UNC93B1 recruits syntenin-1 to dampen TLR7 signalling and prevent autoimmunity.

At least two members of the Toll-like receptor (TLR) family, TLR7 and TLR9, can recognize self-RNA and self-DNA, respectively. Despite the structural and functional similarities between these receptors, their contributions to autoimmune diseases such as systemic lupus erythematosus can differ. For example, TLR7 and TLR9 have opposing effects in mouse models of systemic lupus erythematosus-disease is exacerbated in TLR9-deficient mice but attenuated in TLR7-deficient mice1. However, the mechanisms of negative regulation that differentiate between TLR7 and TLR9 are unknown. Here we report a function for the TLR trafficking chaperone UNC93B1 that specifically limits signalling of TLR7, but not TLR9, and prevents TLR7-dependent autoimmunity in mice. Mutations in UNC93B1 that lead to enhanced TLR7 signalling also disrupt binding of UNC93B1 to syntenin-1, which has been implicated in the biogenesis of exosomes2. Both UNC93B1 and TLR7 can be detected in exosomes, suggesting that recruitment of syntenin-1 by UNC93B1 facilitates the sorting of TLR7 into intralumenal vesicles of multivesicular bodies, which terminates signalling. Binding of syntenin-1 requires phosphorylation of UNC93B1 and provides a mechanism for dynamic regulation of TLR7 activation and signalling. Thus, UNC93B1 not only enables the proper trafficking of nucleic acid-sensing TLRs, but also sets the activation threshold of potentially self-reactive TLR7

A novel method to identify sub-seasonal clustering episodes of extreme precipitation events and their contributions to large accumulation periods

Temporal (serial) clustering of extreme precipitation events on sub-seasonal time scales is a type of compound event. It can cause large precipitation accumulations and lead to floods. We present a novel, count-based procedure to identify episodes of sub-seasonal clustering of extreme precipitation. We introduce two metrics to characterise the frequency of sub-seasonal clustering episodes and their relevance for large precipitation accumulations. The procedure does not require the investigated variable (here precipitation) to satisfy any specific statistical properties. Applying this procedure to daily precipitation from the ERA5 reanalysis data set, we identify regions where sub-seasonal clustering occurs frequently and contributes substantially to large precipitation accumulations. The regions are the east and northeast of the Asian continent (north of Yellow Sea, in the Chinese provinces of Hebei, Jilin and Liaoning; North and South Korea; Siberia and east of Mongolia), central Canada and south of California, Afghanistan, Pakistan, the southwest of the Iberian Peninsula, and the north of Argentina and south of Bolivia. Our method is robust with respect to the parameters used to define the extreme events (the percentile threshold and the run length) and the length of the sub-seasonal time window (here 2–4 weeks). This procedure could also be used to identify temporal clustering of other variables (e.g. heat waves) and can be applied on different time scales (sub-seasonal to decadal). The code is available at the listed GitHub repository

Object-based analysis of simulated thunderstorms in Switzerland: application and validation of automated thunderstorm tracking with simulation data

We present a feasibility study for an object-based method to characterise thunderstorm properties in simulation data from convection-permitting weather models. An existing thunderstorm tracker, the Thunderstorm Identification, Tracking, Analysis and Nowcasting (TITAN) algorithm, was applied to thunderstorms simulated by the Advanced Research Weather Research and Forecasting (AR-WRF) weather model at convection-permitting resolution for a domain centred on Switzerland. Three WRF microphysics parameterisations were tested. The results are compared to independent radar-based observations of thunderstorms derived using the MeteoSwiss Thunderstorms Radar Tracking (TRT) algorithm. TRT was specifically designed to track thunderstorms over the complex Alpine topography of Switzerland. The object-based approach produces statistics on the simulated thunderstorms that can be compared to object-based observation data. The results indicate that the simulations underestimated the occurrence of severe and very large hail compared to the observations. Other properties, including the number of storm cells per day, geographical storm hotspots, thunderstorm diurnal cycles, and storm movement directions and velocities, provide a reasonable match to the observations, which shows the feasibility of the technique for characterisation of simulated thunderstorms over complex terrain

ATM and Artemis promote homologous recombination of radiation-induced DNA double-strand breaks in G2

Homologous recombination (HR) and non‐homologous end joining (NHEJ) represent distinct pathways for repairing DNA double‐strand breaks (DSBs). Previous work implicated Artemis and ATM in an NHEJ‐dependent process, which repairs a defined subset of radiation‐induced DSBs in G1‐phase. Here, we show that in G2, as in G1, NHEJ represents the major DSB‐repair pathway whereas HR is only essential for repair of ∼15% of X‐ or γ‐ray‐induced DSBs. In addition to requiring the known HR proteins, Brca2, Rad51 and Rad54, repair of radiation‐induced DSBs by HR in G2 also involves Artemis and ATM suggesting that they promote NHEJ during G1 but HR during G2. The dependency for ATM for repair is relieved by depleting KAP‐1, providing evidence that HR in G2 repairs heterochromatin‐associated DSBs. Although not core HR proteins, ATM and Artemis are required for efficient formation of single‐stranded DNA and Rad51 foci at radiation‐induced DSBs in G2 with Artemis function requiring its endonuclease activity. We suggest that Artemis endonuclease removes lesions or secondary structures, which inhibit end resection and preclude the completion of HR or NHEJ

High Microbial Diversity Despite Extremely Low Biomass in a Deep Karst Aquifer

Despite the importance of karst aquifers as a source of drinking water, little is known about the role of microorganisms in maintaining the quality of this water. One of the limitations in exploring the microbiology of these environments is access, which is usually limited to wells and surface springs. In this study, we compared the microbiology of the Madison karst aquifer sampled via the potentiometric lakes of Wind Cave with surface sampling wells and a spring. Our data indicated that only the Streeter Well (STR), which is drilled into the same hydrogeologic domain as the Wind Cave Lakes (WCL), allowed access to water with the same low biomass (1.56–9.25 × 103 cells mL-1). Filtration of ∼300 L of water from both of these sites through a 0.2 μm filter allowed the collection of sufficient cells for DNA extraction, PCR amplification of 16S rRNA gene sequences, and identification through pyrosequencing. The results indicated that bacteria (with limited archaea and no detectable eukaryotic organisms) dominated both water samples; however, there were significant taxonomic differences in the bacterial populations of the samples. The STR sample was dominated by a single phylotype within the Gammaproteobacteria (Order Acidithiobacillales), which dramatically reduced the overall diversity and species richness of the population. In WCL, despite less organic carbon, the bacterial population was significantly more diverse, including significant contributions from the Gammaproteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Planctomycetes, Fusobacter, and Omnitrophica phyla. Comparisons with similar oligotrophic environments suggest that karst aquifers have a greater species richness than comparable surface environs. These data also demonstrate that Wind Cave provides a unique opportunity to sample a deep, subterranean aquifer directly, and that the microbiology of such aquifers may be more complex than previously anticipated

CtIP and MRN promote non-homologous end-joining of etoposide-induced DNA double-strand breaks in G1

Topoisomerases class II (topoII) cleave and re-ligate the DNA double helix to allow the passage of an intact DNA strand through it. Chemotherapeutic drugs such as etoposide target topoII, interfere with the normal enzymatic cleavage/re-ligation reaction and create a DNA double-strand break (DSB) with the enzyme covalently bound to the 5′-end of the DNA. Such DSBs are repaired by one of the two major DSB repair pathways, non-homologous end-joining (NHEJ) or homologous recombination. However, prior to repair, the covalently bound topoII needs to be removed from the DNA end, a process requiring the MRX complex and ctp1 in fission yeast. CtIP, the mammalian ortholog of ctp1, is known to promote homologous recombination by resecting DSB ends. Here, we show that human cells arrested in G0/G1 repair etoposide-induced DSBs by NHEJ and, surprisingly, require the MRN complex (the ortholog of MRX) and CtIP. CtIP's function for repairing etoposide-induced DSBs by NHEJ in G0/G1 requires the Thr-847 but not the Ser-327 phosphorylation site, both of which are needed for resection during HR. This finding establishes that CtIP promotes NHEJ of etoposide-induced DSBs during G0/G1 phase with an end-processing function that is distinct to its resection function

ChAInGeS: The Chandra Arp Interacting Galaxies Survey

We have conducted a statistical analysis of the ultra-luminous X-ray point sources (ULXs; L(X) >= 10^39 erg/s) in a sample of galaxies selected from the Arp Atlas of Peculiar Galaxies. We find a possible enhancement of a factor of ~2-4 in the number of ULXs per blue luminosity for the strongly interacting subset. Such an enhancement would be expected if ULX production is related to star formation, as interacting galaxies tend to have enhanced star formation rates on average. For most of the Arp galaxies in our sample, the total number of ULXs compared to the far-infrared luminosity is consistent with values found earlier for spiral galaxies. This suggests that for these galaxies, ULXs trace recent star formation. However, for the most infrared-luminous galaxies, we find a deficiency of ULXs compared to the infrared luminosity. For these very infrared-luminous galaxies, AGNs may contribute to powering the far-infrared; alternatively, ULXs may be highly obscured in the X-ray in these galaxies and therefore not detected by these Chandra observations. We determined local UV/optical colors within the galaxies in the vicinity of the candidate ULXs using GALEX UV and SDSS optical images. In most cases, the distributions of colors are similar to the global colors of interacting galaxies. However, the u - g and r - i colors at the ULX locations tend to be bluer on average than these global colors, suggesting that ULXs are preferentially found in regions with young stellar populations. In the Arp sample there is a possible enhancement of a factor of ~2 - 5 in the fraction of galactic nuclei that are X-ray bright compared to more normal spirals.Comment: 28 pages, 7 figures, Astronomical Journal, in pres

γH2AX foci analysis for monitoring DNA double-strand break repair: Strengths, limitations and optimization

DNA double-strand breaks (DSBs) represent an important radiation-induced lesion and impaired DSB repair provides the best available correlation with radiosensitivity. Physical techniques for monitoring DSB repair require high, non-physiological doses and cannot reliably detect subtle defects. One outcome from extensive research into the DNA damage response is the observation that H2AX, a variant form of the histone H2A, undergoes extensive phosphorylation at the DSB, creating γH2AX foci that can be visualised by immunofluorescence. There is a close correlation between γH2AX foci and DSB numbers and between the rate of foci loss and DSB repair, providing a sensitive assay to monitor DSB repair in individual cells using physiological doses. However, γH2AX formation can occur at single-stranded DNA regions which arise during replication or repair and thus does not solely correlate with DSB formation. Here, we present and discuss evidence that following exposure to ionising radiation, γH2AX foci analysis can provide a sensitive monitor of DSB formation and repair and describe techniques to optimise the analysis. We discuss the limitations and benefits of the technique, enabling the procedure to be optimally exploited but not misused

The Maintenance of ATM Dependent G2/M Checkpoint Arrest Following Exposure to Ionizing Radiation

The G2/M checkpoint is important in preventing cells with unrepaired DNA double strand breaks (DSBs) entering mitosis, an event which is likely to result in genomic instability. We recently reported that checkpoint arrest is maintained until close to completion of DSB repair and that the duration of checkpoint arrest depends on the dose and DSB repair capacity rather than lasting for a fixed period of time. ATM leads to phosphorylation of Chk1/2 in G2 phase following exposure to ionizing radiation. These transducer kinases can phosphorylate and inhibit Cdc25 activity, which is the phosphatase regulating mitotic entry. In this study we dissect three processes that contribute to the maintenance of checkpoint arrest in irradiated G2 phase cells. First, the ATR-Chk1 pathway contributes to maintaining checkpoint arrest, although it is dispensable for the initial activation of checkpoint arrest. Second, ongoing ATM to Chk2 signalling from unrepaired DSBs contributes to checkpoint arrest. This process plays a greater role in a repair defective background. Finally, slow decay of the initially activated Chk2 also contributes to the maintenance of checkpoint arrest. 53BP1 and MDC1 defective cells show an initial checkpoint defect after low doses but are proficient in initial activation of arrest after high doses. After higher radiation doses, however, 53BP1-/- and MDC1-/- MEFs fail to maintain checkpoint arrest. Furthermore 53BP1-/- and MDC1-/- MEFs display elevated mitotic breakage even after high doses. We show that the defect in the maintenance of checkpoint arrest conferred by 53BP1 and MDC1 deficiency substantially enhances chromosome breakage

Haplotype tagging reveals parallel formation of hybrid races in two butterfly species.

Genetic variation segregates as linked sets of variants or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. Yet, genomic data often omit haplotype information due to constraints in sequencing technologies. Here, we present "haplotagging," a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species, the geographic clines for the major wing-pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the center of the hybrid zone. We propose that shared warning signaling (Müllerian mimicry) may couple the cline shifts seen in both species and facilitate the parallel coemergence of a novel hybrid morph in both comimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations