Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “GUT”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11

A realistic theory of E6 unification through novel intermediate symmetries

Abstract We propose a non-supersymmetric E 6 GUT with the scalar sector consisting of650⨁351′ ⨁27. Making use of the first representation for the initial symmetry breaking to an intermediate stage, and the latter two representations for second-stage breaking to the Standard Model and a realistic Yukawa sector, this theory represents the minimal E 6 GUT that proceeds through one of the intermediate stages that are novel compared to SU(5) or SO(10) GUT: trinification SU(3) C × SU(3) L × SU(3) R , SU(6) × SU(2) and flipped SO(10) × U(1). We analyze these possibilities under the choice of vacuum that preserves a ℤ 2 “spinorial parity”, which disentangles the chiral and vector-like fermions of E 6 and provides a dark matter candidate in the form of a (scalar) inert doublet. Three cases are shown to consistently unify under the extended survival hypothesis (with minimal fine-tuning): trinification symmetry SU(3) C × SU(3) L × SU(3) R with eitherLRorCRparity, and SU(6) CR × SU(2) L . Although the successful cases give a large range for proton lifetime estimates, all of them include regions consistent with current experimental bounds and within reach of forthcoming experiments. The scenario investigated in this paper essentially represents the unique (potentially) viable choice in the class of E 6 GUTs proceeding through a novel-symmetry intermediate stage, since non-minimal alternatives seem to be intrinsically non-perturbative.

Physics↗

Protecting honey bees through microbiome engineering

Honey bees are indispensable insects. Their pollination services support modern agriculture and natural ecosystems. Managed honey bee colonies face increasing threats to their survival, ranging from environmental stressors that include agrochemicals to infestations of arthropod pests and infections with microbial pathogens. Like humans, honey bees have a native gut microbiome that supports their health. However, the bee gut microbiome has a simpler composition than the gut microbiome of mammals, and its main constituent bacterial species can be easily cultured outside of the host. Furthermore, this experimental tractability and the need for new methods for protecting hive health have made honey bees a testbed for synthetic microbiomes augmented with probiotic bacteria and engineered DNA. Here, we discuss the natural benefits of bee gut bacteria, recent progress in genetically modifying these bacteria, and how symbiont-mediated RNA interference and other microbiome engineering approaches can boost bee immunity and suppress bee pathogens and parasites. Finally, we discuss how emerging methods for microbiome engineering and biocontainment could be applied to honey bees and used to address challenges in translating these proof-of-principle achievements into safe and effective technologies for field applications at scale.

Biological and medical sciences↗

Separation of life stages within anaerobic fungi (Neocallimastigomycota) highlights differences in global transcription and metabolism

Anaerobic gut fungi of the phylum Neocallimastigomycota are microbes proficient in valorizing low-cost but difficult-to-breakdown lignocellulosic plant biomass. Characterization of different fungal life stages and how they contribute to biomass breakdown are critical for biotechnological applications, yet we lack foundational knowledge about the transcriptional, metabolic, and enzyme secretion behavior of different life stages of anaerobic gut fungi: zoospores, germlings, immature thalli, and mature zoosporangia. A Miracloth-based technique was developed to enrich cell pellets with zoospores - the free-swimming, flagellated, young life stage of anaerobic gut fungi. By contrast, fungal mats contained relatively more vegetative, encysted, mature sporangia that form films. Global gene expression profiles were compared from two sample types (zoospore-enriched cell pellets vs. mature mats) harvested from the anaerobic gut fungal strain Neocallimastix californiae G1. Despite cultures being grown on glucose, the fungal zoospore-enriched samples were transcriptionally primed to encounter plant matter substrate, as evidenced by upregulation of catabolic carbohydrate-active enzymes and putative carbohydrate transporters. Furthermore, we report significant differential gene expression for gene annotation groups, including putative secondary metabolites and transcription factors. Understanding global gene expression differences between the fungal zoospore-enriched cells and mature fungi aid in characterizing fungal development, unmasking gene function, and guiding cultivation conditions and engineering targets to promote enzyme secretion.

59 BASIC BIOLOGICAL SCIENCES↗

Dark dimension and the grand unification of forces

The dark dimension scenario, predicting one extra mesoscopic dimension in the micron range, has emerged by applying various swampland principles to the dark energy. In this note we find that realizing the grand unification of gauge forces is highly constraining in this context. Without actually constructing any grand unified theory (GUT) models, we argue that the mere assumption of grand unification of forces in this scenario, together with the experimental bounds on massive replicas of the Standard Model gauge bosons, predicts an upper bound for the GUT scale, 𝑀 GUT ≲ 10 16 GeV. Combined with the experimental bound on the proton lifetime, this predicts that the 𝑋 gauge boson mediating proton decay is a 5D solitonic string of Planckian tension stretched across a length scale 𝐿 ∼ (1–10 TeV) −1 ending on gauge branes of the same diameter ∼𝐿. This leads to a mass of 𝑀 𝑋 ∼ 10 15 –10 16 GeV. In particular assuming grand unification in the dark dimension scenario results in a tower of Kaluza-Klein excitations of Standard Model gauge bosons on the gauge branes in the 1–10 TeV range. This suggests that the diameter/separation 𝐿 of the gauge branes correlates with both the weak scale ∼1/𝐿 near a TeV and the GUT scale ∼𝑀$^2_5$⁢𝐿 at 10 16 GeV.

branes↗

Supersymmetric proton decay revisited

Encouraged by the advent of a new generation of underground detectors – JUNO, DUNE and Hyper-Kamiokande – that are projected to improve significantly on the present sensitivities to various baryon decay modes, we revisit baryon decay in the minimal supersymmetric SU(5) GUT. We discuss the phenomenological uncertainties associated with hadronic matrix elements and the value of the strong coupling αs – which are the most important – the weak mixing angle θ W , quark masses including one-loop renormalization effects, quark mixing and novel GUT phases that are not visible in electroweak interaction processes. We apply our analysis to a variety of CMSSM, super- and sub-GUT scenarios in which soft supersymmetry-breaking parameters are assumed to be universal at, above and below the GUT scale, respectively. In many cases, we find that the next generation of underground detectors should be able to probe models with sparticle masses that are O(10) TeV, beyond the reach of the LHC.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Gestational exposure to HIV drugs alters intestinal mucosa-associated microbial diversity in adult rat offspring

The antiretroviral (ARV) drug combination of abacavir sulfate, dolutegravir, and lamivudine [ABC/DTG/3TC; Tri combination Anti-retroviral therapy (TC-ART)] has revolutionized HIV treatment by effectively targeting different stages of viral replication. Despite its therapeutic efficiency for maintaining low viremia in the mother during pregnancy, there are concerns for long-term liabilities in offspring that are indirectly exposed during vulnerable periods of development. The commensal microbiota plays a crucial role in maintaining overall gut health, and disruption of the microbiome is often linked to various extraintestinal effects such as immune dysregulation and inflammation. We recently reported the effects of this drug combination in altering fecal microbiome composition of aged rats perinatally exposed to ABC/DTG/3TC-ART. The fecal microbiome can provide only a snapshot of the composition of microbial community at the end of the digestive tract, which may not reflect the microbial population interacting with ileal mucosa. Thus, the current work reports the effects of this drug combination in the gut mucosa-associated microbiome of the same animals, which showed significant microbial diversity and species richness in high dose exposed female adult offspring, along with dose-dependent changes in Firmicutes/Bacteroidetes ratio. The high dose exposure also showed an increase in opportunistic bacterial species in male animals. Overall, we found that, similar to the fecal microbiome, perinatal exposure to TC-ART led to sex- and dose-dependent alterations in the gut mucosa-associated microbial population in aged rats, suggesting that early life exposure to these drugs may influence gut mucosa-associated immune responses and intestinal permeability.

Research & Experimental Medicine↗

Magnesium Oxide Reduces Anxiety-like Behavior in Mice by Inhibiting Sulfate-Reducing Bacteria

The gut microbiota–brain axis allows for bidirectional communication between the microbes in our gastrointestinal (GI) tract and the central nervous system. Psychological stress has been known to disrupt the gut microbiome (dysbiosis) leading to anxiety-like behavior. Pathogens administered into the gut have been reported to cause anxiety. Whether commensal bacteria affect the gut–brain axis is not well understood. In this study, we examined the impact of a commensal sulfate-reducing bacteria (SRB) and its metabolite, hydrogen sulfide (H2S), on anxiety-like behavior. We found that mice gavaged with SRB had increased anxiety-like behavior as measured by the open field test. We also tested the effects of magnesium oxide (MgO) on SRB growth both in vitro and in vivo using a water avoidance stress (WAS) model. We found that MgO inhibited SRB growth and H2S production in a dose-dependent fashion. Mice that underwent psychological stress using the WAS model were observed to have an overgrowth (bloom) of SRB (Deferribacterota) and increased anxiety-like behavior. However, WAS-induced overgrowth of SRB and anxiety-like behavioral effects were attenuated in animals fed a MgO-enriched diet. These findings supported a potential MgO-reversible relationship between WAS-induced SRB blooms and anxiety-like behavior.

60 APPLIED LIFE SCIENCES↗

Thirdhand cigarette smoke leads to age-dependent and persistent alterations in the cecal microbiome of mice

The gut microbiome composition is influenced by many factors including environmental exposures. Here, we investigated the effect of thirdhand cigarette smoke (THS) and exposure age on gut microbiome diversity. C57BL/6 mice were exposed to THS at human exposure relevant levels for three weeks during three different life stages: postnatal (0–3 weeks of age), pubescent (4–7 weeks of age), and adult (9–12 weeks of age), respectively. Cecal microbiome profiles were assessed at 17 weeks of age by 16S rRNA gene sequencing. We found that age at THS exposure strongly influenced the cecal microbiome composition. Although postnatal THS exposure significantly influenced the microbial composition, pubescent and adulthood exposures only had minor effects. The microbiome of postnatally THS-exposed mice significantly increased several degradation pathways that regulate glycolysis and pyruvate decarboxylation, and significantly decreased coenzyme A biosynthesis and pyrimidine deoxyribonucleoside salvage. Our results indicate that mouse postnatal development is particularly susceptible to persistent THS exposure effects on the gut microbiome.

16S rRNA gene sequencing↗

Herbivorous Fish Microbiome Adaptations to Sulfated Dietary Polysaccharides

Marine herbivorous fish that feed primarily on macroalgae, such as those from the genus Kyphosus, are essential for maintaining coral health and abundance on tropical reefs. Here, deep metagenomic sequencing and assembly of gut compartment-specific samples from three sympatric, macroalgivorous Hawaiian kyphosid species have been used to connect host gut microbial taxa with predicted protein functional capacities likely to contribute to efficient macroalgal digestion. Bacterial community compositions, algal dietary sources, and predicted enzyme functionalities were analyzed in parallel for 16 metagenomes spanning the mid- and hindgut digestive regions of wild-caught fishes. Gene colocalization patterns of expanded carbohydrate (CAZy) and sulfatase (SulfAtlas) digestive enzyme families on assembled contigs were used to identify likely polysaccharide utilization locus associations and to visualize potential cooperative networks of extracellularly exported proteins targeting complex sulfated polysaccharides. These insights into the gut microbiota of herbivorous marine fish and their functional capabilities improve our understanding of the enzymes and microorganisms involved in digesting complex macroalgal sulfated polysaccharides.

09 BIOMASS FUELS↗

Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish

ABSTRACT Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce genomic information about the microbiota that perform this degradation. This study explores the potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae through in silico study of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) from previously described Kyphosus gut metagenomes and newly sequenced bioreactor enrichments reveals differences in enzymatic capabilities between the major microbial taxa in Kyphosus guts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzyme collections able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from the Bacillota (genus Vallitalea ) and Verrucomicrobiota (order Kiritimatiellales ) highlight the importance of metabolic contributions from multiple phyla to broaden polysaccharide degradation capabilities. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level among Kyphosus symbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors. IMPORTANCE Seaweed has long been considered a promising source of sustainable biomass for bioenergy and aquaculture feed, but scalable industrial methods for decomposing terrestrial compounds can struggle to break down seaweed polysaccharides efficiently due to their unique sulfated structures. Fish of the genus Kyphosus feed on seaweed by leveraging gastrointestinal bacteria to degrade algal polysaccharides into simple sugars. This study reconstructs metagenome-assembled genomes for these gastrointestinal bacteria to enhance our understanding of herbivorous fish digestion and fermentation of algal sugars. Investigations at the gene level identify Kyphosus guts as an untapped source of seaweed-degrading enzymes ripe for further characterization. These discoveries set the stage for future work incorporating marine enzymes and microbial communities in the industrial degradation of algal polysaccharides.

59 BASIC BIOLOGICAL SCIENCES↗

Effects of Six Sequential Charged Particle Beams on Behavioral and Cognitive Performance in B6D2F1 Female and Male Mice

The radiation environment astronauts are exposed to in deep space includes galactic cosmic radiation (GCR) with different proportions of all naturally occurring ions. To assist NASA with assessment of risk to the brain following exposure to a mixture of ions broadly representative of the GCR, we assessed the behavioral and cognitive performance of female and male C57BL/6J × DBA2/J F1 (B6D2F1) mice two months following rapidly delivered, sequential 6 beam irradiation with protons (1 GeV, LET = 0.24 keV, 50%), 4 He ions (250 MeV/n, LET = 1.6 keV/μm, 20%), 16 O ions (250 MeV/n, LET = 25 keV/μm 7.5%), 28 Si ions (263 MeV/n, LET = 78 keV/μm, 7.5%), 48Ti ions (1 GeV/n, LET = 107 keV/μm, 7.5%), and 56 Fe ions (1 GeV/n, LET = 151 keV/μm, 7.5%) at 0, 25, 50, or 200 cGy) at 4–6 months of age. When the activity over 3 days of open field habituation was analyzed in female mice, those irradiated with 50 cGy moved less and spent less time in the center than sham-irradiated mice. Sham-irradiated female mice and those irradiated with 25 cGy showed object recognition. However, female mice exposed to 50 or 200 cGy did not show object recognition. When fear memory was assessed in passive avoidance tests, sham-irradiated mice and mice irradiated with 25 cGy showed memory retention while mice exposed to 50 or 200 cGy did not. The effects of radiation passive avoidance memory retention were not sex-dependent. There was no effect of radiation on depressive-like behavior in the forced swim test. There was a trend toward an effect of radiation on BDNF levels in the cortex of males, but not for females, with higher levels in male mice irradiated with 50 cGy than sham-irradiated. Finally, sequential 6-ion irradiation impacted the composition of the gut microbiome in a sex-dependent fashion. Taxa were uncovered whose relative abundance in the gut was associated with the radiation dose received. Thus, exposure to sequential six-beam irradiation significantly affects behavioral and cognitive performance and the gut microbiome.

60 APPLIED LIFE SCIENCES↗

An efficient cre‐based workflow for genomic integration and expression of large biosynthetic pathways in Eubacterium limosum

Abstract Acetogenic Clostridia are obligate anaerobes that have emerged as promising microbes for the renewable production of biochemicals owing to their ability to efficiently metabolize sustainable single‐carbon feedstocks. Additionally, Clostridia are increasingly recognized for their biosynthetic potential, with recent discoveries of diverse secondary metabolites ranging from antibiotics to pigments to modulators of the human gut microbiota. Lack of efficient methods for genomic integration and expression of large heterologous DNA constructs remains a major challenge in studying biosynthesis in Clostridia and using them for metabolic engineering applications. To overcome this problem, we harnessed chassis‐independent recombinase‐assisted genome engineering (CRAGE) to develop a workflow for facile integration of large gene clusters (>10 kb) into the human gut acetogen Eubacterium limosum . We then integrated a non‐ribosomal peptide synthetase gene cluster from the gut anaerobe Clostridium leptum , which previously produced no detectable product in traditional heterologous hosts. Chromosomal expression in E. limosum without further optimization led to production of phevalin at 2.4 mg/L. These results further expand the molecular toolkit for a highly tractable member of the Clostridia, paving the way for sophisticated pathway engineering efforts, and highlighting the potential of E. limosum as a Clostridial chassis for exploration of anaerobic natural product biosynthesis.

Sanford, Patrick A.↗

Dark Grand Unification in the axiverse: decaying axion dark matter and spontaneous baryogenesis

The quantum chromodynamics axion with a decay constant near the Grand Unification (GUT) scale has an ultralight mass near a neV. We show, however, that axion-like particles with masses near the keV–PeV range with GUT-scale decay constants are also well motivated in that they naturally arise from axiverse theories with dark c gauge groups. We demonstrate that the correct dark matter abundance may be achieved by the heavy axions in these models through the misalignment mechanism in combination with a period of early matter domination from the long-lived dark glueballs of the same gauge group. Heavy axion dark matter may decay to two photons, yielding mono-energetic electromagnetic signatures that may be detectable by current or next-generation space-based telescopes. We project the sensitivity of next-generation telescopes including Athena, AMEGO, and e-ASTROGAM to such decaying axion dark matter. If the dark sector contains multiple confining gauge groups, then the observed primordial baryon asymmetry may also be achieved in this scenario through spontaneous baryogenesis. We present explicit orbifold constructions where the dark gauge groups unify with the SM at the GUT scale and axions emerge as the fifth components of dark gauge fields with bulk Chern-Simons terms.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Challenges and physiological implications of wood feeding in termites

Termites are fascinating insects for a number of reasons, one of which being their specialization on diets of wood lignocellulose. The goal of this review is to consider stress-inducing characteristics of wood and apparent molecular-physiological adaptations in termite guts to overcome these stressors. Defensive factors present in wood include extractive secondary plant metabolites, lignin and related phenolics, crystalline cellulose, and low nitrogen content. Molecular-physiological adaptations of the termite gut to deal with these factors include robust detoxification and antioxidant machinery, the production of a peritrophic matrix and a wide range of cellulases from host and symbiotic sources, and creation of niches available to nitrogen-fixing bacterial symbionts. Considering termite gut physiology and symbioses in the context of stress-response has applied implications. Overall, these outcomes can include development of efficient biomass breakdown strategies, protection of microbes during industrial processing applications, and safeguarding wooden structures from termite damage.

54 ENVIRONMENTAL SCIENCES↗

Earthworms Exposed to Polyethylene and Biodegradable Microplastics in Soil: Microplastic Characterization and Microbial Community Analysis

While much is known about microplastics in aquatic environments, only few studies have focused on how microplastics interact with terrestrial organisms. The objective of our study was to investigate the interactions of earthworms with microplastics in a natural environment with environmentally realistic plastic concentrations. Here we investigated whether earthworms would ingest microplastics and incorporate them into their bodies and cast, and whether microplastics would alter the intestinal and soil microbiome. Lumbricus terrestris was exposed to two types of mi croplastics, biodegradable polybutylene adipate terephthalate (PBAT) and low-density polyethylene (LDPE) in mesocosoms filled with natural soil. Microplastics were mixed with poplar leaves and earthworms were allowed to forage for food for 20 days. Surface and bulk soil, earthworm cast, and earthworms themselves were sampled and analyzed for plastic content and microbial communities. Earthworms did not show macroscopic health deterioration (weight loss, vitality). We observed microplastics particles in earthworm casts and guts. Raman spectroscopy indicated that PBAT in guts and cast had degraded to some extent; however, LDPE remained unchanged among the different samples. Microbial analysis showed that soil and casts has similar microbial communities; however, they were signicantly different from the guts samples. Microplastic treatments did not result in a statistically signicant change in bacterial richness, diversity or community composition compared to controls. Taken together, our results suggest that, at environmentally realistic concentrations and short exposure times, PBAT and LDPE microplastics do not have adverse effects on Lumbricus terrestris earthworms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

The human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs. Designing precision medicine approaches that incorporate microbial metabolism would require strain- and molecule-resolved, scalable computational modeling. Here, we extend our previous resource of genome-scale metabolic reconstructions of human gut microorganisms with a greatly expanded version. AGORA2 (assembly of gut organisms through reconstruction and analysis, version 2) accounts for 7,302 strains, includes strain-resolved drug degradation and biotransformation capabilities for 98 drugs, and was extensively curated based on comparative genomics and literature searches. The microbial reconstructions performed very well against three independently assembled experimental datasets with an accuracy of 0.72 to 0.84, surpassing other reconstruction resources and predicted known microbial drug transformations with an accuracy of 0.81. We demonstrate that AGORA2 enables personalized, strain-resolved modeling by predicting the drug conversion potential of the gut microbiomes from 616 patients with colorectal cancer and controls, which greatly varied between individuals and correlated with age, sex, body mass index and disease stages. AGORA2 serves as a knowledge base for the human microbiome and paves the way to personalized, predictive analysis of host–microbiome metabolic interactions.

59 BASIC BIOLOGICAL SCIENCES↗

An integrated host-microbiome response to atrazine exposure mediates toxicity in Drosophila

Abstract The gut microbiome produces vitamins, nutrients, and neurotransmitters, and helps to modulate the host immune system—and also plays a major role in the metabolism of many exogenous compounds, including drugs and chemical toxicants. However, the extent to which specific microbial species or communities modulate hazard upon exposure to chemicals remains largely opaque. Focusing on the effects of collateral dietary exposure to the widely used herbicide atrazine, we applied integrated omics and phenotypic screening to assess the role of the gut microbiome in modulating host resilience in Drosophila melanogaster . Transcriptional and metabolic responses to these compounds are sex-specific and depend strongly on the presence of the commensal microbiome. Sequencing the genomes of all abundant microbes in the fly gut revealed an enzymatic pathway responsible for atrazine detoxification unique to Acetobacter tropicalis . We find that Acetobacter tropicalis alone, in gnotobiotic animals, is sufficient to rescue increased atrazine toxicity to wild-type, conventionally reared levels. This work points toward the derivation of biotic strategies to improve host resilience to environmental chemical exposures, and illustrates the power of integrative omics to identify pathways responsible for adverse health outcomes.

59 BASIC BIOLOGICAL SCIENCES↗

Pseudosmooth tribrid inflation in SU(5)

A realistic tribrid model of sneutrino inflation is constructed in an R-symmetric SU(5) grand unified theory (GUT). To avoid the monopole problem, a pseudosmooth inflationary trajectory is generated with the help of an additional Z 5 symmetry which is broken during and after inflation. The predictions of inflationary parameters are made at the central value of the scalar spectral index, n s =0.968. The largest possible value of the tensor to scalar ratio, r ≲ 0.0027, is obtained with sub-Planckian field values (≲m P ). A successful realization of reheating and leptogenesis is achieved by avoiding the gravitino problem with a reheat temperature as low as 10 6 GeV. The predicted range of the gauge symmetry breaking scale, 5 × 10 16 ≲ M/GeV ≲ 5 × 10 17 , turns out to be somewhat larger than the typical GUT scale. Finally, with additional vector-like families, a successful gauge coupling unification is achieved by avoiding the no-go theorem related to R-symmetric SU(5) GUT.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗