Double-strand break toxicity is chromatin context independent

Cells respond to double-strand breaks (DSBs) by activating DNA damage response pathways, including cell cycle arrest. We have previously shown that a single double-strand break generated via CRISPR/Cas9 is sufficient to delay cell cycle progression and compromise cell viability. However, we also found that the cellular response to DSBs can vary, independent of the number of lesions. This implies that not all DSBs are equally toxic, and raises the question if the location of a single double-strand break could influence its toxicity. To systematically investigate if DSB-location is a determinant of toxicity we performed a CRISPR/Cas9 screen targeting 6237 single sites in the human genome. Next, we developed a data-driven framework to design CRISPR/Cas9 sgRNA (crRNA) pools targeting specific chromatin features. The chromatin context was defined using ChromHMM states, Lamin-B1 DAM-iD, DNAseI hypersensitivity, and RNA-sequencing data. We computationally designed 6 distinct crRNA pools, each containing 10 crRNAs targeting the same chromatin state. We show that the toxicity of a DSB is highly similar across the different ChromHMM states. Rather, we find that the major determinants of toxicity of a sgRNA are cutting efficiency and off-target effects. Thus, chromatin features have little to no effect on the toxicity of a single CRISPR/Cas9-induced DSB.     

A gut‐centric view of aging: Do intestinal epithelial cells contribute to age‐associated microbiota changes,inflammaging, and immunosenescence?

Intestinal epithelial cells (IECs) serve as both a physical and an antimicrobial barrier against the microbiota, as well as a conduit for signaling between the microbiota and systemic host immunity. As individuals age, the balance between these systems undergoes a myriad of changes due to age‐associated changes to the microbiota, IECs themselves, immunosenescence, and inflammaging. In this review, we discuss emerging data related to age‐associated loss of intestinal barrier integrity and posit that IEC dysfunction may play a central role in propagating age‐associated alterations in microbiota composition and immune homeostasis.     

Animal use of fence crossings in southwestern rangelands

Net‐wire fencing built to confine livestock is common on rangelands in the Southwestern USA, yet the impacts of livestock fencing on wildlife are largely unknown. Many wildlife species cross beneath fences at defined crossing locations because they prefer to crawl underneath rather than jump over fences. Animals occasionally become entangled jumping or climbing over fences, leading to injury or death. More commonly, repeated crossings under net‐wire fencing by large animals lead to fence damage, though the damage is often tolerated by landowners until the openings affect the ability to enclose livestock. The usage, placement, characteristics, and passage rates of fence crossings beneath net‐wire fencing are poorly understood. We monitored 20 randomly selected fence crossings on net‐wire livestock fencing across two study sites on rangelands in South Texas, USA, from April 2018 to March 2019. We assessed the characteristics of fence‐crossing locations (openings beneath the fence created by animals to aid in crossing) and quantified crossing rates and the probability of crossing by all species of animals via trail cameras. We documented 10,889 attempted crossing events, with 58% (n = 6271) successful. Overall, 15 species of medium‐ and large‐size mammals and turkey (Meleagris gallopavo) contributed to crossing events. Crossing locations received 3–4 crossing attempts per day on average, but the number of attempts and probability of successful crossing varied by location and fence condition. The probability of crossing attempts was most consistently influenced by the opening size of the crossing and season; as crossing size (opening) increased, the probability of successful crossing significantly increased for all species. Peaks in crossing activity corresponded with species'' daily and seasonal movements and activity. The density and size of fence‐crossing locations were dependent on fence maintenance and not associated with vegetation communities or habitat variables. However, crossing locations were often re‐established in the same locations after fence repairs. This is one of the few studies to monitor how all animal species present interacted with net‐wire livestock fencing in rangelands. Our results will help land managers understand the impact of net‐wire livestock fencing on animal movement.     

Scale‐dependent spatial patterns in benthic communities around a tropical island seascape

Understanding and predicting patterns of spatial organization across ecological communities is central to the field of landscape ecology, and a similar line of inquiry has begun to evolve sub‐tidally among seascape ecologists. Much of our current understanding of the processes driving marine community patterns, particularly in the tropics, has come from small‐scale, spatially‐discrete data that are often not representative of the broader seascape. Here we expand the spatial extent of seascape ecology studies and combine spatially‐expansive in situ digital imagery, oceanographic measurements, spatial statistics, and predictive modeling to test whether predictable patterns emerge between coral reef benthic competitors across scales in response to intra‐island gradients in physical drivers. We do this around the entire circumference of a remote, uninhabited island in the central Pacific (Jarvis Island) that lacks the confounding effects of direct human impacts. We show, for the first time, that competing benthic groups demonstrate predictable scaling patterns of organization, with positive autocorrelation in the cover of each group at scales < ~1 km. Moreover, we show how gradients in subsurface temperature and surface wave power drive spatially‐abrupt transition points in group dominance, explaining 48–84% of the overall variation in benthic cover around the island. Along the western coast, we documented ten times more sub‐surface cooling‐hours than any other part of the coastline, with events typically resulting in a drop of 1–4°C over a period of < 5 h. These high frequency temperature fluctuations are indicative of upwelling induced by internal waves and here result in localized nitrogen enrichment (NO₂ + NO₃) that promotes hard coral dominance around 44% of the island's perimeter. Our findings show that, in the absence of confounding direct human impacts, the spatial organization of coral reef benthic competitors are predictable and somewhat bounded across the seascape by concurrent gradients in physical drivers.     

Solar radiation and functional traits explain the decline of forest primary productivity along a tropical elevation gradient

One of the major challenges in ecology is to understand how ecosystems respond to changes in environmental conditions, and how taxonomic and functional diversity mediate these changes. In this study, we use a trait‐spectra and individual‐based model, to analyse variation in forest primary productivity along a 3.3 km elevation gradient in the Amazon‐Andes. The model accurately predicted the magnitude and trends in forest productivity with elevation, with solar radiation and plant functional traits (leaf dry mass per area, leaf nitrogen and phosphorus concentration, and wood density) collectively accounting for productivity variation. Remarkably, explicit representation of temperature variation with elevation was not required to achieve accurate predictions of forest productivity, as trait variation driven by species turnover appears to capture the effect of temperature. Our semi‐mechanistic model suggests that spatial variation in traits can potentially be used to estimate spatial variation in productivity at the landscape scale.     

A lateral-displacement flume for fish behavior and stranding studies during simulated pulsed flows

In regulated rivers, fluctuating water depths associated with pulsed discharges may strand small fish in side channels and pools. Quantitative assessments of stranded fish are difficult in field studies (e.g., due to unknown effects of avian and terrestrial vertebrate predators). To assess such lateral displacement and stranding on juvenile stream fishes, we designed, constructed, and tested (with three species) a 2 × 1-m, lateral-displacement flume. The flume featured a main channel that never drained and a raised, wide “floodplain” channel that alternately flooded, with a simulated pulse, and became dewatered. The floodplain contained four pools, with different shapes and draining capacities, in which fish could become stranded as the water level subsided. Fish-stranding rates (8%) in this relatively compact laboratory flume, after exposure to simulated pulsed stream flows, were comparable to those observed in past investigations using larger, artificial streams.     

Mitochondrial oxidative phosphorylation compensation may preserve vision in patients with OPA1-linked autosomal dominant optic atrophy

Autosomal Dominant Optic Atrophy (ADOA) is the most common inherited optic atrophy where vision impairment results from specific loss of retinal ganglion cells of the optic nerve. Around 60% of ADOA cases are linked to mutations in the OPA1 gene. OPA1 is a fission-fusion protein involved in mitochondrial inner membrane remodelling. ADOA presents with marked variation in clinical phenotype and varying degrees of vision loss, even among siblings carrying identical mutations in OPA1. To determine whether the degree of vision loss is associated with the level of mitochondrial impairment, we examined mitochondrial function in lymphoblast cell lines obtained from six large Australian OPA1-linked ADOA pedigrees. Comparing patients with severe vision loss (visual acuity [VA]<6/36) and patients with relatively preserved vision (VA>6/9) a clear defect in mitochondrial ATP synthesis and reduced respiration rates were observed in patients with poor vision. In addition, oxidative phosphorylation (OXPHOS) enzymology in ADOA patients with normal vision revealed increased complex II+III activity and levels of complex IV protein. These data suggest that OPA1 deficiency impairs OXPHOS efficiency, but compensation through increases in the distal complexes of the respiratory chain may preserve mitochondrial ATP production in patients who maintain normal vision. Identification of genetic variants that enable this response may provide novel therapeutic insights into OXPHOS compensation for preventing vision loss in optic neuropathies.     

Diel variability of mercury phase and species distributions in the Florida Everglades

Preliminary studies of mercury (Hg) cycling in the Everglades revealed that dissolved gaseous mercury (DGM), total mercury (Hg_T), and reactive mercury (Hg_R) show reproducible, diel trends. Peak water-column DGM concentrations were observed on or about noon, with a 3 to 7 fold increase over night-time concentrations. Production of DGM appears to cease during dark periods, with nearly constant water column concentrations that were at or near saturation with respect to the overlying air. A simple mass balance shows that the flux of Hg to the atmosphere from diel DGM production and evasion represents about 10% of the annual input from atmospheric deposition. Production of DGM is likely the result of an indirect photolysis reaction that involves the production of reductive species and/or reduction by electron transfer. Diel variability in Hg_T and Hg_R appears to be controlled by two factors: inputs from rainfall and photolytic sorption/desorption processes. A possible mechanism involves photolysis of chromophores on the surface of a solid substrate (e.g., the periphyton mat) giving rise to destabilization of sorbed mercury and net desorption during daylight. At night, the sorption reactions predominate and the water-column Hg_T decreases. Methylmercury (MeHg) also showed diel trends in concentration but were not clearly linked to the solar cycle or rainfall at the study site.