Comprehensive Functional Analysis Research Articles

Mulea: An R package for enrichment analysis using multiple ontologies and empirical false discovery rate

Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. mulea employs a progressive empirical false discovery rate (eFDR) method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. mulea expands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis, mulea provides gene sets (in standardised GMT format) for 27 model organisms, covering 22 ontology types from 16 databases and various identifiers resulting in almost 900 files. Additionally, the muleaData ExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally, mulea's architecture allows for easy integration of user-defined ontologies, or GMT files from external sources (e.g., MSigDB or Enrichr), expanding its applicability across diverse research areas. mulea is distributed as a CRAN R package downloadable from https://cran.r-project.org/web/packages/mulea/ and https://github.com/ELTEbioinformatics/mulea. It offers researchers a powerful and flexible toolkit for functional enrichment analysis, addressing limitations of traditional tools with its progressive eFDR and by supporting a variety of ontologies. Overall, mulea fosters the exploration of diverse biological questions across various model organisms.

The cardiac, vasomotor and myocardial branches of the baroreflex in hypotension: indications of reduced venous return to the heart.

Alterations of autonomic cardiovascular control are implicated in the origin of chronic low blood pressure (BP) (hypotension), but comprehensive analysis of baroreflex function is still lacking. This study explored baroreflex function in its cardiac, vascular and myocardial branches METHODS: Continuous BP was recorded at rest and during a mental arithmetic task in 40 hypotensive and 40 normotensive participants. Assessed cardiovascular variables included stroke volume (SV) (calculated by the Modelflow method), heart rate (HR), cardiac output (CO), total peripheral resistance (TPR) and heart rate variability (HRV). Baroreflex sensitivity (BRS) was calculated using the spontaneous sequence method. Hypotensive participants exhibited greater BRS in the three baroreflex branches, in addition to lower SV, HR and CO and higher HRV and TPR. Reactivity for BP, HRV and CO during the stress task was reduced in hypotensive individuals. The greater cardiac BRS can explain the lower HR and higher HRV observed in hypotension, suggestive of increased vagal cardiac influences. The higher vasomotor BRS may contribute to the greater TPR observed in the hypotensive participants. Abnormal associations between myocardial BRS and SV arose, suggesting aberrant autonomic control of myocardial contractility in hypotension. The results indicate that hemodynamic deficits in hypotension are related to preload factors, probably triggered by hypovolemia and reduced unstressed blood reserves, resulting in lower venous return, ventricular preload and SV. In contrast, afterload mechanisms seem to work appropriately.

RE(HSeO3)(SeO3)(H2O)·(H2O) (RE = Y, Gd): Two Rare-Earth Selenite Nonlinear Optical Crystals with Wide Band Gaps.

The band gap is one of the significant parameters for nonlinear optical (NLO) materials, which is the key factor in their application band in laser technology. This study reports the synthesis of two rare-earth selenite NLO crystals, namely, RE(HSeO3)(SeO3)(H2O)·(H2O) (RE = Y, Gd), utilizing the hydrothermal technique. The two compounds are isostructural, and both belong to the orthorhombic chiral space group of P212121 and possess three-dimensional structures consisting of two-dimensional rare-earth selenite layers connected by hydrogen bonds (O-H··O). These two compounds exhibit a moderate second harmonic generation intensity of 0.5/0.8 × KDP and wide energy band gaps reaching 4.8 eV. Comprehensive density functional theory analyses based on first-principles were carried out to unravel the relationship between the structural and corresponding properties. This work provides an approach for band gap enlargement in rare-earth selenite systems and is beneficial to the design of future NLO materials.

Arrayed CRISPRi library to suppress genes required for Schizosaccharomyces pombe viability.

The fission yeast, Schizosaccharomyces pombe, is an excellent eukaryote model organism for studying essential biological processes. Its genome contains ∼1,200 genes essential for cell viability, most of which are evolutionarily conserved. To study these essential genes, resources enabling conditional perturbation of target genes are required. Here, we constructed comprehensive arrayed libraries of plasmids and strains to knock down essential genes in S. pombe using dCas9-mediated CRISPRi. These libraries cover ∼98% of all essential genes in fission yeast. We estimate that in ∼60% of these strains, transcription of a target gene was repressed so efficiently that cell proliferation was significantly inhibited. To demonstrate the usefulness of these libraries, we performed metabolic analyses with knockdown strains and revealed flexible interaction among metabolic pathways. Libraries established in this study enable comprehensive functional analyses of essential genes in S. pombe and will facilitate the understanding of essential biological processes in eukaryotes.

Key factors uncovered by transcriptomic analysis in the regulation of glutamic acid repressing the browning of fresh-cut potatoes

Enzymatic browning is a major problem that seriously impacts the quality of fresh-cut potatoes. Our previous study found that glutamic acid (Glu) treatment could repress the discoloration of fresh-cut potatoes, but the molecular mechanism was still unknown. Herein, it was found that the content of total phenolic, H2O2, O2.- and the activities of PPO, POD and PAL were repressed, but the activities of CAT, APX, SOD and GPX were improved by Glu treatment. Moreover, transcriptomic analysis showed that an abundant number of differentially expressed genes (DEGs) were selected from fresh-cut potatoes browning between Glu and control groups. A comprehensive functional enrichment analysis showed that the metabolic pathways of glutathione metabolism, flavonoid biosynthesis, phenylalanine metabolism, phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction were markedly enriched, which transcriptional levels were markedly altered by Glu treatment. RT-qPCR confirmed the results of RNA-Seq that Glu repressed the transcription of StPPO2, StPPO3, StPPO7, and StERF-BR1-like. More importantly, as a nuclear protein, StERF-BR1-like activated the transcription of StPPO2 by directly binding with its promoter. Overall, these data indicate that Glu could repress the browning of fresh-cut potatoes by regulating the pathways mentioned above, and StERF-BR1-like may involve this process by stimulating the expression of StPPO2.

Comprehensive pulmonary function analysis identifies predominant obstructive phenotype in former premature infants around one year of age.

Preterm infants suffer from significant respiratory morbidity during the first years of life, but the underlying lung pathophysiology is not fully understood. This study aimed to comprehensively characterize the pulmonary functions of preterm infants using full infant pulmonary function testing (iPFT). Between 2008 and 2019, we recruited 150 infants (Mage 10.5 ± 6 months) of them 104 preterm infants (median gestational age [GA] = 34 weeks (28-36), n = 23 with bronchopulmonary disease [BPD]) and 46 controls born at term. We compared full iPFT parameters of preterm infants to a control group of term infants. Subanalysis included a comparison of preterm infants by BPD status and GA. Preterm infants had impaired flow parameters, reduced compliance, and air trapping, compared to term infants. Only 15% (n = 14) of the preterm group had normal iPFT, compared to 69% (n = 31) of the term group. The majority of the impaired iPFT in preterm infants were obstructive and 72% (n = 69) had no response to bronchodilators. Reduced maximal flow at the functional residual capacity point (V'maxFRC) was associated with low birth weight and GA. There were no major differences between preterm infants with or without BPD. Preterm infants in the first year of life, demonstrated a high prevalence of obstructive iPFT unresponsive to bronchodilators. BPD status did not add to the degree of pulmonary impairment. These data reveal an airway-predominant pathology of the modern-era prematurity-associated lung disease. Pulmonary function screening tests at an early age may be of value in determining the presence and severity of lung disease in the preterm population. V'maxFRC may provide a good assessment of pulmonary impairment in preterm infants.

DNAH17 deficiency causes disruption in the assembly and docking of sperm flagellar ODAs but not total fertilization failure after ICSI

Research questionAre there other variants in DNAH17 related to male infertility? What is the correlation between total fertilization failure and DNAH17 deficiency? DesignWhole-exome sequencing and Sanger sequencing were performed in a cohort of 75 Chinese patients with MMAF to identify potential novel gene variants. Papanicolaou staining and electron microscopy were employed to observe sperm morphology and ultrastructure. Proteomic analysis and comprehensive functional analysis were performed to elucidate the relationship between DNAH17 deficiency and total fertilization failure at the molecular level. ResultsTen novel variants in DNAH17 were identified in five unrelated families with six infertile males. These identified variants exhibited an autosomal recessive inheritance pattern and caused the deficiency of DNAH17 in sperm. Papanicolaou staining and electron microscopy demonstrated typical MMAF characteristics and deformations in flagellar ultrastructure of DNAH17-deficient sperm. Furthermore, our comprehensive functional analysis revealed that DNAH17 deficiency impaired the assembly and docking of ODAs, affected the acrosome reaction, and disrupted mitochondrial function. Interestingly, the fertilization-related proteins such as ACTL7A and PICK1 were normal, while reduced yet ≥30% PLCζ levels were detected, implying an indirect correlation between DNAH17 deficiency and total fertilization failure. Moreover, four of the affected couples got transferable embryos successfully through intracytoplasmic sperm injection (ICSI) without artificial oocyte activation (AOA). ConclusionsOur findings significantly broaden the variant spectrum of DNAH17 and illuminate the complex molecular basis of male infertility associated with DNAH17 deficiency, particularly its heterogeneous impact on fertilization. The favourable fertility outcomes of ICSI will provide vital insights for genetic diagnosis and counselling in males affected by MMAF.

Exploring the thermal and optical characteristics of Ti3C2 MXene for enhanced photothermal conversion

Ti3C2 MXene, a member of the two-dimensional (2D) transition metal carbides family, has garnered significant attention for its exceptional photothermal properties. To understand the mechanistic underpinnings of this feature, we conducted a comprehensive first-principles density functional theory analysis. This study was aimed at investigating the electronic band structure and vibrational characteristics of Ti3C2 MXene to unravel its microscopic process of photothermal conversion. After obtaining its optical and thermal properties, the process by which the material moves from light absorption to heat release is elucidated. The presence of localized surface plasmon resonance (LSPR) effects in Ti3C2 is proved by Finite-difference time-domain (FDTD) simulations. The synergy between the high thermal conductivity network in the Ti layers and the LSPR phenomenon is believed to be responsible for the superior photothermal conversion capabilities. This investigation enhances the understanding of the intrinsic properties of Ti3C2 MXene, confirming its status as an ultrahigh photothermal conversion material.

A Comprehensive Functional Analysis Indicates CNDP1 Mitigates Hepatocellular Carcinoma and May Be Associated with Immune Cell Infiltration and m6A-Related Genes

A Comprehensive Functional Analysis Indicates CNDP1 Mitigates Hepatocellular Carcinoma and May Be Associated with Immune Cell Infiltration and m6A-Related Genes

Investigation of transverse exchange-springs in electrodeposited nano-heterostructured films through first-order reversal curve analysis

The prerequisite of efficient exchange-spring nano-heterostructures, i.e., tuning both hard and soft phases at a nanometer level, has posed significant preparation challenges to ensure effective exchange-coupling. Here, we present a novel approach to fabricate transverse exchange-spring nano-heterostructures using single starting material through an “in situ” electrodeposition technique at room temperature. Utilizing modified acidic bath chemistry and controlled hydrogen evolution, we successfully prepared stress-free, shiny, fine-grained amorphous, and nanocrystalline Co-rich cobalt phosphorus films. These nano-heterostructured films exhibit a unique non-collinear anisotropy-driven transverse exchange-spring behavior, investigated systematically under ambient conditions. The comprehensive functional analyses reveal that intricate interplay between in-plane (IP) anisotropy of amorphous phase and out-of-plane (OOP) anisotropy generating from a nanocrystalline structure compete with each other, while producing characteristic stripe domain structures to novel corrugated stripe domain shapes. The angle-dependent first-order reversal curve distributions demonstrate new insights into the magnetic reversal mechanisms, further confirming the non-exchange-spring and exchange-spring nature of the films depending on the prevalent interfacial exchange coupling. Formation of anisotropy-driven metastable-state due to competition between IP and OOP anisotropy at a particular OOP orientation has led the normal exchange-spring structures to a transverse exchange-spring structure. Micromagnetic simulations, in excellent agreement with experimental data, further elucidate the formation of characteristic stripe domain patterns and the influence of anisotropy on the magnetic properties. The innovative methodology and detailed functional analysis presented here offer significant understanding to the field of exchange-spring magnetic materials, including anisotropy-driven metastable states, demonstrating the potential for scalable and cost-effective fabrication of advanced nano-heterostructures with tailored magnetic properties.

Mendelian randomization reveals potential causal relationships between cellular senescence-related genes and multiple cancer risks

Cellular senescence is widely acknowledged as having strong associations with cancer. However, the intricate relationships between cellular senescence-related (CSR) genes and cancer risk remain poorly explored, with insights on causality remaining elusive. In this study, Mendelian Randomization (MR) analyses were used to draw causal inferences from 866 CSR genes as exposures and summary statistics for 18 common cancers as outcomes. We focused on genetic variants affecting gene expression, DNA methylation, and protein expression quantitative trait loci (cis-eQTL, cis-mQTL, and cis-pQTL, respectively), which were strongly linked to CSR genes alterations. Variants were selected as instrumental variables (IVs) and analyzed for causality with cancer using both summary-data-based MR (SMR) and two-sample MR (TSMR) approaches. Bayesian colocalization was used to unravel potential regulatory mechanisms underpinning risk variants in cancer, and further validate the robustness of MR results. We identified five CSR genes (CNOT6, DNMT3B, MAP2K1, TBPL1, and SREBF1), 18 DNA methylation genes, and LAYN protein expression which were all causally associated with different cancer types. Beyond causality, a comprehensive analysis of gene function, pathways, and druggability values was also conducted. These findings provide a robust foundation for unravelling CSR genes molecular mechanisms and promoting clinical drug development for cancer.

Impact of Exogenous dsRNA on miRNA Composition in Arabidopsis thaliana.

The application of double-stranded RNAs (dsRNAs) to plant surfaces has emerged as a promising tool for manipulating gene expression in plants and pathogens, offering new opportunities for crop improvement. While research has shown the capability of exogenous dsRNAs to silence genes, the full spectrum of their impact, particularly on the intricate network of microRNAs (miRNAs), remains largely unexplored. Here, we show that the exogenous application of chalcone synthase (CHS)-encoding dsRNA to the rosette leaves of Arabidopsis thaliana induced extensive alterations in the miRNA profile, while non-specific bacterial neomycin phosphotransferase II (NPTII) dsRNA had a minimal effect. Two days after treatment, we detected 60 differentially expressed miRNAs among the 428 miRNAs found in the A. thaliana genome. A total of 59 miRNAs were significantly changed after AtCHS-dsRNA treatment compared with water and NPTII-dsRNA, and 1 miRNA was significantly changed after AtCHS-dsRNA and NPTII-dsRNA compared with the water control. A comprehensive functional enrichment analysis revealed 17 major GO categories enriched among the genes potentially targeted by the up- and downregulated miRNAs. These categories included processes such as aromatic compound biosynthesis (a pathway directly related to CHS activity), heterocycle biosynthesis, RNA metabolism and biosynthesis, DNA transcription, and plant development. Several predicted targets of upregulated and downregulated miRNAs, including APETALA2, SCL27, SOD1, GRF1, AGO2, PHB, and PHV, were verified by qRT-PCR. The analysis showed a negative correlation between the expression of miRNAs and the expression of their predicted targets. Thus, exogenous plant gene-specific dsRNAs induce substantial changes in the plant miRNA composition, ultimately affecting the expression of a wide range of genes. These findings have profound implications for our understanding of the effects of exogenously induced RNA interference, which can have broader effects beyond targeted mRNA degradation, affecting the expression of other genes through miRNA regulation.

Evolution and post-transcriptional regulation insights of m6A writers, erasers, and readers in plant epitranscriptome.

As a dynamic and reversible post-transcriptional marker, N6-methyladenosine (m6A) plays an important role in the regulation of biological functions, which are mediated by m6A pathway components including writers (MT-A70, FIP37, VIR and HAKAI family), erasers (ALKBH family) and readers (YTH family). There is an urgent need for a comprehensive analysis of m6A pathway components across species at evolutionary levels. In this study, we identified 4062 m6A pathway components from 154 plant species including green algae, utilizing large-scale phylogenetic to explore their origin and evolution. We discovered that the copy number of writers was conserved among different plant lineages, with notable expansions in the ALKBH and YTH families. Synteny network analysis revealed conserved genomic contexts and lineage-specific transpositions. Furthermore, we used Direct RNA Sequencing (DRS) to reveal the Poly(A) length (PAL) and m6A ratio profiles in six angiosperms species, with a particular focus on the m6A pathway components. The ECT1/2-Poeaece4 sub-branches (YTH family) with unique genomic contexts exhibited significantly higher expression level than genes of other ECT1/2 poeaece sub-branches (ECT1/2-Poeaece1-3), accompanied by lower m6A modification and PAL. Besides, conserved m6A sites distributed in CDS and 3'UTR were detected in the ECT1/2-Poaceae4, and the dual-luciferase assay further demonstrated that these conserved m6A sites in the 3'UTR negatively regulated the expression of Firefly luciferase (LUC) gene. Finally, we developed transcription factor regulatory networks for m6A pathway components, using yeast one-hybrid assay demonstrated that PheBPC1 could interact with the PheECT1/2-5 promoter. Overall, this study presents a comprehensive evolutionary and functional analysis of m6A pathway components and their modifications in plants, providing a valuable resource for future functional analysis in this field.

Multi-omics Analysis of Umbilical Cord Hematopoietic Stem Cells from a Multi-ethnic Cohort of Hawaii Reveals the Transgenerational Effect of Maternal Pre-Pregnancy Obesity.

Maternal obesity is a health concern that may predispose newborns to a high risk of medical problems later in life. To understand the transgenerational effect of maternal obesity, we conducted a multi-omics study, using DNA methylation and gene expression in the CD34+/CD38-/Lin- umbilical cord blood hematopoietic stem cells (uHSCs) and metabolomics of the cord blood, all from a multi-ethnic cohort (n=72) from Kapiolani Medical Center for Women and Children in Honolulu, Hawaii (collected between 2016 and 2018). Differential methylation (DM) analysis unveiled a global hypermethylation pattern in the maternal pre-pregnancy obese group (BH adjusted p<0.05), after adjusting for major clinical confounders. Comprehensive functional analysis showed hypermethylation in promoters of genes involved in cell cycle, protein synthesis, immune signaling, and lipid metabolism. Utilizing Shannon entropy on uHSCs methylation, we discerned notably higher quiescence of uHSCs impacted by maternal obesity. Additionally, the integration of multi-omics data-including methylation, gene expression, and metabolomics-provided further evidence of dysfunctions in adipogenesis, erythropoietin production, cell differentiation, and DNA repair, aligning with the findings at the epigenetic level. Furthermore, the CpG sites associated with maternal obesity from these pathways also predicted highly accurately (average AUC = 0.8687) between cancer vs. normal tissues in 14 cancer types in The Cancer Genome Atlas (TCGA). This study revealed the significant correlation between pre-pregnancy maternal obesity and multi-omics level molecular changes in the uHSCs of offspring, particularly in DNA methylation. Moreover, these maternal obesity epigenetic markers in uHSCs may predispose offspring to higher cancer risks.

Pathogenic R163W Variant of the Copper Chaperone for Sod1 (Ccs) Functions as an Anti-chaperone.

The copper chaperone for Sod1 (Ccs) is a metallochaperone that plays a multifaceted role in the maturation of Cu,Zn superoxide dismutase (Sod1). The Ccs mutation R163W was identified in an infant with fatal neurological abnormalities. Based on a comprehensive structural and functional analysis, we developed the first data-driven model for R163W-related pathogenic phenotypes. The work here confirms previous findings that the substitution of arginine with tryptophan at this site, which is located adjacent to a conserved Zn binding site, creates an unstable Zn-deficient protein that loses its ability to efficiently activate Sod1. Intriguingly, R163W Ccs can reduce copper (i.e., Cu(II) → Cu(I)) bound in its Sod1-like domain (D2), and this novel redox event is accompanied by disulfide bond formation. The loss of Zn binding, along with the unusual ability to bind copper in D2, diverts R163W Ccs toward aggregation. The remarkably high affinity of D2 Cu(I) binding converts R163W from a Cu chaperone to a Cu scavenger that accelerates Sod1 deactivation (i.e., an Anti-chaperone). Overall, these findings present a first-of-its-kind molecular mechanism for Ccs dysfunction that leads to pathogenesis in humans.

Unveiling the Catalytic Roles of DsBBS1 and DsBBS2 in the Bibenzyl Biosynthesis of Dendrobium sinense.

Dendrobium sinense, an endemic medicinal herb in Hainan Island, is rich in bibenzyl compounds. However, few studies have explored the molecular mechanisms of bibenzyl biosynthesis. This study presents a comprehensive analysis of DsBBS1 and DsBBS2 function in D. sinense. A molecular docking simulation revealed high-resolution three-dimensional structural models with minor domain orientation differences. Expression analyses of DsBBS1 and DsBBS2 across various tissues indicated a consistent pattern, with the highest expression being found in the roots, implying that they play a pivotal role in bibenzyl biosynthesis. Protein expression studies identified optimal conditions for DsBBS2-HisTag expression and purification, resulting in a soluble protein with a molecular weight of approximately 45 kDa. Enzyme activity assays confirmed DsBBS2's capacity to synthesize resveratrol, exhibiting higher Vmax and lower Km values than DsBBS1. Functional analyses in transgenic Arabidopsis demonstrated that both DsBBS1 and DsBBS2 could complement the Atchs mutant phenotype. The total flavonoid content in the DsBBS1 and DsBBS2 transgenic lines was restored to wild-type levels, while the total bibenzyl content increased. DsBBS1 and DsBBS2 are capable of catalyzing both bibenzyl and flavonoid biosynthesis in Arabidopsis. This study provides valuable insights into the molecular mechanisms underlying the biosynthesis of bibenzyl compounds in D. sinense.

Comprehensive Transcriptome Analysis Expands lncRNA Functional Profiles in Breast Cancer.

Breast cancer is a heterogeneous disease that arises as a multi-stage process involving multiple cell types. Patients diagnosed with the same clinical stage and pathological classification may have different prognoses and therapeutic responses due to alterations in molecular genetics. As an essential marker for the molecular subtyping of breast cancer, long non-coding RNAs (lncRNAs) play a crucial role in gene expression regulation, cell differentiation, and the maintenance of genomic stability. Here, we developed a modular framework for lncRNA identification and applied it to a breast cancer cohort to identify novel lncRNAs not previously annotated. To investigate the potential biological function, regulatory mechanisms, and clinical relevance of the novel lncRNAs, we elucidated the genomic and chromatin features of these lncRNAs, along with the associated protein-coding genes and putative enhancers involved in the breast cancer regulatory networks. Furthermore, we uncovered that the expression patterns of novel and annotated lncRNAs identified in breast cancer were related to the hormone response in the PAM50 subtyping criterion, as well as the immune response and progression states of breast cancer across different immune cells and immune checkpoint genes. Collectively, the comprehensive identification and functional analysis of lncRNAs revealed that these lncRNAs play an essential role in breast cancer by altering gene expression and participating in the regulatory networks, contributing to a better insight into breast cancer heterogeneity and potential avenues for therapeutic intervention.

Genomic characterization of bZIP gene family and patterns of gene regulation on Cercospora beticola Sacc resistance in sugar beet (Beta vulgaris L.).

Sugar beet (Beta vulgaris L.) is one of the most important sugar crops, accounting for nearly 30% of the world's annual sugar production. And it is mainly distributed in the northwestern, northern, and northeastern regions of China. However, Cercospora leaf spot (CLS) is the most serious and destructive foliar disease during the cultivation of sugar beet. In plants, the bZIP gene family is one of important family of transcription factors that regulate many biological processes, including cell and tissue differentiation, pathogen defense, light response, and abiotic stress signaling. Although the bZIP gene family has been mentioned in previous studies as playing a crucial role in plant defense against diseases, there has been no comprehensive study or functional analysis of the bZIP gene family in sugar beet with respect to biotic stresses. In this study, we performed a genome-wide analysis of bZIP family genes (BvbZIPs) in sugar beet to investigate their phylogenetic relationships, gene structure and chromosomal localization. At the same time, we observed the stomatal and cell ultrastructure of sugar beet leaf surface during the period of infestation by Cercospora beticola Sacc (C. beticola). And identified the genes with significant differential expression in the bZIP gene family of sugar beet by qRT-PCR. Finally we determined the concentrations of SA and JA and verified the associated genes by qRT-PCR. The results showed that 48 genes were identified and gene expression analysis indicated that 6 BvbZIPs were significantly differential expressed in C. beticola infection. It is speculated that these BvbZIPs are candidate genes for regulating the response of sugar beet to CLS infection. Meanwhile, the observation stomata of sugar beet leaves infected with C. beticola revealed that there were also differences in the surface stomata of the leaves at different periods of infection. In addition, we further confirmed that the protein encoded by the SA signaling pathway-related gene BVRB_9g222570 in high-resistant varieties was PR1, which is closely related to systemic acquired resistance. One of the protein interaction modes of JA signal transduction pathway is the response of MYC2 transcription factor caused by JAZ protein degradation, and there is a molecular interaction between JA signal transduction pathway and auxin. Despite previous reports on abiotic stresses in sugar beet, this study provides very useful information for further research on the role of the sugar beet bZIP gene family in sugar beet through experiments. The above research findings can promote the development of sugar beet disease resistance breeding.

Unified Aedes aegypti Protein Resource Database (UAAPRD): An Integrated High-Throughput In Silico Platform for Comprehensive Protein Structure Modeling and Functional Target Analysis to Enhance Vector Control Strategies.

A comprehensive examination of Aedes aegypti's proteome to detect key proteins that can be targeted with small molecules can disrupt blood feeding and disease transmission. However, research currently only focuses on finding repellent-like compounds, limiting studies on identifying unexplored proteins in its proteome. High-throughput analysis generates vast amounts of data, raising concerns about accessibility and usability. Establishing a dedicated database is a solution, centralizing information on identified proteins, functions, and modeled structures for easy access and research. This study focuses on scrutinizing key proteins in A. aegypti, modeling their structures using RaptorX standalone tool, identification of druggable binding sites using BiteNet, validating the models via Ramachandran plot studies and refining them via 50-ns molecular dynamic simulations using Schrodinger Maestro. By analyzing ~ 18k proteins in the proteome of A. aegypti in our previous studies, all proteins involved in the light and dark circadian rhythm of the mosquito, inclusive of proteins in blood feeding, metabolism, etc. were chosen for the current study. The outcome is UAAPRD, a unique repository housing information on hundreds of previously unmodeled and un-simulated mosquito proteins. This robust MYSQL database ( https://uaaprd.onrender.com/user ) houses data on 309 modeled & simulated proteins of A. aegypti. It allows users to obtain protein data, view evolutionary analysis data of the protein categories, visualize proteins of interest, and send request to screen against the pharmacophore models present in UAAPRD against ligand of interest. This study offers crucial insights for developing targeted studies, which will ultimately contribute to more effective vector control strategies.

Unprecedented Diversity of the Glycoside Hydrolase Family 70: A Comprehensive Analysis of Sequence, Structure, and Function.

The glycoside hydrolase family 70 (GH70) contains bacterial extracellular multidomain enzymes, synthesizing α-glucans from sucrose or starch-like substrates. A few dozen have been biochemically characterized, while crystal structures cover only the core domains and lack significant parts of auxiliary domains. Here we present a systematic overview of GH70 enzymes and their 3D structural organization and bacterial origin. A representative set of 234 permuted and 25 nonpermuted GH70 enzymes was generated, covering 12 bacterial families and 3 phyla and containing 185 predicted glucansucrases (GS), 15 branching sucrases (BrS), 8 "twin" GS-BrSs, and 51 α-glucanotransferases (α-GT). Analysis of AlphaFold models of all 259 entries showed that, apart from the core domains, the structural variation regarding auxiliary domains is far greater than anticipated, with nine different domain types. We analyzed the phylogenetic distribution and discuss the possible roles of auxiliary domains as well as possible correlations between enzyme specificity, auxiliary domain type, and bacterial origin.