Search

Background Aims Methods Results Conclusions Inefficient nitrogen (N) use leads to economic losses and environmental harm. Improving N use efficiency (NUE) is crucial. The use of plant biostimulants (PBs), integrated with good agronomic practices, offers a sustainable solution.The study explores the potential use of exhausted cell culture media from plant cell cultures (Nicotiana sp. and Gardenia sp.) as PBs, assessing their role in enhancing plant physiological status and NUE. It also compares their effectiveness against commercial PBs.Two experiments (Experiments 1 and 2) were conducted using cherry tomato plants. In the first one, the two media were applied at different concentrations as a foliar spray to define the optimal dose. This outcome was used to set up Experiment 2, in which both media were compared to commercial PBs under optimal and reduced N supply. Measurements included plant growth, chlorophyll (Chl) content, and NUE indices. Moreover, Experiment 2 examined gene expression related to N assimilation, transport, and response to oxidative stress.Both experiments demonstrated a significant increase in leaf area (≈11%) and aboveground biomass (≈13%) using exhausted media. Furthermore, Experiment 2 demonstrated enhancements in Chl content (≈10%) and plant N accumulation (≈20%). These findings indicate that exhausted media has a comparable efficacy to commercial PBs.The study underscores the practical viability of exhausted cell culture media as effective PBs for tomato growth in both N conditions. This approach aligns with sustainability objectives by repurposing by‐products to enhance plant resilience against abiotic stress and potentially improve the efficiency of N fertilizers. [ABSTRACT FROM AUTHOR]

Summary Stevia rebaudiana Bertoni is popular source of plant‐derived low/no‐calorie natural sweeteners (LNCSs), collectively known as steviol glycosides (SGs). Nevertheless, genetic predisposition for targeted biosynthesis of SGs is complex due to multi‐substrate functionality of key uridine diphosphate glycosyltransferases (UGTs). Here, we created a high‐quality monoploid assembly of 1.34 Gb with N50 value of 110 Mb, 55 551 predicted protein‐coding genes, and ~80% repetitive regions in Rebaudioside‐A (Reb‐A) enriched cultivar of S. rebaudiana. Additionally, a haplotype‐based chromosome assembly consisting of haplotype A and haplotype B with an overall genome size of 2.33Gb was resolved, harbouring 639 634 variants including single nucleotide polymorphisms (SNPs), indels and structural variants (SVs). Furthermore, a lineage‐specific whole genome duplication analysis revealed that gene families encoding UGTs and Cytochrome‐P450 (CYPs) were tandemly duplicated. Additionally, expression analysis revealed five tandemly duplicated gene copies of UGT76G1 having significant correlations with Reb‐A content, and identified key residue (leu200val) in the glycosylation of Reb‐A. Furthermore, missense variations identified in the acceptor region of UGT76G1 in haplotype resolve genome, transcriptional and molecular docking analysis were confirmed with resequencing of 10 diverse stevia genotypes (~25X). Gene regulatory network analysis identified key transcription factors (MYB, bHLH, bZIP and AP2‐ERF) as potential regulators of SG biosynthesis. Overall, this study provides haplotype‐resolved chromosome‐level genome assembly for genome editing and enhancing breeding efforts for targeted biosynthesis of SGs in S. rebaudiana. [ABSTRACT FROM AUTHOR]

ABSTRACT Light is crucial for flower bud development in plants, serving as both signal and energy source. However, the mechanisms by which daylength and light intensity regulate flowering in modern roses remain unclear. In Rosa hybrida ‘Carola’, insufficient light delays flowering and reduces the sugar content in terminal buds. RNA sequencing identified the Trehalose‐6‐phosphate phosphatase F (RhTPPF) gene as a key responder to insufficient light, modulating Tre6P metabolism. Overexpression of RhTPPF in rose calli enhanced sugar accumulation and suppressed the synthesis of RhCO/FT. In tobacco, overexpression of RhTPPF delayed the transition from vegetative growth to flowering, while silencing RhTPPF in roses accelerated flowering. Silencing RhTPPF in roses elevated trehalose‐6‐phosphate (Tre6P) levels and decreased trehalose. Transcriptome data showed that the expression level of RhTPPF was highly correlated with the circadian rhythm gene LATE ELONGATED HYPOCOTYL (RhLHY). Yeast one‐hybrid assays, dual luciferase assays and EMSA revealed that RhLHY directly binds to the RhTPPF promoters. Overexpression of RhLHY suppressed flowering, while silencing RhLHY promoted flowering. Furthermore, altering the expression of RhLHY influenced Tre6P synthesis and the expression of sucrose‐related transport genes. These findings suggest a RhLHY‐RhTPPF‐Tre6P regulatory module that maintains sugar balance and inhibits flower formation under reduced light conditions by modulating sugar distribution. [ABSTRACT FROM AUTHOR]

ABSTRACT Biosynthesis of specific secondary metabolites in plants involves fine regulation of gene expression. Camellia chekiangoleosa has important economic value: the seeds contain high‐quality unsaturated fatty acids and the pericarp is rich in tea saponins. As an important posttranscriptional regulator, the role of microRNAs (miRNAs) in controlling secondary metabolism in C. chekiangoleosa is not fully studied. Here, we investigated the role of miRNAs and their targets in the secondary metabolic regulatory network by comprehensively analyzing small RNAs, transcriptomes, and degradomes from different tissues. We identified 168 known miRNAs and 74 novel miRNAs in the C. chekiangoleosa genome and revealed 15 tandem clusters containing 35 miRNAs. By establishing a gene regulatory network containing miRNAs, target genes, and transcription factors, we unravelled the multiplicity of miRNA tissue‐specific regulation of gene expression, which may be tightly linked to the synthesis of secondary metabolites. Furthermore, we characterized a novel long‐noncoding miRNA gene (cch‐miR3633) that targeted a UDP‐transferase gene (CchUGT94E5). We showed that, ectopic expression of CchUGT94E5 caused outgrowth of shoot branching and changes in cytokinin contents in Arabidopsis, indicating a potential role of regulating secondary metabolism. This work provides valuable information for the study of miRNA regulation of secondary metabolism. [ABSTRACT FROM AUTHOR]

Convergent evolution of similar phenotypes suggests some predictability in the evolutionary trajectories of organisms, due to strong and repeated selective pressures, and/or developmental constraints. In adaptive radiations, particularly in cichlid fish radiations, convergent phenotypes are commonly found within and across geographical settings. Cichlids show major repeated axes of morphological diversification. Recurrent changes in body patterns reveal adaption to alternative habitats, and modifications of the trophic apparatus respond to the exploitation of different food resources. Here we compare morphologically and genetically two Neotropical cichlid assemblages, the Mexican desert cichlid and the Nicaraguan Midas cichlid, with similar polymorphic body and trophic adaptations despite their independent evolution. We found a common morphological axis of differentiation in trophic structures in both cichlid radiations, but two different axes of differentiation in body shape, defining two alternative limnetic body patterns. Adaptation to limnetic habitats implied regulation of immune functions in the Midas cichlid, while morphogenesis and metabolic functions in the desert cichlid. Convergent phenotypic adaptions could be associated to divergent gene regulation. [ABSTRACT FROM AUTHOR]

Comprehensive Summary: DNA 5‐formylcytosine (5fC) is a prominent epigenetic modification within biological systems. Recent investigations have shed light on its pivotal role in governing cell fate, gene expression, and disease pathways. However, our comprehension of the precise control of the 5fC site structure to influence its functionality remains limited. In this study, we have successfully achieved precise control over 5fC activity by harnessing the interaction between streptavidin and biotin. This research underscores the potential application of interactions between biomacromolecules and small molecules in advancing the field of DNA epigenetic functional regulation. [ABSTRACT FROM AUTHOR]

Summary: Kiwifruit ripening is a complex and highly coordinated process that occurs in conjunction with the formation of fruit edible quality. The significance of epigenetic changes, particularly the impact of N6‐methyladenosine (m6A) RNA modification on fruit ripening and quality formation, has been largely overlooked.We monitored m6A levels and gene expression changes in kiwifruit at four different stages using LC‐MS/MS, MeRIP, RNA‐seq, and validated the function of AcALKBH10 through heterologous transgenic expression in tomato.Notable m6A modifications occurred predominantly at the stop codons and the 3′ UTRs and exhibited a gradual reduction in m6A levels during the fruit ripening process. Moreover, these m6A modifications in the aforementioned sites demonstrated a discernible inverse relationship with the levels of mRNA abundance throughout the ripening process, suggesting a repression effect of m6A modification in the modulation of kiwifruit ripening.We further demonstrated that AcALKBH10 rather than AcECT9 predominantly regulates m6A levels in ripening‐related genes, thereby exerting the regulatory control over the ripening process and the accumulation of soluble sugars and organic acids, ultimately influencing fruit ripening and quality formation. In conclusion, our findings illuminate the epi‐regulatory mechanism involving m6A in kiwifruit ripening, offering a fresh perspective for cultivating high‐quality kiwifruit with enhanced nutritional attributes. [ABSTRACT FROM AUTHOR]

This article examines the role of FIO1, an RNA methyltransferase, in alternative splicing and its impact on flowering regulation in Arabidopsis thaliana. The authors analyze previous studies and find that differences in conclusions may be due to variations in experimental conditions and data analysis methods. They also compare different tools for detecting differential splicing and find that exon-based tools have higher recall rates, while event-based tools have higher precision rates. The study provides insights into the molecular functions of FIO1 and emphasizes the importance of considering experimental conditions and data analysis in research. Additionally, the article explores the potential influence of FIO1 on flowering time but acknowledges the need for further research to fully understand its mechanisms and environmental adaptation. [Extracted from the article]

Summary: The genetic control underlying natural variation in lignin content and composition in trees is not fully understood. We performed a systems genetic analysis to uncover the genetic regulation of lignin biosynthesis in a natural 'SwAsp' population of aspen (Populus tremula) trees.We analyzed gene expression by RNA sequencing (RNA‐seq) in differentiating xylem tissues, and lignin content and composition using Pyrolysis‐GC‐MS in mature wood of 268 trees from 99 genotypes.Abundant variation was observed for lignin content and composition, and genome‐wide association study identified proteins in the pentose phosphate pathway and arabinogalactan protein glycosylation among the top‐ranked genes that are associated with these traits. Variation in gene expression and the associated genetic polymorphism was revealed through the identification of 312 705 local and 292 003 distant expression quantitative trait loci (eQTL). A co‐expression network analysis suggested modularization of lignin biosynthesis and novel functions for the lignin‐biosynthetic CINNAMYL ALCOHOL DEHYDROGENASE 2 and CAFFEOYL‐CoA O‐METHYLTRANSFERASE 3. PHENYLALANINE AMMONIA LYASE 3 was co‐expressed with HOMEOBOX PROTEIN 5 (HB5), and the role of HB5 in stimulating lignification was demonstrated in transgenic trees.The systems genetic approach allowed linking natural variation in lignin biosynthesis to trees´ responses to external cues such as mechanical stimulus and nutrient availability. [ABSTRACT FROM AUTHOR]

Summary: Changes in the plant microbiota composition are intimately associated with the health of the plant, but factors controlling the microbial community in flowers are poorly understood. In this study, we used apple flowers and fire blight as a model system to investigate the effects of floral microbiota and microbial competition on disease development and suppression.To compare changes in microbial flora with the RNA expression patterns of plants, the flower samples were collected in three different flowering stages (Bud, Popcorn, and Full‐bloom). Using advanced sequencing technology, we analyzed the data and conducted both in vitro and in vivo experiments to validate our findings.Our results show that the Erwinia amylovora use arabinogalactan, which is secreted on the flowers, for early colonization of apple flowers. Pantoea agglomerans was more competitive for arabinogalactan than E. amylovora. Additionally, P. agglomerans suppressed the expression of virulence factors of E. amylovora by using arabinose, which is a major component of arabinogalactan, which induces virulence gene expression.The present data provide new insights into developing control strategies for diverse plant diseases, including fire blight, by highlighting the importance of nutrients in disease development or suppression. [ABSTRACT FROM AUTHOR]

Summary: Gene silencing is crucial in crop breeding for desired trait development. RNA interference (RNAi) has been used widely but is limited by ectopic expression of transgenes and genetic instability. Introducing an upstream start codon (uATG) into the 5′untranslated region (5′UTR) of a target gene may 'silence' the target gene by inhibiting protein translation from the primary start codon (pATG).Here, we report an efficient gene silencing method by introducing a tailor‐designed uATG‐containing element (ATGE) into the 5′UTR of genes in plants, occupying the original start site to act as a new pATG.Using base editing to introduce new uATGs failed to silence two of the tested three rice genes, indicating complex regulatory mechanisms. Precisely inserting an ATGE adjacent to pATG achieved significant target protein downregulation. Through extensive optimization, we demonstrated this strategy substantially and consistently downregulated target protein expression. By designing a bidirectional multifunctional ATGE4, we enabled tunable knockdown from 19% to 89% and observed expected phenotypes. Introducing ATGE into Waxy, which regulates starch synthesis, generated grains with lower amylose, revealing the value for crop breeding.Together, we have developed a programmable and robust method to knock down gene expression in plants, with potential for biological mechanism exploration and crop enhancement. See also the Commentary on this article by Li & Wei, 243: 2052–2054. [ABSTRACT FROM AUTHOR]

Comprehensive Summary: DNA 5‐formylcytosine (5fC) is a prominent epigenetic modification within biological systems. Recent investigations have shed light on its pivotal role in governing cell fate, gene expression, and disease pathways. However, our comprehension of the precise control of the 5fC site structure to influence its functionality remains limited. In this study, we have successfully achieved precise control over 5fC activity by harnessing the interaction between streptavidin and biotin. This research underscores the potential application of interactions between biomacromolecules and small molecules in advancing the field of DNA epigenetic functional regulation. [ABSTRACT FROM AUTHOR]

Disease progression is a major problem in ovarian cancer. There are very few treatment options for patients with platinum‐resistant ovarian cancer (PROC), and therefore, these patients have a particularly poor prognosis. The aim of the present study was to identify markers for monitoring the response of 123 PROC patients enrolled in the Phase I/II GANNET53 clinical trial, which evaluated the efficacy of Ganetespib in combination with standard chemotherapy versus standard chemotherapy alone. In total, 474 blood samples were collected, comprising baseline samples taken before the first administration of the study drugs and serial samples taken during treatment until further disease progression (PD). After microfluidic enrichment, 27 gene transcripts were analyzed using quantitative polymerase chain reaction and their utility for disease monitoring was evaluated. At baseline, ERCC1 was associated with an increased risk of PD (hazard ratio [HR] 1.75, 95% confidence interval [CI]: 1.20–2.55; p = 0.005), while baseline CDH1 and ESR1 may have a risk‐reducing effect (CDH1 HR 0.66, 95% CI: 0.46–0.96; p = 0.024; ESR1 HR 0.58, 95% CI: 0.39–0.86; p = 0.002). ERCC1 was observed significantly more often (72.7% vs. 53.9%; p = 0.032) and ESR1 significantly less frequently (59.1% vs. 78.3%; p = 0.018) in blood samples taken at radiologically confirmed PD than at controlled disease. At any time during treatment, ERCC1‐presence and ESR1‐absence were associated with short PFS and with higher odds of PD within 6 months (odds ratio 12.77, 95% CI: 4.08–39.97; p < 0.001). Our study demonstrates the clinical relevance of ESR1 and ERCC1 and may encourage the analysis of liquid biopsy samples for the management of PROC patients. [ABSTRACT FROM AUTHOR]

ABSTRACT In E. coli K‐12, the absence of unphosphorylated PtsN (unphospho‐PtsN) has been proposed to cause an L‐leucine‐sensitive growth phenotype (LeuS) by hyperactivated K+ uptake mediated impairment of the expression of the ilvBN operon, encoding subunits of the L‐valine (Val)‐sensitive acetohydroxyacid synthase I (AHAS I) that renders residual AHAS activity susceptible to inhibition by Leu and K+. This leads to AHAS insufficiency and a requirement for L‐isoleucine (Ile). Herein, we provide an alternate mechanism for the LeuS of the ∆ptsN mutant. Genetic and physiological studies with suppressors of the LeuS indicate that impaired expression of the ilvBN operon jointly caused by the absence of unphospho‐PtsN and the presence of Leu coupled to Leu‐mediated repression of expression of AHAS III leads to AHAS insufficiency rendering residual AHAS activity susceptible to chronic Val stress that may be generated by exogenous Leu. Hyperactivated K+ uptake and an elevated α‐ketobutyrate level mediate elevation of ilvBN expression and alleviate the LeuS. The requirement of unphospho‐PtsN as a positive regulator of ilvBN expression may buffer Ile biosynthesis against Leu‐mediated AHAS insufficiency and protect AHAS I function from chronic endogenous Val generated by Leu and could be realized in certain environments that impair AHAS function. [ABSTRACT FROM AUTHOR]

Neuronal information processing depends on converting membrane depolarizations into compartmentalized biochemical signals that can modify neuronal activity and structure. However, our understanding of how neurons translate electrical signals into specific biochemical responses remains limited, especially in the soma where gene expression and ion channel function are crucial for neuronal activity. Here, I emphasize the importance of physically compartmentalizing action potential‐triggered biochemical reactions within the soma. Emerging evidence suggests that somatic endoplasmic reticulum–plasma membrane (ER‐PM) junctions are specialized organelles that coordinate electrical and biochemical signaling. The juxtaposition of ion channels and signaling proteins at a prominent subset of these sites enables compartmentalized calcium and cAMP‐dependent protein kinase (PKA) signaling. I explore the hypothesis that these PKA‐containing ER‐PM junctions serve as critical sites for translating membrane depolarizations into PKA signals and identify key gaps in knowledge of the assembly, regulation, and neurobiological functions of this somatic signaling system. [ABSTRACT FROM AUTHOR]

BACKGROUND RESULTS CONCLUSION Dictyophora indusiata polysaccharide is an important bioactive component of D. indusiata, playing an important role in alleviating inflammation. The present study aimed to investigate the anti‐inflammatory effect and mechanism of D. indusiata polysaccharide on lipopolysaccharide (LPS)‐induced intestinal inflammation in mice.Our results indicated that D. indusiata polysaccharide ameliorated intestinal inflammation of mice by increasing the body weight, the number of goblet cells and decreasing inflammatory cell infiltration. In addition, D. indusiata polysaccharide significantly up‐regulated expression of ZO‐1, Occuldin mRNA, which were 2.55‐fold and 2.28‐fold higher than the LPS group, respectively. In particular, D. indusiata polysaccharide effectively inhibited the Toll‐like receptor 4 (TLR4)/ c‐Jun NH2‐terminal kinase (JNK) signalling pathway which was 0.34‐fold and 0.49‐fold of gene expression and 0.41‐fold and 0.39‐fold of protein expression in the LPS group, respectively.The results of the present study suggested that D. indusiata polysaccharide exerted anti‐inflammatory and intestinal protective effects by inhibiting the TLR4/JNK signaling pathway, which will provide a basis for the potential value of D. indusiata polysaccharide as prebiotics in food applications. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Amyloid‐beta peptide oligomers (AβO) have been considered “primum movens” for a cascade of events that ultimately cause selective neuronal death in Alzheimer's disease (AD). However, initial events triggered by AβO have not been clearly defined. Synaptic (Syn) N‐methyl‐d‐aspartate receptors (NMDAR) are known to activate cAMP response element‐binding protein (CREB), a transcriptional factor involved in gene expression related to cell survival, memory formation and synaptic plasticity, whereas activation of extrasynaptic (ESyn) NMDARs was linked to excitotoxic events. In AD brain, CREB phosphorylation/activation was shown to be altered, along with dyshomeostasis of intracellular Ca2+ (Ca2+i). Thus, in this work, we analyze acute/early and long‐term AβO‐mediated changes in CREB activation involving Syn or ESyn NMDARs in mature rat cortical neurons. Our findings show that acute AβO exposure produce early increase in phosphorylated CREB, reflecting CREB activity, in a process occurring through Syn NMDAR‐mediated Ca2+ influx. Data also demonstrate that AβO long‐term (24 h) exposure compromises synaptic function related to Ca2+‐dependent CREB phosphorylation/activation and nuclear CREB levels and related target genes, namely Bdnf, Gadd45γ, and Btg2. Data suggest a dual effect of AβO following early or prolonged exposure in mature cortical neurons through the activation of the CREB signaling pathway, linked to the activation of Syn NMDARs. [ABSTRACT FROM AUTHOR]

This article explores the potential of gene editing in the marine algae Neopyropia yezoensis to improve breeding techniques. The study successfully edited a target gene using the CRISPR/Cas9 system, creating gene knockout mutants. This breakthrough paves the way for molecular breeding in N. yezoensis and positions it as a potential model species for marine algae research. The document also discusses the use of P2A as a connector to enhance the efficiency of resistance enrichment screening in gene editing. This advancement in macroalgal gene editing methodologies has implications for precision breeding and the economic seaweed industry. The article acknowledges the contributions of various individuals and organizations to the research. [Extracted from the article]

The functional role and molecular mechanisms of small‐nucleolar RNA host gene 14 (SNHG14) in triple‐negative breast cancer (TNBC) progression remain unclear. The expression levels of SNHG14 in breast cancer samples and cell lines were determined using real‐time quantitative polymerase chain reaction. Cell proliferation, migration, and invasion abilities were detected using MTS and transwell assays. By RNA sequencing, differentially expressed genes were identified between the SNHG14 siRNA and the negative control group. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were used to predict the targets and pathways regulated by SNHG14. pRAF, pMEK, and pERK expression were measured by western blot. The xenograft model was constructed to access the biological function of SNHG14 in vivo. A minimal patient‐derived xenograft model was established to evaluate the sensitivity to chemotherapy drugs. Our data indicated that SNHG14 expression was increased in TNBC tissues and cell lines. SNHG14 knockdown attenuated the proliferation, migration, and invasion abilities of TNBC cells both in vivo and in vitro. High SNHG14 expression was associated with lymph node metastasis and a high Ki67 index. The targets of SNHG14 were mainly enriched in the MAPK signaling pathway. pRAF, pMEK, and pERK expression were downregulated after being transfected with SNHG14 siRNA. Compared with the negative control group, the expression of CACNA1I, DUSP8, FGF17, FGFR4, FOS, PDGFRB, and DDIT3 was increased, and the expression of MKNK1 was decreased in the SNHG14 siRNA group. Minimal patient‐derived xenograft model demonstrated that knockdown of SNHG14 enhanced the sensitivity to Docetaxel in vivo. Compared with the DMSO group, the proliferation of Docetaxel‐resistant MDA‐MB‐231 cells was decreased in Dabrafenib, PD184352, and FR180204 treatment groups. SNHG14 knockdown inhibits TNBC progression by regulating the ERK/MAPK signaling pathway, which provides evidence for SNHG14 as a potential target for TNBC therapy. [ABSTRACT FROM AUTHOR]

The origin of sociality represents one of the most important evolutionary transitions. Insect sociality evolved in some hemipteran aphids, which can produce soldiers and normal nymphs with distinct morphology and behaviour through parthenogenesis. The lack of genomic data resources has hindered the investigations into molecular mechanisms underlying their social evolution. Herein, we generated the first chromosomal‐level genome of a social hemipteran (Pseudoregma bambucicola) with highly specialized soldiers and performed comparative genomic and transcriptomic analyses to elucidate the molecular signatures and regulatory mechanisms of caste differentiation. P. bambucicola has a larger known aphid genome of 582.2 Mb with an N50 length of 11.24 Mb, and about 99.6% of the assembly was anchored to six chromosomes with a scaffold N50 of 98.27 Mb. A total of 14,027 protein‐coding genes were predicted and 37.33% of the assembly were identified as repeat sequences. The social evolution is accompanied by a variety of changes in genome organization, including expansion of gene families related to transcription factors, transposable elements, as well as species‐specific expansions of certain sugar transporters and UGPases involved in carbohydrate metabolism. We also characterized large candidate gene sets linked to caste differentiation and found evidence of expression regulation and positive selection acting on energy metabolism and muscle structure, explaining the soldier‐specific traits including morphological and behavioural specialization, developmental arrest and infertility. Overall, this study offers new insights into the molecular basis of social aphids and the evolution of insect sociality and also provides valuable data resources for further comparative and functional studies. [ABSTRACT FROM AUTHOR]

The Nascent polypeptide‐Associated Complex (NAC) family is among the largest plant‐specific TF families and plays an important role in plant growth, development, and stress responses. NAC TFs have been extensively studied in plants such as rice and Arabidopsis; however, their characterization, functions, evolution, and expression patterns in Manihot esculenta (cassava) under environmental stress remain largely unexplored. Here, we used bioinformatic analyses and biotic stress responses to investigate the physicochemical properties, chromosome location, phylogeny, gene structure, expression patterns, and cis‐elements in promoter regions of the NAC TFs in cassava. We identified 119 M. esculenta NAC (MeNAC) gene families, unevenly distributed on 16 chromosomes. We investigated expression patterns of all identified MeNAC TFs under Xanthomonas axonopodis pv. manihotis (Xam) infection, strain CHN11, at different time points. Only 20 MeNAC TFs showed expression of significant bacterial resistance. Six MeNACs (MeNAC7, 26, 63, 65, 77, and 113) were selected for functional analysis. qRT‐PCR assays revealed that MeNAC7, 26, 63, 65, 77, and 113 were induced in response to XamCHN11 infection and may participate in the molecular interaction of cassava and bacterial blight. Interestingly, MeNAC26, MeNAC63, MeNAC65, and MeNAC113 responded to XamCHN11 infection at 3 h post‐inoculation. Furthermore, we identified 13 stress‐related cis‐elements in promoter regions of the MeNAC genes that are involved in diverse environmental stress responses. Phylogenetic analysis revealed that MeNAC genes with similar structures and motif distributions were grouped. This study provides valuable insights into the evolution, diversity, and characterization of MeNAC TFs. It lays the groundwork for a better understanding of their biological roles and molecular mechanisms in cassava. [ABSTRACT FROM AUTHOR]

SUMMARY Flooding impairs plant growth through oxygen deprivation, which activates plant survival and acclimation responses. Transcriptional responses to low oxygen are generally associated with the activation of group VII ETHYLENE‐RESPONSE FACTOR (ERFVII) transcription factors. However, the exact mechanisms and molecular components by which ERFVII factors initiate gene expression are not fully elucidated. Here, we show that the ERFVII factors RELATED TO APETALA 2.2 (RAP2.2) and RAP2.12 cooperate with the Mediator complex subunit AtMED25 to coordinate gene expression under hypoxia in Arabidopsis thaliana. Respective med25 knock‐out mutants display reduced low‐oxygen stress tolerance. AtMED25 physically associates with a distinct set of hypoxia core genes and its loss partially impairs transcription under hypoxia due to decreased RNA polymerase II recruitment. Association of AtMED25 with target genes requires the presence of ERFVII transcription factors. Next to ERFVII protein stabilisation, also the composition of the Mediator complex including AtMED25 is potentially affected by hypoxia stress as shown by protein‐complex pulldown assays. The dynamic response of the Mediator complex to hypoxia is furthermore supported by the fact that two subunits, AtMED8 and AtMED16, are not involved in the establishment of hypoxia tolerance, whilst both act in coordination with AtMED25 under other environmental conditions. We furthermore show that AtMED25 function under hypoxia is independent of ethylene signalling. Finally, functional conservation at the molecular level was found for the MED25‐ERFVII module between A. thaliana and the monocot species Oryza sativa, pointing to a potentially universal role of MED25 in coordinating ERFVII‐dependent transcript responses to hypoxia in plants. [ABSTRACT FROM AUTHOR]

SUMMARY Genome‐wide association study (GWAS) with single nucleotide polymorphisms (SNPs) has been widely used to explore genetic controls of phenotypic traits. Alternatively, GWAS can use counts of substrings of length k from longer sequencing reads, k‐mers, as genotyping data. Using maize cob and kernel color traits, we demonstrated that k‐mer GWAS can effectively identify associated k‐mers. Co‐expression analysis of kernel color k‐mers and genes directly found k‐mers from known causal genes. Analyzing complex traits of kernel oil and leaf angle resulted in k‐mers from both known and candidate genes. A gene encoding a MADS transcription factor was functionally validated by showing that ectopic expression of the gene led to less upright leaves. Evolution analysis revealed most k‐mers positively correlated with kernel oil were strongly selected against in maize populations, while most k‐mers for upright leaf angle were positively selected. In addition, genomic prediction of kernel oil, leaf angle, and flowering time using k‐mer data resulted in a similarly high prediction accuracy to the standard SNP‐based method. Collectively, we showed k‐mer GWAS is a powerful approach for identifying trait‐associated genetic elements. Further, our results demonstrated the bridging role of k‐mers for data integration and functional gene discovery. [ABSTRACT FROM AUTHOR]

Kawakawa (Piper excelsum) is an endemic medicinal plant widely consumed by Māori in New Zealand. Presence of diverse biologically active phytochemicals in kawakawa may underpin its putative therapeutic anti‐inflammatory properties. However, no human studies on its anti‐inflammatory effects are yet undertaken. Blood samples from a randomized controlled dietary intervention exploring the impact of kawakawa compared to control on postprandial microRNAs (miRNA) abundances and their respective gene and protein targets in a cohort of healthy human volunteers (n = 26; Age; 33.6 ± 1.9 year and BMI; 22.5 ± 0.4 kg/m2) were analyzed. Postprandial levels of nine miRNAs showed differential abundances; hsa‐miR‐17‐5p, ‐21‐5p, ‐320a‐5p, let‐7g‐5p, ‐16‐5p, ‐122‐5p, and ‐144‐3p was upregulated while as hsa‐miR‐221‐3p and ‐223‐3p was downregulated in response to kawakawa compared to control. In silico analysis indicated enrichment of miRNAs in multiple inflammation‐related pathways, including apoptosis, cytokine signaling, MAPK signaling, and MTOR pathways. Furthermore, gene expression of IL‐8 (p = .03), IL‐6 (p = .01), and PPAR‐γ were significantly reduced following kawakawa intake compared to control. While as plasma IL‐6 showed a significant increase over 120 min in the kawakawa arm. These results highlight kawakawa to exert anti‐inflammatory effects by modulating the expression of miRNAs and their target genes and proteins in the inflammatory signaling pathways. [ABSTRACT FROM AUTHOR]

SUMMARY Hydathodes are small organs found on the leaf margins of vascular plants which release excess xylem sap through a process called guttation. While previous studies have hinted at additional functions of hydathode in metabolite transport or auxin metabolism, experimental support is limited. We conducted comprehensive transcriptomic, metabolomic and physiological analyses of mature Arabidopsis hydathodes. This study identified 1460 genes differentially expressed in hydathodes compared to leaf blades, indicating higher expression of most genes associated with auxin metabolism, metabolite transport, stress response, DNA, RNA or microRNA processes, plant cell wall dynamics and wax metabolism. Notably, we observed differential expression of genes encoding auxin‐related transcriptional regulators, biosynthetic processes, transport and vacuolar storage supported by the measured accumulation of free and conjugated auxin in hydathodes. We also showed that 78% of the total content of 52 xylem metabolites was removed from guttation fluid at hydathodes. We demonstrate that NRT2.1 and PHT1;4 transporters capture nitrate and inorganic phosphate in guttation fluid, respectively, thus limiting the loss of nutrients during this process. Our transcriptomic and metabolomic analyses unveil an organ with its specific physiological and biological identity. [ABSTRACT FROM AUTHOR]

SUMMARY Plant long noncoding RNAs (lncRNAs) exhibit features such as tissue‐specific expression, spatiotemporal regulation, and stress responsiveness. Although diverse studies support the regulatory role of lncRNAs in model plants, our knowledge about lncRNAs in crops is limited. We employ a custom pipeline on a dataset of over 1000 RNA‐seq samples across nine representative species of the family Cucurbitaceae to predict 91 209 nonredundant lncRNAs. The lncRNAs were characterized according to three confidence levels and classified by their genomic context into intergenic, natural antisense, intronic, and sense‐overlapping. Compared with protein‐coding genes, lncRNAs were, on average, expressed at low levels and displayed significantly higher specificity when considering tissue, developmental stages, and stress responsiveness. The evolutionary analysis indicates higher positional conservation than sequence conservation, probably linked to the conserved modular motifs within syntenic lncRNAs. Moreover, a positive correlation between the expression of intergenic/natural antisense lncRNAs and their closest/parental gene was observed. For those intergenic, the correlation decreases with the distance to the neighboring gene, supporting that their potential cis‐regulatory effect is within a short‐range. Furthermore, the analysis of developmental studies showed that a conserved NAT‐lncRNA family is differentially expressed in a coordinated way with their cognate sense protein‐coding genes. These genes code for proteins associated with phloem development, thus providing insights about the potential involvement of some of the identified lncRNAs in a developmental process. We expect that this extensive inventory will constitute a valuable resource for further research lines focused on elucidating the regulatory mechanisms mediated by lncRNAs in cucurbits. [ABSTRACT FROM AUTHOR]

Introduction Methods Results Conclusion Epigenetics has been shown to be relevant in oncology: BMI1 overexpression has been reported in leukemias, EZH2 mutations have been found in follicular lymphoma, and USP22 seems to stabilize BMI1 protein. In this study, we measured the expression of BMI1, EZH2, and USP22 in lymph nodes from 56 diffuse large B‐cell lymphoma (DLBCL) patients.A new multiplex digital droplet PCR (ddPCR) has been set up to measure the expression of 4 genes (BMI1, EZH2, USP22, and GAPDH) in the same reaction on RNA extracted from paraffin‐embedded tissues.The specificity of ddPCR was confirmed by a 100% alignment on the BLAST platform and its repeatability demonstrated by duplicates. A strict correlation between expression of BMI1 and EZH2 and BMI1 and USP22 has been found, and high expression of these genes was correlated with extra‐nodal lymphomas. Progression‐free survival (PFS) and overall survival (OS) were conditioned by IPI, bone marrow infiltration, and the complete response achievement. High levels of BMI1 and USP22 did not condition the response to therapy, but impaired the PFS, especially for patients defined at “high risk” based on the cell of origin (no germinal center [GCB]), high BCL2 expression, and IPI 3‐5. In this subgroup, the probability of relapse/progression was twice higher than that of patients carrying low BMI1 and USP22 levels.High expression of BMI1 and of USP22 might be a poor prognostic factor in DLBCL, and might represent the target for novel inhibitors. [ABSTRACT FROM AUTHOR]

How organ size is determined is a fundamental question in life sciences. Recent studies have highlighted the importance of the Hippo pathway in regulating organ size. This pathway controls cell proliferation and cell death to maintain the proper number of cells. The activity of the Hippo pathway is tightly fine‐tuned through various post‐translational modifications, such as phosphorylation and ubiquitination. Here, we discover that miR‐927 is a novel regulator of wing size. Overexpression of miR‐927 decreases wing size, which can be rescued by co‐expressing miR‐927‐sponge. Next, we show that miR‐927 stimulates apoptosis and suppresses the expression of Drosophila inhibitor of apoptosis protein 1, a well‐known target gene of the Hippo pathway. Genetic epistatic analyses position miR‐927 upstream of Yorkie (Yki) to modulate the Hippo pathway. In addition, there is a matching miR‐927 seed site in the yki 3′ untranslated region (3′‐UTR), and we demonstrate that yki 3′‐UTR is the direct target of miR‐927. Ultimately, our study reveals that the targeting of yki by miR‐927 to regulate the Hippo pathway is conserved in Helicoverpa armigera. Administration of miR‐927 via star polycation (SPc) nanocarrier effectively inhibits wing development in H. armigera. Taken together, our findings uncover a novel mechanism by which Yki is silenced at the post‐transcriptional level by miR‐927, and provide a new perspective on pest management. [ABSTRACT FROM AUTHOR]

ABSTRACT Sorghum (Sorghum bicolor (L.) Moench) is a highly nutritional multipurpose millet crop. However, the genetic and molecular regulatory mechanisms governing sorghum grain development and the associated agronomic traits remain unexplored. In this study, we performed a comprehensive transcriptomic analysis of pistils collected 1–2 days before pollination, and developing seeds collected –2, 10, 20 and 30 days after pollination of S. bicolor variety M35‐1. Out of 31 337 genes expressed in these stages, 12 804 were differentially expressed in the consecutive stages of seed development. These exhibited 10 dominant expression patterns correlated with the distinct pathways and gene functions. Functional analysis, based on the pathway mapping, transcription factor enrichment and orthology, delineated the key patterns associated with pollination, fertilization, early seed development, grain filling and seed maturation. Furthermore, colocalization with previously reported quantitative trait loci (QTLs) for grain weight/size revealed 48 differentially expressed genes mapping to these QTL regions. Comprehensive literature mining integrated with QTL mapping and expression data shortlisted 25, 17 and 8 core candidates for engineering grain size, starch and protein content, respectively. [ABSTRACT FROM AUTHOR]

ABSTRACT The freezing temperature greatly limits the growth, development and productivity of plants. The C‐repeat/DRE binding factor (CBF) plays a major role in cold acclimation, enabling plants to increase their freezing tolerance. Notably, the INDUCER OF CBF EXPRESSION1 (ICE1) protein has garnered attention for its pivotal role in bolstering plants' resilience against freezing through transcriptional upregulation of DREB1A/CBF3. However, the research on the interaction between ICE1 and other transcription factors and its function in regulating cold stress tolerance is largely inadequate. In this study, we found that a R2R3 MYB transcription factor CDC5 interacts with ICE1 and regulates the expression of CBF3 by recruiting RNA polymerase II, overexpression of ICE1 can complements the freezing deficient phenotype of cdc5 mutant. CDC5 increases the expression of CBF3 in response to freezing. Furthermore, CDC5 influences the expression of CBF3 by altering the chromatin status through H3K4me3 and H3K27me3 modifications. Our work identified a novel component that regulates CBF3 transcription in both ICE1‐dependent and ICE1‐independent manner, improving the understanding of the freezing signal transduction in plants. [ABSTRACT FROM AUTHOR]

ABSTRACT Leaf flattening plays a pivotal role in optimizing light capture and enhancing photosynthesis efficiency. While extensive research has clarified the molecular mechanisms governing the initial stages of leaf flattening, understanding the maintenance of this process in mature leaves remains limited. Our investigation focused on sly‐miR398b in tomatoes and revealed its crucial role in maintaining leaf flattening. In situ hybridization experiments indicated predominant expression of sly‐miR398b in the abaxial side. Disrupting sly‐miR398b using CRISPR/Cas9 relieved its suppression on target gene (Cu/Zn‐SOD, SlCSD1), elevating SlCSD1 levels specifically on the abaxial side. Consequently, this asymmetrical expression of SlCSD1 increased hydrogen peroxide (H2O2) levels in the abaxial side, hindering auxin influx genes while promoting auxin efflux gene expression. This shift reduced auxin response gene expression in the abaxial side of mature leaves compared to the adaxial side, leading to leaf epinasty in sly‐miR398b mutants. Exogenous H2O2 spraying induced leaf epinasty, downregulating SlGH3.5 and upregulating SlPIN3 and SlPIN4. Remarkably, spraying with 1‐naphthalacetic acid (NAA) restored leaf flattening in sly‐miR398b mutants. Our findings offer novel insights into mature leaf flattening maintenance via sly‐miR398b's regulation of auxin and H2O2 signalling pathways. [ABSTRACT FROM AUTHOR]

Every year, unfavorable environmental factors significantly affect crop productivity and threaten food security. Plants are sessile; they cannot move to escape unfavorable environmental conditions, and therefore, they activate a variety of defense pathways. Among them are processes regulated by stress‐associated proteins (SAPs). SAPs have a specific zinc finger domain (A20) at the N‐terminus and either AN1 or C2H2 at the C‐terminus. SAP proteins are involved in many biological processes and in response to various abiotic or biotic constraints. Most SAPs play a role in conferring transgenic stress resistance and are stress‐inducible. The emerging field of SAPs in abiotic or biotic stress response regulation has attracted the attention of researchers. Although SAPs interact with various proteins to perform their functions, the exact mechanisms of these interactions remain incompletely understood. This review aims to provide a comprehensive understanding of SAPs, covering their diversity, structure, expression, and subcellular localization. SAPs play a pivotal role in enabling crosstalk between abiotic and biotic stress signaling pathways, making them essential for developing stress‐tolerant crops without yield penalties. Collectively, understanding the complex regulation of SAPs in stress responses can contribute to enhancing tolerance against various environmental stresses through several techniques such as transgenesis, classical breeding, or gene editing. [ABSTRACT FROM AUTHOR]

Background Methods Results Conclusions Inositol‐requiring enzyme 1 (IRE1) is an endoplasmic reticulum (ER)‐resident transmembrane protein that senses ER stress and mediates an essential arm of the unfolded protein response (UPR). IRE1 reduces ER stress by upregulating the expression of multiple ER chaperones through activation of X‐box‐binding protein 1 (XBP1). Emerging lines of evidence have revealed that IRE1‐XBP1 axis serves as a multipurpose signal transducer during oncogenic transformation and cancer development. In this study, we explore how IRE1‐XBP1 signaling promotes chemoresistance in lung cancer.The expression patterns of UPR components and MRP1 were examined by Western blot. qRT‐PCR was employed to determine RNA expression. The promoter activity was determined by luciferase reporter assay. Chemoresistant cancer cells were analyzed by viability, apoptosis. CUT & Tag (Cleavage under targets and tagmentation)‐qPCR analysis was used for analysis of DNA‐protein interaction.Here we show that activation of IRE1α‐XBP1 pathway leads to an increase in MDR‐related protein 1 (MRP1) expression, which facilitates drug extrusion and confers resistance to cytotoxic chemotherapy. At the molecular level, XBP1‐induced c‐Myc is necessary for SREBP1 expression, and SREBP1 binds to the MRP1 promoter to directly regulate its transcription.We conclude that IRE1α‐XBP1 had important role in chemoresistance and appears to be a novel prognostic marker for lung cancer. [ABSTRACT FROM AUTHOR]

Alpha‐smooth muscle actin (α‐SMA) expression in the stroma is linked to the presence of cancer‐associated fibroblasts and is known to correlate with worse outcomes in various tumors. In this study, using a GeoMx digital spatial profiling approach, we characterized the gene expression of the tumor and α‐SMA‐expressing stromal cell compartments in pancreatic neuroendocrine tumors (PanNETs). The profiling was performed on tissues from eight retrospective cases (three grade 1, four grade 2, and one grade 3). Selected regions of interest were segmented geometrically based on tissue morphology and fluorescent signals from synaptophysin and α‐SMA markers. The α‐SMA‐expressing stromal‐cell‐associated genes were involved in pathways of extracellular matrix modification, whereas, in tumor cells, the gene expression profiles were associated with pathways involved in cell proliferation. The comparison of gene expression profiles across all three PanNET grades revealed that the differences between grades are not only present at the level of the tumor but also in the α‐SMA‐expressing stromal cells. Furthermore, the tumor cells from regions with a rich presence of adjacent α‐SMA‐expressing stromal cells revealed an upregulation of matrix metalloproteinase‐9 (MMP9) expression in grade 3 tumors. This study provides an in‐depth characterization of gene expression profiles in α‐SMA‐expressing stromal and tumor cells, and outlines potential crosstalk mechanisms. [ABSTRACT FROM AUTHOR]

The common carp is one of the most economically valuable freshwater fish worldwide and its aquaculture can be severely affected by the koi sleepy disease (KSD)/carp edema virus disease (CEVD). This study explores a natural outbreak of CEVD in a pond containing both clinically healthy and diseased fish of various origins exposed to the virus. We investigated mRNA expression of genes associated with known antiviral immune mechanisms, such as type I interferon signalling and cell‐mediated cytotoxicity, and performed a comprehensive protein expression analysis to highlight differences between the two groups in various organs. Significant differences in expression profiles of common carp with and without clinical signs were found to be strongly dependent on the organ from which the sample originated. Components of the complement cascade, including various C3 proteins, exhibited upregulation only in less affected organs, specifically the head kidney and spleen. Other complement proteins such as B/C2 and C9 showed upregulation in the kidney, spleen, and gills but not in the skin. Conversely, lysozymes C and G, were observed to be upregulated in the most affected organs of the skin and gills. This study submits the first description of the immune system related proteome using a mass spectrometry on the samples isolated from fish infected with CEV. It also offers a unique comparison of immune reaction of CEV infected and healthy fish under an infectious pressure. [ABSTRACT FROM AUTHOR]

Type III secretion system (T3SS) is an important virulence system in Gram‐negative bacteria. In this investigation, different environmental conditions that regulate the expression of T3SS genes in Yersinia ruckeri were investigated aimed at obtaining a better understanding about its modulation after various environmental challenges. Four isolates of Y. ruckeri CSF007‐82, ATCC29473, A7959‐11 and YRNC10 were cultivated under the diverse in vitro challenges iron depletion, high salt, low pH and in the presence of fish serum or in the fish cell culture (Chinook Salmon Embryo – CHSE). The transcriptional modulation of the chromosomal genes ysaV, ysaC, ysaJ and prgH of ysa were investigated using quantitative real‐time PCR. The expression of prgH, ysaV, ysaC and ysaJ was differentially expressed in all four strains under evaluation. The highest gene expression levels were observed for Y. ruckeri YRNC10 AN after addition of 0.3 M NaCl in Luria Bertani broth. The results obtained from this study provide initial insights into T3SS responses in Y. ruckeri, which pave the way for further studies aimed at expanding our knowledge on the functional roles of the T3SS genes in Y. ruckeri. [ABSTRACT FROM AUTHOR]

Eukaryotic cells respond to stress by altering coding and non‐coding gene expression programs. Alongside many approaches and regulatory mechanisms, long non‐coding RNAs (lncRNA) are finding a significant place in gene regulation, suggesting an involvement in various cellular processes and pathophysiology. LncRNAs are regulated by many transcription factors, including SMAR1 and p53, which are tumor suppressor genes. SMAR1 inhibits cancer cell metastasis and invasion and is also known to inhibit apoptosis during low‐dose stress in coordination with p53. Data mining analysis suggested that these tumor suppressor genes might coregulate the lncRNA RP11‐431M3.1 in colon cancer cells. Importantly, RP11‐431M3.1 expression was found to be negatively correlated with patient survival rates in a number of cancers. Oxidative stress occurs when an imbalance in the body is caused by reactive oxygen species (ROS). This imbalance is known to be important in the development/pathogenesis of colon cancer. We are researching the role and control of this lncRNA in HCT116 cells under conditions of oxidative stress. We observed a dose‐dependent differential expression of lncRNA upon H2O2 treatment and found that p53 and SMAR1 bind differentially to the promoter in response to the dose of stress inducer used. RP11‐431M3.1 was observed to sponge miR‐138 which has an important target gene, hypoxia‐inducible factor (HIF1A). miR‐138 was observed to bind differentially to RP11‐431M3.1 and HIF1A RNA depending on the dose of oxidative stress. Furthermore, the knockdown of RP11‐431M3.1 decreased the migration and proliferation of colon cancer cells. Our results suggest a previously undescribed regulatory mechanism through which RP11‐431M3.1 is transcriptionally regulated by SMAR1 and p53, target HIF1A through miR‐138, and highlight its potential as a therapeutic and diagnostic marker for cancer. [ABSTRACT FROM AUTHOR]

Diffuse large B‐cell lymphoma (DLBCL) is the most common subtype of non‐Hodgkin lymphoma and is associated with a poor prognosis. Data from the Gene Expression Profiling Interactive Analysis (GEPIA) database revealed dysregulated expression of several ubiquitin‐specific proteases (USPs) in DLBCL tissues (DLBCL vs. non‐DLBCL = 47 vs. 337), including USP19 (log2fold change = 1.17, P < 0.05). USP19 is closely linked to tumorigenesis, but its role in DLBCL progression remains largely unknown. Here, we investigated the role of USP19 in DLBCL development. Genetic manipulation of USP19 using adenovirus‐based vectors was performed in two DLBCL cell lines, SUDHL4 and DB cells. The results showed that USP19 knockdown suppressed the proliferation, anchorage‐independent growth and xenograft tumor formation of DLBCL cells and arrested the cell cycle at the G1 stage. In parallel, DLBCL cells overexpressing USP19 acquired a more malignant phenotype. Next, to explore USP19 interactors, we performed co‐immunoprecipitation/liquid chromatography–mass spectrometry and identified potential interacting proteins. Among them, Parkinson disease protein 7 (PARK7), a member of the peptidase C56 family known to be involved in carcinogenesis, was further validated to bind with and be stabilized by USP19. Additionally, we found that USP19 induced PARK7 deubiquitylation in both DLBCL cell lines, and PARK7 acted as a downstream effector of USP19 in regulating the growth of DLBCL cells. Collectively, USP19 exerts a tumor‐promoting role in DLBCL through interacting with and stabilizing PARK7. [ABSTRACT FROM AUTHOR]

Abnormal mechanical loading is one of the major risk factors for articular cartilage degeneration. Engineered mesenchymal stromal cell (MSC)‐derived cartilage holds great promise for cell‐based cartilage repair. However, physiological loading protocols were shown to reduce matrix synthesis of MSC‐derived neocartilage in vitro and the regulators of this undesired mechanoresponse remain poorly understood. Parathyroid hormone‐related protein (PTHrP) is involved in cartilage development and can affect extracellular matrix (ECM) production during MSC chondrogenesis opposingly, depending on a continuous or transient exposure. PTHrP is induced by various mechanical cues in multiple tissues and species; but whether PTHrP is regulated in response to loading of human engineered neocartilage and may affect matrix synthesis in a positive or negative manner is unknown. The aim of this study was to investigate whether dynamic loading adjusts PTHrP‐signaling in human MSC‐derived neocartilage and whether it regulates matrix synthesis and other factors involved in the MSC mechanoresponse. Interestingly, MSC‐derived chondrocytes significantly upregulated PTHrP mRNA (PTHLH) expression along with its second messenger cAMP in response to loading in our custom‐built bioreactor. Exogenous PTHrP(1‐34) induced the expression of known mechanoresponse genes (FOS, FOSB, BMP6) and significantly decreased glycosaminoglycan (GAG) and collagen synthesis similar to loading. The adenylate‐cyclase inhibitor MDL‐12,330A rescued the load‐mediated decrease in GAG synthesis, indicating a direct involvement of cAMP‐signaling in the reduction of ECM production. According to COL2A1‐corrected hypertrophy‐associated marker expression, load and PTHrP treatment shared the ability to reduce expression of MEF2C and PTH1R. In conclusion, the data demonstrate a significant mechanoinduction of PTHLH and a negative contribution of the PTHrP‐cAMP signaling axis to GAG synthesis in MSC‐derived chondrocytes after loading. To improve ECM synthesis and the mechanocompetence of load‐exposed neocartilage, inhibition of PTHrP activity should be considered for MSC‐based cartilage regeneration strategies. [ABSTRACT FROM AUTHOR]

Premise Methods Conclusions The extraction of high‐quality RNA is the critical first step for the analysis of gene expression and gene space. This remains particularly challenging in plants, and especially in ferns, where the disruption of the cell wall and separation of organic compounds from nucleic acids is not trivial.We developed a cetyltrimethylammonium bromide (CTAB)‐based RNA extraction protocol that consistently performs well across a large phylogenetic breadth of ferns—a lineage of plants high in secondary compounds—and in an array of tissue types. Two alternative options (precipitation vs. clean‐up without intermediate precipitation) are presented, both of which yield high‐quality RNA extracts with optical density (OD) ratios of OD 260/280 = 1.9–2.1 and OD 260/230 > 1.6, and RNA integrity numbers >7.This study presents an efficient protocol for the extraction of high‐quality RNA from multiple tissues and across the fern phylogeny, a clade of plants that still lags behind other major lineages in the development of genomic resources. We hope that this method can be used to help facilitate the closing of this gap. [ABSTRACT FROM AUTHOR]

Dapagliflozin (DPG) is a sodium‐glucose cotransporter‐2 (SGLT2) inhibitor that has been suggested to possess anti‐inflammatory properties in diabetes. The aim of this study is to evaluate the role of DPG administration in preventing lipopolysaccharide (LPS)‐induced damage in the female genital system. Thirty‐two female Wistar Albino rats were randomly allocated into four groups: control group, LPS group, LPS + DPG group and DPG group. At the end of the experimental phase, ovary, fallopian tube and uterus tissues were collected for histopathological, immunohistochemical, genetic and biochemical analyses. The findings showed that LPS caused histopathological changes characterized by marked hyperaemia, mild to moderate haemorrhage, oedema and neutrophil leucocyte infiltrations and degenerative and necrotic changes in the female genital tract. In addition, it decreased total antioxidant status (TAS), increased total oxidant status (TOS) and oxidative stress index (OSI) levels. LPS also increased the expressions of Cas‐3, G‐CSF and IL‐1β in the ovary, fallopian tubes and uterus immunohistochemically. While Claudin‐1 expression decreased, NLRP3 and AQP4 gene expressions increased due to LPS. However, DPG treatment prevented all these changes. The results of this study indicate that, DPG can be used to prevent LPS‐induced lesions in the female reproductive system. [ABSTRACT FROM AUTHOR]

ABSTRACT The leguminous chickpea is a good source of protein, but its yield potential is frequently constrained by biotic stresses, primarily Helicoverpa armigera, a major havoc for cultivation of the crop. To develop host plant resistance for minimizing the losses due to the pod borer, five kabuli parents with desired traits for pod borer tolerance were crossed in diallel mating design to produce 10 crosses which were analysed for traits related to pod borer and nutrition. Based on correlation studies, trichome density was found positively correlated with phenol content, but both the traits were negatively associated with number of damaged seeds. Therefore, the tolerant genotypes were identified on the basis of phenol content, trichome density, number of damaged seeds and field rating. Among parents ICC 12197 was found superior in terms of yield and borer tolerance features with an intermediate pest resistance susceptible rating in addition to higher Fe content. However, significant sca effects for higher phenol content and seed yield in ICC 11764 × ICC 14190 were recorded with reduced number of damaged seeds in addition to higher Fe and Zn content. It was observed that the specific combination involved good and poor combiners for each trait. The same cross also showed significant standard heterosis in desirable direction for phenol content, trichome density, number of damaged seeds and seed yield. Additionally, the ratio of σ2 GCA to σ2 SCA revealed nonadditive gene action in controlling the expression of phenol content, trichome density, number of damaged seeds and Fe and Zn content. Thus, breeder may focus efforts on desirable cross utilizing selection in further segregating generations for higher phenol content, trichome density and Fe and Zn content in addition to yield‐related traits while lesser number of damaged seeds per plant to concentrate for development of pod borer resilient high yielding kabuli genotypes to combat micronutrient deficiency. [ABSTRACT FROM AUTHOR]

The tibial tuberosity has a superficial patellar tendon‐embedded portion and a deep uncalcified cartilage portion. Suppressed calcification of the tibial tuberosity leads to Osgood–Schlatter disease. The tibial tuberosity calcifies with age; load reduction degrades the cartilage matrix and promotes calcification, suggesting that reduced mechanical stimulation of the tibial tuberosity promotes calcification. However, this is yet to be clarified. Therefore, in this study, we aimed to investigate the effects of mechanical stimulation reduction on the tibial tuberosity tissue structure and calcification mechanism. Specifically, we examined the effect of load reduction on tibial tuberosity calcification in 20 male 7‐week‐old Wistar rats classified into two groups: hind‐limb suspension (HS, n = 10) and control (CO, n = 10). We observed superficial and deep tibial tuberosities in both groups. The tibial tuberosity in the HS group had narrower areas of deep portions than did those in the CO group (p = 0.000539), and immature bone tissue and cartilage tissue were observed in the HS group. Enpp1 expression did not significantly differ between the groups (p = 0.804). In contrast, Alpl (p = 0.001) and Mmp3 (p = 0.006) expression increased whereas Timp3 expression decreased (p = 0.002) in the HS group. Thus, these results showed a maturing of bone ossification, and this gene expression trend was similar to that observed in a murine join instability model of osteoarthritis with articular cartilage calcification and ossification. The HS tibial tuberosity also showed immature bone tissue. In conclusion, reduced mechanical stimulation caused tibial tuberosity calcification and pathological changes. These findings highlight the importance of optimal exercise to avoid premature pathological structural changes in bones and joints. [ABSTRACT FROM AUTHOR]

Transposable elements (TEs) are mobile genetic modules of viral derivation that have been co-opted to become modulators of mammalian gene expression. TEs are a major source of endogenous dsRNAs, signaling molecules able to coordinate inflammatory responses in various physiological processes. Here, we provide evidence for a positive involvement of TEs in inflammation-driven bone repair and mineralization. In newly fractured mice bone, we observed an early transient upregulation of repeats occurring concurrently with the initiation of the inflammatory stage. In human bone biopsies, analysis revealed a significant correlation between repeats expression, mechanical stress and bone mineral density. We investigated a potential link between LINE-1 (L1) expression and bone mineralization by delivering a synthetic L1 RNA to osteoporotic patient-derived mesenchymal stem cells and observed a dsRNA-triggered protein kinase (PKR)-mediated stress response that led to strongly increased mineralization. This response was associated with a strong and transient inflammation, accompanied by a global translation attenuation induced by eIF2α phosphorylation. We demonstrated that L1 transfection reshaped the secretory profile of osteoblasts, triggering a paracrine activity that stimulated the mineralization of recipient cells. Synopsis: Transposable elements (TEs) are selfish genetic modules that have, in certain contexts, evolved into modulators of mammalian gene expression. This study provides evidence for a role of TEs in promoting an inflammatory response that is required for bone repair and mineralization via dsRNA sensing-dependent PKR activation. In mice, TE expression is transiently upregulated shortly after a bone fracture concurrently with the onset of the inflammatory process. In humans, mechanically loaded bones upregulate TE expression, which correlates with local bone mineral density. Transfection with LINE-1 (L1) TE RNA stimulates mineralization activity in human osteoblasts in vitro. Cytoplasmic L1 RNA accumulation in differentiating osteoblasts triggers PKR-dependent translational shutdown, inflammation, and reshaping of the secretome. The secretome of L1 RNA-primed osteoblasts induces the mineralization activity of recipient osteoblasts. Bone fracture is associated with upregulation of transient transposable element RNA expression triggering bone mineralization via a paracrine, secretome mediated process. [ABSTRACT FROM AUTHOR]

The btuB riboswitch is a regulatory RNA sequence controlling gene expression of the outer membrane B12 transport protein BtuB by specifically binding coenzyme B12 (AdoCbl) as its natural ligand. The B12 sensing riboswitch class is known to accept various B12 derivatives, leading to a division into two riboswitch subclasses, dependent on the size of the apical ligand. Here we focus on the role of side chains b and e on affinity and proper recognition, i. e. correct structural switch of the btuB RNA, which belongs to the AdoCbl‐binding class I. Chemical modification of these side chains disturbs crucial hydrogen bonds and/or electrostatic interactions with the RNA, its effect on both affinity and switching being monitored by in‐line probing. Chemical modifications at sidechain b of vitamin B12 show larger effects indicating crucial B12‐RNA interactions. When introducing the same modification to AdoCbl the influence of any side‐chain modification tested is reduced. This renders the impact of the adenosyl‐ligand for B12‐btuB riboswitch recognition clearly beyond the known role in affinity. [ABSTRACT FROM AUTHOR]

Background Results Conclusion Carotenoids have various physiological functions, such as immune regulation and cancer prevention. Germination could further improve the content of carotenoids in maize seeds. In this study, yellow maize seeds (Suyu 29) were soaked and germinated with different concentrations of 24‐epibrassinolide. The changes of germination percentage, sprout length, bioactive components, antioxidant capacity and carotenoid content of the maize seeds were analyzed. Additionally, the relative expression of key genes in the carotenoid synthesis pathway was investigated.The results showed that the sprout length, germination percentage, soluble protein, free amino acids, proline, endogenous abscisic acid, vitamin C, total phenolics and carotenoids displayed a significant increasing trend compared with the control group (P < 0.05). The activity of superoxide dismutase and peroxidase increased by 55.1% and 58.5% versus the control group, and the antioxidant capacity of 2,2‐diphenyl‐1‐picrylhydrazyl, 2,2‐azinobis(3‐ethylbenzothiazoline‐6‐sulfonic acid) and ferric reducing antioxidant power was 19.8%, 13.4% and 44.1% higher than that of the control group (P < 0.05). Compared with the control group, the expression of genes was significantly up‐regulated (P < 0.05). Under the treatment of 0.1 mg L−1 of 24‐epibrassinolide, carotenoid content reached the highest value. The carotenoids showed a positive correspondence with antioxidant enzyme activity, antioxidant capacity and total phenolics content (P < 0.05).This study showed that 0.1 mg L−1 of exogenous 24‐epibrassinolide promoted the accumulation of carotenoids and improved the antioxidant capacity and the quality of germinated maize seeds. It could provide a method for the development of germinated maize products enriched in carotenoids. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Microsporidia, a group of unicellular eukaryotic parasites, rely intensely on secretory effectors for successful invasion and proliferation within host cells. This review focuses on the identification, characterization, and functional roles of effectors, including secretory proteins and microRNAs. The adhesion proteins like the Ricin‐B‐lectin facilitate initial invasion, which binds to the host cell surface. Once inside, microsporidia deploy a range of effectors to modulate host immune responses, such as serpin proteins, and redirect host cell metabolism to meet the parasite's nutritional needs through hexokinase. Some effectors such as microRNAs, alter the host gene expression to create a more favorable intracellular parasitic environment. In conclusion, the secretory effectors of microsporidia play a pivotal role spanning from host cell invasion to intracellular establishment. In the future, more effectors secreted by microsporidia will be studied, which will not only help to elucidate the molecular mechanism of pathogenic manipulation of the host but also help to provide the potential targets for anti‐parasitic treatments. [ABSTRACT FROM AUTHOR]

Background Objective Methods Results Conclusions Primary familial brain calcification (PFBC) is a monogenic disorder characterized by bilateral calcifications in the brain. The genetic basis remains unknown in over half of the PFBC patients, indicating the existence of additional novel causative genes. NAA60 was a recently reported novel causative gene for PFBC.The aim was to identify the probable novel causative gene in an autosomal recessive inherited PFBC family.We performed a comprehensive genetic study on a consanguineous Chinese family with 3 siblings diagnosed with PFBC. We evaluated the effect of the variant in a probable novel causative gene on the protein level using Western blot, immunofluorescence, and coimmunoprecipitation. Possible downstream pathogenic mechanisms were further explored in gene knockout (KO) cell lines and animal models.We identified a PFBC co‐segregated homozygous variant of c.460_461del (p.D154Lfs*113) in NAA60. Functional assays showed that this variant disrupts NAA60 protein localization to Golgi and accelerated protein degradation. The mutant NAA60 protein alters its interaction with the PFBC‐related proteins PiT2 and XPR1, affecting intracellular phosphate homeostasis. Further mass spectrometry analysis in NAA60 KO cell lines revealed decreased expression of multiple brain calcification–associated proteins, including reduced folate carrier (RFC), a folate metabolism–related protein.Our study replicated the identification of NAA60 as a novel causative gene for autosomal recessive PFBC, demonstrating our causative variant leads to NAA60 loss of function. The NAA60 loss of function disrupts not only PFBC‐related proteins (eg, PiT2 and XPR1) but also a wide range of other brain calcification–associated membrane protein substrates (eg, RFC), and provided a novel probable pathogenic mechanism for PFBC. © 2024 International Parkinson and Movement Disorder Society. [ABSTRACT FROM AUTHOR]

In mammals, imprinted genes are characterised by a monoallelic expression, which is based on parental origin and is essential for both foetal and placental development. The ZFAT gene encodes a transcriptional factor, and its non‐coding antisense RNA, ZFAT‐AS1, overlaps with the ZFAT locus. Both ZFAT and ZFAT‐AS1 are maternally imprinted in human placentas. In bovines, the imprinting status of the ZFAT and ZFAT‐AS1 genes has yet to be reported. In this study, we analysed the allelic expression of three transcript variants (X1–X3) of the bovine ZFAT and ZFAT‐AS1 genes in somatic tissues and placentas using a single nucleotide polymorphism‐based method. The results showed that bovine ZFAT exhibited isoform‐specific paternal expression. The ZFAT X2 variant exhibited monoallelic expression in the bovine placentas and biallelic expression in the six bovine somatic tissues (heart, liver, spleen, lung, kidney and brain). However, the ZFAT X1 and X3 variants were biallelically expressed in both bovine tissues and placentas. A 311 bp bovine ZFAT‐AS1 complementary DNA (cDNA) sequence was obtained by aligning the human ZFAT‐AS1 cDNA sequence with the bovine genome and conducting reverse transcription polymerase chain reaction amplification. Bovine ZFAT‐AS1 have monoallelic expression in bovine placentas and somatic tissues. In addition, the DNA methylation of two regions was characterised, including the partial promoter, and exon 1 and intron 1 regions of ZFAT, and there were no differentially methylated regions. [ABSTRACT FROM AUTHOR]