klhl41, Fabp4, Hspb7, Myot, Ankrd2, Hrc, Cox6a2, Obscn, Col2a1, Mybpc1, and 3 inflammation-related genes(Fabp4, Adipoq and Pck1) were finally acquired. The 15 differential genes were annotated into main biological processes, cell composition and molecular function in the GO function classification analysis. The 15 differential genes were then enriched into different KEGG pathways, including the peroxisome proliferatorsactivated receptor (PPAR) signaling pathway, Adipocytokine signaling pathway. The mRNA and protein expressions of Fabp4, Adipoq and Pck1 in spinal cord detected by qRT-PCR and Western blot were significantly increased in the model group (P<0.001, P<0.01), while these were significantly decreased in the EA group relevant to the model group(P<0.001, P<0.01, P<0.05). EA can promote the repair of nerve function and improve inflammatory infiltration in SCI mice. The mechanism may be closely related to the down-regulation of inflammatory factors Fabp4, Adipoq and Pck1 expression, and the regulation of PPAR and Adipocytokine signaling pathways.

The comparison of gut gene expression and bacterial community in Diaphorina citri (Hemiptera: Liviidae) adults fed on Murraya exotica and ‘Shatangju’ mandarin (Citrus reticulate cv. Shatangju)

BackgroundDiaphorina citri Kuwayama is an important citrus pest. It serves as the vector for the transmission of Candidatus Liberibacter asiaticus (CLas), which induced a destructive disease, Huanglongbing, and caused huge economic losses. During the interaction between insects and plants, insects have evolved a series of mechanisms to adapt to various host plants. Murraya exotica and ‘Shatangju’ mandarin (Citrus reticulate cv. Shatangju) are the Rutaceae species from different genera that have been discovered as suitable hosts for D. citri adults. While the adaptation mechanism of this pest to these two host plants is unclear.ResultsIn this study, RNA-seq and 16 S rDNA amplification sequencing were performed on the gut of D. citri adults reared on M. exotica and ‘Shatangju’ mandarin. RNA-seq results showed that a total of 964 differentially expressed genes were found in different gut groups with two host plant treatments. The impacted genes include those that encode ribosomal proteins, cathepsins, and mitochondrial respiratory chain complexes. According to 16 S rDNA sequencing, the compositions of the gut bacterial communities were altered by different treatments. The α and β diversity analyses confirmed that the host plant changes influenced the gut microbial diversity. The functional classification analysis by Tax4Fun revealed that 27 KEGG pathways, mostly those related to metabolism, including those for nucleotide metabolism, energy metabolism, metabolism of cofactors and vitamins, amino acid metabolism, carbohydrate metabolism, xenbiotics biodegradation and metabolism, lipid metabolism, and biosynthesis of other secondary metabolites, were significantly altered.ConclusionOur preliminary findings shed light on the connection between D. citri and host plants by showing that host plants alter the gene expression profiles and bacterial community composition of D. citri adults.

A root-knot nematode effector manipulates the rhizosphere microbiome for establishing parasitism relationship with hosts.

Root-knot nematode (RKN; Meloidogyne spp.) is one of the most infamous soilborne plant diseases, causing severe crop losses every year. Effector proteins secreted by RKNs play crucial roles during plant-nematode interaction. However, less is known about whether RKN effector proteins can impact the rhizosphere microbial environment. In this study, we investigated the rhizosphere microbiome community of MiMIF-2 (a plant immunity-modulating effector) transgenic Arabidopsis thaliana with or without nematode infection using the Illumina high-throughput sequencing analysis. The results showed that the bacterial species richness index increased, while the fungi species richness index decreased in M. incognita-infected MiMIF-2 transgenic A. thaliana plants. The relative abundance of genera such as Clitopilus, Komagataeibacter, Lactobacillus, Prevotella, Moritella, Vibrio, Escherichia-Shigella, and Pseudomonas was reduced in MiMIF-2 transgenic A. thaliana plants compared to wild type, but was significantly increased after inoculation with M. incognita. The Cluster of Orthologous Genes (COG) function classification analysis revealed a decrease in the relative abundance of defense mechanisms, secondary metabolite biosynthesis, transport, and nematode infection catabolism-related functions in MiMIF-2 lines compared to the wild type. These differences may be the reason for the increased susceptibility of MiMIF-2 transgenic A. thaliana to nematode infection. Our results provide a new insight into RKN effector proteins and their association with the microbial community, host, and plant pathogens, which will lead to the exploration of new innovative ideas for future biological control of RKNs.

Transcriptome analysis reveals key regulatory genes for root growth related to potassium utilization efficiency in rapeseed (Brassica napus L.).

Root system architecture (RSA) is the primary predictor of nutrient intake and significantly influences potassium utilization efficiency (KUE). Uncertainty persists regarding the genetic factors governing root growth in rapeseed. The root transcriptome analysis reveals the genetic basis driving crop root growth. In this study, RNA-seq was used to profile the overall transcriptome in the root tissue of 20 Brassica napus accessions with high and low KUE. 71,437 genes in the roots displayed variable expression profiles between the two contrasting genotype groups. The 212 genes that had varied expression levels between the high and low KUE lines were found using a pairwise comparison approach. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification analysis revealed that the DEGs implicated in hormone and signaling pathways, as well as glucose, lipid, and amino acid metabolism, were all differently regulated in the rapeseed root system. Additionally, we discovered 33 transcription factors (TFs) that control root development were differentially expressed. By combining differential expression analysis, weighted gene co-expression network analysis (WGCNA), and recent genome-wide association study (GWAS) results, four candidate genes were identified as essential hub genes. These potential genes were located fewer than 100 kb from the peak SNPs of QTL clusters, and it was hypothesized that they regulated the formation of the root system. Three of the four hub genes' homologs-BnaC04G0560400ZS, BnaC04G0560400ZS, and BnaA03G0073500ZS-have been shown to control root development in earlier research. The information produced by our transcriptome profiling could be useful in revealing the molecular processes involved in the growth of rapeseed roots in response to KUE.

Plasma Proteomic Analysis Reveals the Potential Role of Lectin and Alternative Complement Pathways in IgA Vasculitis Pathogenesis.

IgA vasculitis (IgAV) is the most common form of childhood vasculitis. A better understanding of its pathophysiology is required to identify new potential biomarkers and treatment targets. to assess the underlying molecular mechanisms in the pathogenesis of IgAV using an untargeted proteomics approach. Thirty-seven IgAV patients and five healthy controls were enrolled. Plasma samples were collected on the day of diagnosis before any treatment was initiated. We used nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS) to investigate the alterations in plasma proteomic profiles. For the bioinformatics analyses, databases including Uniprot, PANTHER, KEGG, Reactome, Cytoscape, and IntAct were used. Among the 418 proteins identified in the nLC-MS/MS analysis, 20 had significantly different expressions in IgAV patients. Among them, 15 were upregulated and 5 were downregulated. According to the KEGG pathway and function classification analysis, complement and coagulation cascades were the most enriched pathways. GO analyses showed that the differentially expressed proteins were mainly involved in defense/immunity proteins and the metabolite interconversion enzyme family. We also investigated molecular interactions in the identified 20 proteins of IgAV patients. We extracted 493 interactions from the IntAct database for the 20 proteins and used Cytoscape for the network analyses. Our results clearly suggest the role of the lectin and alternate complement pathways in IgAV. The proteins defined in the pathways of cell adhesion may serve as biomarkers. Further functional studies may lead the way to better understanding of the disease and new therapeutic options for IgAV treatment.

Genome-wide identification of Kanamycin B binding RNA in Escherichia coli

BackgroundThe aminoglycosides are established antibiotics that inhibit bacterial protein synthesis by binding to ribosomal RNA. Additional non-antibiotic aminoglycoside cellular functions have also been identified through aminoglycoside interactions with cellular RNAs. The full extent, however, of genome-wide aminoglycoside RNA interactions in Escherichia coli has not been determined. Here, we report genome-wide identification and verification of the aminoglycoside Kanamycin B binding to Escherichia coli RNAs. Immobilized Kanamycin B beads in pull-down assays were used for transcriptome-profiling analysis (RNA-seq).ResultsOver two hundred Kanamycin B binding RNAs were identified. Functional classification analysis of the RNA sequence related genes revealed a wide range of cellular functions. Small RNA fragments (ncRNA, tRNA and rRNA) or small mRNA was used to verify the binding with Kanamycin B in vitro. Kanamycin B and ibsC mRNA was analysed by chemical probing.ConclusionsThe results will provide biochemical evidence and understanding of potential extra-antibiotic cellular functions of aminoglycosides in Escherichia coli.

Porcine salivary proteome analysis identifies potential early pregnancy-specific protein biomarkers

Early diagnosis of pregnancy is of utmost importance to optimize profit in pig husbandry. Identifying candidate protein biomarkers for early diagnosis of pregnancy in a non-invasive sample such as saliva may produce a colossallead to accomplish the purpose. Therefore, in this study, comparative salivary proteome profile of day 12 of gestation, representing elongation of blastocysts stage and non-pregnant sows was explored by label-free quantitation (LFQ) based mass spectrometry approach to identify early pregnancy biomarkers. A total of 115 proteins were identified as differentially expressed proteins (DEPs) with significant difference between non-pregnant and early pregnancy groups. Among the DEPs, majority of the proteins (82 out of 115 DEPs) were found to be down-regulated in early pregnancy group (fold change &gt;2) compared to non-pregnant control. Functional classification and pathway analysis of the DEPs revealed involvement of most of the proteins in integrin signalling pathways, blood coagulation, carbohydrate metabolism, oxidative stress response and regulation of protein folding. Few DEPs with higher fold change during early pregnancy such as thioredoxin, heat shock 70 kDa protein 1A, alpha 1-S haptoglobin, and glutathione S-transferase pi 1 may have potential as biomarkers for early pregnancy diagnosis in pigs based on their recognized role in different pregnancy related activities. Overall, our results provide a set of salivary proteins which can be used as potential biomarkers for early pregnancy diagnosis after large scale validation.