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At least 73 records · Page 4

Tonoplast Sucrose Transporter SUT4-Dependent Sugar Partitioning Modulates Phenological Transitions and Reproductive Success in Poplar

Climate uncertainty is intensifying the need for greater plasticity in carbohydrate reserve utilization to support winter survival and spring growth in woody perennials. In poplar, the single-copy SUT4, which encodes a tonoplast-localized sucrose transporter, and the SUT5/SUT6 genome duplicates, which encode plasma membrane-localized transporters, are expressed year-round, with SUT4 showing the highest expression during cool seasons. Given its role in vacuolar sucrose efflux and winter-predominant expression, SUT4 may play a key role in modulating seasonal carbohydrate dynamics. While SUT4-knockdown and knockout effects have been studied under greenhouse conditions, their impact under field conditions remains unexplored. Here, we report a field-based study comparing CRISPR knockout mutants of winter-expressed SUT4 and SUT5/SUT6 in Populus tremula x alba. We show that sut4, but not sut5/6, mutants exhibited earlier autumn leaf senescence, delayed spring bud flush, reduced stem growth, and altered sugar partitioning in winter xylem and bark relative to controls. After 2 years in the field, all genotypes flowered before leaf flush in early spring; however, sut4 mutants produced sterile ovules despite developing normal-looking catkins. Metabolic profiling revealed disrupted sucrose and raffinose dynamics in elongating sut4 catkins. This was accompanied by transcriptomic signatures of elevated stress and downregulation of proanthocyanidin biosynthesis and circadian clock genes. These findings highlight the critical role of SUT4 in coordinating sugar allocation, stress responses, and seasonal development in poplar.

09 BIOMASS FUELS↗

Data for Metabolic Engineering of Nonmodel Yeast Issatchenkia orientalis SD108 for 5-Aminolevulinic Acid Production

Biological production of 5‐aminolevulinic acid (5‐ALA) has received growing attentionover theyears.However, thereis the tradeoff between 5‐ALA biosynthesis and cell growth because the fermentation broth will become acidic due to the production of 5‐ALA. To address this limitation, we engineered an acid‐tolerant yeast, Issatchenkia orientalis SD108, for 5‐ALA production. We first discovered that the cell growth rate of I. orientalis SD108 was boosted by 5‐ALA and its endogenous ALA synthetase (ALAS) showed higher activity than those homologs from other yeasts. The titer of 5‐ALA was improved from 28mg/L to 120‐, 150‐, and 300mg/L, by optimizing plasmid design, overexpressing a transporter, and increasing gene copy number, respectively. After redirecting the metabolic flux using the pyruvate decarboxylase (PDC) knockout strain (SD108ΔPDC) and culturing with urea, we increased the titer of 5‐ALA to 510mg/L, a 13‐fold enhancement, proving the importance of the newly identified IoALAS with higher activity and the strategic selection of nitrogen sources for knockout strains. This study demonstrates the acid‐tolerant I. orientalis SD108ΔPDC has a high potential for 5‐ALA production at a large scale in the future.

Bioproducts↗

Photo- and Electro-Induced Hadron Production from Nuclei at Jefferson Laboratory

Understanding many-body knockout processes is crucial for nuclear physics, particularly in photo- and electro-induced reactions. In turn, understanding two- and three-body forces, including higher-order forces, is vital for a complete understanding of atoms. We present photo-induced many-proton knockout processes, with multiplicities from 1 to 6, using 12C, CH2, and C4H9OH targets in the g9a FROST dataset. Our analysis covers photon energies from 600 to 4500 MeV, significantly expanding current world data. Comparing our experimental data to the state-of-the-art GiBUU model offers a new challenge in the model’s theoretical description of many-body processes. GiBUU reasonably describes the data at lower photon energies but struggles at higher energies and missing masses, likely due to missing processes, such as initial 3-pion photoproduction. Our results will inform future developments in describing proton knockout processes, indicating GiBUU’s overall reasonable description of many-proton knockout data up to around 2.2 GeV. We also assess various electro-induced reactions using 2D, 12C, and 40Ar targets in the RGM dataset. Our results, obtained at electron beam energies of 2, 4, and 6 GeV, are compared in detail to GENIE and GiBUU, two widely used theory models in neutrino oscillation experiments. Discrepancies between model predictions and experimental data underscore the need for refining the two theoretical models. Despite discrepancies, GiBUU provides a more accurate modelling of electro-induced reactions, especially for 40Ar - crucial for future neutrino oscillation facilities such as DUNE. Understanding the fundamental nuclear physics involved in neutrino-nuclei interactions is essential for reducing the systematic uncertainties in extracting neutrino oscillation parameters. Many-body processes significantly contribute to the background processes observed in neutrino-nuclei interactions, hence the results from both analyses are crucial for developing the theoretical framework for the underlying nuclear physics.

Williams, Rhidian↗

New Perspectives on Spectroscopic Factor Quenching from Reactions

The evolution of single-particle strengths as the neutron-to-proton asymmetry changes informs us of the importance of short- and long-range correlations in nuclei and has therefore been extensively studied for the last two decades. Surprisingly, the strong asymmetry dependence of these strengths and their extreme values for highly asymmetric nuclei inferred from knockout reaction measurements on a target nucleus are not consistent with what is extracted from electron-induced, transfer, and quasi-free reaction data, constituting a two-decade old puzzle. This work presents the first consistent analysis of one-nucleon transfer and one-nucleon knockout data, in which theoretical uncertainties associated with the nucleon-nucleus effective interactions considered in the reaction models are quantified using a Bayesian analysis. Here, our results demonstrate that, taking into account these uncertainties, the spectroscopic strengths of loosely bound nucleons extracted from both probes agree with each other and, although there are still discrepancies for deeply bound nucleons, the slope of the asymmetry dependence of the single-particle strengths inferred from transfer and knockout reactions are consistent within 1 σ . Both probes are consistent with a small asymmetry dependence of these strengths. The uncertainties obtained in this work represent a lower bound and are already significantly larger than the original estimates.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Determination and analysis of sex ratios in heme oxygenase 1 gene targeted mouse embryos

Abstract Heme oxygenase 1 or Hmox1 enzyme is involved in catalyzing the first and rate‐limiting step in heme breakdown reactions. Many studies have reported a partial lethality of Hmox1 knockout mice obtained from heterozygous breeding pairs. Similar results were obtained in our transgenic mice colony and a sex specific bias was observed in the favor of males in the adult mice. Hmox1 independent factors which could have caused this bias were initially analyzed and it was found that those factors were not a reason behind this anomaly. Certain studies involving gene knockout hinted toward a prenatal or neonatal lethality of female knockout mice embryos or pups, respectively. In order to check if this bias was occurring in embryonic stages, that is, either if mutant female embryos were dying or if heterozygous mothers were not carrying embryos to term, we analyzed the sex‐ratios in mid‐ and late‐gestational ages (9.5–13.5 dpc and 14.5–18.5 dpc, respectively). Our results did not indicate any significant difference in the sex ratios in embryonic stages; hence, it was concluded that females are not dying in embryonic stages. It can be speculated that these deaths were probably occurring at neonatal age. More studies are required to confirm that the lack of Hmox1 gene products is the sole reason for this female lethality.

Jain, Sidhant↗

Induced protein expression in Leptospira spp. and its application to CRISPR/Cas9 mutant generation

Abstract Expanding the genetic toolkit for Leptospira spp. is a crucial step toward advancing our understanding of the biology and virulence of these atypical bacteria. Pathogenic Leptospiraare responsible for over 1 million human leptospirosis cases annually and significantly impact domestic animals. Bovine leptospirosis causes substantial financial losses due to abortion, stillbirths, and suboptimal reproductive performance. The advent of the CRISPR/Cas9 system has marked a turning point in genetic manipulation, with applications across multiple Leptospira species. However, incorporating controlled protein expression into existing genetic tools could further expand their utility. We developed and demonstrated the functionality of IPTG-inducible heterologous protein expression in Leptospira spp. This system was applied for regulated expression of dead Cas9 (dCas9) to generate knockdown mutants, and Cas9 to produce knockout mutants by inducing double-strand breaks (DSB) into desired targets. IPTG-induced dCas9 expression enabled validation of essential genes and non-coding RNAs. Additionally, IPTG-controlled Cas9 expression combined with a constitutive non-homologous end-joining (NHEJ) system allowed for successful recovery of knockout mutants, even in the absence of IPTG. These newly controlled protein expression systems will advance studies on the basic biology and virulence ofLeptospira, as well as facilitate knockout mutant generation for improved veterinary vaccines.

Science & Technology - Other Topics↗

Considering nonlocality in the optical potentials within eikonal models

Background: For its simplicity, the eikonal method is the tool of choice to analyze nuclear reactions at high energies (E > 100 MeV/nucleon), including knockout reactions. However, so far, the effective interactions used in this method are assumed to be fully local. Purpose: Given the recent studies on nonlocal optical potentials, in this work we assess whether nonlocality in the optical potentials is expected to impact reactions at high energies and then explore different avenues for extending the eikonal method to include nonlocal interactions. Method: We compare angular distributions obtained for nonlocal interactions (using the exact R-matrix approach for elastic scattering and the adiabatic distorted wave approximation for transfer) with those obtained using their local-equivalent interactions. Results: Our results show that transfer observables are significantly impacted by nonlocality in the high-energy regime. Because knockout reactions are dominated by stripping (transfer to inelastic channels), nonlocality is expected to have a large effect on knockout observables too. Three approaches are explored for extending the eikonal method to nonlocal interactions, including an iterative method and a perturbation theory. Conclusions: None of the derived extensions of the eikonal model provide a good description of elastic scattering. Here, this paper suggests that nonlocality removes the formal simplicity associated with the eikonal model.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

CRISPR/Cas9-Induced fad2 and rod1 Mutations Stacked With f ae1 Confer High Oleic Acid Seed Oil in Pennycress (Thlaspi arvense L.)

Pennycress (Thlaspi arvense L.) is being domesticated as an oilseed cash cover crop to be grown in the off-season throughout temperate regions of the world. With its diploid genome and ease of directed mutagenesis using molecular approaches, pennycress seed oil composition can be rapidly tailored for a plethora of food, feed, oleochemical and fuel uses. Here, we utilized Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 technology to produce knockout mutations in the FATTY ACID DESATURASE2 (FAD2) and REDUCED OLEATE DESATURATION1 (ROD1) genes to increase oleic acid content. High oleic acid (18:1) oil is valued for its oxidative stability that is superior to the polyunsaturated fatty acids (PUFAs) linoleic (18:2) and linolenic (18:3), and better cold flow properties than the very long chain fatty acid (VLCFA) erucic (22:1). When combined with a FATTY ACID ELONGATION1 (fae1) knockout mutation, fad2 fae1 and rod1 fae1 double mutants produced ~90% and ~60% oleic acid in seed oil, respectively, with PUFAs in fad2 fae1 as well as fad2 single mutants reduced to less than 5%. MALDI-MS spatial imaging analyses of phosphatidylcholine (PC) and triacylglycerol (TAG) molecular species in wild-type pennycress embryo sections from mature seeds revealed that erucic acid is highly enriched in cotyledons which serve as storage organs, suggestive of a role in providing energy for the germinating seedling. In contrast, PUFA-containing TAGs are enriched in the embryonic axis, which may be utilized for cellular membrane expansion during seed germination and seedling emergence. Under standard growth chamber conditions, rod1 fae1 plants grew like wild type whereas fad2 single and fad2 fae1 double mutant plants exhibited delayed growth and overall reduced heights and seed yields, suggesting that reducing PUFAs below a threshold in pennycress had negative physiological effects. Taken together, our results suggest that combinatorial knockout of ROD1 and FAE1 may be a viable route to commercially increase oleic acid content in pennycress seed oil whereas mutations in FAD2 will likely require at least partial function to avoid fitness trade-offs.

09 BIOMASS FUELS↗

Base Excision Repair: Mechanisms and Impact in Biology, Disease, and Medicine

Base excision repair (BER) corrects forms of oxidative, deamination, alkylation, and abasic single-base damage that appear to have minimal effects on the helix. Since its discovery in 1974, the field has grown in several facets: mechanisms, biology and physiology, understanding deficiencies and human disease, and using BER genes as potential inhibitory targets to develop therapeutics. Within its segregation of short nucleotide (SN-) and long patch (LP-), there are currently six known global mechanisms, with emerging work in transcription- and replication-associated BER. Knockouts (KOs) of BER genes in mouse models showed that single glycosylase knockout had minimal phenotypic impact, but the effects were clearly seen in double knockouts. However, KOs of downstream enzymes showed critical impact on the health and survival of mice. BER gene deficiency contributes to cancer, inflammation, aging, and neurodegenerative disorders. Medicinal targets are being developed for single or combinatorial therapies, but only PARP and APE1 have yet to reach the clinical stage.

5′-Gap↗

Augmentation of progestin signaling rescues testis organization and spermatogenesis in zebrafish with the depletion of androgen signaling

Disruption of androgen signaling is known to cause testicular malformation and defective spermatogenesis in zebrafish. However, knockout of cyp17a1 , a key enzyme responsible for the androgen synthesis, in ar -/- male zebrafish paradoxically causes testicular hypertrophy and enhanced spermatogenesis. Because Cyp17a1 plays key roles in hydroxylation of pregnenolone and progesterone (P4), and converts 17α-hydroxypregnenolone to dehydroepiandrosterone and 17α-hydroxyprogesterone to androstenedione, we hypothesize that the unexpected phenotype in cyp17a1 -/-; androgen receptor ( ar )-/- zebrafish may be mediated through an augmentation of progestin/nuclear progestin receptor (nPgr) signaling. In support of this hypothesis, we show that knockout of cyp17a1 leads to accumulation of 17α,20β-dihydroxy-4-pregnen-3-one (DHP) and P4. Further, administration of progestin, a synthetic DHP mimetic, is sufficient to rescue testicular development and spermatogenesis in ar -/- zebrafish, whereas knockout of npgr abolishes the rescue effect of cyp17a1 -/- in the cyp17a1 -/-; ar -/- double mutant. Analyses of the transcriptomes among the mutants with defective testicular organization and spermatogenesis ( ar -/-, ar -/-; npgr -/- and cyp17a -/-; ar -/-; npgr -/-), those with normal phenotype (control and cyp17a1 -/-), and rescued phenotype ( cyp17a1 -/-; ar -/-) reveal a common link between a downregulated expression of insl3 and its related downstream genes in cyp17a -/-; ar -/-; npgr -/- zebrafish. Taken together, our data suggest that genetic or pharmacological augmentation of the progestin/nPgr pathway is sufficient to restore testis organization and spermatogenesis in zebrafish with the depletion of androgen signaling.

Zhai, Gang↗

Forward production of protons in relativistic 12C-nucleus collisions

The production of protons in heavy ion collisions through the knockout mechanism (abrasion) is described using the Glauber model. The multiple knockouts from the projectile, including the inelastic collision series with the target, are considered using a closure approximation in treating energy conservation. Calculations for reactions of 12C projectiles with several targets at energies of 1 and 2A GeV arc compared to experiments. For large secondary proton momentum a strong dependence on the target mass is found and attributed to multiple scattering of the projectile knockouts.

NASA Discipline Radiation Health↗

Metabolic Engineering of Nonmodel Yeast Issatchenkia orientalis SD108 for 5–Aminolevulinic Acid Production

Biological production of 5-aminolevulinic acid (5-ALA) has received growing attention over the years. However, there is the tradeoff between 5-ALA biosynthesis and cell growth because the fermentation broth will become acidic due to the production of 5-ALA. To address this limitation, we engineered an acid-tolerant yeast, Issatchenkia orientalis SD108, for 5-ALA production. We first discovered that the cell growth rate of I. orientalis SD108 was boosted by 5-ALA and its endogenous ALA synthetase (ALAS) showed higher activity than those homologs from other yeasts. The titer of 5-ALA was improved from 28 mg/L to 120-, 150-, and 300 mg/L, by optimizing plasmid design, overexpressing a transporter, and increasing gene copy number, respectively. After redirecting the metabolic flux using the pyruvate decarboxylase (PDC) knockout strain (SD108ΔPDC) and culturing with urea, we increased the titer of 5-ALA to 510 mg/L, a 13-fold enhancement, proving the importance of the newly identified IoALAS with higher activity and the strategic selection of nitrogen sources for knockout strains. This study demonstrates the acid-tolerant I. orientalis SD108ΔPDC has a high potential for 5-ALA production at a large scale in the future.

59 BASIC BIOLOGICAL SCIENCES↗

The effect of a BRN 3.1 deletion on the temperature response to 2G

Researchers studied the effect of 2G exposure on body temperature in Wild type and BRN 3.1 Knockout mice to determine the feasibility to using BRN 3.1 Knockout mice as an animal model of the effects of altered gravitational fields on vestibular system physiology.

NASA Discipline Neuroscience↗

Transforming growth factor-beta1 mediates cellular response to DNA damage in situ

Transforming growth factor (TGF)-beta1 is rapidly activated after ionizing radiation, but its specific role in cellular responses to DNA damage is not known. Here we use Tgfbeta1 knockout mice to show that radiation-induced apoptotic response is TGF-beta1 dependent in the mammary epithelium, and that both apoptosis and inhibition of proliferation in response to DNA damage decrease as a function of TGF-beta1 gene dose in embryonic epithelial tissues. Because apoptosis in these tissues has been shown previously to be p53 dependent, we then examined p53 protein activation. TGF-beta1 depletion, by either gene knockout or by using TGF-beta neutralizing antibodies, resulted in decreased p53 Ser-18 phosphorylation in irradiated mammary gland. These data indicate that TGF-beta1 is essential for rapid p53-mediated cellular responses that mediate cell fate decisions in situ.

Non-NASA Center↗

Genome‐wide CRISPR‐Cas9 screen reveals a persistent null‐hyphal phenotype that maintains high carotenoid production in Yarrowia lipolytica

Abstract Yarrowia lipolytica is a metabolic engineering host of growing industrial interest due to its ability to metabolize hydrocarbons, fatty acids, glycerol, and other renewable carbon sources. This dimorphic yeast undergoes a stress‐induced transition to a multicellular hyphal state, which can negatively impact biosynthetic activity, reduce oxygen and nutrient mass transfer in cell cultures, and increase culture viscosity. Identifying mutations that prevent the formation of hyphae would help alleviate the bioprocess challenges that they create. To this end, we conducted a genome‐wide CRISPR screen to identify genetic knockouts that prevent the transition to hyphal morphology. The screen identified five mutants with a null‐hyphal phenotype— ΔRAS2 , ΔRHO5 , ΔSFL1 , ΔSNF2 , and ΔPAXIP1 . Of these hits, only ΔRAS2 suppressed hyphal formation in an engineered lycopene production strain over a multiday culture. The RAS2 knockout was also the only genetic disruption characterized that did not affect lycopene production, producing more than 5 mg L −1 OD −1 from a heterologous pathway with enhanced carbon flux through the mevalonate pathway. These data suggest that a ΔRAS2 mutant of Y. lipolytica could prove useful in engineering a metabolic engineering host of the production of carotenoids and other biochemicals.

59 BASIC BIOLOGICAL SCIENCES↗

Treatment of cholinergic‐induced status epilepticus with polytherapy targeting GABA and glutamate receptors

Abstract Despite new antiseizure medications, the development of cholinergic‐induced refractory status epilepticus (RSE) continues to be a therapeutic challenge as pharmacoresistance to benzodiazepines and other antiseizure medications quickly develops. Studies conducted by Epilepsia . 2005;46:142 demonstrated that the initiation and maintenance of cholinergic‐induced RSE are associated with trafficking and inactivation of gamma‐aminobutyric acid A receptors (GABA A R) thought to contribute to the development of benzodiazepine pharmacoresistance. In addition, Dr. Wasterlain's laboratory reported that increased N‐methyl‐ d ‐aspartate receptors (NMDAR) and alpha‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid receptors (AMPAR) contribute to enhanced glutamatergic excitation ( Neurobiol Dis . 2013;54:225; Epilepsia . 2013;54:78). Thus, Dr. Wasterlain postulated that targeting both maladaptive responses of reduced inhibition and increased excitation that is associated with cholinergic‐induced RSE should improve therapeutic outcome. We currently review studies in several animal models of cholinergic‐induced RSE that demonstrate that benzodiazepine monotherapy has reduced efficacy when treatment is delayed and that polytherapy with drugs that include a benzodiazepine (eg midazolam and diazepam) to counter loss of inhibition, concurrent with an NMDA antagonist (eg ketamine) to reduce excitation provide improved efficacy. Improved efficacy with polytherapy against cholinergic‐induced seizure is demonstrated by reduction in (1) seizure severity, (2) epileptogenesis, and (3) neurodegeneration compared with monotherapy. Animal models reviewed include pilocarpine‐induced seizure in rats, organophosphorus nerve agent (OPNA)‐induced seizure in rats, and OPNA‐induced seizure in two mouse models: (1) carboxylesterase knockout (Es1 −/− ) mice which, similarly to humans, lack plasma carboxylesterase and (2) human acetylcholinesterase knock‐in carboxylesterase knockout (KIKO) mice. We also review studies showing that supplementing midazolam and ketamine with a third antiseizure medication (valproate or phenobarbital) that targets a nonbenzodiazepine site rapidly terminates RSE and provides further protection against cholinergic‐induced SE. Finally, we review studies on the benefits of simultaneous compared with sequential drug treatments and the clinical implications that lead us to predict improved efficacy of early combination drug therapies. The data generated from seminal rodent studies of efficacious treatment of cholinergic‐induced RSE conducted under Dr. Wasterlain's guidance suggest that future clinical trials should treat the inadequate inhibition and temper the excess excitation that characterize RSE and that early combination therapies may provide improved outcome over benzodiazepine monotherapy.

59 BASIC BIOLOGICAL SCIENCES↗

First measurement of differential cross sections for muon neutrino charged current interactions on argon with a two-proton final state using the MicroBooNE detector

We present the first measurement of differential cross sections for charged-current muon neutrino interactions on argon with one muon, two protons, and no pions in the final state. These final states are dominated by two-nucleon knockout interactions, which are complicated to model and for which there is currently limited information about the characteristics of these interactions in existing neutrino-nucleus scattering data. Detailed investigations of two-nucleon knockout are vital to support upcoming experiments exploring the nature of the neutrino. Among the different kinematic quantities measured, the opening angle between the two protons, the angle between the total proton momentum and the muon, and the total transverse momentum of the final state system are most sensitive to the underlying physics processes as embodied in various theoretical models.

2-particle 2-hole states↗

HAND transcription factors cooperatively specify the aorta and pulmonary trunk

Congenital heart defects (CHDs) affecting the cardiac outflow tract (OFT) constitute a significant cause of morbidity and mortality. The OFT develops from migratory cell populations which include the cardiac neural crest cells (cNCCs) and secondary heart field (SHF) derived myocardium and endocardium. The related transcription factors HAND1 and HAND2 have been implicated in human CHDs involving the OFT. Although Hand1 is expressed within the OFT, Hand1 NCC-specific conditional knockout mice (H1CKOs) are viable. Here we show that these H1CKOs present a low penetrance of OFT phenotypes, whereas SHF-specific Hand1 ablation does not reveal any cardiac phenotypes. Further, HAND1 and HAND2 appear functionally redundant within the cNCCs, as a reduction/ablation of Hand2 on an NCC-specific H1CKO background causes pronounced OFT defects. Double conditional Hand1 and Hand2 NCC knockouts exhibit persistent truncus arteriosus (PTA) with 100% penetrance. NCC lineage-tracing and Sema3c in situ mRNA expression reveal that Sema3c-expressing cells are mis-localized, resulting in a malformed septal bridge within the OFTs of H1CKO;H2CKO embryos. Interestingly, Hand1 and Hand2 also genetically interact within the SHF, as SHF H1CKOs on a heterozygous Hand2 background exhibit Ventricular Septal Defects (VSDs) with incomplete penetrance. Previously, we identified a BMP, HAND2, and GATA-dependent Hand1 OFT enhancer sufficient to drive reporter gene expression within the nascent OFT and aorta. Using these transcription inputs as a probe, we identify a novel Hand2 OFT enhancer, suggesting that a conserved BMP-GATA dependent mechanism transcriptionally regulates both HAND factors. These findings support the hypothesis that HAND factors interpret BMP signaling within the cNCCs to cooperatively coordinate OFT morphogenesis.

59 BASIC BIOLOGICAL SCIENCES↗