Search Results (33)

The uterine microbiome plays a critical role in maintaining pH balance, modulating the immune system, and influencing fertility, especially in artificial breeding contexts. This study examined the impact of uterine microbiota on pregnancy success in cows following embryo transfer (ET), using Illumina 16S rRNA gene sequencing of the V4 hypervariable region of samples collected from the uterine horn (UH) and the uterine body (UB) of cows during the estrous cycle preceding synchronization for ET in the Amazon region. Microbiomes from the uterine horn (UH) and the uterine body (UB) were analyzed before embryo transfer. Cows that became pregnant (UH-P and UB-P) and those that did not (UH-NP and UB-NP) were compared. Fifteen cows were grouped as follows: UB-P (three), UB-NP (five), UH-P (three), and UH-NP (four). Linear discriminant analysis effect size and heat tree analyses identified Sphingobacterium and Stenotrophomonas spp. as significantly enriched in the UB-P and UH-NP groups, respectively. Additionally, non-pregnant cows exhibited more distinctive genera than pregnant ones. These findings suggest that cows achieving pregnancy have lower microbial diversity and fewer potentially pathogenic genera. This study contributes to the emerging field of pre-pregnancy uterine microbiome research in cattle, offering evidence that microbial composition may influence reproductive success, and highlights specific taxa as potential biomarkers for pregnancy outcomes following embryo transfer. Full article

Seed weight is a key agronomic trait determining soybean yield and quality, yet only a few of genes regulating this trait have been functionally characterized to date. In this study, we identified 155 homologous genes in the soybean genome through BLAST searches using 78 functionally validated rice grain weight-related genes as queries. Haplotype analysis prioritized 40 candidate genes exhibiting significant differences in seed weight between haplotypes. To further refine the candidate list, we integrated haplotype frequency analysis, expression–trait association mapping, and tissue-specific expression profiling, ultimately delineating eight key genes. Given the established role of ubiquitination in seed development, we focused on homologs of OsUBP15 and identified three candidate genes, GmUBP5, GmUBP11, and GmUBP33, that exhibited significant haplotype-dependent variation in seed weight. Subcellular localization assays confirmed their nuclear localization. Haplotype frequency analysis revealed that the superior haplotypes of these genes have been preferentially retained during modern breeding and are widely distributed across major soybean-producing regions. Leveraging non-synonymous SNP variants, we developed and validated robust KASP markers that efficiently discriminate germplasm with contrasting seed weight phenotypes. Collectively, our study provides not only high-confidence genetic targets and actionable molecular markers but also insights into pyramiding breeding strategies for improving seed weight in soybean. Full article

Indocalamus tessellatus (Munro) P. C. Keng is a bamboo species with significant economic and ecological value, and exhibits considerable resistance to abiotic stresses. However, systematic evaluation of reference genes for gene expression analysis in this species is lacking. Analysis of multi-tissue transcriptomes yielded 3801 relatively stable genes; from these, we selected eleven new candidates along with nine widely adopted reference genes. We then evaluated these candidates under four conditions: drought (15% PEG-6000), salt (200 mM NaCl), waterlogging (root submergence in water), and a multi-tissue panel (leaf, leaf sheath, culm, shoot, and root). Under stress, early and sustained time points were sampled to capture dynamic transcriptional responses. Expression stability was assessed using geNorm, NormFinder, BestKeeper, and ΔCt, and results were integrated with RefFinder to generate comprehensive stability rankings for each condition. The most stable reference genes were condition-dependent: MD10B and PP2A under drought, eIF1A and Ite23725 under salt stress, PP2A and eIF4A under waterlogging, and 60S and UBP1 across different tissues. Notably, commonly used genes such as UBI and Actin7 were less stable. Peroxidase (POD) was used as a validation marker because it is a known stress-responsive gene, providing a sensitive readout of normalization accuracy. Validation confirmed that selecting suitable reference genes is essential for dependable expression quantification. These findings provide a robust set of reference genes for qRT-PCR studies in I. tessellatus, supporting future molecular and functional research in bamboo. Full article

Stress granules (SGs) are dynamic membrane-less structures assembled in response to stress. The formation of stress granules in plants is poorly understood, especially the mechanism of mRNA recruitment. The problem of the specificity of mRNA interaction with stress granule proteins is unexplored. Oligouridylate binding protein 1B (UBP1B) is considered as the core element of plant SGs. In this study, we expressed the AtUBP1b protein from Arabidopsis thaliana in E. coli cells. Mass spectroscopic analysis showed that the AtUBP1b protein expressed in E. coli cells is phosphorylated at serine, threonine, and tyrosine residues. We also performed a de novo phosphorylation reaction in wheat germ extracts with the addition of radioactively labeled phosphorus and showed AtUBP1b phosphorylation in plant extracts. We hypothesized that phosphorylation or dephosphorylation of AtUBP1b in plant cells is a signal for protein binding to RNA. The purified protein was tested for its ability to bind to mRNA in vitro. In gel-shifting assays we demonstrated that AtUBP1b protein binds specifically to 5′-untranslated regions (5′UTR) of mRNA. When AtUBP1b was added to a cell-free wheat germ translation system, it exerted different effects on protein synthesis. We showed that AtUBP1b had a significant inhibitory effect on the expression of mRNAs containing 5′UTRs that were shown to bind to the protein in the gel-shifting reaction. Full article

Deubiquitination plays a pivotal role in regulating plant responses to abiotic stress, growth, and development. Among the deubiquitinase (DUB) families, ubiquitin-specific proteases (UBPs) constitute the largest group. Despite this, limited research has been conducted on the functional characteristics of the UBP gene family in soybean (Glycine max). In this study, we identified 52 UBP gene family members in soybean, all of which harbored UCH (ubiquitin C-terminal hydrolase) domains with short yet evolutionarily conserved Cys-box and His-box. These genes were phylogenetically classified into 14 distinct groups; GmUBP genes within the same group shared analogous patterns of conserved domains and motifs. Moreover, a synteny analysis reveals that the GmUBP family has undergone extensive gene duplication events and shares a close evolutionary relationship with Arabidopsis thaliana. We conducted a focused analysis on GmUBP7, which is a gene exhibiting high expression levels in soybean seeds. Intriguingly, this gene exhibited several haplotypes in natural soybean varieties, with significant differences being observed in relation to seed traits, such as 100-seed weight, total fatty acid content, and protein content among different haplotypes. Collectively, the findings from this study provide a foundation for the functional characterization of GmUBP genes, offering new insights into the regulatory network underlying seed development in soybean. Full article

The Alternaria alternata tangerine pathotype causes Alternaria brown spot, a devastating disease of susceptible tangerine varieties and their hybrids. Alternaria citri toxin (ACT) is the primary virulence factor, but the regulatory mechanisms governing ACT synthesis remain unclear. Deubiquitinating enzymes maintain ubiquitination homeostasis and regulate fungal pathogenicity, yet their role in A. alternata remains unexplored. We characterized 13 ubiquitin-specific protease (UBP) family members in A. alternata tangerine pathotype. Six UBP genes (Aaubp2, Aaubp3, Aaubp4, Aaubp6, Aaubp14, and Aaubp15) regulated mycelial growth. Aaubp14 deletion abolished sporulation, while mutations of Aaubp3, Aaubp4, Aaubp6, Aaubp8, and Aaubp15 altered conidial morphology. qRT-PCR demonstrated distinct host-induced expression patterns among Aaubp genes. Pathogenicity tests showed that ΔAaubp6, ΔAaubp14, and ΔAaubp15 mutants failed to produce lesions on Citrus reticulata cv. Hongjv leaves. Moreover, Aaubp14 deletion significantly suppressed ACT biosynthesis gene expression and blocked ACT production. Comparative proteomics showed Aaubp14 regulates ACT biosynthesis by modulating protein ubiquitination in metabolic pathways and controls pathogenicity via a complex network. Our findings elucidate Aaubp gene function in development and pathogenicity, particularly the Aaubp14-mediated regulation mechanism, providing insights into ubiquitination-mediated pathogenicity in phytopathogenic fungi. Full article

The ubiquitin-specific protease (UBP) family constitutes the largest group within the deubiquitinating enzymes (DUBs) and plays a crucial role in regulating the cell cycle, growth, and developmental processes in living organisms. By utilizing genomic and transcriptomic databases, we employed bioinformatics tools to identify UBP family members within pepper genomes and to analyze the expression profiles of CaUBP genes under various abiotic stresses, as well as in different tissues and organs. Our findings revealed the presence of 40 CaUBPs in peppers, exhibiting significant variation in their physicochemical properties. Subcellular localization studies indicated that all CaUBPs are localized in the nucleus. Phylogenetic analysis categorized the 40 CaUBPs into 11 distinct subfamilies (G1–G11), with the largest subfamily comprising seven members. Members within the same subfamily displayed similar domain and motif structures. The promoter regions of CaUBP genes were found to be enriched with elements responsive to light, stress, and hormones. Syntenic analysis revealed that 12 CaUBPs were mapped to the Arabidopsis thaliana genome, suggesting potential functional conservation. Additionally, tandem duplications were observed in the alignment of two sets of genes within the pepper genome. CaUBPs were implicated in the stress response and organ growth, with CaUBP17/34/35 showing significant changes in expression under heat stress. While most genes were not expressed in leaves, the expression of several genes (CaUBP3/17/27/32/35/38) in flowers was significantly altered. This study establishes a foundation for further exploration of the roles of CaUBPs in pepper growth, development, and stress response mechanisms. Full article

To reduce labor costs in aquaculture and enhance the level of automated management, this study designed and developed a multifunctional unmanned boat platform (UBP) by integrating technologies such as sensors, satellite positioning, and artificial intelligence. The platform contains three major modules for data collection, underwater vision, and motion control, enabling functions like cruise path planning, water quality monitoring, identification of aquaculture products, and bait feeding. To verify its reliability and practicality, verification experiments were conducted in the aquaculture area of Lianyungang, China. The results show that the UBP can efficiently distribute feed to an area of 10,000 square meters within 20 min based on feeding points, outperforming the 47 min required for manual feeding. Over a two-month period, the weight of sea cucumbers raised by unmanned boats increased by 67.7% compared to those raised manually, with a 24.33% reduction in feed usage. Additionally, the unmanned boat reduced daily aquaculture costs from 225 RMB to 120.2 RMB, a total reduction of 46.7%. In conclusion, this platform reduces labor costs by improving aquaculture efficiency, and addresses limitations of the existing aquaculture feeding machinery in adaptability and real-time responsiveness, which can provide a feasible solution for aquaculture automation. Full article

Chickens possess a well-developed vision that allows them to perceive a wide range of the color spectrum. In addition, they display an inherent sensitivity toward specific light spectra, which suggests that coloring feed could influence feed preference, feed intake and growth performance. This trial assessed the effect of feed coloring on broiler feed color preferences. A total of 216 day-old Cobb by-product males were randomly distributed into 18 battery cages, each containing 12 chicks and subjected to three dietary treatments from 1 to 21 days, resulting in six replicates per dietary treatment. Feed color treatments consisted of a common corn–soybean meal-based undyed basal (UB) broiler starter diet, which was dyed to obtain blue-colored (B) and purple-colored (P) diets, resulting in a total of three diets used to create the feed combinations. Two feed troughs were affixed to each cage, allowing for the assignment of dietary treatments as follows: UB-B, UB-P, and B-P. The birds had ad libitum access to feed and water throughout the study. Feed consumption data were collected at 7-day intervals. Additionally, bird weights were measured at 1 and 21 days. The data were analyzed as a completely randomized design using the SAS GLIMMIX and TTEST procedures. Overall, broilers exhibited a preference for the UB diet compared to the B and P diets. Broilers had a 27.5 and 29.2% higher (p < 0.05) feed consumption of UB feed compared to P feed from 1 to 14 and 1 to 21 days, respectively. In addition, broilers tended to have a higher (p = 0.098) consumption of UB feed compared to B feed from 1 to 14 days. No differences were observed in feed consumption between B and P diets during the experimental period. Based on feed consumption data, broilers displayed a preference towards the UB feed when paired with B or P diets. Feed coloring did not impact the mortality of broilers and did not result in adverse growth. Overall, broilers preferred the UB diet over the B and P diets and showed no preference between B and P diets. Based on the results of this trial, diets that appear more conventional, compared to dyed diets, can promote consumption. Special care must be taken to avoid ingredients that could alter the diet’s coloration. Full article

Focusing on the COVID-19 period in Japan, this study identifies the effectiveness of a municipal unit-based pricing (UBP) system on household waste reduction through a panel data analysis targeting 770 cities for 2013–2022. It focuses on simple unit pricing (SUP) and two-tiered pricing (TTP) systems as the UBP components. As previous studies have not considered the COVID-19 period when assessing UBP, this study significantly contributes to the literature by providing new evidence. The main findings are as follows: First, SUP effectively reduced household waste even during the COVID-19 period; however, its effectiveness was slightly neutralized owing to the pandemic environment. Second, TTP also restrained household waste efficiently; however, its effect was smaller than that of SUP, and its reduction effect accelerated during the COVID-19 period (in 2020) because people became cautious about excessive waste volumes beyond the TTP criteria. The study implicates the need to expand the municipal adoption of the UBP system for household waste reduction. Full article

Ubiquitin-specific proteases (UBPs), the largest subfamily of deubiquitinating enzymes (DUBs), are critical for plant growth and development as well as abiotic-stress responses. In this study, we discovered that the expression of the ubiquitin-specific protease 15 (UBP15) gene was induced by salt, mannitol and abscisic acid (ABA) treatments. Further research revealed that UBP15 is involved in modulation of salt, drought tolerance and ABA signaling during seed germination, early seedling development, post-germination root growth or adult-plant stage. Enrichment analysis showed that many genes related to abiotic stresses and metabolic pathways were altered in the ubp15-1 mutant. Through the joint analysis of the quantitative real-time polymerase chain reaction (qRT-PCR) and differentially-expressed gene relationship network, we found that UBP15 may mainly regulate salt-stress tolerance by modulating the dwarf and delayed flowering 1 (DDF1) pathway through a cascade reaction. In the regulation of drought-stress responses, ring domain ligase1 (RGLG1) may be a direct substrate of UBP15. Moreover, we cannot exclude the possibility that UBP15 acts in a feed-forward loop mechanism in the regulation of drought-stress responses via ethylene response factor 53 (ERF53) and its ubiquitin (Ub) ligase RGLG1. In ABA signal transduction, UBP15 may play a role in at least three aspects of the ABA signaling pathway: ABA synthesis, stomatal closure regulated by ABA signaling, and transcription factors in the ABA pathway. Taken together, our results suggest that UBP15 is involved in salt, osmotic, and drought-stress tolerance and the ABA signaling pathway by directly regulating the stability of key substrates or indirectly affecting the expression of genes related to abiotic stresses in Arabidopsis thaliana. Our research provides new germplasm resources for stress-resistant crops cultivation. These results demonstrate that UBP15 is a key regulator of salt, drought and ABA tolerance in Arabidopsis. Full article

The ubiquitin-specific protease (UBP) family represents a type of deubiquitinase (DUB) that plays a significant role in plant abiotic stress responses, growth, and development. Although UBP genes have been characterized in many species, a genome-wide systematic analysis and the potential functions under abiotic stresses have not yet been reported in rice (Oryza sativa L.). In this study, we identified 21 UBP gene family members in the genome of rice, all of which had UCH domains containing short but highly conserved Cys-box and His-box. The DUF4220 and DUF594 domains, which are found in monocotyledonous plants, were unique. Phylogenetic analysis suggested that OsUBP7 and OsUBP12 genes had the closest genetic relationships with AtUBP12 and AtUBP13, implying that OsUBP7 and OsUBP12 might have similar biological functions to AtUBP12 and AtUBP13. Synteny analysis revealed that OsUBP genes were expanded through segmental duplication under purifying selection. Meanwhile, they had closer evolutionary relationships with monocotyledonous plants. Additionally, all OsUBP genes had an ABRE cis-element, which was related to abscisic acid (ABA) stress hormone response. Protein interaction analysis suggested that OsUBP22 might modulate gene regulation through OsGCN5- and OsADA2-mediated chromatin modification, and OsUBP10 might regulate salt stress through modulating OsDNA2_4 stability. Specifically, the expression profiles and the transcriptional levels of 11 representative OsUBPs suggested the potential important functions of OsUBP9 and OsUBP17 under drought and cold stresses. Taken together, our study provided a systematic analysis of OsUBPs and preliminarily explored their potential roles under abiotic stresses. Our results lay a foundation for further research on the functions of the OsUBP gene family under abiotic stresses. Full article

Cancer metastasis accounts for approximately 90% of cancer deaths, and elucidating markers in metastasis is the first step in its prevention. To characterize metastasis marker genes (MGs) of breast cancer, XGBoost models that classify metastasis status were trained with gene expression profiles from TCGA. Then, a metastasis score (MS) was assigned to each gene by calculating the inner product between the feature importance and the AUC performance of the models. As a result, 54, 202, and 357 genes with the highest MS were characterized as MGs by empirical p-value cutoffs of 0.001, 0.005, and 0.01, respectively. The three sets of MGs were compared with those from existing metastasis marker databases, which provided significant results in most comparisons (p-value < 0.05). They were also significantly enriched in biological processes associated with breast cancer metastasis. The three MGs, SPPL2C, KRT23, and RGS7, showed highly significant results (p-value < 0.01) in the survival analysis. The MGs that could not be identified by statistical analysis (e.g., GOLM1, ELAVL1, UBP1, and AZGP1), as well as the MGs with the highest MS (e.g., ZNF676, FAM163B, LDOC2, IRF1, and STK40), were verified via the literature. Additionally, we checked how close the MGs were to each other in the protein–protein interaction networks. We expect that the characterized markers will help understand and prevent breast cancer metastasis. Full article

Abnormal depolarization of neuronal membranes called paroxysmal depolarization shift (PDS) represents a cellular correlate of interictal spikes. The mechanisms underlying the generation of PDSs or PDS clusters remain obscure. This study aimed to investigate the role of ionotropic glutamate receptors (iGluRs) in the generation of PDS and dependence of the PDS pattern on neuronal membrane potential. We have shown that significant depolarization or hyperpolarization (by more than ±50 mV) of a single neuron does not change the number of individual PDSs in the cluster, indicating the involvement of an external stimulus in PDS induction. Based on this data, we have suggested reliable protocols for stimulating single PDS or PDS clusters. Furthermore, we have found that AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptors are necessary for PDS generation since AMPAR antagonist NBQX completely suppresses bicuculline-induced paroxysmal activity. In turn, antagonists of NMDA (N-methyl-D-aspartate) and kainate receptors (D-AP5 and UBP310, respectively) caused a decrease in the amplitude of the first action potential in PDSs and in the amplitude of the oscillations of intracellular Ca²⁺ concentration occurring alongside the PDS cluster generation. The effects of the NMDAR (NMDA receptor) and KAR (kainate receptor) antagonists indicate that these receptors are involved only in the modulation of paroxysmal activity. We have also shown that agonists of some G_i-coupled receptors, such as A₁ adenosine (A₁Rs) or cannabinoid receptors (CBRs) (N₆-cyclohexyladenosine and WIN 55,212-2, respectively), completely suppressed PDS generation, while the A₁R agonist even prevented it. We hypothesized that the dynamics of extracellular glutamate concentration govern paroxysmal activity. Fine-tuning of neuronal activity via action on G_i-coupled receptors or iGluRs paves the way for the development of new approaches for epilepsy pharmacotherapy. Full article

The Jakarta metropolitan region (the Jakarta megacity), located in the fourth most populous country in the world (Indonesia), is the largest urban agglomeration in the Global South—continues to grow, especially in its outer suburbs (Bekasi Regency). The governments (Central and Local) tend to implement an urban-biased policy (UBP) to connect Bekasi Regency into global production networks and boost Bekasi Regency’s income. However, previous case studies of China and Vietnam have revealed that the UBP increases economic disparities between urban and rural areas. Therefore, this study probes urban–rural economic disparities and their characteristics at a microregional level (desa/kelurahan) in the Bekasi Regency. The methods applied in this study are geographically weighted regression (GWR), RULT index, and quantitative zoning. The results show that almost all desa/kelurahan in the high poverty (HPv) cluster are rural neighborhoods (desa/kelurahan with rural characteristics). By contrast, only 5% of desa/kelurahan with urban characteristics are HPvs, while the remainder are in the low poverty (LPv) cluster. Rural neighborhoods with HPv tend to have a high percentage of households dependent on agriculture. Thus, empirical results (with a case of a Global South megacity suburb) further support previous evidence that the UBP has caused urban–rural economic disparities. Full article