Isolation of homozygous mutant mouse embryonic stem cells using a dual selection system.

Obtaining random homozygous mutants in mammalian cells for forward genetic studies has always been problematic due to the diploid genome. With one mutation per cell, only one allele of an autosomal gene can be disrupted, and the resulting heterozygous mutant is unlikely to display a phenotype. In cells with a genetic background deficient for the Bloom's syndrome helicase, such heterozygous mutants segregate homozygous daughter cells at a low frequency due to an elevated rate of crossover following mitotic recombination between homologous chromosomes. We constructed DNA vectors that are selectable based on their copy number and used these to isolate these rare homozygous mutant cells independent of their phenotype. We use the piggyBac transposon to limit the initial mutagenesis to one copy per cell, and select for cells that have increased the transposon copy number to two or more. This yields homozygous mutants with two allelic mutations, but also cells that have duplicated the mutant chromosome and become aneuploid during culture. On average, 26% of the copy number gain events occur by the mitotic recombination pathway. We obtained homozygous cells from 40% of the heterozygous mutants tested. This method can provide homozygous mammalian loss-of-function mutants for forward genetic applications

Bromodomain-containing Protein 4 regulates innate inflammation via modulation of alternative splicing

IntroductionBromodomain-containing Protein 4 (BRD4) is a transcriptional regulator which coordinates gene expression programs controlling cancer biology, inflammation, and fibrosis. In the context of airway viral infection, BRD4-specific inhibitors (BRD4i) block the release of pro-inflammatory cytokines and prevent downstream epithelial plasticity. Although the chromatin modifying functions of BRD4 in inducible gene expression have been extensively investigated, its roles in post-transcriptional regulation are not well understood. Given BRD4's interaction with the transcriptional elongation complex and spliceosome, we hypothesize that BRD4 is a functional regulator of mRNA processing.MethodsTo address this question, we combine data-independent analysis - parallel accumulation-serial fragmentation (diaPASEF) with RNA-sequencing to achieve deep and integrated coverage of the proteomic and transcriptomic landscapes of human small airway epithelial cells exposed to viral challenge and treated with BRD4i.ResultsWe discover that BRD4 regulates alternative splicing of key genes, including Interferon-related Developmental Regulator 1 (IFRD1) and X-Box Binding Protein 1 (XBP1), related to the innate immune response and the unfolded protein response (UPR). We identify requirement of BRD4 for expression of serine-arginine splicing factors, splicosome components and the Inositol-Requiring Enzyme 1 IREα affecting immediate early innate response and the UPR.DiscussionThese findings extend the transcriptional elongation-facilitating actions of BRD4 in control of post-transcriptional RNA processing via modulating splicing factor expression in virus-induced innate signaling

Isotropy of the velocity of light and the Sagnac effect

In this paper, it is shown, using a geometrical approach, the isotropy of the velocity of light measured in a rotating frame in Minkowski space-time, and it is verified that this result is compatible with the Sagnac effect. Furthermore, we find that this problem can be reduced to the solution of geodesic triangles in a Minkowskian cylinder. A relationship between the problems established on the cylinder and on the Minkowskian plane is obtained through a local isometry.Comment: LaTeX, 13 pages, 3 eps figures; typos corrected, added references, minor changes; to appear in "Relativity in Rotating Frames", ed. G. Rizzi G. and M.L. Ruggiero, Kluwer Academic Publishers, Dordrecht (2003

Single-electron charge transfer into putative Majorana and trivial modes in individual vortices

Majorana bound states are putative collective excitations in solids that exhibit the self-conjugate property of Majorana fermions - they are their own antiparticles. In iron-based superconductors, zero-energy states in vortices have been reported as potential Majorana bound states, but the evidence remains controversial. Here, we use scanning tunneling noise spectroscopy to study the tunneling process into vortex bound states in the conventional superconductor NbSe2, and in the putative Majorana platform FeTe0.55Se0.45. We find that tunneling into vortex bound states in both cases exhibits charge transfer of a single electron charge. Our data for the zero-energy bound states in FeTe0.55Se0.45 exclude the possibility of Yu-Shiba-Rusinov states and are consistent with both Majorana bound states and trivial vortex bound states. Our results open an avenue for investigating the exotic states in vortex cores and for future Majorana devices, although further theoretical investigations involving charge dynamics and superconducting tips are necessary.Comment: 15 pages, 4 figures, and 16 pages for supplementary informatio

Contrasting physical properties of black carbon in urban Beijing between winter and summer

Black carbon (BC) is known to have major impacts on both human health and climate. The populated megacity represents the most complex anthropogenic BC emissions where the sources and related impacts are very uncertain. This study provides source attribution and characterization of BC in the Beijing urban environment during the joint UK–China APHH (Air Pollution and Human Health) project, in both winter (November–December 2016) and summer (May–June 2017). The size-resolved mixing state of BC-containing particles was characterized by a single-particle soot photometer (SP2) and their mass spectra was measured by a soot particle aerosol mass spectrometer (SP-AMS). The refractory BC (rBC) mass loading was around a factor of 2 higher in winter relative to summer, and more variable coatings were present, likely as a result of additional surface emissions from the residential sector and favourable condensation in the cold season. The characteristics of the BC were relatively independent of air mass direction in summer, whereas in winter air masses from the Northern Plateau were considerably cleaner and contained less-coated and smaller BC, but the BC from the Southern Plateau had the largest core size and coatings. We compare two online source apportionment methods using simultaneous measurements made by the SP2, which measures physical properties of BC, and the chemical approach using the positive matrix factorization (PMF) of mass spectra from the SP-AMS for the first time. A method is proposed to isolate the BC from the transportation sector using a mode of small BC particles (core diameter Dc0.18 µm and ct  200 nm) to the total rBC mass increased with pollution level in winter but was minor in summer. These large BC particles importantly enhanced the absorption efficiency at high pollution levels – in winter when PM1 > 100 µg m−3 or BC > 2 µg m−3, the absorption efficiency of BC increased by 25 %–70 %. The reduction of emissions of these large BC particles and the precursors of the associated secondary coating will be an effective way of mitigating the heating effect of BC in urban environments

Why shot noise does not generally detect pairing in mesoscopic superconducting tunnel junctions

The shot noise in tunneling experiments reflects the Poissonian nature of the tunneling process. The shot noise power is proportional to both the magnitude of the current and the effective charge of the carrier. Shot-noise spectroscopy thus enables - in principle - to determine the effective charge q of the charge carriers that tunnel. This can be used to detect electron pairing in superconductors: in the normal state, the noise corresponds to single electron tunneling (q = 1e), while in the paired state, the noise corresponds to q = 2e, because of Andreev reflections. Here, we use a newly developed amplifier to reveal that in typical mesoscopic superconducting junctions, the shot noise does not reflect the signatures of pairing and instead stays at a level corresponding to q = 1e. We show that transparency can control the shot noise and this q = 1e is due to the large number of tunneling channels with each having very low transparency. At such transparencies, the shot noise in the junction resembles that of a metallic instead of a superconducting tunnel junction. Our results indicate that in typical mesoscopic superconducting junctions one should expect q = 1e noise, and lead to design guidelines for junctions that allow the detection of electron pairing

Primary extraskeletal osteosarcoma of omentum majus

Extraskeletal osteosarcoma is a rare malignant soft tissue tumor. Here we present a case of a primary extraskeletal osteosarcoma arising from omentum majus in a 40-year-old Chinese woman. Ultrasonography of the pelvic cavity showed a large soft tissue mass with marked calcification. Complete surgical resection of the primary tumor was performed and the histopathological diagnosis was extraskeletal osteosarcoma of omentum majus. She was followed up without adjuvant radiotherapy and chemotherapy, and died from widespread intra-abdominal, lung and liver metastases 7 months postoperatively

Puddle formation, persistent gaps, and non-mean-field breakdown of superconductivity in overdoped (Pb,Bi)2Sr2CuO6+{\delta}

The cuprate high-temperature superconductors exhibit many unexplained electronic phases, but it was often thought that the superconductivity at sufficiently high doping is governed by conventional mean-field Bardeen-Cooper-Schrieffer (BCS) theory[1]. However, recent measurements show that the number of paired electrons (the superfluid density) vanishes when the transition temperature Tc goes to zero[2], in contradiction to expectation from BCS theory. The origin of this anomalous vanishing is unknown. Our scanning tunneling spectroscopy measurements in the overdoped regime of the (Pb,Bi)2Sr2CuO6+{\delta} high-temperature superconductor show that it is due to the emergence of puddled superconductivity, featuring nanoscale superconducting islands in a metallic matrix[3,4]. Our measurements further reveal that this puddling is driven by gap filling, while the gap itself persists beyond the breakdown of superconductivity. The important implication is that it is not a diminishing pairing interaction that causes the breakdown of superconductivity. Unexpectedly, the measured gap-to-filling correlation also reveals that pair-breaking by disorder does not play a dominant role and that the mechanism of superconductivity in overdoped cuprate superconductors is qualitatively different from conventional mean-field theory

Microbes in beach sands : integrating environment, ecology and public health

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Reviews in Environmental Science and Bio/Technology 13 (2014): 329-368, doi:10.1007/s11157-014-9340-8.Beach sand is a habitat that supports many microbes, including viruses, bacteria, fungi and protozoa (micropsammon). The apparently inhospitable conditions of beach sand environments belie the thriving communities found there. Physical factors, such as water availability and protection from insolation; biological factors, such as competition, predation, and biofilm formation; and nutrient availability all contribute to the characteristics of the micropsammon. Sand microbial communities include autochthonous species/phylotypes indigenous to the environment. Allochthonous microbes, including fecal indicator bacteria (FIB) and waterborne pathogens, are deposited via waves, runoff, air, or animals. The fate of these microbes ranges from death, to transient persistence and/or replication, to establishment of thriving populations (naturalization) and integration in the autochthonous community. Transport of the micropsammon within the habitat occurs both horizontally across the beach, and vertically from the sand surface and ground water table, as well as at various scales including interstitial flow within sand pores, sediment transport for particle-associated microbes, and the large-scale processes of wave action and terrestrial runoff. The concept of beach sand as a microbial habitat and reservoir of FIB and pathogens has begun to influence our thinking about human health effects associated with sand exposure and recreational water use. A variety of pathogens have been reported from beach sands, and recent epidemiology studies have found some evidence of health risks associated with sand exposure. Persistent or replicating populations of FIB and enteric pathogens have consequences for watershed/beach management strategies and regulatory standards for safe beaches. This review summarizes our understanding of the community structure, ecology, fate, transport, and public health implications of microbes in beach sand. It concludes with recommendations for future work in this vastly under-studied area.2015-05-0

Imbalanced decision hierarchy in addicts emerging from drug-hijacked dopamine spiraling circuit

Despite explicitly wanting to quit, long-term addicts find themselves powerless to resist drugs, despite knowing that drug-taking may be a harmful course of action. Such inconsistency between the explicit knowledge of negative consequences and the compulsive behavioral patterns represents a cognitive/behavioral conflict that is a central characteristic of addiction. Neurobiologically, differential cue-induced activity in distinct striatal subregions, as well as the dopamine connectivity spiraling from ventral striatal regions to the dorsal regions, play critical roles in compulsive drug seeking. However, the functional mechanism that integrates these neuropharmacological observations with the above-mentioned cognitive/behavioral conflict is unknown. Here we provide a formal computational explanation for the drug-induced cognitive inconsistency that is apparent in the addicts' “self-described mistake”. We show that addictive drugs gradually produce a motivational bias toward drug-seeking at low-level habitual decision processes, despite the low abstract cognitive valuation of this behavior. This pathology emerges within the hierarchical reinforcement learning framework when chronic exposure to the drug pharmacologically produces pathologicaly persistent phasic dopamine signals. Thereby the drug hijacks the dopaminergic spirals that cascade the reinforcement signals down the ventro-dorsal cortico-striatal hierarchy. Neurobiologically, our theory accounts for rapid development of drug cue-elicited dopamine efflux in the ventral striatum and a delayed response in the dorsal striatum. Our theory also shows how this response pattern depends critically on the dopamine spiraling circuitry. Behaviorally, our framework explains gradual insensitivity of drug-seeking to drug-associated punishments, the blocking phenomenon for drug outcomes, and the persistent preference for drugs over natural rewards by addicts. The model suggests testable predictions and beyond that, sets the stage for a view of addiction as a pathology of hierarchical decision-making processes. This view is complementary to the traditional interpretation of addiction as interaction between habitual and goal-directed decision systems