Box Element Research Articles

Nanoscale heat transport analysis of magnetized trihybrid nanofluid over wedge artery: Keller Box and Finite element scheme combination

Nanoscale heat transport analysis of magnetized trihybrid nanofluid over wedge artery: Keller Box and Finite element scheme combination

GhWRKY4 binds to the histone deacetylase GhHDA8 promoter to regulate drought and salt tolerance in Gossypium hirsutum

Soil drought and salinization, caused by water deficiency, have become the greatest concerns limiting crop production. Up to now, the WRKY transcription factor and histone deacetylase have been shown to be involved in drought and salt responses. However, the molecular mechanism underlying their interaction remains unclear in cotton. Herein, we identified GhWRKY4, a member of WRKY gene family, which is induced by drought and salt stress and is located in the nucleus. The ectopic expression of GhWRKY4 in Arabidopsis enhanced drought and salt tolerance, and suppressing GhWRKY4 in cotton increased susceptibility to drought and salinity. Subsequently, DAP-seq analysis revealed that the W box element in the promoter of stress-induced genes could potentially be the binding target for GhWRKY4 protein. GhWRKY4 binds to the promoters of GhHDA8 and GhNHX7 via W box element, and the expression level of GhHDA8 was increased in GhWRKY4-silenced plants. In addition, GhHDA8-overexpressed Arabidopsis were found to be hypersensitive to drought and salt stress, while silencing of GhHDA8 enhanced drought and salt tolerance in cotton. The stress-related genes, such as GhDREB2A, GhRD22, GhP5CS, and GhNHX7, were induced in GhHDA8-silenced plants. Our findings indicate that the GhWRKY4-GhHDA8 module regulates drought and salt tolerance in cotton. Collectively, the results provide new insights into the coordination of transcription factors and histone deacetylases in regulating drought and salt stress responses in plants.

Molecular regulation of oil gland development and biosynthesis of essential oils in Citrus spp.

Secretory structures in terrestrial plants serve as reservoirs for a variety of secondary metabolites. Among these, the secretory cavity of the Rutaceae family is notable for containing essential oils with a wide range of applications. However, the molecular basis underlying secretory cavity development is unknown. Here, we reveal a molecular framework for Citrus oil gland formation. Using genetic mapping and genome editing, we demonstrated that this process requires LATE MERISTEM IDENTITY1 (LMI1), a key regulator of leaf serration. A conserved GCC box element of the LMI1 promoter recruits DORNROSCHEN-like (DRNL) for transcriptional activation. This DRNL-LMI1 cascade triggers MYC5 activation, facilitating the development of oil glands and the biosynthesis of essential oils. Our findings spotlight cis-regulatory divergence within leaf shape genes, propelling novel functional tissue formation.

Qualitative investigations into floodways under extreme flood loading

AbstractThe Australian use of the term floodway refers to a trafficable transverse structure designed to facilitate the safe crossing of watercourses. Floodways are also commonly referred to as fords and causeways. This research explores areas of focus through experimental, numerical and survey methods to improve floodway resilience with regard to flood risk management. The industry‐based survey provides a dataset relating to user experiences, deduces the likeliness of floodways to sustain damage, defines several key focus areas, and reveals that the current risk levels are primarily managed without significant investigation into design. A floodway experimental and numerical simulation program was developed to investigate the lateral forces induced through debris impact using scaled models in a soil box and finite element analysis. Qualitatively, crack propagation and displacement correlated closely with the strain concentrations and displacements in the numerical simulation, with failure attributed to tensile strength being exceeded, followed by plastic strain development within the soil elements. It was concluded through this research that floodway failure during flood is complex and can be attributed to several different failure modes including concrete failure, yielding of adjoining soil material, and hydraulically via scour.

Load bearing capacity analysis of concrete sidewalk system designed to ensure comfort of walking for people with a motor disability

The paper looks at a novel structural solution to sidewalks. The proposed system consists of a box element as a substructure and a concrete slab with openings for rainwater infiltration. Such a design will make the sidewalk comfortable for pedestrians with motor impairments, friendly for urban tree root systems and durable. The article provides stress and strain calculations for the variants of the new design. We used the finite element method for the analysis. The results confirm that the proposed variants meet the assumed strength criteria and can therefore be used in the next research steps, that is, permeability tests, rain-water retention simulations, laboratory testing. Highlights Concrete paving slab with environmental approach. Concrete paving slab for people with motor disabilities. The first study implementing FEM method supported by the Barcelona model to analyse stresses and strains in sidewalk pavement.

Taf1 N-terminal domain 2 (TAND2) of TFIID promotes formation of stable and mobile unstable TBP-TATA complexes

In eukaryotes, TATA-binding protein (TBP) occupancy of the core promoter globally correlates with transcriptional activity of class II genes. Elucidating how TBP is delivered to the TATA box or TATA-like element is crucial to understand the mechanisms of transcriptional regulation. A previous study demonstrated that the inhibitory DNA binding (IDB) surface of human TBP plays an indispensable role during the two-step formation of the TBP-TATA complex, first assuming an unstable and unbent intermediate conformation, and subsequently converting slowly to a stable and bent conformation. The DNA binding property of TBP is altered by physical contact of this surface with TBP regulators. In the present study, we examined whether the interaction between Taf1 N-terminal domain 2 (TAND2) and the IDB surface affected DNA binding property of yeast TBP by exploiting TAND2-fused TBP derivatives. TAND2 promoted formation of two distinct types of TBP-TATA complexes, which we arbitrarily designated as complex I and II. While complex I was stable and similar to the well-characterized original TBP-TATA complex, complex II was unstable and moved along DNA. Removal of TAND2 from TBP after complex formation revealed that continuous contact of TAND2 with the IDB surface was required for formation of complex II but not complex I. Further, TFIIA could be incorporated into the complex of TAND2-fused TBP and the TATA box, which was dependent on the amino-terminal non-conserved region of TBP, implying that this region could facilitate the exchange between TAND2 and TFIIA on the IDB surface. Collectively, these findings provide novel insights into the mechanism by which TBP is relieved from the interaction with TAND to bind the TATA box or TATA-like element within promoter-bound TFIID.

Expression Profiling Reveals the Possible Involvement of the Ubiquitin-Proteasome Pathway in Abiotic Stress Regulation in Gracilariopsis lemaneiformis.

Gracilariopsis lemaneiformis is an economically important red macroalga, the cultivation of which is affected by abiotic stresses. This research intends to study the response mechanism of various components of the ubiquitin-protease pathway to abiotic stress in G. lemaneiformis. The algae were treated with five common external stresses (high temperature, low temperature, O3, PEG, and water shortage) to study the macroscopic and microscopic manifestations of the ubiquitin-proteasome pathway. Firstly, the changes in soluble protein and ubiquitin were detected during the five treatments, and the results showed that the content of soluble protein and ubiquitin significantly increased under most stresses. The content of the soluble protein increased the most on the second day after 20% PEG treatment, which was 1.38 times higher than that of the control group, and the content of ubiquitin increased the most 30 min after water shortage treatment, which was 3.6 times higher than that of the control group. Then, 12 key genes (E1, E2, UPL1, HRD1, UFD1, Cul3, Cul4, DDB2, PIAS1, FZR1, APC8, and COP1) of the ubiquitin-proteasome pathway were studied, including an estimation of the probably regulatory elements in putative promoter regions and an analysis of transcript levels. The results showed that CAAT box, LTR, GC motif, and MBS elements were present in the putative promoter regions, which might have endowed the genes with the ability to respond to stress. The transcript analysis showed that under high temperature, low temperature, PEG, O3, and water shortage, all of the genes exhibited instant and significant up-regulation, and different genes had different response levels to different stresses. Many of them also showed the synergistic effect of transcript up-regulation under various stress treatments. In particular, E1, E2, Cul3, Cul4, UPL1, HRD1, and COP1 performed most significantly under the five stresses. Collectively, our exploration of the ubiquitin-proteasome pathway and the transcript levels of key genes suggest a significant role to cope with adversity, and potential candidate genes can be selected for transformation to obtain stress-resistant strains.

GA20ox Family Genes Mediate Gibberellin and Auxin Crosstalk in Moso bamboo (Phyllostachys edulis).

Moso bamboo (Phyllostachys edulis) is one of the fastest growing plants. Gibberellin (GA) is a key phytohormone regulating growth, but there are few studies on the growth of Moso bamboo regulated by GA. The gibberellin 20 oxidase (GA20ox) gene family was targeted in this study. Chromosomal distribution and collinearity analysis identified 10 GA20ox genes evenly distributed on chromosomes, and the family genes were relatively conservative in evolution. The genetic relationship of GA20ox genes had been confirmed to be closest in different genera of plants in a phylogenetic and selective pressure analysis between Moso bamboo and rice. About 1/3 GA20ox genes experienced positive selective pressure with segmental duplication being the main driver of gene family expansion. Analysis of expression patterns revealed that only six PheGA20ox genes were expressed in different organs of shoot development and flowers, that there was redundancy in gene function. Underground organs were not the main site of GA synthesis in Moso bamboo, and floral organs are involved in the GA biosynthesis process. The auxin signaling factor PheARF47 was located upstream of PheGA20ox3 and PheGA20ox6 genes, where PheARF47 regulated PheGA20ox3 through cis-P box elements and cis-AuxRR elements, based on the result that promoter analysis combined with yeast one-hybrid and dual luciferase detection analysis identified. Overall, we identified the evolutionary pattern of PheGA20ox genes in Moso bamboo and the possible major synthesis sites of GA, screened for key genes in the crosstalk between auxin and GA, and laid the foundation for further exploration of the synergistic regulation of growth by GA and auxin in Moso bamboo.

Role of circadian clock in the chronoefficacy and chronotoxicity of clopidogrel.

The role of circadian locomotor output cycles kaput (CLOCK) in regulating drug chronoefficacy and chronotoxicity remains elusive. Here, we aimed to uncover the impact of CLOCK and dosing time on clopidogrel efficacy and toxicity. The antiplatelet effect, toxicity and pharmacokinetics experiments were conducted with Clock-/- mice and wild-type mice, after gavage administration of clopidogrel at different circadian time points. The expression levels of drug-metabolizing enzymes were determined by quantitative polymerase chain reaction (qPCR) and western blotting. Transcriptional gene regulation was investigated using luciferase reporter and chromatin immunoprecipitation assays. The antiplatelet effect and toxicity of clopidogrel in wild-type mice showed a dosing time-dependent variation. Clock ablation reduced the antiplatelet effect of clopidogrel, but increased clopidogrel-induced hepatotoxicity, with attenuated rhythms of clopidogrel active metabolite (Clop-AM) and clopidogrel, respectively. We found that Clock regulated the diurnal variation of Clop-AM formation by modulating the rhythmic expression of CYP1A2 and CYP3A1, and altered clopidogrel chronopharmacokinetics by regulation of CES1D expression. Mechanistic studies revealed that CLOCK activated Cyp1a2 and Ces1d transcription by directly binding to the enhancer box (E-box) elements in their promoters, and promoted Cyp3a11 transcription through enhancing the transactivation activity of albumin D-site-binding protein (DBP) and thyrotroph embryonic factor (TEF). CLOCK regulates the diurnal rhythmicity in clopidogrel efficacy and toxicity through regulation of CYP1A2, CYP3A11 and CES1D expression. These findings may contribute to optimizing dosing schedules for clopidogrel and may deepen understanding of the circadian clock and chronopharmacology.

Genome-Wide Analysis and Identification of 1-Aminocyclopropane-1-Carboxylate Synthase (ACS) Gene Family in Wheat (Triticum aestivum L.).

Ethylene has an important role in regulating plant growth and development as well as responding to adversity stresses. The 1-aminocyclopropane-1-carboxylate synthase (ACS) is the rate-limiting enzyme for ethylene biosynthesis. However, the role of the ACS gene family in wheat has not been examined. In this study, we identified 12 ACS members in wheat. According to their position on the chromosome, we named them TaACS1-TaACS12, which were divided into four subfamilies, and members of the same subfamilies had similar gene structures and protein-conserved motifs. Evolutionary analysis showed that fragment replication was the main reason for the expansion of the TaACS gene family. The spatiotemporal expression specificity showed that most of the members had the highest expression in roots, and all ACS genes contained W box elements that were related to root development, which suggested that the ACS gene family might play an important role in root development. The results of the gene expression profile analysis under stress showed that ACS members could respond to a variety of stresses. Protein interaction prediction showed that there were four types of proteins that could interact with TaACS. We also obtained the targeting relationship between TaACS family members and miRNA. These results provided valuable information for determining the function of the wheat ACS gene, especially under stress.

The Mobilome-Enriched Genome of the Competence-Deficient Streptococcus pneumoniae BM6001, the Original Host of Integrative Conjugative Element Tn5253, Is Phylogenetically Distinct from Historical Pneumococcal Genomes.

Streptococcus pneumoniae is an important human pathogen causing both mild and severe diseases. In this work, we determined the complete genome sequence of the S. pneumoniae clinical isolate BM6001, which is the original host of the ICE Tn5253. The BM6001 genome is organized in one circular chromosome of 2,293,748 base pairs (bp) in length, with an average GC content of 39.54%; the genome harbors a type 19F capsule locus, two tandem copies of pspC, the comC1-comD1 alleles and the type I restriction modification system SpnIII. The BM6001 mobilome accounts for 15.54% (356,521 bp) of the whole genome and includes (i) the ICE Tn5253 composite; (ii) the novel IME Tn7089; (iii) the novel transposon Tn7090; (iv) 3 prophages and 2 satellite prophages; (v) 5 genomic islands (GIs); (vi) 72 insertion sequences (ISs); (vii) 69 RUPs; (viii) 153 BOX elements; and (ix) 31 SPRITEs. All MGEs, except for the GIs, produce excised circular forms and attB site restoration. Tn7089 is 9089 bp long and contains 11 ORFs, of which 6 were annotated and code for three functions: integration/excision, mobilization and adaptation. Tn7090 is 9053 bp in size, flanked by two copies of ISSpn7, and contains seven ORFs organized as a single transcriptional unit, with genes encoding for proteins likely involved in the uptake and binding of Mg2+ cations in the adhesion to host cells and intracellular survival. BM6001 GIs, except for GI-BM6001.4, are variants of the pneumococcal TIGR4 RD5 region of diversity, pathogenicity island PPI1, R6 Cluster 4 and PTS island. Overall, prophages and satellite prophages contain genes predicted to encode proteins involved in DNA replication and lysogeny, in addition to genes encoding phage structural proteins and lytic enzymes carried only by prophages. ΦBM6001.3 has a mosaic structure that shares sequences with prophages IPP69 and MM1 and disrupts the competent comGC/cglC gene after chromosomal integration. Treatment with mitomycin C results in a 10-fold increase in the frequency of ΦBM6001.3 excised forms and comGC/cglC coding sequence restoration but does not restore competence for genetic transformation. In addition, phylogenetic analysis showed that BM6001 clusters in a small lineage with five other historical strains, but it is distantly related to the lineage due to its unique mobilome, suggesting that BM6001 has progressively accumulated many MGEs while losing competence for genetic transformation.

Investigating the sequence landscape in the Drosophila initiator core promoter element using an enhanced MARZ algorithm.

The core promoter elements are important DNA sequences for the regulation of RNA polymerase II transcription in eukaryotic cells. Despite the broad evolutionary conservation of these elements, there is extensive variation in the nucleotide composition of the actual sequences. In this study, we aim to improve our understanding of the complexity of this sequence variation in the TATA box and initiator core promoter elements in Drosophila melanogaster. Using computational approaches, including an enhanced version of our previously developed MARZ algorithm that utilizes gapped nucleotide matrices, several sequence landscape features are uncovered, including an interdependency between the nucleotides in position 2 and 5 in the initiator. Incorporating this information in an expanded MARZ algorithm improves predictive performance for the identification of the initiator element. Overall our results demonstrate the need to carefully consider detailed sequence composition features in core promoter elements in order to make more robust and accurate bioinformatic predictions.

The transcription factor NtERF13a enhances abiotic stress tolerance and phenylpropanoid compounds biosynthesis in tobacco

The AP2/ERF (APETALA2/ETHYLENE RESPONSE FACTOR) transcription factors play multiple roles in modulating the biosynthesis of diverse specialized metabolites in response to various environmental stresses. ERF13 has been shown to participate in plant resistance to biotic stress as well as in repressing the synthesis of fatty acid. However, its full roles in regulating plant metabolism and stress resistance still remains to be further studied. In this study, we identified two NtERF genes from N. tabacum genome that belong to Ⅸa subgroup of ERF family. Over-expression and knock-out of NtERF13a showed that NtERF13a could enhance plant resistance to salt and drought stresses, as well as promoted the biosynthesis of chlorogenic acid (CGA), flavonoids, and lignin in tobacco. Transcriptome analysis between WT and NtERF13a-OE plants revealed 6 differentially expressed genes (DEGs) that encode enzymes catalyzing the key steps of phenylpropanoid pathway. Chromatin immunoprecipitation, Y1H, and Dual-Luc assays further clarified that NtERF13a could directly bind to the fragments containing GCC box or DRE element in the promoters of NtHCT, NtF3'H, and NtANS genes to induce the transcription of these genes. Knock-out of NtHCT, NtF3'H, or NtANS in the NtERF13a-OE background significantly repressed the increase of phenylpropanoid compound contents caused by over-expression of NtERF13a, indicating that the promotion of NtERF13a on the phenylpropanoid compound contents depends on the activity of NtHCT, NtF3'H, and NtANS. Our study demonstrated new roles of NtERF13a in promoting plant resistance to abiotic stresses, and provided a promising target for modulating the biosynthesis of phenylpropanoid compounds in tobacco.

Unraveling the Mechanism of StWRKY6 in Potato (Solanum tuberosum)'s Cadmium Tolerance for Ensuring Food Safety.

The WRKY transcription factor plays a crucial role in plant stress adaptation. Our research has found that WRKY6 in Solanum tuberosum (potatoes) is closely related to cadmium (Cd) tolerance. Therefore, investigating the mechanism of StWRKY6 in plant resistance to Cd toxicity is of great scientific importance for food safety. This research further analyzed the gene structure and functional regions of the nuclear transcription factor WRKY6 in potatoes, discovering that StWRKY6 contains W box, GB/box, ABRE, and other elements that can act as a nuclear transcription regulatory factor to execute multiple functional regulations. The results of the heterologous expression of StWRKY6 in Arabidopsis under Cd stress showed that the overexpression line (StWRKY6-OE) had significantly higher SAPD values and content of reactive oxygen species scavenging enzymes than the wild type, indicating that StWRKY6 plays a crucial role in protecting the photosynthetic system and promoting carbohydrate synthesis. Transcriptome analysis also revealed that the Cd-induced expression of StWRKY6 up-regulated many potential gene targets, including APR2, DFRA, ABCG1, VSP2, ERF013, SAUR64/67, and BBX20, which are involved in Cd chelation (APR2, DFRA), plant defense (VSP2, PDF1.4), toxic substance efflux (ABCG1), light morphology development (BBX20), and auxin signal (SAUR64/67). These genes coordinate the regulation of Cd tolerance in the StWRKY6 overexpression line. In summary, this study identified a potential gene set of the co-expression module of StWRKY6, providing useful evidence for the remediation of Cd-contaminated soil and the genetic breeding of low Cd-accumulating crops, thereby ensuring food safety.

Thermal Performance of Slotted Light Steel-Framed Composite Wall

In this study, calibrated hot box and finite element simulation methods were used to study the influence of a slotted web on the thermal performance of a lightweight steel stud composite wall. By comparing the results from the simulations and experiments, the accuracy of the finite element method was verified; this method was then used for parameter analyses. The results showed that the wall’s thermal transfer coefficient is inversely proportional to increases in the length of the slot and height of the stud web, leading to improvements in the thermal insulation effect; vice versa, the wall thermal transfer coefficient increases when the slot transverse spacing and stud thickness increase, and the insulation effect correspondingly worsens. The stud spacing influences the insulation performance of the wall by changing the proportion of studs within a certain wall. The greater the proportion of studs, the greater the stud thermal bridging, the faster the thermal loss, and the worse the insulation effect of the wall. In practice, the height of the stud web can be set as required. Preferably, for practical applications, the number of rows of slots is 5–7, the length of the slots is 70–80 mm, the transverse distance of the slots is 6–8 mm, the thickness of each stud is 1 or 1.2 mm, and the distance of each stud is 600 mm.

Calculation of compelled fluctuations of panel buildings

The article discusses the dynamic calculation of the elements of the box structure of buildings under the action of seismic effects, taking into account the spatial work of the box elements, given by the displacement of their lower part according to a sinusoidal law. The equations of motion for each of the plate and beam elements of the box structure of the building are constructed based on the Kirchhoff-Love theory. Expressions for the forces, moments, and stresses of the plate elements, which balance the box elements' displacement, the boundary conditions, and the conditions of full contact through displacements and force factors in the contact zones of the plate and beam elements, are compiled. The general solution to the problem is constructed by decomposing the movement of box elements according to their shapes using the finite difference method. The calculation results are shown in graphs for the height of the box of bending moments, plate elements working in bending, and shear stresses of plate elements.

Identification of SBP Gene Family and Analysis of Expression Patterns Under Salt Stress in Quinoa

This study aimed to identify the Squamosa promoter Binding Protein (SBP) transcription factor from the whole genome of quinoa by analyzing its phylogenetic relationship, gene structure, chromosome location, gene replication, upstream cis-regulatory elements, tissue expression, and construction of the SBP protein interaction network, as well as the characteristics of its tissue expression pattern under salt stress. The researchers found that 23 genes of the CqSBP family were identified through bioinformatics analysis and showed diversity in their amino acid physical and chemical properties. These proteins were hydrophilic and all 23 CqSBPs were located in the nucleus. The SBP family genes were unevenly distributed across the 12 chromosomes of quinoa, mostly on the B chromosome group. The upstream cis-acting element analysis revealed the presence of 49 elements with plant hormones, stress, light response, and tissue-specific expression, and all CqSBPs contained one or more Tata box elements. Protein interaction network analysis showed that all CqSBP proteins appeared in the known interaction network of Arabidopsis. Different SBP genes were differently expressed in different organs and periods of quinoa, and SBP genes were expressed with certain tissue specificity. The expression of CqSBP showed many changes under salt stress.

An image-based coal network model for simulating hydro-mechanical gas flow in coal: An application to carbon dioxide geo-sequestration

CO2 geo-sequestration is a practical approach to achieve net-zero carbon target. However, one of the main challenges for successful CO2 geo-sequestration is the reduced coal permeability and injectivity that are caused by coal swelling. Coal has complex and heterogenous internal pore and fracture structure. The processes of gases adsorbing, desorbing, and transporting within multiscale heterogeneous coal structures are more complicated compared with conventional rocks. This paper aims to gain insights about the gas transport behaviours in coal by developing a coupled model to simulate gas flow multiphysics as well as dynamic coal deformation. This work develops an image-based 3D fracture network model, called Fracture Box Model (FBNM). In this model, each fracture is described by arrays of box elements such that the regional change of fracture opening widths can be preserved. Compared with other fracture models (e.g. discrete fracture network), FBNM can simulate complicated multiphysical gas transport more efficiently, but also be able to simulate corresponding coal matrix deformation. By comparing permeability results between direct simulation method with FBNM, it is found that FBNM can effectively estimate the permeability of original fracture networks, but requiring significantly less computational cost. To study the implications of gas types, effective stress, gas adsorption, and thermal expansion on coal permeability, gas injection pressures, gas types, coal seam temperatures are varied and investigated in the simulations. In addition to the advantage of computational efficiency, FBNM is more preferable for complicated flow transport simulations where direct simulation methods are still challenging. This work provides a promising framework which could be further developed for multiphase and multicomponent flow simulations for CO2 geo-sequestration projects.

Forced vibrations of a box element of a multi-story building under dynamic impact

Forced vibrations of a box element of a multi-story building under dynamic impact

Molecular biology of the cell

Molecular biology of the cell