SnapShot: Fanconi anemia and associated proteins.

Fanconi anemia is a genetic disorder resulting from biallelic mutations in one of the 17 FANC genes. It is characterized by congenital abnormalities, bone marrow failure, and cancer predisposition. The underlying cause is genomic instability resulting from the deficiency in replication-dependent DNA interstrand crosslink repair pathway commonly referred to as the Fanconi anemia-BRCA pathway. This SnapShot presents the key factors involved.

Distinct roles of BRCA2 in replication fork protection in response to hydroxyurea and DNA interstrand cross-links.

DNA interstrand cross-links (ICLs) are a form of DNA damage that requires the interplay of a number of repair proteins including those of the Fanconi anemia (FA) and the homologous recombination (HR) pathways. Pathogenic variants in the essential gene BRCA2/FANCD1, when monoallelic, predispose to breast and ovarian cancer, and when biallelic, result in a severe subtype of Fanconi anemia. BRCA2 function in the FA pathway is attributed to its role as a mediator of the RAD51 recombinase in HR repair of programmed DNA double-strand breaks (DSB). BRCA2 and RAD51 functions are also required to protect stalled replication forks from nucleolytic degradation during response to hydroxyurea (HU). While RAD51 has been shown to be necessary in the early steps of ICL repair to prevent aberrant nuclease resection, the role of BRCA2 in this process has not been described. Here, based on the analysis of BRCA2 DNA-binding domain (DBD) mutants (c.8488-1G>A and c.8524C>T) discovered in FA patients presenting with atypical FA-like phenotypes, we establish that BRCA2 is necessary for the protection of DNA at ICLs. Cells carrying BRCA2 DBD mutations are sensitive to ICL-inducing agents but resistant to HU treatment consistent with relatively high HR repair in these cells. BRCA2 function at an ICL protects against DNA2-WRN nuclease-helicase complex and not the MRE11 nuclease that is implicated in the resection of HU-induced stalled replication forks. Our results also indicate that unlike the processing at HU-induced stalled forks, the function of the SNF2 translocases (SMARCAL1, ZRANB3, or HLTF), implicated in fork reversal, are not an integral component of the ICL repair, pointing to a different mechanism of fork protection at different DNA lesions.

A comparative genomics examination of desiccation tolerance and sensitivity in two sister grass species.

Desiccation tolerance is an ancient and complex trait that spans all major lineages of life on earth. Although important in the evolution of land plants, the mechanisms that underlay this complex trait are poorly understood, especially for vegetative desiccation tolerance (VDT). The lack of suitable closely related plant models that offer a direct contrast between desiccation tolerance and sensitivity has hampered progress. We have assembled high-quality genomes for two closely related grasses, the desiccation-tolerant Sporobolus stapfianus and the desiccation-sensitive Sporobolus pyramidalis Both species are complex polyploids; S. stapfianus is primarily tetraploid, and S. pyramidalis is primarily hexaploid. S. pyramidalis undergoes a major transcriptome remodeling event during initial exposure to dehydration, while S. stapfianus has a muted early response, with peak remodeling during the transition between 1.5 and 1.0 grams of water (gH2O) g-1 dry weight (dw). Functionally, the dehydration transcriptome of S. stapfianus is unrelated to that for S. pyramidalis A comparative analysis of the transcriptomes of the hydrated controls for each species indicated that S. stapfianus is transcriptionally primed for desiccation. Cross-species comparative analyses indicated that VDT likely evolved from reprogramming of desiccation tolerance mechanisms that evolved in seeds and that the tolerance mechanism of S. stapfianus represents a recent evolution for VDT within the Chloridoideae. Orthogroup analyses of the significantly differentially abundant transcripts reconfirmed our present understanding of the response to dehydration, including the lack of an induction of senescence in resurrection angiosperms. The data also suggest that failure to maintain protein structure during dehydration is likely critical in rendering a plant desiccation sensitive.

The generality of cryptic dietary niche differences in diverse large-herbivore assemblages.

Ecological niche differences are necessary for stable species coexistence but are often difficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth forms but are agnostic toward food plant species identity. Empirical support for these models is variable, suggesting that additional mechanisms of resource partitioning may be important in sustaining large-herbivore diversity in African savannas. We used DNA metabarcoding to conduct a taxonomically explicit analysis of large-herbivore diets across southeastern Africa, analyzing ∼4,000 fecal samples of 30 species from 10 sites in seven countries over 6 y. We detected 893 food plant taxa from 124 families, but just two families-grasses and legumes-accounted for the majority of herbivore diets. Nonetheless, herbivore species almost invariably partitioned food plant taxa; diet composition differed significantly in 97% of pairwise comparisons between sympatric species, and dissimilarity was pronounced even between the strictest grazers (grass eaters), strictest browsers (nongrass eaters), and closest relatives at each site. Niche differentiation was weakest in an ecosystem recovering from catastrophic defaunation, indicating that food plant partitioning is driven by species interactions, and was stronger at low rainfall, as expected if interspecific competition is a predominant driver. Diets differed more between browsers than grazers, which predictably shaped community organization: Grazer-dominated trophic networks had higher nestedness and lower modularity. That dietary differentiation is structured along taxonomic lines complements prior work on how herbivores partition plant parts and patches and suggests that common mechanisms govern herbivore coexistence and community assembly in savannas.

Grazing herbivores reduce herbaceous biomass and fire activity across African savannas.

Fire and herbivory interact to alter ecosystems and carbon cycling. In savannas, herbivores can reduce fire activity by removing grass biomass, but the size of these effects and what regulates them remain uncertain. To examine grazing effects on fuels and fire regimes across African savannas, we combined data from herbivore exclosure experiments with remotely sensed data on fire activity and herbivore density. We show that, broadly across African savannas, grazing herbivores substantially reduce both herbaceous biomass and fire activity. The size of these effects was strongly associated with grazing herbivore densities, and surprisingly, was mostly consistent across different environments. A one-zebra increase in herbivore biomass density (~100 kg/km2 of metabolic biomass) resulted in a ~53 kg/ha reduction in standing herbaceous biomass and a ~0.43 percentage point reduction in burned area. Our results indicate that fire models can be improved by incorporating grazing effects on grass biomass.

Syntrichia ruralis: emerging model moss genome reveals a conserved and previously unknown regulator of desiccation in flowering plants.

Water scarcity, resulting from climate change, poses a significant threat to ecosystems. Syntrichia ruralis, a dryland desiccation-tolerant moss, provides valuable insights into survival of water-limited conditions. We sequenced the genome of S. ruralis, conducted transcriptomic analyses, and performed comparative genomic and transcriptomic analyses with existing genomes and transcriptomes, including with the close relative S. caninervis. We took a genetic approach to characterize the role of an S. ruralis transcription factor, identified in transcriptomic analyses, in Arabidopsis thaliana. The genome was assembled into 12 chromosomes encompassing 21 169 protein-coding genes. Comparative analysis revealed copy number and transcript abundance differences in known desiccation-associated gene families, and highlighted genome-level variation among species that may reflect adaptation to different habitats. A significant number of abscisic acid (ABA)-responsive genes were found to be negatively regulated by a MYB transcription factor (MYB55) that was upstream of the S. ruralis ortholog of ABA-insensitive 3 (ABI3). We determined that this conserved MYB transcription factor, uncharacterized in Arabidopsis, acts as a negative regulator of an ABA-dependent stress response in Arabidopsis. The new genomic resources from this emerging model moss offer novel insights into how plants regulate their responses to water deprivation.

First Dark Matter Search Results from the LUX-ZEPLIN (LZ) Experiment.

The LUX-ZEPLIN experiment is a dark matter detector centered on a dual-phase xenon time projection chamber operating at the Sanford Underground Research Facility in Lead, South Dakota, USA. This Letter reports results from LUX-ZEPLIN's first search for weakly interacting massive particles (WIMPs) with an exposure of 60 live days using a fiducial mass of 5.5 t. A profile-likelihood ratio analysis shows the data to be consistent with a background-only hypothesis, setting new limits on spin-independent WIMP-nucleon, spin-dependent WIMP-neutron, and spin-dependent WIMP-proton cross sections for WIMP masses above 9 GeV/c^{2}. The most stringent limit is set for spin-independent scattering at 36 GeV/c^{2}, rejecting cross sections above 9.2×10^{-48} cm at the 90% confidence level.

Racial/Ethnic Variability in Use of General Anesthesia for Pediatric Magnetic Resonance Imaging.

BACKGROUND: Children increasingly undergo diagnostic imaging procedures, sometimes with general anesthesia (GA). It is unknown whether the use of GA differs by race/ethnicity among children undergoing magnetic resonance imaging (MRI) scans. METHODS: This is a retrospective cohort study of GA use for pediatric patients from 0 to 21 years of age who underwent MRIs from January 1, 2004 to May 31, 2019. The study sample was stratified into 5 age groups: 0 to 1, 2 to 5, 6 to 11, 12 to 18, and 19 to 21. Analysis was performed separately for each age group. RESULTS: Among 457,314 MRI patients, 29,108 (6.4%) had GA. In the adjusted regression models, Asian patients aged 0 to 1 (adjusted relative risk [aRR] [95% confidence interval {CI}] of 1.11 [1.05-1.17], P < .001) and aged 2 to 5 (aRR [95% CI], 1.04 [1.00-1.09], P = .03), Black patients aged 2 to 5 (aRR [95% CI], 1.04 [1.01-1.08], P = .02) and aged 6 to 11 (aRR [95% CI], 1.13 [1.06-1.20], P < .001), and Hispanic patients aged 0 to 1 (aRR [95% CI], 1.07 [1.03-1.12], P < .001) were more likely to receive GA for MRIs than White patients. CONCLUSIONS: Asian, Black, and Hispanic children of some ages were more likely to receive GA during MRI scans than White children in the same age group. Future research is warranted to delineate whether this phenomenon signifies disparate care for children based on their race/ethnicity.

Health Care Burden Associated With Adolescent Prolonged Opioid Use After Surgery.

BACKGROUND: Prolonged opioid use after surgery (POUS), defined as the filling of at least 1 opioid prescription filled between 90 and 180 days after surgery, has been shown to increase health care costs and utilization in adult populations. However, its economic burden has not been studied in adolescent patients. We hypothesized that adolescents with POUS would have higher health care costs and utilization than non-POUS patients. METHODS: Opioid-naive patients 12 to 21 years of age in the United States who received outpatient prescription opioids after surgery were identified from insurance claim data from the Optum Clinformatics Data Mart Database from January 1, 2003, to June 30, 2019. The primary outcomes were total health care costs and visits in the 730-day period after the surgical encounter in patients with POUS versus those without POUS. Multivariable regression analyses were used to determine adjusted health care cost and visit differences. RESULTS: A total of 126,338 unique patients undergoing 132,107 procedures were included in the analysis, with 4867 patients meeting criteria for POUS for an incidence of 3.9%. Adjusted mean total health care costs in the 730 days after surgery were $4604 (95% confidence interval [CI], $4027-$5181) higher in patients with POUS than that in non-POUS patients. Patients with POUS had increases in mean adjusted inpatient length of stay (0.26 greater [95% CI, 0.22-0.30]), inpatient visits (0.07 greater [95% CI, 0.07-0.08]), emergency visits (0.96 greater [95% CI, 0.89-1.03]), and outpatient/other visits (5.78 greater [95% CI, 5.37-6.19]) in the 730 days after surgery ( P < .001 for all comparisons). CONCLUSIONS: In adolescents, POUS was associated with increased total health care costs and utilization in the 730 days after their surgical encounter. Given the increased health care burden associated with POUS in adolescents, further investigation of preventative measures for high-risk individuals and additional study of the relationship between opioid prescription and outcomes may be warranted.

Fasciitis ossificans: imaging features, histology, and differential diagnosis.

AIM: To describe the imaging features of fasciitis ossificans and its histopathological features. MATERIALS AND METHODS: Using a word search of existing pathology reports at the Mayo Clinic, six cases of fasciitis ossificans were identified. The clinical history, histology, and available imaging of the affected area were reviewed. RESULTS: Imaging consisted of radiographs, mammograms, ultrasound images, bone scintigraphs, computed tomography (CT), and magnetic resonance imaging (MRI) images. All cases demonstrated a soft-tissue mass. The characteristic MRI appearance was a T2 hyperintense enhancing mass with surrounding soft-tissue oedema. Peripheral calcifications were seen on radiographs, CT, and/or ultrasound. Histological sections showed distinct zonation, with nodular fasciitis-like zones of myofibroblastic proliferation, which merged with osteoblasts that rim the ill-defined trabeculae of woven bone and became continuous with the mature lamellar bone surrounded by a thin layer of compressed fibrous tissue. CONCLUSION: Imaging features of fasciitis ossificans are that of an enhancing soft-tissue mass located within a fascial plane with prominent surrounding oedema and mature peripheral calcification. Imaging and histology are that of myositis ossificans but occurring within the fascia. It is important that radiologists are aware of the diagnosis of fasciitis ossificans and appreciate its similarity to myositis ossificans. This is particularly important in anatomical locations with fascias but no muscle. Given the radiographic and histological overlap between these entities, nomenclature that encompasses both could be considered in the future.

A Dominant Mutation in Human RAD51 Reveals Its Function in DNA Interstrand Crosslink Repair Independent of Homologous Recombination.

Repair of DNA interstrand crosslinks requires action of multiple DNA repair pathways, including homologous recombination. Here, we report a de novo heterozygous T131P mutation in RAD51/FANCR, the key recombinase essential for homologous recombination, in a patient with Fanconi anemia-like phenotype. In vitro, RAD51-T131P displays DNA-independent ATPase activity, no DNA pairing capacity, and a co-dominant-negative effect on RAD51 recombinase function. However, the patient cells are homologous recombination proficient due to the low ratio of mutant to wild-type RAD51 in cells. Instead, patient cells are sensitive to crosslinking agents and display hyperphosphorylation of Replication Protein A due to increased activity of DNA2 and WRN at the DNA interstrand crosslinks. Thus, proper RAD51 function is important during DNA interstrand crosslink repair outside of homologous recombination. Our study provides a molecular basis for how RAD51 and its associated factors may operate in a homologous recombination-independent manner to maintain genomic integrity.

New Theory Illustrates the Formation of Enamel CUP-Shaped Lesions on Occlusal Surfaces.

We propose a new theory for enamel cupping lesions formation. At early stages, naturally formed cupping lesions showed increased porosity at two structural prismatic traits: the central cone extending into the enamel-dentine junction and the type-I Hunther-Schreger bands (HSB), suggesting them to be the main drivers for cupping lesion formation and development. In addition, these lesions were circumscribed by type-II HSBs, which present lower surface porosity and higher resistance to wear. This theory was verified in in vitro observations, where both the central cone and the type-I HSB of cuspal enamel showed higher susceptibility to wear, potentially elucidating the mechanisms involved on cupping lesion formation.

To dry perchance to live: Insights from the genome of the desiccation-tolerant biocrust moss Syntrichia caninervis.

With global climate change, water scarcity threatens whole agro/ecosystems. The desert moss Syntrichia caninervis, an extremophile, offers novel insights into surviving desiccation and heat. The sequenced S. caninervis genome consists of 13 chromosomes containing 16 545 protein-coding genes and 2666 unplaced scaffolds. Syntenic relationships within the S. caninervis and Physcomitrella patens genomes indicate the S. caninervis genome has undergone a single whole genome duplication event (compared to two for P. patens) and evidence suggests chromosomal or segmental losses in the evolutionary history of S. caninervis. The genome contains a large sex chromosome composed primarily of repetitive sequences with a large number of Copia and Gypsy elements. Orthogroup analyses revealed an expansion of ELIP genes encoding proteins important in photoprotection. The transcriptomic response to desiccation identified four structural clusters of novel genes. The genomic resources established for this extremophile offer new perspectives for understanding the evolution of desiccation tolerance in plants.

Search for Relativistic Magnetic Monopoles with Eight Years of IceCube Data.

We present an all-sky 90% confidence level upper limit on the cosmic flux of relativistic magnetic monopoles using 2886 days of IceCube data. The analysis was optimized for monopole speeds between 0.750c and 0.995c, without any explicit restriction on the monopole mass. We constrain the flux of relativistic cosmic magnetic monopoles to a level below 2.0×10^{-19} cm^{-2} s^{-1} sr^{-1} over the majority of the targeted speed range. This result constitutes the most strict upper limit to date for magnetic monopoles with ß≳0.8 and up to ß∼0.995 and fills the gap between existing limits on the cosmic flux of nonrelativistic and ultrarelativistic magnetic monopoles.

Search for Unstable Sterile Neutrinos with the IceCube Neutrino Observatory.

We present a search for an unstable sterile neutrino by looking for a resonant signal in eight years of atmospheric ν_{µ} data collected from 2011 to 2019 at the IceCube Neutrino Observatory. Both the (stable) three-neutrino and the 3+1 sterile neutrino models are disfavored relative to the unstable sterile neutrino model, though with p values of 2.8% and 0.81%, respectively, we do not observe evidence for 3+1 neutrinos with neutrino decay. The best-fit parameters for the sterile neutrino with decay model from this study are Δm_{41}^{2}=6.7_{-2.5}^{+3.9} eV^{2}, sin^{2}2θ_{24}=0.33_{-0.17}^{+0.20}, and g^{2}=2.5π±1.5π, where g is the decay-mediating coupling. The preferred regions of the 3+1+decay model from short-baseline oscillation searches are excluded at 90% C.L.

Strong Constraints on Neutrino Nonstandard Interactions from TeV-Scale ν_{µ} Disappearance at IceCube.

We report a search for nonstandard neutrino interactions (NSI) using eight years of TeV-scale atmospheric muon neutrino data from the IceCube Neutrino Observatory. By reconstructing incident energies and zenith angles for atmospheric neutrino events, this analysis presents unified confidence intervals for the NSI parameter ε_{µτ}. The best-fit value is consistent with no NSI at a p value of 25.2%. With a 90% confidence interval of -0.0041≤ε_{µτ}≤0.0031 along the real axis and similar strength in the complex plane, this result is the strongest constraint on any NSI parameter from any oscillation channel to date.

First-year Acacia seedlings are anisohydric "water-spenders" but differ in their rates of water use.

PREMISE: First-year seedlings (FYS) of tree species may be a critical demographic bottleneck in semi-arid, seasonally dry ecosystems such as savannas. Given the highly variable water availability and potentially strong FYS-grass competition for water, FYS water-use strategies may play a crucial role in FYS establishment in savannas and, ultimately, in tree-grass competition and coexistence. METHODS: We examined drought responses in FYS of two tree species that are dominant on opposite ends of an aridity gradient in Serengeti, Acacia (=Vachellia) tortilis and A. robusta. In a glasshouse experiment, gas exchange and whole-plant hydraulic conductance (Kplant ) were measured as soil water potential (Ψsoil ) declined. Trajectory of the Ψleaf /Ψsoil relationship during drought elucidated the degree of iso/anisohydry. RESULTS: Both species were strongly anisohydric "water-spenders," allowing rapid wet-season C gain after pulses of moisture availability. Despite being equally vulnerable to declines in Kplant under severe drought, they differed in their rates of water use. Acacia tortilis, which occurs in the more arid regions, initially had greater Kmax , transpiration (E), and photosynthesis (Anet ) than A. robusta. CONCLUSIONS: This work demonstrates an important mechanism of FYS establishment in savannas: Rather than investing in drought tolerance, savanna FYS maximize gas exchange during wet periods at the expense of desiccation during dry seasons. FYS establishment appears dependent on high C uptake during the pulses of water availability that characterize habitats dominated by these species. This study increases our understanding of species-scale plant ecophysiology and ecosystem-scale patterns of tree-grass coexistence.

Integrative modelling reveals mechanisms linking productivity and plant species richness.

How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems.

Anisotropic spin-orbit torque generation in epitaxial SrIrO3 by symmetry design.

Spin-orbit coupling (SOC), the interaction between the electron spin and the orbital angular momentum, can unlock rich phenomena at interfaces, in particular interconverting spin and charge currents. Conventional heavy metals have been extensively explored due to their strong SOC of conduction electrons. However, spin-orbit effects in classes of materials such as epitaxial 5d-electron transition-metal complex oxides, which also host strong SOC, remain largely unreported. In addition to strong SOC, these complex oxides can also provide the additional tuning knob of epitaxy to control the electronic structure and the engineering of spin-to-charge conversion by crystalline symmetry. Here, we demonstrate room-temperature generation of spin-orbit torque on a ferromagnet with extremely high efficiency via the spin-Hall effect in epitaxial metastable perovskite SrIrO3 We first predict a large intrinsic spin-Hall conductivity in orthorhombic bulk SrIrO3 arising from the Berry curvature in the electronic band structure. By manipulating the intricate interplay between SOC and crystalline symmetry, we control the spin-Hall torque ratio by engineering the tilt of the corner-sharing oxygen octahedra in perovskite SrIrO3 through epitaxial strain. This allows the presence of an anisotropic spin-Hall effect due to a characteristic structural anisotropy in SrIrO3 with orthorhombic symmetry. Our experimental findings demonstrate the heteroepitaxial symmetry design approach to engineer spin-orbit effects. We therefore anticipate that these epitaxial 5d transition-metal oxide thin films can be an ideal building block for low-power spintronics.

Ferumoxytol Nanoparticles Target Biofilms Causing Tooth Decay in the Human Mouth.

Severe tooth decay has been associated with iron deficiency anemia that disproportionally burdens susceptible populations. Current modalities are insufficient in severe cases where pathogenic dental biofilms rapidly accumulate, requiring new antibiofilm approaches. Here, we show that ferumoxytol, a Food and Drug Administration-approved nanoparticle formulation for treating iron deficiency, exerts an alternative therapeutic activity via the catalytic activation of hydrogen peroxide, which targets bacterial pathogens in biofilms and suppresses tooth enamel decay in an intraoral human disease model. Data reveal the potent antimicrobial specificity of ferumoxytol iron oxide nanoparticles (FerIONP) against biofilms harboring Streptococcus mutans via preferential binding that promotes bacterial killing through in situ free-radical generation. Further analysis indicates that the targeting mechanism involves interactions of FerIONP with pathogen-specific glucan-binding proteins, which have a minimal effect on commensal streptococci. In addition, we demonstrate that FerIONP can detect pathogenic biofilms on natural teeth via a facile colorimetric reaction. Our findings provide clinical evidence and the theranostic potential of catalytic nanoparticles as a targeted anti-infective nanomedicine.