Search Results (21)

MIKC-type MADS-box transcription factors constitute one of the largest gene families in plants, playing pivotal roles in regulating plant growth and development, hormone signaling transduction, and responses to biotic and abiotic stresses. However, there have been no reports on the systematic identification and characterization of MIKC-type MADS-box proteins in walnuts. In this study, we identified 52 JrMADS genes in the walnut genome and transcriptome, and categorized them into 14 subfamilies through structural domain and phylogenetic tree analysis. It was found that these genes were unevenly distributed across 16 chromosomes. Within the MIKC-type MADS-box gene family, we identified three pairs of tandem-duplicated genes and 40 pairs of segmental duplicated genes, indicating that segmental duplication was the primary mechanism of gene amplification in walnut. Ka/Ks analysis showed that the family genes have undergone purifying selection during evolutionary processes. The promoter was predicted to contain cis-acting elements related to growth, development, plant hormones, and stress response. Expression profile analysis showed that JrMADS genes have different expression patterns in various tissues and developmental stages of male and female flower buds. Notably, an ancient clade of TM8 (JrMADS43) genes was found, which is absent in Arabidopsis but present in other flowering plants. Another gene, TM6 gene (JrMADS4), belongs to the AP3 subfamily and is a clade that has diverged from tomatoes. Through qPCR analysis, we verified the differential expression of JrMADS genes at different developmental stages (MB-1/2/3 and FB-1/2/3), with JrMADS5, JrMADS8, JrMADS14, JrMADS24, JrMADS40, JrMADS46, JrMADS47, JrGA3ox1, and JrGA3ox3 showing significantly higher expression in male than in female flower buds. In summary, our results provide valuable information for further biological functions research on MIKC-type MADS-box genes in walnut, such as flower organ development, and lays a solid foundation for future studies. Full article

Plant U-box E3 ubiquitin ligases (PUBs) serve as crucial regulators of protein degradation and are fundamentally involved in plant developmental processes and stress response mechanisms. Despite their well-characterized roles in model plant species, the PUB gene family in the hybrid poplar (Populus alba × P. tremula var. glandulosa) remains poorly understood. By conducting a comprehensive genome-wide analysis, we identified 152 PUB genes in poplar and phylogenetically classified them into five distinct clades based on a comparative analysis with Arabidopsis thaliana and tomato PUB homologs. The structural characterization revealed that numerous PagPUB proteins possess additional functional domains, including ARM and WD40 repeats, which are indicative of potential functional diversification. Genomic distribution and synteny analyses demonstrated that the expansion of the PUB gene family predominantly resulted from whole-genome duplication (WGD) events, with evolutionary constraint analyses (Ka/Ks ratios < 1) suggesting strong purifying selection. An examination of the promoter region uncovered an abundance of stress-responsive cis-elements, particularly ABRE and MYB binding sites associated with abiotic stress and hormonal regulation. Transcriptome profiling demonstrated both tissue-specific expression patterns and dynamic regulation under diverse stress conditions, including drought, salinity, temperature extremes, and pathogen infection. Our findings provide the first systematic characterization of the PUB gene family in poplar and establish a valuable framework for elucidating their evolutionary history and functional significance in environmental stress adaptation. Full article

Wheat (Triticum aestivum) is one of the most important cereal crops globally, with significant economic value. The Arabidopsis Tóxicos en Levadura (ATL) gene family, which comprises members of ubiquitin ligase enzymes (E3s), functions in substrate protein tagging during ubiquitin-mediated protein modification. Recent studies have demonstrated its involvement in stress responses. However, the ATL gene family in wheat remains poorly characterized. This study aimed to identify the members of the ATL gene family in wheat and investigate their roles under salt stress. We identified 334 TaATL genes in the wheat genome, all of which contain either RING-H2, RING U-box, or RAD18 superfamily domains, exhibiting a remarkably low proportion of intron-containing genes. The Ka/Ks (non-synonymous to synonymous substitution rate) analysis and cis-acting element analysis of the TaATL gene family indicate that its sequences are highly conserved and functionally constrained, suggesting that it may participate in abiotic stress responses through the ABA, MeJA, and MYB signaling pathways. Both RNA-seq analysis and RT-qPCR data demonstrated that the expression levels of the TaATL gene family were significantly upregulated under stress conditions, indicating their crucial roles in stress responses. This study demonstrates that the targeted regulation of stress-responsive signaling pathways mediated by superior TaATL gene family members can effectively enhance wheat salt tolerance, thereby providing a viable strategy for the development of high-yielding cultivars adapted to saline agricultural ecosystems. Full article

The B-box (BBX) protein has an impact on flowering physiology, photomorphogenesis, shade effects, and responses to both biotic and abiotic stresses. Although recent research described the BBX gene family in numerous plants, knowledge of the BBX gene in Trichosanthes kirilowii was sparse. In this study, we identified a total of 25 TkBBX genes, and phylogenetic analysis showed that these genes were divided into five subfamilies. Analyses of gene structure and motifs for each group found relative conservation. Ka/Ks values showed that most TkBBX genes have undergone negative selection. qRT-PCR analyses revealed that TkBBX1, TkBB4, TkBBX5, TkBBX7, TkBBX15, TkBBX16, TkBBX17, TkBBX19, and TkBBX21 genes respond to salt and drought treatment. Furthermore, we cloned TkBBX7 and TkBBX17 genes and performed a subcellular localization experiment, which revealed that these two genes were both located in the nucleus. Transgenic yeast experiments demonstrated that TkBBX7 and TkBBX17 enhanced yeast tolerance to both salt and drought stresses. These findings provide a theoretical foundation for further investigation on the functions of TkBBX genes in Trichosanthes kirilowii. Full article

Hazardous substances such as hydrogen and chlorine are used in semiconductor manufacturing. When these gasses are discharged, they are mixed with outside air and are connected to a treatment facility through a duct inside a gas box. This study investigated an optimal exhaust design to prevent fire explosions and toxic exposure by optimizing the exhaust volume when hazardous substances leak from the gas box of semiconductor manufacturing equipment. In this study, carbon monoxide was used for modeling. A 75 mm duct was used, and the tracer gas was released into the gas box at 15.4 LPM. The concentrations were measured at nine points inside and outside the gas box. According to the test results, in an experiment designed with 0% air intake, the internal leakage concentration was measured to be more than 25% of the LEL (lower explosive limit) for 10 min when leakage occurred due to stagnant flow, and the outside toxicity concentration was also measured to be more than 50% of the TWA (time-weighted average) value. When the air intake ratio was designed to be 100%, there was a point on the outside that exceeded 50% of the TWA, confirming that excessive air intake could also cause gas to leak outside. Finally, when the intake ratio was designed to be 50% in both directions, it was confirmed that the airflow was maintained smoothly, and the hazardous gasses were safely diluted and discharged through the duct. This study was conducted to improve the safety of workers in the field in the event of leakage of flammable and toxic gasses by testing the location and area of the air intake hole in the gas box exhaust port. Through this effort, the aim is to present specific standards for gas box design and to assist in establishing a legal framework or standardized guidelines. Full article

B-box (BBX) proteins, a subfamily of zinc-finger transcription factors, are involved in various environmental signaling pathways. In this study, we conducted a comprehensive analysis of BBX family members in Brassica crops. The 482 BBX proteins were divided into five groups based on gene structure, conserved domains, and phylogenetic analysis. An analysis of nonsynonymous substitutions and (Ka)/synonymous substitutions (Ks) revealed that most BBX genes have undergone purifying selection during evolution. An analysis of transcriptome data from rapeseed (Brassica napus) organs suggested that BnaBBX3d might be involved in the development of floral tissue-specific RNA-seq expression. We identified numerous light-responsive elements in the promoter regions of BnaBBX genes, which were suggestive of participation in light signaling pathways. Transcriptomic analysis under shade treatment revealed 77 BnaBBX genes with significant changes in expression before and after shading treatment. Of these, BnaBBX22e showed distinct expression patterns in yellow- vs. black-seeded materials in response to shading. UPLC-HESI-MS/MS analysis revealed that shading influences the accumulation of 54 metabolites, with light response BnaBBX22f expression correlating with the accumulation of the flavonoid metabolites M46 and M51. Additionally, BnaBBX22e and BnaBBX22f interact with BnaA10.HY5. These results suggest that BnaBBXs might function in light-induced pigment accumulation. Overall, our findings elucidate the characteristics of BBX proteins in six Brassica species and reveal a possible connection between light and seed coat color, laying the foundation for further exploring the roles of BnaBBX genes in seed development. Full article

Floor mats are commonly used to improve the impact sound performance of existing homes, but actual impact sound reductions do not consistently appear, as they depend on the test-bed conditions used to determine impact sound performance. Therefore, this study evaluated the effects of the environmental conditions of the test bed on the impact sound reduction performances of different floor mats. The Korean industrial standard KS F 2865 specifies the measurement method in the test room and sets the thickness range of the available target floor structure to bare slabs with thicknesses ranging from 120 mm to 210 mm. The evaluation method is ∆L, which is the difference in standardized impact sound levels before and after the installation of the floor finishing material. In this study, a total of eight types of floor mats were tested in four different test beds according to KS F 2865. The impact sources used were tapping, bang machines, and a rubber ball, and we used these sources to consider both light-weight and heavy-weight impact sounds. The results were derived as the impact sound reduction performance for each frequency band and a single-number quantity. The results showed that light impact sound had a similar minimum reduction characteristic of at least 38 dB, regardless of the floor structure on which the mat was installed. However, the heavy-weight impact sound showed different tendencies depending on the floor mat and the characteristics of the floor structure of the test bed when a bang machine and a rubber ball were used. In particular, the reduction achieved by the bang machine showed less than half the tendency of the reduction by the rubber ball, and the tendency of the heavy-weight impact sound was shown to be reducible depending on how the floor mat was maintained, but the reductions differed depending on the test bed. The reductions were larger in the box-type test room than in the real-life-type test room, and among the box-type test rooms, the one with a thicker bare slab showed a relatively larger reduction. In addition, the reliability of the measurement results was evaluated through a correlation analysis between the single-number quantities depending on the thicknesses of the bare slabs of the test beds. Full article

Malate dehydrogenase (MDH; EC 1.1.1.37) plays a vital role in plant growth and development as well as abiotic stress responses, and it is widely present in plants. However, the MDH family genes have not been explored in sweet potato. In this study, nine, ten, and ten MDH genes in sweet potato (Ipomoea batatas) and its two diploid wild relatives, Ipomoea trifida and Ipomoea triloba, respectively, were identified. These MDH genes were unevenly distributed on seven different chromosomes among the three species. The gene duplications and nucleotide substitution analysis (Ka/Ks) revealed that the MDH genes went through segmental duplications during their evolution under purifying selection. A phylogenetic and conserved structure divided these MDH genes into five subgroups. An expression analysis indicated that the MDH genes were omni-presently expressed in distinct tissues and responded to various abiotic stresses. A transcription factor prediction analysis proved that Dof, MADS-box, and MYB were the main transcription factors of sweet potato MDH genes. These findings provide molecular features of the MDH family in sweet potato and its two diploid wild relatives, which further supports functional characterizations. Full article

Highly flammable substances such as hydrogen and silane are used in the semiconductor manufacturing process. When gas leaks, it is mixed with outside air and connected to a treatment facility through the duct inside the gas box. This study investigated optimal exhaust design to prevent fire explosions and health problems by optimizing the exhaust volume when hydrogen leaks from the gas box of semiconductor manufacturing equipment. After selecting the leakage rate amount based on the KS C IEC 60079-10-1, SEMI S6-0707E, and SEMI F-15 standards, a gas box was manufactured. Subsequently, the fan speed required to ventilate the gas box more than five times per minute according to the SEMI standard and the opening area and location that can reduce the lower explosive limit (LEL) to less than 25% in the event of hydrogen leakage were determined. When the air intakes were placed on the left and right, the flow rate was measured at 32 L per minute (LPM), and the maximum concentration was measured at 9111 ppm. This is less than 25% of the LEL of hydrogen and is believed to be capable of preventing fire and explosion, even if a similarly flammable gas leaks inside the gas box. Full article

Members of the WRKY transcription factor (TF) family are unique to plants and serve as important regulators of diverse physiological processes, including the ability of plants to manage biotic and abiotic stressors. However, the functions of specific WRKY family members in the context of maize responses to fungal pathogens remain poorly understood, particularly in response to Ustilago maydis (DC.) Corda (U. maydis), which is responsible for the devastating disease known as corn smut. A systematic bioinformatic approach was herein employed for the characterization of the maize WRKY TF family, leading to the identification of 120 ZmWRKY genes encoded on 10 chromosomes. Further structural and phylogenetic analyses of these TFs enabled their classification into seven different subgroups. Segmental duplication was established as a major driver of ZmWRKY family expansion in gene duplication analyses, while the Ka/Ks ratio suggested that these ZmWRKY genes had experienced strong purifying selection. When the transcriptional responses of these genes to pathogen inoculation were evaluated, seven U. maydis-inducible ZmWRKY genes were identified, as validated using a quantitative real-time PCR approach. All seven of these WKRY proteins were subsequently tested using a yeast one-hybrid assay approach, which revealed their ability to directly bind the ZmSWEET4b W-box element, thereby controlling the U. maydis-inducible upregulation of ZmSWEET4b. These results suggest that these WRKY TFs can control sugar transport in the context of fungal infection. Overall, these data offer novel insight into the evolution, transcriptional regulation, and functional characteristics of the maize WRKY family, providing a basis for future research aimed at exploring the mechanisms through which these TFs control host plant responses to common smut and other fungal pathogens. Full article

The MYB gene family is significant in plants, playing a role in numerous plant development processes, including metabolism, hormone signal transduction, cell identity, and biotic and abiotic stresses. Due to the recent availability of the Melastoma candidum genome, this is the first time that the MYB gene family has been identified in this species. This study identified 421 MYB gene members in the M. candidum genome using the HMMER search and BLASTp method. These MYBs were further divided into 10 sub-types, including R2R3, R-R, CPC-like, CCA1-like, TBP-like, R1R2R3, I-box, atypical MYB, MYB-CC, and MYB-like. Domain and conservation analyses revealed that each type of MYB was characterized by a different number and combination of SANTs/myb DNA-binding domains. Collinearity analysis revealed several gene duplication events within the MYB gene family. The Ka to Ks ratio suggested that most of the MYB genes underwent purifying selection during the evolution process. Phylogenetic analysis among three species confirmed our findings and displayed the evolutionary relationship of MYB genes in different species. RNA-seq of three developmental stages of flowers and WGCNA analysis identified McMYB113h, McMYB21b, and McGLK1c as playing a pivotal role during flower development in M. candidum. Finally, we conducted qRT-PCR experiments for 20 flower-development-related MYBs across 9 tissues to illustrate their expression patterns in M. candidum. This study establishes a foundation for exploring MYB gene resources and their potential applications in related industries of M. candidum. Full article

MADS-box is a class of transcriptional regulators that are ubiquitous in plants and plays important roles in the process of plant growth and development. Identification and analysis of blueberry MADS-box genes can lay a foundation for their function investigations. In the present study, 249 putative MADS-box genes were identified in the blueberry genome. Those MADS-box genes were distributed on 47 out of 48 chromosomes. The phylogenetic and evolutionary analyses showed that blueberry MADS-box genes were divided into 131 type I members and 118 type II members. The type I genes contained an average of 1.89 exons and the type II genes contained an average of 7.83 exons. Motif analysis identified 15 conserved motifs, of which 4 were related to the MADS domain and 3 were related to the K-box domain. A variety of cis-acting elements were found in the promoter region of the blueberry MADS-box gene, indicating that the MADS-box gene responded to various hormones and environmental alterations. A total of 243 collinear gene pairs were identified, most of which had a Ka/Ks value of less than 1. Nine genes belonging to SEP, AP3/PI, and AGL6 subfamilies were screened based on transcriptomic data. The expression patterns of those nine genes were also verified using quantitative PCR, suggesting that VcMADS6, VcMADS35, VcMADS44, VcMADS58, VcMADS125, VcMADS188, and VcMADS212 had potential functions in blueberry fruit ripening. The results of this study provide references for an in-depth understanding of the biological function of the blueberry MADS-box genes and the mechanism of blueberry fruit ripening. Full article

WRKY transcription factors have been found in most plants and play an important role in regulating organ growth and disease response. Outlining the profile of WRKY genes is a very useful project for studying morphogenesis and resistance formation. In the present study, a total of 63 WRKY genes consisting of 13 class I, 41 class II, and 9 class III genes were identified from the newly published A. trifoliata genome, of which 62 were physically distributed on all 16 chromosomes. Structurally, two AkWRKY genes (AkWRKY6 and AkWRKY52) contained four domains, and AkWRKY17 lacked the typical heptapeptide structure. Evolutionarily, 42, 16, and 5 AkWRKY genes experienced whole genome duplication (WGD) or fragmentation, dispersed duplication, and tandem duplication, respectively; 28 Ka/Ks values of 30 pairs of homologous genes were far lower than 1, while those of orthologous gene pairs between AkWRKY41 and AkWRKY52 reached up to 2.07. Transcriptome analysis showed that many of the genes were generally expressed at a low level in 12 fruit samples consisting of three tissues, including rind, flesh, and seeds, at four developmental stages, and interaction analysis between AkWRKY and AkNBS genes containing W-boxes suggested that AkWRKY24 could play a role in plant disease resistance by positively regulating AkNBS18. In summary, the WRKY gene family of A. trifoliata was systemically characterized for the first time, and the data and information obtained regarding AkWRKY could be very useful in further theoretically elucidating the molecular mechanisms of plant development and response to pathogens and practically improving favorable traits such as disease resistance. Full article

Compost amendment is a widespread agronomic practice, but little information is available about the short- and medium-term effects on clay soils. In this investigation, we selected three soil compost rates (treatments, T), i.e., fertilizer (T2 = 1.5 kg m⁻²), amending (T3 = 15 kg m⁻²), and organic (T4 = 75 kg m⁻²), that were compared to a control (T1). Our research accounts for the effects reached on representative large boxes (about 0.75 m³), without crops and for about eighteen months. An overall assessment of the physical and hydraulic properties of the soil was made, including infiltration rate or saturated hydraulic conductivity (K_s), water content and water retention (θ) of the soil, bulk density and structure, and several physical quality indicators obtained from the water retention curve, accounting for the optimal balance between water/air into the soil, pore volume distribution function, and soil features in the inflection point of the soil water retention curve. Additionally, the temporal changes of K_s were evaluated. The main results showed that (i) after eighteen months, and regardless of T, θ significantly improved by a factor of 1.2–1.3, but these improvements (up to 1%) were detected only close to water saturation (i.e., until 6 cm of soil pressure head) when little (T2) or no compost (T1) addition was considered, while a larger range was detected (until 60 cm) when higher rates (T3–T4) were used; (ii) K_s determination allowed to establish that compost effects vanished after about eleven months, but it was not possible to verify that composting increased the permeability of the investigated clay soil within that time frame; (iii) some significant correlations between K_s and some soil physical indicators estimated from both the inflection point of the water retention curve or bulk density suggested possible improvements in soil permeability. Because some factors (water content of the soil above all) could have affected the comparison of K_s measurements, further research on this topic is needed. Full article

In this study, the effects of multi-perforated gypsum boards on floor impact noises were investigated in a box-type test building and an actual apartment building. In a box-type test building with 150 mm thick slab, various design factors such as hole pattern, hole size, opening ratio, backing, or finishing materials were considered. Heavy-weight impact sources of bang machine and rubber ball were employed. The test procedure followed KS F 2810-2, and then, a single number rating was derived in accordance with KS F 2863-2. As a result, reduction of heavy-weight impact noise by applying multi-perforated gypsum boards as a ceiling material was expected maximumly up to 3 dB for bang machine and 5 dB for rubber ball. Regarding the reduction of floor impact sounds at frequencies above 125 Hz, the installed area of the employed multi-perforated gypsum board was shown as the most dominant factor. Then, an in situ investigation using standard impact sources and five children was carried out in an actual living space of an actual apartment dwelling unit. Comparing before and after installation of multi-perforated gypsum board, 1–2 dB of heavy-weight impact noises was reduced. In addition, subjective impressions of the reduced impact noise were discussed based on the field questionnaire survey using actual children’s running situations. Full article