Element Binding Research Articles

Genome-wide profiling of soybean WRINKLED1 transcription factor binding sites provides insight into seed storage lipid biosynthesis

Understanding the regulatory mechanisms controlling storage lipid accumulation will inform strategies to enhance seed oil quality and quantity in crop plants. The WRINKLED1 transcription factor (WRI1 TF) is a central regulator of lipid biosynthesis. We characterized the genome-wide binding profile of soybean (Gm)WRI1 and show that the TF directly regulates genes encoding numerous enzymes and proteins in the fatty acid and triacylglycerol biosynthetic pathways. GmWRI1 binds primarily to regions downstream of target gene transcription start sites. We showed that GmWRI1-bound regions are enriched for the canonical WRI1 DNA binding element, the ACTIVATOR of Spomin::LUC1/WRI1 (AW) Box (CNTNGNNNNNNNCG), and another DNA motif, the CNC Box (CNCCNCC). Functional assays showed that both DNA elements mediate transcriptional activation by GmWRI1. We also show that GmWRI1 works in concert with other TFs to establish a regulatory state that promotes fatty acid and triacylglycerol biosynthesis. In particular, comparison of genes targeted directly by GmWRI1 and by GmLEC1, a central regulator of the maturation phase of seed development, reveals that the two TFs act in a positive feedback subcircuit to control fatty acid and triacylglycerol biosynthesis. Together, our results provide unique insights into the genetic circuitry in which GmWRI1 participates to regulate storage lipid accumulation during seed development.

Heritage clay brick characterization and assessment with compatible contemporary bricks for retrofitting of heritage monuments

Various mughal architecture clay brick masonry monuments were built in the Punjab state of northern India from the late 14th to late 19th centuries. Nanakshahi monuments (era of 1st Sikh Guru-Guru Nanak Dev Ji) are gigantic clay brick masonry structures constructed of lime and lime surkhi mortar (a powdered form of red burnt clay brick). Currently, this study is focused on identifying a suitable material for repairing and strengthening heritage clay brick monuments. Using the mineralogical composition of heritage Nanakshahi clay bricks (NSCB), the study compares them with contemporary clay bricks (CCB) from the same region, and then compares them to newly prepared clay bricks (NPCB), which have similar composition and dimensions to NSCB. The X-ray fluorescence confirms that the NSCB samples of southeast Punjab have an elemental composition consisting of filler SiO2 and binding elements like Al2O3, Fe2O3, CaO, K2O and MgO. The average density of ancient NSCB and CCB has been found to be similar; the ancient NSCB has a lower water absorption rate and porosity in contrast to the present-day clay bricks. The Initial rate of absorption of an ancient NSCB is quite higher. In comparison to the heritage NSCB, the CCB's compressive strength value is lower and uniaxial compression strength of newly prepared clay bricks (NPCB) of similar mineralogical composition and dimensions is comparable to that of the heritage NSCB from Punjab districts. The significance of the study is to suggest a compatible material for strengthening of heritage clay brick monuments of northern India.

The homeodomain regulates stable DNA binding of prostate cancer target ONECUT2.

The CUT and homeodomain are ubiquitous DNA binding elements often tandemly arranged in multiple transcription factor families. However, how the CUT and homeodomain work concertedly to bind DNA remains unknown. Using ONECUT2, a driver and therapeutic target of advanced prostate cancer, we show that while the CUT initiates DNA binding, the homeodomain thermodynamically stabilizes the ONECUT2-DNA complex through allosteric modulation of CUT. We identify an arginine pair in the ONECUT family homeodomain that can adapt to DNA sequence variations. Base interactions by this ONECUT family-specific arginine pair as well as the evolutionarily conserved residues are critical for optimal DNA binding and ONECUT2 transcriptional activity in a prostate cancer model. The evolutionarily conserved base interactions additionally determine the ONECUT2-DNA binding energetics. These findings provide insights into the cooperative DNA binding by CUT-homeodomain proteins.

Distilling the Essential Elements of Nuclear Binding via Neural-Network Quantum States.

To distill the essential elements of nuclear binding, we seek the simplest Hamiltonian capable of modeling atomic nuclei with percent-level accuracy. A critical aspect of this endeavor consists of accurately solving the quantum many-body problem without incurring an exponential computing cost with the number of nucleons. We address this challenge by leveraging a variational MonteCarlo method based on a highly expressive neural-network quantum state ansatz. In addition to computing binding energies and charge radii of nuclei with up to A=20 nucleons, by evaluating their magnetic moments, we demonstrate that neural-network quantum states are able to correctly capture the self-emerging nuclear shell structure. To this end, we introduce a novel computational protocol based on adding an external magnetic field to the nuclear Hamiltonian, which allows the neural network to learn the preferred polarization of the nucleus within the given magnetic field.

Phylogenomic instructed target analysis reveals ELAV complex binding to multiple optimally spaced U-rich motifs.

ELAV/Hu RNA-binding proteins are gene-specific regulators of alternative pre-mRNA processing. ELAV/Hu family proteins bind to short AU-rich motifs which are abundant in pre-mRNA, making it unclear how they achieve gene specificity. ELAV/Hu proteins multimerize, but how multimerization contributes to decode degenerate sequence environments remains uncertain. Here, we show that ELAV forms a saturable complex on extended RNA. Through phylogenomic instructed target analysis we identify the core binding motif U5N2U3, which is repeated in an extended binding site. Optimally spaced short U5N2U3 binding motifs are key for high-affinity binding in this minimal binding element. Binding strength correlates with ELAV-regulated alternative poly(A) site choice, which is physiologically relevant through regulation of the major ELAV target ewg in determining synapse numbers. We further identify a stem-loop secondary structure in the ewg binding site unwound upon ELAV binding at three distal U motifs. Base-pairing of U motifs prevents ELAV binding, but N6-methyladenosine (m6A) has little effect. Further, stem-loops are enriched in ELAV-regulated poly(A) sites. Additionally, ELAV can nucleate preferentially from 3' to 5'. Hence, we identify a decisive mechanism for ELAV complex formation, addressing a fundamental gap in understanding how ELAV/Hu family proteins decode degenerate sequence spaces for gene-specific mRNA processing.

Metabolomics-Based Study of the Protective Effect of 4-Hydroxybenzyl Alcohol on Ischemic Astrocytes.

Ischemic stroke is a common and dangerous disease in clinical practice. Astrocytes (ASs) are essential for maintaining the metabolic balance of the affected regions during the disease process. 4-Hydroxybenzyl alcohol (4HBA) from Gastrodia elata Bl. has potential neuroprotective properties due to its ability to cross the blood-brain barrier. In an in vitro experiment, we replicated the oxygen-glucose deprivation/reoxygenation model, and used methyl thiazoly tertrazolium, flow cytometry, kits, and other technical means to clarify the protective effect of 4HBA on primary ASs. In in vivo experiments, the 2VO model was replicated, and immunofluorescence and immunohistochemistry techniques were used to clarify the protective effect of 4HBA on ASs and the maintenance of the blood-brain barrier. Differential metabolites and related pathways were screened and verified using metabolomics analysis and western blot. 4HBA noticeably amplified AS cell survival, reduced mitochondrial dysfunction, and mitigated oxidative stress. It demonstrated a protective effect on ASs in both environments and was instrumental in stabilizing the blood-brain barrier. Metabolomic data indicated that 4HBA regulated nucleic acid and glutathione metabolism, influencing purines, pyrimidines, and amino acids, and it activated the N-methyl-D-aspartate/p-cAMP-response element binding protein/brain-derived neurotrophic factor signaling pathway via N-methyl-D-aspartate R1/N-methyl-D-aspartate 2C receptors. Our findings suggest that 4HBA is a potent neuroprotective agent against ischemic stroke, enhancing AS cell survival and function while stabilizing the blood-brain barrier. The N-methyl-D-aspartate/p-cAMP-response element binding protein/brain-derived neurotrophic factor signaling pathway is activated by 4HBA.

A transcriptional regulatory mechanism of genes in the tricarboxylic acid cycle in the heart

The tricarboxylic acid (TCA) cycle plays a crucial role in mitochondrial ATP production in the healthy heart. However, in heart failure, the TCA cycle becomes dysregulated. Understanding the mechanism by which TCA cycle genes are transcribed in the healthy heart is an important prerequisite to understanding how these genes become dysregulated in the failing heart. PGC-1α is a transcriptional coactivator that broadly induces genes involved in mitochondrial ATP production. PGC-1α potentiates its effects through coactivation of coupled transcription factors, such as ERR, Nrf1, Gabpa, and YY1. We hypothesized that PGC-1α plays an essential role in transcription of TCA cycle genes. Thus, by utilizing localization peaks of PGC-1α to TCA cycle gene promoters, it would allow the identification of coupled transcription factors. PGC-1α potentiated the transcription of 13 out of 14 TCA cycle genes, partly through ERR, Nrf1, Gabpa, and YY1. ChIP-sequencing showed PGC-1α localization peaks in TCA cycle gene promoters. Transcription factors with binding elements that were found proximal to PGC-1α peak localization were generally essential for transcription of the gene. These transcription factor binding elements were well conserved between mice and humans. Among the four transcription factors, ERR and Gabpa played a major role in potentiating transcription when compared to Nrf1 and YY1. These transcription factor-dependent PGC-1α recruitment was verified with Idh3a, Idh3g, and Sdha promoters with DNA binding assay. Taken together, this study clarifies the mechanism by which TCA cycle genes are transcribed, which could be useful to understand how those genes are dysregulated in pathological conditions.

A Droplet Digital Polymerase Chain Reaction-Based Tool to Aid in Melanoma Diagnosis.

Detecting copy number variations (CNVs) at certain loci can aid in the diagnosis of histologically ambiguous melanocytic neoplasms. Droplet digital polymerase chain reaction (ddPCR) is a rapid, automated, and inexpensive method for CNV detection in other cancers, but not yet melanoma. To evaluate the performance of a 4-gene ddPCR panel that simultaneously tests for ras responsive binding element protein 1 (RREB1) gain; cyclin-dependent kinase inhibitor 2A (CDKN2A) loss; MYC proto-oncogene, bHLH transcription factor (MYC) gain; and MYB proto-oncogene, transcription factor (MYB) loss in melanocytic neoplasms. One hundred sixty-four formalin-fixed, paraffin-embedded skin samples were used to develop the assay, of which 65 were used to evaluate its performance. Chromosomal microarray analysis (CMA) data were used as the gold standard. ddPCR demonstrated high concordance with CMA in detecting RREB1 gain (sensitivity, 86.7%; specificity, 88.9%), CDKN2A loss (sensitivity, 80%; specificity, 100%), MYC gain (sensitivity, 70%; specificity, 100%), and MYB loss (sensitivity, 71.4%; specificity, 100%). When one CNV was required to designate the test as positive, the 4-gene ddPCR panel distinguished nevi from melanomas with a sensitivity of 78.4% and a specificity of 71.4%. For reference, CMA had a sensitivity of 86.2% and a specificity of 78.6%. Our data also revealed interesting relationships with histology, namely (1) a positive correlation between RREB1 ddPCR copy number and degree of tumor progression; (2) a statistically significant correlation between MYC gain and nodular growth; and (3) a statistically significant correlation between MYB loss and a sheetlike pattern of growth. With further validation, ddPCR may aid both in our understanding of melanomagenesis and in the diagnosis of challenging melanocytic neoplasms.

Xanthomonas oryzae pv. oryzicola effector Tal10a directly activates rice OsHXK5 expression to facilitate pathogenesis.

Bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzicola (Xoc), is a major bacterial disease in rice. Transcription activator-like effectors (TALEs) from Xanthomonas can induce host susceptibility (S) genes and facilitate infection. However, knowledge of the function of Xoc TALEs in promoting bacterial virulence is limited. In this study, we demonstrated the importance of Tal10a for the full virulence of Xoc. Through computational prediction and gene expression analysis, we identified the hexokinase gene OsHXK5 as a host target of Tal10a. Tal10a directly binds to the gene promoter region and activates the expression of OsHXK5. CRISPR/Cas9-mediated gene editing in the effector binding element (EBE) of OsHXK5 significantly increases rice resistance to Xoc, while OsHXK5 overexpression enhances the susceptibility of rice plants and impairs rice defense responses. Moreover, simultaneous editing of the promoters of OsSULTR3;6 and OsHXK5 confers robust resistance to Xoc in rice. Taken together, our findings highlight the role of Tal10a in targeting OsHXK5 to promote infection and suggest that OsHXK5 represents a potential target for engineering rice resistance to Xoc.

Advocating harder soft governance for the European Green Deal. Stakeholder perspectives on the revision of the EU governance regulation

The Governance Regulation is the central coordination instrument for the European Unions' energy and climate policy. The Regulation is scheduled for revision, as it is misaligned with the updated EU framework and exhibits implementation and enforcement deficits. Our analysis reviews 136 submissions of institutional stakeholders participating in the European Commission's public consultations on the Governance Regulation and interlinked sectoral legislation. Employing a combined quantitative and qualitative text analysis, we examine the most salient issues for different stakeholder groups. We focus on stakeholder demands that address the implementation and enforcement deficits by introducing harder soft governance elements. While we find broad support among stakeholder groups for a revision and the improvement of implementation, Public Authorities exhibit reluctance for further binding elements, with the exception of demands for more precise enforcement mechanisms. While the inclusion of harder soft governance is only of subsidiary interest for non-public stakeholders demands for stronger obligations (e.g. binding national targets), justifications and public participation can be identified. The analysis finally discusses how the further introduction of harder soft governance elements has the potential to advance the EU's energy and climate framework.

Bioluminescent aptamer-based microassay for detection of melanoma inhibitory activity protein (MIA).

Melanoma inhibitory activity protein (MIA) does obviously offer the potential to reveal clinical manifestations of melanoma. Despite a pressing need for effective diagnosis of this highly fatal disease, there are no clinically approved MIA detection ELISA kits available. A recommended MIA threshold has not yet been defined, mostly by reason of variability in immunoglobulins' affinity and stability, the difference in sample preparation and assay conditions. Here we present a pair of high-affinity DNA aptamers developed as an alternative recognition and binding element for MIA detection. Their stability and reproducible synthesis are expected to ensure this analysis under standard conditions. The devised aptamer-based solid-phase microassay of model standard and control human sera involves luciferase NLuc as a highly sensitive reporter. Bioluminescence dependence on MIA concentration ranges in a linear manner from 2.5 to 250 ng mL-1, providing a MIA detection limit of 1.67 ± 0.57 ng mL-1.

Dimerization of assimilatory NADPH-dependent sulfite reductase reveals elements for diflavin reductase binding at a minimal interface.

Escherichia coli NADPH-dependent assimilatory sulfite reductase is responsible for fixing sulfur for incorporation into sulfur-containing biomolecules. The oxidoreductase is composed of two subunits, an NADPH, FMN, and FAD-binding diflavin reductase and an iron siroheme and Fe4S4-containing oxidase. How they interact has been an unknown for over 50 years because the complex is highly flexible, thus has been intransigent for traditional X-ray or cryo-EM structural analysis. Using a combination of the chameleon plunging system with a fluorinated lipid we overcame the challenge of preserving the minimal dimer between the subunits for high-resolution cryo-EM analysis. Here, we report the first structure of the complex between the reductase and oxidase, revealing how they interact in a minimal interface. Further, we determined the structural elements that discriminate between the pairing of a siroheme-containing oxidase with a diflavin reductase or a ferredoxin partner to channel the six electrons that reduce sulfite to sulfide.

A higher order PUF complex is central to regulation of C. elegans germline stem cells.

PUF RNA-binding proteins are broadly conserved stem cell regulators. Nematode PUF proteins maintain germline stem cells (GSCs) and, with key partner proteins, repress differentiation mRNAs, including gld-1. Here we report that PUF protein FBF-2 and its partner LST-1 form a ternary complex that represses gld-1 via a pair of adjacent FBF-2 binding elements (FBEs) in its 3ÚTR. One LST-1 molecule links two FBF-2 molecules via motifs in the LST-1 intrinsically-disordered region; the gld-1 FBE pair includes a well-established 'canonical' FBE and a newly-identified noncanonical FBE. Remarkably, this FBE pair drives both full RNA repression in GSCs and full RNA activation upon differentiation. Discovery of the LST-1-FBF-2 ternary complex, the gld-1 adjacent FBEs, and their in vivo significance predicts an expanded regulatory repertoire of different assemblies of PUF-partner complexes in nematode germline stem cells. It also suggests analogous PUF controls may await discovery in other biological contexts and organisms.

Revealing and targeting metabolic drivers contributing to treatment escape in diffuse midline glioma.

10038 Background: Diffuse midline glioma (DMG) is an aggressive pediatric brain tumor that predominately affects children, with a median survival of 9-11 months. DMGs are driven by self-renewing, stem-like glioma cells that have been stalled in an oligodendrocyte precursor cell (OPC)-like state and that highly express PDGFRA. This overexpression of PDGFRA has been shown to be pivotal in DMG development. Thus, targeting PDGFRA may serve as a viable treatment approach for DMG. In our previous studies, we revealed that avapritinib, a next generation tyrosine kinase inhibitor of PDGFRA, is highly effective in DMG cells. While a subset of patients receiving treatment with avapritinib experienced a promising clinical response, all patients eventually experienced tumor progression due to treatment escape. In this study, we investigated which mechanisms DMG cells use to escape avapritinib treatment, and how we can therapeutically exploit these resistance mechanisms. Methods: Transcriptomic profiling and functional assays were performed on patient-derived DMG cell lines. A combinatorial drug screening identified drug candidates evaluated in this study. Results: Bulk RNA sequencing analysis of two patient derived DMG cell lines revealed an upregulation of genes associated with both fatty acid metabolism and oxidative phosphorylation (OXPHOS) following avapritinib treatment. Functional assays confirmed elevated OXPHOS in avapritinib-treated cells with significant increases in mitochondrial energy transduction, palmitate- (a product of fatty acid metabolism) driven oxygen consumption rates, and incorporation of palmitate-derived carbons into the tricarboxylic acid (TCA) cycle. CRISPR-Cas9-mediated knockout of PDGFRAin one DMG cell line confirmed the metabolic changes observed following avapritinib treatment. Analysis of bulk RNA sequencing data revealed an upregulation of key fatty acid- related transcription factors in avapritinib-treated DMG cells. Specifically, Peroxisome Proliferator-Activated Receptor alpha (PPAR-alpha), Sterol Regulatory Binding Element Binding Transcription Factors 1 and 2, and Fatty Acid Synthase (FASN) were most prominently upregulated. To determine which therapies could target the dependency of avapritinib-treated cells on fatty acid metabolism, we performed a combinatorial drug screening and found three lipid pathway inhibitors that have synergistic cytotoxic effects with avapritinib. Specifically, a FASN inhibitor, cholesterol pathway inhibitor, and PPAR-alpha inhibitor. Conclusions: In this study, we revealed metabolic drivers that may contribute to avapritinib resistance in DMG cells, and identified compounds capable of inhibiting these drivers that demonstrate synergy with avapritinib. We now intend on testing these combination therapies in vivo as we aim to provide a long-term clinical benefit to DMG patients receiving avapritinib.

Abstract 1147: Crosstalk Between Alk5 And Mtorc1 Signaling Promotes VSMC Differentiation And The Therapeutic Effect Of Rapamycin

Background: Vascular smooth muscle cells (VSMC) phenotypic switching contributes to vascular repair and remodeling but also to pathologies including intimal hyperplasia. The mTORC1 inhibitor rapamycin is an effective drug-eluting stent agent that promotes VSMC differentiation. TGFβ also promotes VSMC differentiation through SMAD transcription factors. We investigated unexpected convergence between these pathways in VSMC plasticity. Methods: We assessed the interactions between rapamycin and the TGFβ1 (ALK5) signaling in human coronary artery SMCs and in vascular remodeling using inducible SMC-specific knockout mice (ALK5iKO). Results: Genome-wide histone H3K27 acetylation analysis unexpectedly identified SMAD binding elements as the motif most enriched after rapamycin treatment of hCASMCs. Treatment with rapamycin promoted rapid phosphorylation of SMAD2/3. Extensive signaling studies revealed that this phosphorylation required ALK5 activity but not TGF-β ligand. Surprisingly, ALK5 and SMAD2/3 were required for rapamycin-induced differentiation. We determined that rapamycin relieves FKBP12 inhibition of ALK5 to promote ligand independent Smad signaling, and FKBP12 knockdown was sufficient to induce contractile genes. Notably, rapamycin treatment induced an interaction between TET2 and SMAD2/3, and these SMADs were required for differentiation-associated chromatin remodeling, including DNA hydroxymethylation and H3K27 acetylation at contractile genes, suggesting that SMADs and TET2 function in concert at SBE- and CArG-containing promoter regions. Furthermore, ALK5iKO mice exhibited severe intimal hyperplasia after carotid artery injury compared to controls and were entirely resistant to the therapeutic effect of rapamycin, despite persistent inhibition of mTORC1. Consistent with in vitro findings, treatment with rapamycin elevated pSmad3 staining post-injury in the medial layer of control but not ALK5iKO mice. Conclusions: We report the surprising observation that rapamycin requires FKBP12/ALK5/SMAD2/3 signaling in order to promote TET2-dependent chromatin remodeling and SMC differentiation. Understanding these mechanisms may reveal new therapeutic strategies for treating vascular diseases.

구비공식구로 본 <새끼 서 발> 설화의 인물 성격과 서사적 의미

This provides an in-depth analysis of the characters and narrative significance of the Korean folktale Saekki Seo-Bal(An Unfinished Short Straw Rope) focusing on the oral-formulaic phrases of characters “Eating a meal in the warmer part and pooping in the colder part in the same room.” This oral-formulaic phrase, “Eating a meal in the warmer part and pooping in the colder part in the same room,” is fixedly and regularly combined with the folktales Saekki Seo-Bal and Chamkkaenamu(Sesame Tree). Therefore, the characters in the two folktales were named “Saekki Seo-Bal” type characters.
 The oral-formulaic phrase which appears in the character of Saekki Seo-Bal, is an essential binding element of the introductory narrative structure, linking to the success narrative of the ending section. This oral-formulaic phrase is not a rhetorical expression representing the character’s lazy behavior but a metaphorical expression of the character's deliberation or plan ahead of his social initiation. In other words, it defines the protagonist as an active person with emergent thinking who prepares to become independent from his mother and move into the world rather than as a problematic person with a lazy personality. This study interprets the folktale Saekki Seo-Bal, which is combined with the oral-formulaic phrase “Eating a Meal in the Warmer Part and Pooping in the Colder Part in the Same Room” as an initiation tale depicting a son growing from an individual to a social being.
 The social initiation process of characters consists of three stages: the preparatory stage for initiation, the stage of accumulating experiences and growth, and finally, social approval. In the first stage, characters prepare for social initiation through acts of oral-formulaic phrases. They demonstrate qualities as beginners in society by engaging in activities with materials provided by the community, such as “twisting straw ropes” in Saekki Seo-Bal and “sowing seeds” in Chamkkaenamu. The second stage appears in the narrative where the protagonist acquires the maiden who will become his wife through continuous bartering, starting with the “Saekki Seo-Bal.” Therefore, the character accumulates experience in solving problems in relationships with various others and grows into a social being with experience narratives that can solve any problem. In the third stage, the character’s abilities are tested through a “riddle bet” while returning to the community with the maiden who will become his wife. He eventually protects his wife and gains the approval of the social community as a marriage ritual.

Production of a sustainable cement through the usage of clay as binding element

The formulation of a calcined clay-based hydraulic binder is an innovative solution for reducing the carbon footprint in the construction industry. This binder is made from calcined clay, a natural and abundant material that does not require high-temperature firing in the 400C to 950C range. In our study, we worked respectively under the following temperatures: 550C, 650C, 750C and 850C, unlike traditional binders whose clinker is fired at a temperature of around 1450C. The blaine tests showed that the binder had been well ground, resulting in a much finer binder. We then obtained various blaines varying between 5000 and 8000 Cm2/g, unlike the blaine of the traditional binder, which is 3800 Cm2/g; the residue rate is very high compared with that of the traditional binder, due to the grinding carried out in a laboratory ball mill. The results of resistance tests at 30% gave 34.8, 48.8, 36.5 and 46 respectively; those at 40% gave 42.7, 45.4, 44.4 and 44.8, while the resistance of traditional binder gave 42.5. In other words, we obtained strengths comparable to those of the traditional binder. In addition, it was found that the manufacture of calcined clay-based hydraulic binders reduces CO2 emissions compared with traditional binders, which emit very high levels of CO2, making the production of calcined clay-based binders a more environmentally-friendly option for the cement industry. The financial assessment carried out at the end of this study shows that the production of a calcined clay-based binder is more economical than that of a traditional binder (Portland cement).

Generation of transgene-free canker-resistant Citrus sinensis cv. Hamlin in the T0 generation through Cas12a/CBE co-editing.

Citrus canker disease affects citrus production. This disease is caused by Xanthomonas citri subsp. citri (Xcc). Previous studies confirmed that during Xcc infection, PthA4, a transcriptional activator like effector (TALE), is translocated from the pathogen to host plant cells. PthA4 binds to the effector binding elements (EBEs) in the promoter region of canker susceptibility gene LOB1 (EBEPthA4-LOBP) to activate its expression and subsequently cause canker symptoms. Previously, the Cas12a/CBE co-editing method was employed to disrupt EBEPthA4-LOBP of pummelo, which is highly homozygous. However, most commercial citrus cultivars are heterozygous hybrids and more difficult to generate homozygous/biallelic mutants. Here, we employed Cas12a/CBE co-editing method to edit EBEPthA4-LOBP of Hamlin (Citrus sinensis), a commercial heterozygous hybrid citrus cultivar grown worldwide. Binary vector GFP-p1380N-ttLbCas12a:LOBP1-mPBE:ALS2:ALS1 was constructed and shown to be functional via Xcc-facilitated agroinfiltration in Hamlin leaves. This construct allows the selection of transgene-free regenerants via GFP, edits ALS to generate chlorsulfuron-resistant regenerants as a selection marker for genome editing resulting from transient expression of the T-DNA via nCas9-mPBE:ALS2:ALS1, and edits gene(s) of interest (i.e., EBEPthA4-LOBP in this study) through ttLbCas12a, thus creating transgene-free citrus. Totally, 77 plantlets were produced. Among them, 8 plantlets were transgenic plants (#HamGFP1 - #HamGFP8), 4 plantlets were transgene-free (#HamNoGFP1 - #HamNoGFP4), and the rest were wild type. Among 4 transgene-free plantlets, three lines (#HamNoGFP1, #HamNoGFP2 and #HamNoGFP3) contained biallelic mutations in EBEpthA4, and one line (#HamNoGFP4) had homozygous mutations in EBEpthA4. We achieved 5.2% transgene-free homozygous/biallelic mutation efficiency for EBEPthA4-LOBP in C. sinensis cv. Hamlin, compared to 1.9% mutation efficiency for pummelo in a previous study. Importantly, the four transgene-free plantlets and 3 transgenic plantlets that survived were resistant against citrus canker. Taken together, Cas12a/CBE co-editing method has been successfully used to generate transgene-free canker-resistant C. sinensis cv. Hamlin in the T0 generation via biallelic/homozygous editing of EBEpthA4 of the canker susceptibility gene LOB1.

Deciphering the antidepressant effects of Rosa damascena essential oil mediated through the serotonergic synapse signaling pathway

Ethnopharmacological relevanceRosa damascena is an ancient plant with significance in both medicine and perfumery that have a variety of therapeutic properties, including antidepressant, anti-anxiety, and anti-stress effects. Rose damascena essential oil (REO) has been used to treat depression, anxiety and other neurological related disorders in Iranian traditional medicine. However, its precise mechanism of action remains elusive. Aim of the studyThe aim of this study was to investigate the impact and mechanism underlying the influence of REO on chronic unpredictable mild stress (CUMS) rats. Materials and methodsGas chromatography-mass spectrometry (GC-MS) technique coupling was used to analyze of the components of REO. A CUMS rat model was replicated to assess the antidepressant effects of varying doses of REO. This assessment encompassed behavioral evaluations, biochemical index measurements, and hematoxylin-eosin staining. For a comprehensive analysis of hippocampal tissues, we employed transcriptomics and incorporated weighting coefficients by means of network pharmacology. These measures allowed us to explore differentially expressed genes and biofunctional pathways affected by REO in the context of depression treatment. Furthermore, GC-MS metabolomics was employed to assess metabolic profiles, while a joint analysis in Metscape facilitated the construction of a network elucidating the links between differentially expressed genes and metabolites, thereby elucidating potential relationships and clarifying key pathways regulated by REO. Finally, the expression of relevant proteins in the key pathways was determined through immunohistochemistry and Western blot analysis. Molecular docking was utilized to investigate the interactions between active components and key targets, thereby validating the experimental results. ResultsREO alleviated depressive-like behavior, significantly elevated levels of the neurotransmitter 5-hydroxytryptamine (5-HT), and reduced hippocampal neuronal damage in CUMS rats. This therapeutic effect may be associated with the modulation of the serotonergic synapse signaling pathway. Furthermore, REO rectified metabolic disturbances, primarily through the regulation of amino acid metabolic pathways. Joint analysis revealed five differentially expressed genes (EEF1A1, LOC729197, ATP8A2, NDST4, and GAD2), suggesting their potential in alleviating depressive symptoms by modulating the serotonergic synapse signaling pathway and tryptophan metabolism. REO also modulated the 5-HT2A-mediated extracellular regulated protein kinases-cAMP-response element binding protein-brain-derived neurotrophic factor (ERK-CREB-BDNF) pathway. In addition, molecular docking results indicated that citronellol, geraniol and (E,E)-farnesol in REO may serve as key active ingredients responsible for its antidepressant effects. ConclusionsThis study is the first to report that REO can effectively alleviate CUMS-induced depression-like effects in rats. Additionally, the study offers a comprehensive understanding of its intricate antidepressant mechanism from a multi-omics and multi-level perspective. Our findings hold promise for the clinical application and further development of this essential oil.

THE IMPACT OF COMMUNICATION ON LEADERSHIP: A SIGNIFICANT REVIEW

Leadership is vital for organizational growth, necessitating examination of core competencies like communication enabling effective leadership especially in turbulent times. This review consolidates research on linkages between leadership communication and emergent leadership outcomes. While predominant focus remains leader-centric, literature reveals complex bidirectional communication flows across hierarchical levels influencing leadership effectiveness and acceptance. However, consolidated clarity regarding distinguishing facets of communication fundamental for impactful leadership remains lacking. This significant review synthesizes multi-level research connecting communication behaviors and processes with leadership emergence and performance spanning interpersonal, team and organizational contexts via conceptual analysis. A framework integrating competencies characterizing distinguished leader-communicators is also put forth based on evidence aggregated. Analysis points to key aspects ranging from conveying cultural empathy to elevating collective identity through inclusive discourse that distinguished leadership communication fundamentally binds leadership vision to contextual interactions driving performance. Findings also critically highlight need for added communication dimensions encompassing restorative justice where adversity erodes leader legitimacy. This seminal review definitively puts forth communication as the core binding element flowing through formal and informal leadership development conduits that ultimately nourishes organizational resilience fit to navigate unprecedented turbulence. The integrated framework crystallizes distinguished communication-based leadership competencies redressing complex sociotechnical mechanisms that can unambiguously advance scholarship and practice on optimizing human centered, ethical and digitally-enabled leader messaging crucial for collective advancement.