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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 55 records · Page 3

Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s

Like fungi and some prokaryotes, plants use a thiazole synthase (THI4) to make the thiazole precursor of thiamin. Fungal THI4s are suicide enzymes that destroy an essential active-site Cys residue to obtain the sulfur atom needed for thiazole formation. In contrast, certain prokaryotic THI4s have no active-site Cys, use sulfide as sulfur donor, and are truly catalytic. The presence of a conserved active-site Cys in plant THI4s and other indirect evidence implies that they are suicidal. To confirm this, we complemented the Arabidopsistz-1 mutant, which lacks THI4 activity, with a His-tagged Arabidopsis THI4 construct. LC–MS analysis of tryptic peptides of the THI4 extracted from leaves showed that the active-site Cys was predominantly in desulfurated form, consistent with THI4 having a suicide mechanism in planta. Unexpectedly, transcriptome data mining and deep proteome profiling showed that barley, wheat, and oat have both a widely expressed canonical THI4 with an active-site Cys, and a THI4-like paralog (non-Cys THI4) that has no active-site Cys and is the major type of THI4 in developing grains. Transcriptomic evidence also indicated that barley, wheat, and oat grains synthesize thiamin de novo, implying that their non-Cys THI4s synthesize thiazole. Structure modeling supported this inference, as did demonstration that non-Cys THI4s have significant capacity to complement thiazole auxotrophy in Escherichia coli. There is thus a prima facie case that non-Cys cereal THI4s, like their prokaryotic counterparts, are catalytic thiazole synthases. Bioenergetic calculations show that, relative to suicide THI4s, such enzymes could save substantial energy during the grain-filling period.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Differential roles of kinetic on- and off-rates in T-cell receptor signal integration revealed with a modified Fab’-DNA ligand

Antibody-derived T-cell receptor (TCR) agonists are commonly used to activate T cells. While antibodies can trigger TCRs regardless of clonotype, they bypass native T cell signal integration mechanisms that rely on monovalent, membrane-associated, and relatively weakly binding ligand in the context of cellular adhesion. Commonly used antibodies and their derivatives bind much more strongly than native peptide major histocompatibility complex (pMHC) ligands bind their cognate TCRs. Because ligand dwell time is a critical parameter that tightly correlates with physiological function of the TCR signaling system, there is a general need, both in research and therapeutics, for universal TCR ligands with controlled kinetic binding parameters. To this end, we have introduced point mutations into recombinantly expressed α-TCRβ H57 Fab to modulate the dwell time of monovalent Fab binding to TCR. When tethered to a supported lipid bilayer via DNA complementation, these monovalent Fab’-DNA ligands activate T cells with potencies well-correlated with their TCR binding dwell time. Single-molecule tracking studies in live T cells reveal that individual binding events between Fab'-DNA ligands and TCRs elicit local signaling responses closely resembling native pMHC. The unique combination of high on- and off-rates of the H57 R97L mutant enables direct observations of cooperative interplay between ligand binding and TCR-proximal condensation of the linker for activation of T cells, which is not readily visualized with pMHC. This work provides insights into how T cells integrate kinetic information from TCR ligands and introduces a method to develop affinity panels for polyclonal T cells, such as cells from a human patient.

Science & Technology - Other Topics↗

RrA, an enzyme from Rhodospirillum rubrum , is a prototype of a new family of short‐chain L‐asparaginases

Abstract L‐Asparaginases (ASNases) catalyze the hydrolysis of L‐Asn to L‐Asp and ammonia. Members of the ASNase family are used as drugs in the treatment of leukemia, as well as in the food industry. The protomers of bacterial ASNases typically contain 300–400 amino acids (typical class 1 ASNases). In contrast, the chain of ASNase from Rhodospirillum rubrum , reported here and referred to as RrA, consists of only 172 amino acid residues. RrA is homologous to the N‐terminal domain of typical bacterial class 1 ASNases and exhibits millimolar affinity for L‐Asn. In this study, we demonstrate that RrA belongs to a unique family of cytoplasmic, short‐chain ASNases (scASNases). These proteins occupy a distinct region in the sequence space, separate from the regions typically assigned to class 1 ASNases. The scASNases are present in approximately 7% of eubacterial species, spanning diverse bacterial lineages. They seem to be significantly enriched in species that encode for more than one class 1 ASNase. Here, we report biochemical, biophysical, and structural properties of RrA, a member of scASNases family. Crystal structures of the wild‐type RrA, both with and without bound L‐Asp, as well as structures of several RrA mutants, reveal topologically unique tetramers. Moreover, the active site of one protomer is complemented by two residues (Tyr21 and Asn26) from another protomer. Upon closer inspection, these findings clearly outline scASNases as a stand‐alone subfamily of ASNases that can catalyze the hydrolysis of L‐Asn to L‐Asp despite the lack of the C‐terminal domain that is present in all ASNases described structurally to date.

59 BASIC BIOLOGICAL SCIENCES↗

Integrated Transcriptomic and Proteomic Analysis Identifies Plasma Biomarkers of Hepatocellular Failure in Alcohol-Associated Hepatitis

Alcohol-associated hepatitis (AH) is a form of liver failure with high short-term mortality. Recent results have shown that HNF4a defective function and systemic inflammation are major disease drivers of AH. Plasma biomarkers of hepatocyte function could be useful for diagnostic and prognostic purposes. Herein an integrative analysis of hepatic RNAseq and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to identify plasma protein signatures for mild and severe AH patients. Alcohol-related liver disease cirrhosis (ALD)(AC), non-alcoholic fatty liver disease (NALFD), and healthy subjects (HC) were used as comparator groups. Identified proteins primarily involved in hepatocellular function were decreased in AH patients which included hepatokines, clotting factors, complement cascade components, and hepatocyte growth activators. A protein signature of AH disease severity was identified including thrombin (THRB), hepatocyte growth factor alpha (HGFA), clusterin (CLUS), human serum factor H-related protein (FHR1) and kallistatin (KAIN), which exhibited large abundance shifts between severe and non-severe AH. The combination of THRB and HGFA discriminated between severe and non-severe AH with high sensitivity and specificity. These findings were correlated with the liver expression of genes encoding secreted proteins in a similar cohort, finding a highly consistent plasma protein signature reflecting HNF4A and HNF1A functions. This unbiased proteomic-transcriptome analysis identified plasma protein signatures and pathways associated with disease severity, reflecting HNF4A/1A activity useful for diagnostic assessment in AH.

60 APPLIED LIFE SCIENCES↗

Identification, characterization, and structure of a tRNA splicing enzyme RNA 5′-OH kinase from the pathogenic fungi Mucorales

Fungal Trl1 is an essential tRNA splicing enzyme composed of C-terminal cyclic phosphodiesterase and central polynucleotide kinase end-healing domains that convert the 2′,3′-cyclic-PO 4 and 5′-OH ends of tRNA exons into the 3′-OH,2′-PO 4 and 5′-PO 4 termini required for sealing by an N-terminal ATP-dependent ligase domain. Trifunctional Trl1 enzymes are present in most human fungal pathogens and are untapped targets for antifungal drug discovery. Mucorales species, deemed high-priority human pathogens by WHO, elaborate a noncanonical tRNA splicing apparatus in which a stand-alone monofunctional RNA ligase enzyme joins 3′-OH,2′-PO 4 and 5′-PO 4 termini. Here we identify a stand-aloneMucor circinelloidespolynucleotide kinase (MciKIN) and affirm its biological activity in tRNA splicing by genetic complementation in yeast. Recombinant MciKIN catalyzes magnesium-dependent phosphorylation of 5′-OH RNA and DNA ends in vitro. MciKIN displays a strong preference for GTP as the phosphate donor in the kinase reaction, a trait shared with the stand-alone RNA kinase homologs from Mucorales speciesRhizopus azygosporus(RazKIN) andLichtheimia corymbifera(LcoKIN) and with the kinase domains of fungal Trl1 enzymes. We report a 1.65 Å crystal structure of RazKIN in complex with GDP•Mg 2+ that illuminates the basis for guanosine nucleotide specificity.

Biochemistry & Molecular Biology↗

Building Science Education for Solar Decathlon: Emissions and the Built Environment [Slides]

The Solar Decathlon Building Science Education series is designed to educate students and working professionals on building science principles that are paramount to the successful design of high-performance, energy-efficient buildings. Instructional content is presented in modules, covering specific topics. Altogether, this series aims to educate viewers on: 1) where/how energy is used in buildings; 2) how to define zero energy buildings; 3) how to apply the fundamentals of thermodynamics to building envelope design; 4) how to explain the science of how/why buildings use energy; 5) how to apply this knowledge to design comfortable energy efficient buildings. Students and working professionals can use this educational information at no cost to complement academic curriculum and continuing education activities. This is Module 7 which focuses on embodied environmental carbon.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

The Necessity of International Particle Physics Opportunities for American Education

This Snowmass2021 Contributed Paper addresses the role of the Particle Physics community in creating and fostering international connections in American education. It describes the pressing need to introduce students and faculty to the challenges and rewards of international collaboration, not only to develop the next generation of scientists and engineers for particle physics, but to maintain and build U.S. leadership on an increasingly competitive world stage. We present and assess current efforts in education and public engagement with an eye toward identifying those activities in need of change or increased resources to improve audience reach and program efficacy. We also consider possible new activities that might improve upon or complement existing programs, with the common goal of providing all U.S. students with the opportunity to benefit from a quality international scientific experience.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Cosmogenic activation of silicon

In the production of 3 H, 7 Be, and 22 Na by interactions of cosmic-ray particles with silicon can produce radioactive backgrounds in detectors used to search for rare events. Through controlled irradiation of silicon CCDs and wafers with a neutron beam that mimics the cosmic-ray neutron spectrum, followed by direct counting, we determined that the production rate from cosmic-ray neutrons at sea level is (112 ± 24) atoms/( kg day ) for 3 H, (8.1 ± 1.9) atoms/( kg day ) for 7 Be, and (43.0 ± 7.2) atoms/( kg day ) for 22 Na . Complementing these results with the current best estimates of activation cross sections for cosmic-ray particles other than neutrons, we obtain a total sea-level cosmic-ray production rate of (124 ± 25) atoms/(kg day) for 3 H, (9.4 ± 2.0) atoms/( kg day ) for 7 Be, and (49.6 ± 7.4) atoms/( kg day ) for 22 Na. These measurements will help constrain background estimates and determine the maximum time that silicon-based detectors can remain unshielded during detector fabrication before cosmogenic backgrounds impact the sensitivity of next-generation rare-event searches.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

2019 Nevada National Security Site Environmental Report Attachment A: Site Description

This attachment expands on the general description of the Nevada National Security Site (NNSS) presented in the Introduction to the Nevada National Security Site Environmental Report 2019. Included are subsections that summarize the site’s geological, hydrological, climatological, and ecological settings and the cultural resources of the NNSS. The subsections are meant to aid the reader in understanding the complex physical and biological environment of the NNSS. An adequate knowledge of the site’s environment is necessary to assess the environmental impacts of new projects, design and implement environmental monitoring activities for current site operations, and assess the impacts of site operations on the public residing in the vicinity of the NNSS. The NNSS environment contributes to several key features of the site that afford protection to the inhabitants of adjacent areas from potential exposure to radioactivity or other contaminants resulting from NNSS operations. These key features include the general remote location of the NNSS, restricted access, extended wind transport times, the great depths to slow-moving groundwater, little or no surface water, and low population density. This attachment complements the annual summary of monitoring program activities and dose assessments presented in the main body of this report.

54 ENVIRONMENTAL SCIENCES↗

Hydraulic fracture mapping using wavelet-based fusion of wave transmission and emission measurements

Fracture characterization is essential to hydrocarbon and geothermal exploration and production as well as carbon geo-sequestration. Active and passive measurements have been extensively applied to map fractures across various scales. Active and passive methods have inherent advantages and limitations that complement each other. Here, in this study, to improve the mapping of embedded fractures and the surrounding geomechanically altered regions, we integrate active shear-wave transmission measurement with passive acoustic-emission measurement collected during a lab-scale hydraulic-fracturing experiment. The proposed data fusion leverages the advantages of the two modalities of measurements, while minimizing their individual limitations. Polarized shear-wave transmission (active) measurement was collected before and after the hydraulic fracturing, and the acoustic emission (passive) measurement was collected during hydraulic fracturing. Two sets of two-dimensional maps of fracture and fracture-induced damage in axial, median and frontal planes were obtained by separately processing active and passive measurements. These 2D maps are then fed to wavelet-based image fusion technique to integrate the two sources of information for the reliable mapping/imaging of the embedded fractures and the surrounding geomechanically altered regions.

58 GEOSCIENCES↗

Building a Computational and Experimental Rapid Response Pipeline to Counter the Coronavirus Disease 2019 Outbreak and Emerging Biothreats

The LDRD ER “Building a Computational and Experimental Rapid Response Pipeline to Counter the Coronavirus Disease 2019 Outbreak and Emerging Biothreats” was conceived to address a need for rapid, scalable, evaluation of computationally designed therapeutic or prophylactic antibodies and vaccine antigens, two important classes of protein medical countermeasure (MCM). This was done in complement to a computationally driven LDRD 20ERD032 “Active Learning for Rapid Design of Vaccines and Antibodies.” Natural antibodies and antigens are often insufficiently broad or robust across different pathogens and their variants. Leveraging a collaboration of simulation driven machine learning, structural expertise, and high-throughput characterization of candidate antibodies, we successfully re-targeted three different anti-SARS-CoV-1 antibodies to neutralize SARS-CoV-2 in vitro. Our antibody design work reached its most important stage in rapid response to the emergence of the Omicron variant of concern (VOC) in late 2021. In a matter of weeks, we computationally designed derivative antibodies of COV2-2130, one of two antibodies from Vanderbilt that form the basis of the AstraZeneca Evusheld prophylactic drug product. This drug product suffers a serious loss of efficacy against Omicron BA.1 and BA.1.1, the first Omicron strains. Our designs were successful, including a pair of designs which provide potent neutralization of not only Omicron BA.1 and BA.1.1, but also the earlier Delta variant, and subsequent Omicron strains including BA.2, BA.4, BA.5, and BA.2.75, demonstrating that our multi-target design process can, by its nature, produce robust antibody designs that strictly improve over the parental antibody. These results, recognized by a 2022 Director’s Science and Technology award, have enabled the follow-on GUIDE program, to commence in FY23.

59 BASIC BIOLOGICAL SCIENCES↗

WHYMSIE-SGP Field Campaign Report

Through a partnership between the U.S. National Aeronautics and Space Administration (NASA) and the National Oceanic and Atmospheric Administration (NOAA), this field campaign demonstrated first-of-its-kind hyperspectral microwave airborne measurements (Conical Scanning Millimeter-wave Imaging Radiometer [CoSMIR-H]). It was complemented by other passive (infrared, visible) and active (lidar) sensors onboard the NASA ER-2 aircraft. Serving as a future NASA planetary boundary-layer (PBL) mission prototype, the Westcoast and Heartland Hyperspectral Microwave Intensive Experiment (WH 2 yMSIE, formerly WHyMSIE) aimed to capture a wide variety of thermodynamic, moisture, and PBL regimes across a variety of surface types. The intensive operating period of the campaign spanned from October 22, 2024, through November 15, 2024, and included a large network of collaborators.

54 ENVIRONMENTAL SCIENCES↗

The detrimental ratio ( ρ ): A critical metric complementing coulombic loss for long calendar-life silicon-based lithium-ion batteries

Silicon (Si) is a promising high-capacity anode in lithium-ion batteries but suffers from chronic chemical degradation and capacity fading during calendar aging, greatly hindering its automobile applications. Electrolyte engineering currently relies on conventional evaluation criteria of reducing coulombic consumption, which implicitly presume its equivalence to irreversible capacity loss and complicates battery development. Here, we introduce the detrimental ratio p to quantify the fraction of parasitic species that permanently degrades active material. This metric is independent and crucially complements total coulombic consumption for accurate performance evaluation. We systematically investigate multiple electrolyte formulations using high-precision leakage current measurements, open-circuit-voltage experiments, and post-mortem characterizations. Although some electrolytes exhibit similarly low coulombic consumption, they diverge significantly incapacity retention and p. Especially, dimethyl-carbonate-based localized-high concentration electrolyte can synergically achieve low coulombic consumption and detrimental ratio p during calendar aging, owing to its chemically inert and structurally resilient solidelectrolyte interface with minimal isolated Si material. By contrast, increasing fluoroethylene carbonate (FEC) additive content suppresses electrolyte breakdown but suffers aggravated chemical degradation of more LixSi isolation for irreversible capacity loss with arising p. This study critically reveals that the chemistry-characteristic detrimental ratio p establishes physically informed performance evaluation to pave the way for accelerating battery development.

Calendar aging↗

Identifying Dense NiSe 2 /CoSe 2 Heterointerfaces Coupled with Surface High-Valence Bimetallic Sites for Synergistically Enhanced Oxygen Electrocatalysis

Constructing heterostructures with abundant interfaces is essential for integrating the multiple functionalities in single entities. Herein, the synthesis of NiSe 2 /CoSe 2 heterostructures with different interfacial densities via an innovative strategy of successive ion injection is reported. The resulting hybrid electrocatalyst with dense heterointerfaces exhibits superior electrocatalytic properties in an alkaline electrolyte, superior to other benchmarks and precious metal catalysts. Advanced synchrotron techniques, post structural characterizations, and density functional theory (DFT) simulations reveal that the introduction of atomic-level interfaces can lower the oxidation overpotential of bimetallic Ni and Co active sites (whereas Ni$^{2+}$ can be more easily activated than Co$^{2+}$) and induce the electronic interaction between the core selenides and surface in situ generated oxides/hydroxides, which play a critical role in synergistically reducing energetic barriers and accelerating reaction kinetics for catalyzing the oxygen evolution. Hence, the heterointerface structure facilitates the catalytic performance enhancement via increasing the intrinsic reactivity of metallic atoms and enhancing the synergistic effect between the inner selenides and surface oxidation species. This work not only complements the understanding on the origins of the activity of electrocatalysts based on metal selenides, but also sheds light on further surface and interfacial engineering of advanced hybrid materials.

36 MATERIALS SCIENCE↗

Structure and in vivo psoralen DNA crosslink repair activity of mycobacterial Nei2

Mycobacterium smegmatis Nei2 is a monomeric enzyme with AP β-lyase activity on single-stranded DNA. Expression of Nei2, and its operonic neighbor Lhr (a tetrameric 3'-to-5' helicase), is induced in mycobacteria exposed to DNA damaging agents. Here, we find that nei2 deletion sensitizes M. smegmatis to killing by DNA inter-strand crosslinker trimethylpsoralen but not to crosslinkers mitomycin C and cisplatin. By contrast, deletion of lhr sensitizes to killing by all three crosslinking agents. We report a 1.45 Å crystal structure of recombinant Nei2, which is composed of N and C terminal lobes flanking a central groove suitable for DNA binding. The C lobe includes a tetracysteine zinc complex. Mutational analysis identifies the N-terminal proline residue (Pro2 of the ORF) and Lys51, but not Glu3, as essential for AP lyase activity. We find that Nei2 has 5-hydroxyuracil glycosylase activity on single-stranded DNA that is effaced by alanine mutations of Glu3 and Lys51 but not Pro2. Testing complementation of psoralen sensitivity by expression of wild-type and mutant nei2 alleles in Δnei2 cells established that AP lyase activity is neither sufficient nor essential for crosslink repair. By contrast, complementation of psoralen sensitivity of Δlhr cells by mutant lhr alleles depended on Lhr’s ATPase/helicase activities and its tetrameric quaternary structure. The lhr–nei2 operon comprises a unique bacterial system to rectify inter-strand crosslinks.

59 BASIC BIOLOGICAL SCIENCES↗

Unravelling the origin of extended radio emission in narrow-line Seyfert 1 galaxies with the JVLA

Narrow-line Seyfert 1 galaxies (NLS1s) are believed to be active galactic nuclei (AGN) in the early stages of their evolution. Several dozen of them have been found to host relativistic jets, whilst the majority of NLS1s have not even been detected in radio, emphasising the heterogeneity of the class in this band. In this paper, our aim is to determine the predominant source of radio emission in a sample of 44 NLS1s, selected based on their extended kiloparsec-scale radio morphologies at 5.2 GHz. Here, we accomplish this by analysing their spatially resolved radio spectral index maps, centred at 5.2 GHz, as the spectral index carries information about the production mechanisms of the emission. In addition, we utilise several diagnostics based on mid-infrared emission to estimate the star formation activity of their host galaxies. These data are complemented by archival data to draw a more complete picture of each source. We find an extraordinary diversity among our sample. Approximately equal fractions (~10–12 sources) of our sources can be identified as AGN-dominated, composite, and host-dominated. Among the AGN-dominated sources are a few NLS1s with very extended jets, reaching distances of tens of kiloparsecs from the nucleus. One of these, J0814+5609, hosts the most extended jets found in an NLS1 so far. We also identify five NLS1s that could be classified as compact steep-spectrum sources. In addition, one source shows a possible kiloparsec-scale relic that reaches well outside the host galaxy as well as restarted nuclear activity, and one could belong to the sub-class of NLS1s that host relativistic jets that seem to be absorbed at lower radio frequencies (< 10 GHz). We further conclude that, due to the variety seen in NLS1s, simple proxies, such as the star formation diagnostics also employed in this paper and the radio loudness parameter, are not ideal tools for characterising NLS1s. We emphasise the necessity of examining NLS1s as individuals instead of making assumptions based on their classification. When these issues are properly taken into account, NLS1s offer an exceptional environment for studying the interplay between the host galaxy and several AGN-related phenomena, such as jets and outflows.

79 ASTRONOMY AND ASTROPHYSICS↗

Structural and functional insights into the first Bacillus thuringiensis vegetative insecticidal protein of the Vpb4 fold, active against western corn rootworm

The western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte, is a major maize pest in the United States causing significant economic loss. The emergence of field-evolved resistant WCR to Bacillus thuringiensis (Bt) traits has prompted the need to discover and deploy new insecticidal proteins in transgenic maize. In the current study we determined the crystal structure and mode of action (MOA) of the Vpb4Da2 protein (formerly known as Vip4Da2) from Bt, the first identified insecticidal Vpb4 protein with commercial level control against WCR. The Vpb4Da2 structure exhibits a six-domain architecture mainly comprised of antiparallel β-sheets organized into β-sandwich layers. The amino-terminal domains 1–3 of the protein share structural homology with the protective antigen (PA) PA14 domain and encompass a long β-pore forming loop as in the clostridial binary-toxB module. Domains 5 and 6 at the carboxyl-terminal half of Vpb4Da2 are unique as this extension is not observed in PA or any other structurally-related protein other than Vpb4 homologs. These unique Vpb4 domains adopt the topologies of carbohydrate-binding modules known to participate in receptor-recognition. Functional assessment of Vpb4Da2 suggests that domains 4–6 comprise the WCR receptor binding region and are key in conferring the observed insecticidal activity against WCR. The current structural analysis was complemented by in vitro and in vivo characterizations, including immuno-histochemistry, demonstrating that Vpb4Da2 follows a MOA that is consistent with well-characterized 3-domain Bt insecticidal proteins despite significant structural differences.

59 BASIC BIOLOGICAL SCIENCES↗

Direct selection of functional fluorescent-protein antibody fusions by yeast display

Antibodies are important reagents for research, diagnostics, and therapeutics. Many examples of chimeric proteins combining the specific target recognition of antibodies with complementing functionalities such as fluorescence, toxicity or enzymatic activity have been described. However, antibodies selected solely on the basis of their binding specificities are not necessarily ideal candidates for the construction of chimeras. Here, we describe a high throughput method based on yeast display to directly select antibodies most suitable for conversion to fluorescent chimera. A library of scFv binders was converted to a fluorescent chimeric form, by cloning thermal green protein into the linker between VH and VL, and directly selecting for both binding and fluorescent functionality. This allowed us to directly identify antibodies functional in the single chain TGP format, that manifest higher protein expression, easier protein purification, and one-step binding assays.

59 BASIC BIOLOGICAL SCIENCES↗