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Neutrino experiments entering the precision era like DUNE, NOνA, T2K, and others rely heavily on the microscopic modeling of neutrino nucleus interactions for the extraction of neutrino oscillation parameters.
Giant kelp (Macrocystis pyrifera) is a paramount species of immense ecological and economic importance. It forms dense underwater forests, providing crucial habitat and serving as a foundation species for diverse marine ecosystems. Understanding the genetics of giant kelp is essential for conservation and sustainable farming, safeguarding these valuable ecosystems and their benefits. By analyzing mutations based on their impact, we can gain insights into the potential functional consequences and implications for the organism, helping to identify critical genes or regions that may play a significant role in adaptation, development, and environmental response. To achieve this, we annotated the effects and impact of spontaneous mutations in 559 giant kelp individuals from four different populations. We found over 15.9 million mutations in genes of giant kelp, and classified them into modifier, low, moderate, and high impact depending on their predicted effects. The creation of this mutation effect database, attached to the seedbank of these individuals, offers several applications, including enhancing breeding programs, aiding genetic engineering with naturally occurring mutations, and developing strategies to mitigate the impact of environmental changes.
In neutrino event generators, for models for neutrino and electron scattering only inclusive cross sections are implemented. When these models are used to describe a semi-inclusive cross section, the event generator attaches the hadron variables based on some assumptions. In this work we compare the nucleon kinematics given by the method used in the GENIE event generator, e.g. in the implementation of the SuSAv2 model, to a fully unfactorized calculation using the relativistic distorted wave impulse approximation (RDWIA). We focus on kinematics relevant to the $e4\nu$ analysis and show that observables obtained with RDWIA differ significantly from those of the approximate method used in GENIE, the latter should be considered unrealistic.
To enable an accurate determination of oscillation parameters, accelerator-based neutrino experiments require detailed simulations of nuclear interaction physics in the GeV regime. While substantial effort from both theory and experiment is currently being invested to improve the fidelity of these simulations, their present deficiencies typically oblige experimental collaborations to resort to empirical tuning of simulation model parameters. As the precision requirements of the field continue to become more stringent, machine learning techniques may provide a powerful means of handling corresponding growth in the complexity of future neutrino interaction model tuning exercises. To study the suitability of simulation-based inference (SBI) for this physics application, in this paper we revisit a tuned configuration of the GENIE neutrino event generator that was originally developed by the MicroBooNE collaboration. Despite closely reproducing the adopted values of four physics parameters when confronted with the tuned cross-section predictions as input, we find that our trained SBI algorithm prefers modestly different values (within MicroBooNE's assigned uncertainties) and achieves slightly better goodness-of-fit when inference is run on the experimental data set originally used by MicroBooNE. We also find that our trained algorithm can create a fair approximation of an alternative neutrino scattering simulation, NuWro, that shares only a subset of its physics model parameters with GENIE.
Genetic compensation has been proposed to explain phenotypic differences between gene knockouts and knockdowns in several metazoan and plant model systems. With the rapid development of reverse genetic tools such as CRISPR/Cas9 and RNAi in microalgae, it is increasingly important to assess whether genetic compensation affects the phenotype of engineered algal mutants. While exploring triacylglycerol (TAG) biosynthesis pathways in the model alga Chlamydomonas reinhardtii, it was discovered that knockout of certain genes catalyzing rate-limiting steps of TAG biosynthesis, type-2 diacylglycerol acyltransferase genes (DGTTs), triggered genetic compensation under abiotic stress conditions. Genetic compensation of a DGTT1 null mutation by a related PDAT gene was observed regardless of the strain background or mutagenesis approach, for example, CRISPR/Cas 9 or insertional mutagenesis. However, no compensation was found in the PDAT knockout mutant. The effect of PDAT knockout was evaluated in a Δvtc1 mutant, in which PDAT was upregulated under stress, resulting in a 90% increase in TAG content. Knockout of PDAT in the Δvtc1 background induced a 12.8-fold upregulation of DGTT1 and a 272.3% increase in TAG content in Δvtc1/pdat1 cells, while remaining viable. These data suggest that genetic compensation contributes to the genetic robustness of microalgal TAG biosynthetic pathways, maintaining lipid and redox homeostasis in the knockout mutants under abiotic stress. This work demonstrates examples of genetic compensation in microalgae, implies the physiological relevance of genetic compensation in TAG biosynthesis under stress, and provides guidance for future genetic engineering and mutant characterization efforts.
Highlights: • Protein 4.1R knockout promoted the proliferation, migration, and invasion of B16 cells. • Protein 4.1R knockout induced a decrease expression of 5-ALA transporters GAT-1 and GAT-2. • Protein 4.1R knockout reduced the effect of PDT and downregulated the anti-tumor immune response induced by PDT. Melanoma is the most aggressive malignant tumor of skin cancer as it can grow rapidly and metastasize. Photodynamic therapy (PDT) is a promising cancer ablation method for skin tumors, although it lacks efficiency owing to factors such as tumor characteristics, delivery of photosensitizers, immune response in vivo etc. Extensive investigation of molecules that can potentially modulate treatment efficacy is required. Protein 4.1R is a cytoskeletal protein molecule. Previous studies have shown that protein 4.1R knockdown reduces PDT sensitivity in mouse embryonic fibroblast cells. However, the functional role of protein 4.1R in melanoma is unclear. In this study, we aimed to elucidate the effect of protein 4.1R on PDT for melanoma in mice and the mechanism of anti-tumor immunity. Our results indicated that CRISPR/Cas9-mediated protein 4.1R knockout promotes the proliferation, migration, and invasion of B16 cells. We further investigated the potential mechanism of protein 4.1R on tumor cell PDT sensitivity. Our results showed that protein 4.1R knockout reduced the expression of membrane transporters γ-aminobutyric acid transporter (GAT)-1 and (GAT)-2 in B16 cells, which affected 5-ALA transmembrane transport and reduced the efficiency of PDT on B16 cells. Protein 4.1R knockout downregulated the anti-tumor immune response triggered by PDT in vivo. In conclusion, our data suggest that protein 4.1R is an important regulator in PDT for tumors and may promote the progress and efficacy of melanoma treatment.
Highlights: • Protein 4.1R knockout reduced the phagocytosis of M2 macrophages. • Co-culture with 4.1R knockout M2 macrophages enhances the malignancy of colon cancer. • Protein 4.1R knockout upregulates vascular endothelial growth factor A secreted by M2 macrophages. • Protein 4.1R knockout activates the PI3K/AKT signaling pathway and promotes the progression of colon cancer. M2 macrophages are crucial components of the tumour microenvironment and have been shown to be closely related to tumour progression. Co-culture with 4.1R{sup −/−} M2 macrophages enhances the malignancy of colon cancer (CC), but the mechanism remains unclear. Here, we report that protein 4.1R knockout reduced the phagocytosis of M2 macrophages (M-CSF/IL-4-treated bone marrow cells) and promoted MC38 colon cancer cell proliferation, migration, invasion, tumour formation and epithelial-mesenchymal transition (EMT), which are regulated by M2 macrophages. Further mechanistic dissection revealed that the 4.1R knockout upregulated vascular endothelial growth factor A (VEGFA) secreted by M2 macrophages and promoted colon cancer progression by activating the PI3K/AKT signalling pathway. In summary, our present study identified that 4.1R downregulates VEGFA secretion in M2 macrophages and delays the malignant potential of colon cancer by inhibiting the PI3K/AKT signalling pathway.
Abstract Xylan is the predominant hemicellulose in the primary cell walls of grasses, but its synthesis and interactions with other wall polysaccharides are complex and incompletely understood. To probe xylan biosynthesis, we generated CRISPR/Cas9 knockout and amiRNA knockdown lines of BdGT43B2 , an ortholog of the wheat TaGT43‐4 xylan synthase scaffolding protein in the IRX14 clade, in Brachypodium distachyon . Knockout of BdGT43B2 caused stunting and premature death in Brachypodium seedlings. Immunofluorescence labeling of xylans was greatly reduced in homozygous knockout BdGT43B2 mutants, whereas cellulose labeling was unchanged or slightly increased. Biochemical analysis showed reductions in digestible xylan in knockout mutant walls, and cell size was smaller in knockout leaves. BdGT43B2 knockdown plants appeared morphologically normal as adults, but showed slight reductions in seedling growth and small decreases in xylose content in isolated cell walls. Immunofluorescence labeling of xylan and cellulose staining was both reduced in BdGT43B2 knockdown plants. Together, these data indicate that BdGT43B2 functions in the synthesis of a form of xylan that is required for seedling growth and survival in Brachypodium distachyon .
ABSTRACT Leptospirosis, caused by pathogenic bacteria from the genusLeptospira, is a global zoonosis responsible for more than one million human cases and 60,000 deaths annually. The disease also affects many domestic animal species. Historically, genetic manipulation ofLeptospirahas been difficult to perform, resulting in limited knowledge on pathogenic mechanisms of disease and the identification of virulence factors. The application of CRISPR/Cas9 and its variations have helped fill these gaps but the generation of knockout mutants remains challenging because double-strand breaks (DSBs) inflicted by Cas9 nuclease are lethal toLeptospiracells. The novel CRISPR prime editing (PE) strategy is the first precise genome-editing technology that allows deletions, insertions, and base substitutions without introducing DSBs. This revolutionary technique utilizes a nickase Cas9 that cleaves a single strand of DNA, coupled with an engineered reverse transcriptase and a modified single-guide RNA (termed prime editing guide RNA) containing an extended 3′ end with the desired edits. We demonstrate the application of CRISPR-PE in both saprophytic and pathogenicLeptospirafrom multiple species and serovars by introducing deletions or insertions into target DNA with a remarkable precision of just one nucleotide. Additionally, we demonstrate the ability to genetically manipulateLeptospira borgpetersenii, a prevalent pathogenic species of humans, domestic cattle, and wildlife animals. Rapid plasmid loss by mutated strains in liquid culture allows for the generation of knockout strains without selective markers, which can be readily used to elucidate virulence factors and develop optimized bacterin and/or live vaccines against leptospirosis. IMPORTANCE Leptospirosis is a geographically widespread bacterial zoonosis. Genetic manipulation of pathogenicLeptospiraspp. has been laborious and difficult to perform, limiting our ability to understand how leptospires cause disease. The application of the CRISPR/Cas9 system toLeptospiraenhanced our ability to generate knockdown and knockout mutants; however, the latter remains challenging. Here, we demonstrate the application of the CRISPR prime editing technique inLeptospira, allowing the generation of knockout mutants in several pathogenic species, with mutations comprising just a single nucleotide resolution. Notably, we generated a mutant in theLeptospira borgpeterseniibackground, a prevalent pathogenic species of humans and cattle. Our application of this method opens new avenues for studying pathogenic mechanisms ofLeptospiraand the identification of virulence factors across multiple species. These methods can also be used to facilitate the generation of marker-less knockout strains for updated and improved bacterin and/or live vaccines.
The difference in the proton and neutron separation energies (ΔS) of the weakly bound 15 C ground state is -19.86 MeV, an extreme value. Data from intermediate-energy heavy-ion induced (HI-induced) knockout reactions on nuclei spanning -20 ≲ ΔS ≲ +20 MeV, suggest that the degree to which single-particle strength is quenched, R s , has a negative correlation with ΔS, decreasing from unity around -20 MeV to around 0.2 at +20 MeV. For the 15 C ground state (R s = 0.96 (4) in HI-induced knockout), contrasting results have recently been obtained via the neutron-adding transfer reaction, which reveal a value of R s = 0.64 (15), similar to the value observed at modest and more extreme values of ΔS with reaction probes other than HI knockout. In order to explore the any potential differences between adding and removing processes in transfer reactions at extreme ΔS, single-neutron removal transfer reactions on 15 C were performed at 7.1 MeV/u in inverse kinematics. The removal of a valence neutron in 2s 1/2 orbit using both (p, d) and (d, t) reactions shows consistent quenching factors and agrees with those from the neutron-adding reaction. The present results, which can be compared with neutron knockout reaction, suggest that correlations, represented by the quenching factor, show limited dependence on neutron-proton asymmetry under the most extreme asymmetry conditions so far achieved in transfer reactions.
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.
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.
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.
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.
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.
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.
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.
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.