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At least 289 records · Page 16

Imaging Supramolecular Morphogenesis with Confocal Laser Scanning Microscopy at Elevated Temperatures

The morphogenesis of supramolecular assemblies is a highly dynamic process that has only recently been recognized, and our understanding of this phenomenon will require imaging techniques capable of crossing scales. Shape transformations depend both on the complex energy landscapes of supramolecular systems and the kinetically controlled pathways that define their structures and functions. We report here the use of confocal laser scanning microscopy coupled with a custom-designed variable-temperature sample stage that enables in situ observation of such shape changes. The submicrometer resolution of this technique allows for real-time observation of the nanostructures in the native liquid environments in which they transform with thermal energy. We use this technique to study the temperature-dependent morphogenic behavior of peptide amphiphile nanofibers and photocatalytic chromophore amphiphile nanoribbons. Furthermore, the variable-temperature confocal microscopy technique demonstrated in this work can sample a large volume and provides real-time information on thermally induced morphological changes in the solution.

36 MATERIALS SCIENCE↗

Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana

Plants exhibit wide chemical diversity due to the production of specialized metabolites that function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs, as well as sources of insect repellents, health-promoting compounds, and fragrance. We report the chromosome-scale genome assembly of Callicarpa americana L. (American beautyberry), a species within the early-diverging Callicarpoideae clade of Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long-read sequencing and Hi-C scaffolding, we generated a 506.1-Mb assembly spanning 17 pseudomolecules with N50 contig and N50 scaffold sizes of 7.5 and 29.0 Mb, respectively. In all, 32,164 genes were annotated, including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Our analyses revealed 3 putative whole-genome duplication events, which, together with local tandem duplications, contributed to gene family expansion of terpene synthases. Kolavenyl diphosphate is a gateway to many of the bioactive terpenoids in C. americana; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with Tectona grandis L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 C. americana syntelogs. Access to the C. americana genome provides a road map for rapid discovery of genes encoding plant-derived agrichemicals and a key resource for understanding the evolution of chemical diversity in Lamiaceae.

59 BASIC BIOLOGICAL SCIENCES↗

Symmetry Effects in Photoinduced Electron Transfer in Chlorin-Quinone Dyads: Adiabatic Suppression in the Marcus Inverted Region

In donor–acceptor dyads undergoing photoinduced electron transfer (PET), a direction or pathway for electron movement is usually dictated by the redox properties and the separation distance between the donor and acceptor subunits, while the effect of symmetry is less recognized. We have designed and synthesized two isomeric donor–acceptor assemblies in which electronic coupling between donor and acceptor is altered by the orbital symmetry control with the reorganization energy and charge transfer exothermicity being kept unchanged. Analysis of the optical absorption and luminescence spectra, supported by the DFT and TD-DFT calculations, showed that PET in these assemblies corresponds to the Marcus inverted region (MIR) and has larger rate for isomer with weaker electronic coupling. This surprising observation provides the first experimental evidence for theoretically predicted adiabatic suppression of PET in MIR, which unambiguously controlled solely by symmetry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Recent Progress in Electrochemical Nitrogen Reduction on Transition Metal Nitrides

Distributed electrochemical nitrogen reduction reaction (ENRR) powered by renewable energy for the on-site production of ammonia is an attractive alternative to the industrial Haber–Bosch process, which is responsible for roughly 2 % of global energy consumption. Here, in this Review, we summarize recent progress in the ENRR catalyzed by transition metal nitrides (TMNs). The unique electronic structures of TMNs make them promising ENRR catalysts for active and selective ammonia production, which have been predicted theoretically and demonstrated experimentally. Reaction pathways and deactivation mechanisms of the ENRR on different TMNs are surveyed, and current understanding of structure-activity relations is discussed. To develop highly active, selective, and stable TMN catalysts for industrial-scale ENRR, membrane electrode assembly configuration is recommended in catalyst evaluation. Furthermore, we highlight the importance of developing mechanistic understanding on ENRR with different operando spectroscopic techniques.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery

Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways encoded by biosynthetic gene clusters (BGCs). Since the existing genome mining tools predict many putative NRPs synthesized by a given BGC, it remains unclear which of these putative NRPs are correct and how to identify post-assembly modifications of amino acids in these NRPs in a blind mode, without knowing which modifications exist in the sample. To address this challenge, here we report NRPminer, a modification-tolerant tool for NRP discovery from large (meta)genomic and mass spectrometry datasets. We show that NRPminer is able to identify many NRPs from different environments, including four previously unreported NRP families from soil-associated microbes and NRPs from human microbiota. Furthermore, in this work we demonstrate the anti-parasitic activities and the structure of two of these NRP families using direct bioactivity screening and nuclear magnetic resonance spectrometry, illustrating the power of NRPminer for discovering bioactive NRPs.

59 BASIC BIOLOGICAL SCIENCES↗

Pure-Water-Fed Forward-Bias Bipolar Membrane CO 2 Electrolyzer

Coupling renewable electricity to reduce carbon dioxide (CO 2 ) electrochemically into carbon feedstocks offers a promising pathway to produce chemical fuels sustainably. While there has been success in developing materials and theory for CO 2 reduction, the widespread deployment of CO 2 electrolyzers has been hindered by challenges in the reactor design and operational stability due to CO 2 crossover and (bi)carbonate salt precipitation. Herein, we design asymmetrical bipolar membranes assembled into a zero-gap CO 2 electrolyzer fed with pure water, solving both challenges. By investigating and optimizing the anion-exchangelayer thickness, cathode differential pressure, and cell temperature, the forward-bias bipolar membrane CO 2 electrolyzer achieves a CO faradic efficiency over 80% with a partial current density over 200 mA cm –2 at less than 3.0 V with negligible CO 2 crossover. In addition, this electrolyzer achieves 0.61 and 2.1 mV h –1 decay rates at 150 and 300 mA cm –2 for 200 and 100 h, respectively. Postmortem analysis indicates that the deterioration of catalyst/polymer– electrolyte interfaces resulted from catalyst structural change, and ionomer degradation at reductive potential shows the decay mechanism. Furthermore, all these results point to the future research direction and show a promising pathway to deploy CO 2 electrolyzers at scale for industrial applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism

Gmelina arborea Roxb is a fast-growing tree species of commercial importance for tropical countries due to multiple industrial uses of its wood. Wood is primarily composed of thick secondary cell walls of xylem cells which imparts the strength to the wood. Identification of the genes involved in the secondary cell wall biosynthesis as well as their cognate regulators is crucial to understand how the production of wood occurs and serves as a starting point for developing breeding strategies to produce varieties with improved wood quality, better paper pulping or new potential uses such as biofuel production. In order to gain knowledge on the molecular mechanisms and gene regulation related with wood development in white teak, a de novo sequencing and transcriptome assembly approach was used employing secondary cell wall synthesizing cells from young white teak trees. For generation of transcriptome, RNA-seq reads were assembled into 110,992 transcripts and 49,364 genes were functionally annotated using plant databases; 5071 GO terms and 25,460 SSR markers were identified within xylem transcripts and 10,256 unigenes were assigned to KEGG database in 130 pathways. Among transcription factor families, C2H2, C3H, bLHLH and MYB were the most represented in xylem. Differential gene expression analysis using leaves as a reference was carried out and a total of 20,954 differentially expressed genes were identified including monolignol biosynthetic pathway genes. The differential expression of selected genes (4CL, COMT, CCoAOMT, CCR and NST1) was validated using qPCR. We report the very first de novo transcriptome of xylem-related genes in this tropical timber species of commercial importance and constitutes a valuable extension of the publicly available transcriptomic resource aimed at fostering both basic and breeding studies.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluating the effect of membrane-ionomer combinations and supporting electrolytes on the performance of cobalt nanoparticle anodes in anion exchange membrane electrolyzers

In low temperature polymer electrolyte membrane electrolyzers, component choices and membrane electrode assembly (MEA) fabrication have pivotal roles in determining cell performance. Here, cobalt anodes were used in combination with different ionomers, membranes, and supporting electrolytes to delineate their effect on MEA performance in anion exchange membrane (AEM) based electrolyzers. Changes to the ionomer type suppress or enhance catalyst redox and were found to alter the resulting exchange current densities and Tafel slopes. Changes in membrane conductivity account for large differences in performance and overpotential losses among the different MEAs, with higher conductivity minimizing ohmic losses. Within supporting electrolytes, lower concentration results in lower conductivity and lower MEA performance; the performance, however, is higher in potassium hydroxide than bicarbonate. These experiments address the influence of individual components and their integration on cell-level performance, to help develop a pathway to an electrolyte free system while providing a foundation for studying electrode composition and component incorporation into MEAs.

25 ENERGY STORAGE↗

Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan

Thermoflexus hugenholtzii JAD2 T , the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2 T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2 T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus Thermoflexus sinensis.” Genomics was integrated with targeted exometabolomics and 13 C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2 T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2 T using 13 C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13 C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.

59 BASIC BIOLOGICAL SCIENCES↗

Seasonal activities of the phyllosphere microbiome of perennial crops

Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.

59 BASIC BIOLOGICAL SCIENCES↗

Chloroplast phosphatases LPPγ and LPPε1 facilitate conversion of extraplastidic phospholipids to galactolipids

Abstract Galactolipids comprise the majority of chloroplast membranes in plants, and their biosynthesis requires dephosphorylation of phosphatidic acid at the chloroplast envelope membranes. In Arabidopsis (Arabidopsis thaliana), the lipid phosphate phosphatases LPPγ, LPPε1, and LPPε2 have been previously implicated in chloroplast lipid assembly, with LPPγ being essential, as null mutants were reported to exhibit embryo lethality. Here, we show that lppγ mutants are in fact viable and that LPPγ, LPPε1, and LPPε2 do not appear to have central roles in the plastid pathway of membrane lipid biosynthesis. Redundant LPPγ and LPPε1 activity at the outer envelope membrane is important for plant development, and the respective lppγ lppε1 double mutant exhibits reduced flux through the ER pathway of galactolipid synthesis. While LPPε2 is imported and associated with interior chloroplast membranes, its role remains elusive and does not include basal nor phosphate limitation-induced biosynthesis of glycolipids. The specific physiological roles of LPPγ, LPPε1, and LPPε2 are yet to be uncovered, as does the identity of the phosphatidic acid phosphatase required for plastid galactolipid biosynthesis.

Cook, Ron (ORCID:0000000198356205)↗

Probing the solidification of quasicrystals via joint experiment and simulation (Final Report)

Quasicrystals (QCs) possess long-range positional order but non-crystallographic orientational order. Their classically ‘forbidden’ symmetry has long attracted the interest of scientists worldwide. Despite their frequent observation in both metal alloys and soft matter structures in the 35 years since their discovery, little is known about how QCs evolve from a liquid, amorphous, or crystalline precursor. In this project, we sought to resolve the enigma of QC self-assembly through a combined experimental and computational program. The Shahani group employed in situ electron and synchrotron X ray imaging to peer into the growth dynamics of QCs in a liquid, covering a broad range of length scales and solidification pathways. Glotzer's team developed new simulation models incorporating phasonic defects — which are unique to quasicrystals — and used this model to investigate two grains growing together, closely mimicking the experimental conditions. While QCs remain exceptional structures, most compounds in the realm of intermetallics adopt non-trivial geometries. In fact, only around 6% of phases are comprised of the simplest sphere packings that researchers so readily associate with metals. State-of-the-art knowledge of phase transformations at the outset of this collaborative project did not encompass the remaining 94% of intermetallic compounds that possess complex and aperiodic structure types. Therefore, we expect that outcomes from this project will have immediate and profound impact on synthesis and processing science: our efforts will be used to not only explain the growth dynamics of QCs but also complex intermetallics more broadly.

36 MATERIALS SCIENCE↗

Accelerating Optimal Integration of Energy Efficiency Strategies with Industrialized Modular Construction: Preprint

The National Renewable Energy Laboratory's (NREL's) Industrialized Construction Innovation team first introduced the Industrialized Construction Assessment Framework to achieve affordable, net-zero energy (NZE) modular multifamily buildings in the 2020 ACEEE paper "Integrating Energy Efficiency Strategies with Industrialized Construction for our Clean Energy Future." Since then, NREL has continued to drive the ambitious plan to accelerate optimal integration of energy efficiency strategies during industrialized construction with little or no additional cost, labor, and production time. This follow-on paper introduces the Energy in Modular (EMOD) buildings method and presents NREL's research efforts over the last two years in collaboration with industry, including affordable housing partners. NREL has developed an idealized NZE modular multifamily building design that incorporates five energy efficiency strategies well suited for industrialized construction in factories: (1) envelope thermal control, (2) envelope infiltration control, (3) mechanical, electrical, and plumbing systems, (4) smart controls, and (5) solar plus storage. This paper highlights results from leveraging design for manufacturing and assembly principles, testing, and validation pilots with factory partners; demonstrating pod prototypes in test stand at NREL; and performing simulations. Overall, these research efforts address barriers to whole-building system integration, such as poor installation quality of thermal and air barriers; lack of unitized systems for space conditioning, energy recovery and ventilation, and water heating; problematic on-site installation, commissioning, and configuration of controls; and lack of cost-effective integration for grid-friendly design and emerging technologies. Conclusively, the paper delineates next steps for future work with NREL's partners toward developing a transformational pathway for our clean energy future.

affordable housing↗

Fibril Network Strategy Enables High‐Performance Semitransparent Organic Solar Cells

Abstract The development of semitransparent organic solar cells (ST‐OSCs) represents a significant step toward the commercialization of OSCs. However, the trade‐off between power conversion efficiency (PCE) and average visible transmittance (AVT) restricts further improvements of ST‐OSCs. Herein, it is demonstrated that a fibril network strategy can enable ST‐OSCs with a high PCE and AVT simultaneously. A wide‐bandgap polymer PBT1‐C‐2Cl that can self‐assemble into a fibril nanostructure is used as the donor and a near‐infrared small molecule Y6 is adopted as the acceptor. It is found that a tiny amount of PBT1‐C‐2Cl in the blend can form a high speed pathway for hole transport due to the well distributed fibril nanostructure, which increases the transmittance in the visible region. Meanwhile, the acceptor Y6 guarantees sufficient light absorption. Using this strategy, the optimized ST‐OSCs yield a high PCE of 9.1% with an AVT of over 40% and significant light utilization efficiency of 3.65% at donor/acceptor ratio of 0.25:1. This work demonstrates a simple and effective approach to realizing high PCE and AVT of ST‐OSCs simultaneously.

Xie, Yuanpeng↗

Amphiphilic Baskets for Supramolecular Nanoarchitectures at Interfaces: Inverted Monolayer Formation on Water

Interfacial chemistry of molecular baskets remains poorly understood despite their promise for supramolecular applications of detection and sequestration of toxic molecules including those of illicit drugs, organophosphorus compounds, and anticancer agents. We present a fundamental investigation of the interfacial behavior of three amphiphilic supramolecular baskets (ASB 4, 8, and 12), having increasingly longer yet linear alkyl chains at the top of their bowl-shaped cavity. The studies were completed at the air−water interface to elucidate surface activity, interfacial stability, self-assembly, and monolayer organization that drive inverted monolayer formation, in which the molecular arms orient toward the aqueous phase in a configuration opposite to that typically observed for lipids. Herein, surface pressure−area isotherms of ASB 4, 8, 12, deposited on a water surface, were performed in tandem with nonequilibrium relaxation experiments to quantify surface activity, thermodynamic stability, and monolayer compressibility of the baskets’ monolayer assembly. Brewster angle microscopy enabled direct visualization of morphological evolution, aggregation, and packing at the interface. We show that systematic extension of the hydrocarbon arms, from four to 12 methylene groups, progressively modifies intermolecular packing, drives distinct two-dimensional aggregation pathways, and increases number densities at the air−water interface. Atomistic molecular dynamics simulations corroborate many of these experimentally observed trends and provide mechanistic detail on the cooperative roles of basket topology and interfacial concentration in regulating the hydration structure and dynamics within the cavities generated by surface-adsorbing baskets, consistent with observed variations in surface activity and packing. Our results establish how the topology of these unique supramolecules and their concentration govern interfacial organization and offer a rational framework for designing amphiphiles with predictable behavior at soft interfaces.

Hydrocarbons↗

Understanding the dynamic nature of plant lipid anabolic and catabolic metabolism is key to sustainable oilseed engineering

Plant-derived oils are essential sources of reduced carbon and various fatty acid (FA) structures for food, biofuels, and the oleochemical industry. Despite extensive efforts, engineering mainstream oilseed crops to produce high levels of industrially valuable unusual FAs (UFAs) remains challenging. This review synthesizes recent advances in the understanding of lipid metabolic networks, emphasizing how species-specific regulation of FA synthesis, activation, and delivery influences triacylglycerol (TAG) assembly to govern the efficiency of UFA accumulation. Key insights reveal that acyl flux through anabolic and catabolic branches of lipid metabolism is tightly controlled by enzyme substrate selectivities, diacylglycerol (DAG) pool compartmentalization, and metabolic context, including lipid remodeling and degradation pathways. Engineering success is often constrained by incompatibilities between UFA biosynthetic enzymes and endogenous host metabolism, leading to flux imbalances, futile cycles, and undesired phenotypes. We highlight emerging strategies to overcome these barriers, such as the use of UFA-selective acyltransferases, coordinated manipulation of DAG source pools, suppression of competing endogenous enzymes, and exploitation of TAG remodeling mechanisms. This integrated synthesis provides a conceptual framework for logic-based engineering of oilseeds with enhanced UFA content by offering new avenues for sustainable biomanufacturing of valuable lipids.

acyltransferase specificity↗

Chromosome-level genome assembly of Quercus variabilis provides insights into the molecular mechanism of cork thickness

Quercus variabilis is a deciduous woody species with high ecological and economic value and is a major source of cork in East Asia. Cork from thick softwood sheets have higher commercial value than those from thin sheets. It is extremely difficult to genetically improve Q. variabilis to produce high quality softwood due to the lack of genomic information. Here, we present a high-quality chromosomal genome assembly for Q. variabilis with length of 791,89 Mb and 54,606 predicted genes. Comparative analysis of protein sequences of Q. variabilis with 11 other species revealed that specific and expanded gene families were significantly enriched in the "fatty acid biosynthesis" pathway in Q. variabilis, which may contribute to the formation of its unique cork. Additionally, based on weighted correlation network analysis of time-course (i.e., five important developmental ages) gene expression data in thick-cork versus thin-cork genotypes of Q. variabilis, we identified one co-expression gene module associated with the thick-cork trait. Within this co-expression gene module, 10 hub genes were associated with suberin biosynthesis. Furthermore, we identified a total of 198 suberin biosynthesis-related new candidate genes that were up-regulated in trees with a thick cork layer relative to those with a thin cork layer. Also, we found that some genes related to cell expansion and cell division were highly expressed in trees with a thick cork layer. Collectively, our results revealed that two metabolic pathways (i.e., suberin biosynthesis, fatty acid biosynthesis), along with other genes involved in cell expansion, cell division, and transcriptional regulation, were associated with the thick-cork trait in Q. variabilis, providing insights into the molecular basis of cork development and knowledge for informing genetic improvement of cork thickness in Q. variabilis and closely related species.

59 BASIC BIOLOGICAL SCIENCES↗

DNA-caged nanoparticles via electrostatic self-assembly

DNA-modified nanoparticles enable DNA sensing and therapeutics in nanomedicine and are also crucial for nanoparticle self-assembly with DNA-based materials. However, methods to conjugate DNA to nanoparticle surfaces are limited, inefficient, and lack control. Inspired by DNA tile nanotechnology, we demonstrate a new approach to nanoparticle modification based on electrostatic attraction between negatively charged DNA tiles and positively charged nanoparticles. This approach does not disrupt nanoparticle surfaces and leverages the programmability of DNA nanotechnology to control DNA presentation. We demonstrated this approach using a variety of nanoparticles, including polymeric micelles, polystyrene beads, gold nanoparticles, and superparamagnetic iron oxide nanoparticles with sizes ranging from 5–20 nm in diameter. DNA cage formation was confirmed through transmission electron microscopy (TEM), neutralization of zeta potential, and a series of fluorescence experiments. DNA cages present “handle” sequences that can be used for reversible target attachment or self-assembly. Handle functionality was verified in solution, at the solid–liquid interface, and inside fixed cells, corresponding to applications in biosensing, DNA microarrays, and erasable immunocytochemistry. Finally, these experiments demonstrate the versatility of the electrostatic DNA caging approach and provide a new pathway to nanoparticle modification with DNA that will empower further applications of these materials in medicine and materials science.

60 APPLIED LIFE SCIENCES↗