A disease-associated gene desert directs macrophage inflammation through ETS2.

Increasing rates of autoimmune and inflammatory disease present a burgeoning threat to human health1. This is compounded by the limited efficacy of available treatments1 and high failure rates during drug development2, highlighting an urgent need to better understand disease mechanisms. Here we show how functional genomics could address this challenge. By investigating an intergenic haplotype on chr21q22-which has been independently linked to inflammatory bowel disease, ankylosing spondylitis, primary sclerosing cholangitis and Takayasu's arteritis3-6-we identify that the causal gene, ETS2, is a central regulator of human inflammatory macrophages and delineate the shared disease mechanism that amplifies ETS2 expression. Genes regulated by ETS2 were prominently expressed in diseased tissues and more enriched for inflammatory bowel disease GWAS hits than most previously described pathways. Overexpressing ETS2 in resting macrophages reproduced the inflammatory state observed in chr21q22-associated diseases, with upregulation of multiple drug targets, including TNF and IL-23. Using a database of cellular signatures7, we identified drugs that might modulate this pathway and validated the potent anti-inflammatory activity of one class of small molecules in vitro and ex vivo. Together, this illustrates the power of functional genomics, applied directly in primary human cells, to identify immune-mediated disease mechanisms and potential therapeutic opportunities.

Analysis of the B cell receptor repertoire in six immune-mediated diseases.

B cells are important in the pathogenesis of many, and perhaps all, immune-mediated diseases. Each B cell expresses a single B cell receptor (BCR)1, and the diverse range of BCRs expressed by the total B cell population of an individual is termed the 'BCR repertoire'. Our understanding of the BCR repertoire in the context of immune-mediated diseases is incomplete, and defining this could provide new insights into pathogenesis and therapy. Here, we compared the BCR repertoire in systemic lupus erythematosus, anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis, Crohn's disease, Behçet's disease, eosinophilic granulomatosis with polyangiitis, and immunoglobulin A (IgA) vasculitis by analysing BCR clonality, use of immunoglobulin heavy-chain variable region (IGHV) genes and-in particular-isotype use. An increase in clonality in systemic lupus erythematosus and Crohn's disease that was dominated by the IgA isotype, together with skewed use of the IGHV genes in these and other diseases, suggested a microbial contribution to pathogenesis. Different immunosuppressive treatments had specific and distinct effects on the repertoire; B cells that persisted after treatment with rituximab were predominately isotype-switched and clonally expanded, whereas the inverse was true for B cells that persisted after treatment with mycophenolate mofetil. Our comparative analysis of the BCR repertoire in immune-mediated disease reveals a complex B cell architecture, providing a platform for understanding pathological mechanisms and designing treatment strategies.

Interference in multi-user optical wireless communications systems.

Visible light communications (VLC) (including LiFi) represent a subset of the broader field of optical wireless communications. Where narrow beams, typical of free space optical communications are largely free from interference. VLC encompasses use cases involving combined illumination and data access and supporting a wireless access point (AP) model. The use of many units provides scaling of spatial coverage for both lighting and data access. However, AP replication in close proximity creates many interference challenges that motivate the investigation embodied in this paper. In particular, we frame the interference challenge in the context of existing strategies for driving improvements in link performance and consider the impacts of multiple users, multiple sources and multiple cells. Lastly, we review the state of existing research in this area and recommend areas for further study. This article is part of the theme issue 'Optical wireless communication'.

A potential biotechnological process for the sustainable production of vitamin K1.

The primary objective of this review is to propose an approach for the biosynthesis of phylloquinone (vitamin K1) based upon its known sources, its role in photosynthesis and its biosynthetic pathway. The chemistry, health benefits, market, and industrial production of vitamin K are also summarized. Vitamin K compounds (K vitamers) are required for the normal function of at least 15 proteins involved in diverse physiological processes such as coagulation, tissue mineralization, inflammation, and neuroprotection. Vitamin K is essential for the prevention of Vitamin K Deficiency Bleeding (VKDB), especially in neonates. Increased vitamin K intake may also reduce the severity and/or risk of bone fracture, arterial calcification, inflammatory diseases, and cognitive decline. Consumers are increasingly favoring natural food and therapeutic products. However, the bulk of vitamin K products employed for both human and animal use are chemically synthesized. Biosynthesis of the menaquinones (vitamin K2) has been extensively researched. However, published research on the biotechnological production of phylloquinone is restricted to a handful of available articles and patents. We have found that microalgae are more suitable than plant cell cultures for the biosynthesis of phylloquinone. Many algae are richer in vitamin K1 than terrestrial plants, and algal cells are easier to manipulate. Vitamin K1 can be efficiently recovered from the biomass using supercritical carbon dioxide extraction.

Expression, purification and metal utilization of recombinant SodA from Borrelia burgdorferi.

Borrelia are microaerophilic spirochetes capable of causing multisystemic diseases such as Lyme disease and Relapsing Fever. The ubiquitous Fe/Mn-dependent superoxide dismutase (SOD) provides essential protection from oxidative damage by the superoxide anion. Borrelia possess a single SOD enzyme - SodA that is essential for virulence, providing protection against host-derived reactive oxygen species (ROS). Here we present a method for recombinant expression and purification of Borrelia burgdorferi SodA in E. coli. Metal exchange or insertion into the Fe/Mn-SOD is inhibited in the folded state. We therefore present a method whereby the recombinant Borrelia SodA binds to Mn under denaturing conditions and is subsequently refolded by a reduction in denaturant. SodA purified by metal affinity chromatography and size exclusion chromatography reveals a single band on SDS-PAGE. Protein folding is confirmed by circular dichroism. A coupled enzyme assay demonstrates SOD activity in the presence of Mn, but not Fe. The apparent molecular weight determined by size exclusion corresponds to a dimer of SodA; a homology model of dimeric SodA is presented revealing a surface Cys distal to the dimer interface. The method presented of acquiring a target metal under denaturing conditions may be applicable to the refolding of other metal-binding proteins.

Two-Phase Framework for Indoor Positioning Systems Using Visible Light.

Recently with the advancement of solid state lighting and the application thereof to Visible Light Communications (VLC), the concept of Visible Light Positioning (VLP) has been targeted as a very attractive indoor positioning system (IPS) due to its ubiquity, directionality, spatial reuse, and relatively high modulation bandwidth. IPSs, in general, have four major components: (1) a modulation, (2) a multiple access scheme, (3) a channel measurement, and (4) a positioning algorithm. A number of VLP approaches have been proposed in the literature and primarily focus on a fixed combination of these elements and moreover evaluate the quality of the contribution often by accuracy or precision alone. In this article, we provide a novel two-phase indoor positioning algorithmic framework that is able to increase robustness when subject to insufficient anchor luminaries and also incorporate any combination of the four major IPS components.

Beam shaping with tip-tilt varifocal mirror for indoor optical wireless communication.

MEMS mirrors are currently used in many applications to steer beams of light. An area of continued research is developing mirrors with varifocal capability that allows the beam to be shaped and focused. In this work, we study the varifocal capability of a 380 µm diameter, thermally actuated MEMS mirror with a ± 40° tip-tilt angle and a radius of curvature between -0.48 mm to 20.5 mm. Light is coupled to the mirror via a single mode optical fiber, similar to an indoor optical wireless communication architecture. The performance of the mirror is characterized with respect to (1) the profile of the reflected beam as the mirror deforms and (2) the mirror's impact when integrated into an optical communication system. We found that the mirror can focus light to a beam with a 0.18° half-angle divergence. Additionally, the ability to change the shape of fiberized light from a wide to narrow beam provides an unmatched level of dynamic control and significantly improves the bit error rate in an optical communication system.

Electrothermally actuated tip-tilt-piston micromirror with integrated varifocal capability.

MEMS micromirrors have proven to be very important optical devices with applications ranging from steerable mirrors for switches and cross-connects to spatial light modulators for correcting optical distortions. Usually beam steering and focusing are done with different MEMS devices and tilt angles in excess of 10 degrees are seldom obtained. Here we describe a single MEMS device that combines tip/tilt, piston mode and varifocal capability into a single, low cost device with very large tilt angles. Our device consists of a 400 micron diameter mirror driven with thermal bimorphs. We have demonstrated deflection angles of ± 40 degrees along both axes, a tunable focal length which varies between -0.48 mm to + 20.5 mm and a piston mode range of 300 microns - four separately controllable degrees of freedom in a single device. Potential applications range from smart lighting to optical switches and devices for telecom systems.

Reverse polarity optical-OFDM (RPO-OFDM): dimming compatible OFDM for gigabit VLC links.

Visible light communications (VLC) technology permits the exploitation of light-emitting diode (LED) luminaries for simultaneous illumination and broadband wireless communication. Optical orthogonal frequency-division multiplexing (O-OFDM) is a promising modulation technique for VLC systems, in which the real-valued O-OFDM baseband signal is used to modulate the instantaneous power of the optical carrier to achieve gigabit data rates. However, a major design challenge that limits the commercialization of VLC is how to incorporate the industry-preferred pulse-width modulation (PWM) light dimming technique while maintaining a broadband and reliable communication link. In this work, a novel signal format, reverse polarity O-OFDM (RPO-OFDM), is proposed to combine the fast O-OFDM communication signal with the relatively slow PWM dimming signal, where both signals contribute to the effective LED brightness. The advantages of using RPO-OFDM include, (1) the data rate is not limited by the frequency of the PWM signal, (2) the LED dynamic range is fully utilized to minimize the nonlinear distortion of the O-OFDM communication signal, and (3) the bit-error performance is sustained over a large fraction of the luminaire dimming range. In addition, RPO-OFDM offers a practical approach to utilize off-the-shelf LED drivers. We show results of numerical simulations to study the trade-offs between the PWM duty cycle, average electrical O-OFDM signal power, radiated optical flux as well as human perceived light.

Mutation detection and single-molecule counting using isothermal rolling-circle amplification.

Rolling-circle amplification (RCA) driven by DNA polymerase can replicate circularized oligonucleotide probes with either linear or geometric kinetics under isothermal conditions. In the presence of two primers, one hybridizing to the + strand, and the other, to the - strand of DNA, a complex pattern of DNA strand displacement ensues that generates 10(9) or more copies of each circle in 90 minutes, enabling detection of point mutations in human genomic DNA. Using a single primer, RCA generates hundreds of tandemly linked copies of a covalently closed circle in a few minutes. If matrix-associated, the DNA product remains bound at the site of synthesis, where it may be tagged, condensed and imaged as a point light source. Linear oligonucleotide probes bound covalently on a glass surface can generate RCA signals, the colour of which indicates the allele status of the target, depending on the outcome of specific, target-directed ligation events. As RCA permits millions of individual probe molecules to be counted and sorted using colour codes, it is particularly amenable for the analysis of rare somatic mutations. RCA also shows promise for the detection of padlock probes bound to single-copy genes in cytological preparations.

Richer than Gold: the fungal biodiversity of Reserva Los Cedros, a threatened Andean cloud forest.

BACKGROUND: Globally, many undescribed fungal taxa reside in the hyperdiverse, yet undersampled, tropics. These species are under increasing threat from habitat destruction by expanding extractive industry, in addition to global climate change and other threats. Reserva Los Cedros is a primary cloud forest reserve of ~ 5256 ha, and is among the last unlogged watersheds on the western slope of the Ecuadorian Andes. No major fungal survey has been done there, presenting an opportunity to document fungi in primary forest in an underrepresented habitat and location. Above-ground surveys from 2008 to 2019 resulted in 1760 vouchered collections, cataloged and deposited at QCNE in Ecuador, mostly Agaricales sensu lato and Xylariales. We document diversity using a combination of ITS barcode sequencing and digital photography, and share the information via public repositories (GenBank & iNaturalist). RESULTS: Preliminary identifications indicate the presence of at least 727 unique fungal species within the Reserve, representing 4 phyla, 17 classes, 40 orders, 101 families, and 229 genera. Two taxa at Los Cedros have recently been recommended to the IUCN Fungal Red List Initiative (Thamnomyces chocöensis Læssøe and "Lactocollybia" aurantiaca Singer), and we add occurrence data for two others already under consideration (Hygrocybe aphylla Læssøe & Boertm. and Lamelloporus americanus Ryvarden). CONCLUSIONS: Plants and animals are known to exhibit exceptionally high diversity and endemism in the Chocó bioregion, as the fungi do as well. Our collections contribute to understanding this important driver of biodiversity in the Neotropics, as well as illustrating the importance and utility of such data to conservation efforts. RESUMEN: Antecedentes: A nivel mundial muchos taxones fúngicos no descritos residen en los trópicos hiper diversos aunque continúan submuestreados. Estas especies están cada vez más amenazadas por la destrucción del hábitat debido a la expansión de la industria extractivista además del cambio climático global y otras amenazas. Los Cedros es una reserva de bosque nublado primario de ~ 5256 ha y se encuentra entre las últimas cuencas hidrográficas no explotadas en la vertiente occidental de los Andes ecuatorianos. Nunca antes se ha realizado un estudio de diversidad micológica en el sitio, lo que significa una oportunidad para documentar hongos en el bosque primario, en hábitat y ubicación subrepresentatadas. El presente estudio recopila información entre el 2008 y 2019 muestreando material sobre todos los sustratos, reportando 1760 colecciones catalogadas y depositadas en el Fungario del QCNE de Ecuador, en su mayoría Agaricales sensu lato y Xylariales; además se documenta la diversidad mediante secuenciación de códigos de barras ITS y fotografía digital, la información está disponible en repositorios públicos digitales (GenBank e iNaturalist). RESULTADOS: La identificación preliminar indica la presencia de al menos 727 especies únicas de hongos dentro de la Reserva, que representan 4 filos, 17 clases, 40 órdenes, 101 familias y 229 géneros. Recientemente dos taxones en Los Cedros se recomendaron a la Iniciativa de Lista Roja de Hongos de la UICN (Thamnomyces chocöensis Læssøe y "Lactocollybia" aurantiaca Singer) y agregamos datos de presencia de otros dos que ya estaban bajo consideración (Hygrocybe aphylla Læssøe & Boertm. y Lamelloporus americanus Ryvarden). CONCLUSIONES: Se sabe que plantas y animales exhiben una diversidad y endemismo excepcionalmente altos en la bioregión del Chocó y los hongos no son la excepción. Nuestras colecciones contribuyen a comprender este importante promotor de la biodiversidad en el Neotrópico además de ilustrar la importancia y utilidad de dichos datos para los esfuerzos de conservación.

Diagnostic radiography and adult acute myeloid leukaemia: an interview and medical chart review study.

BACKGROUND: Aetiology of acute myeloid leukaemia (AML) is not well understood, perhaps because of its distinct subtypes. High-dose ionising radiation is a known risk factor, but less is known about risk from low-dose exposure such as from diagnostic radiography. METHODS: Subjects were 412 matched case-control pairs. Ten-year subject histories of diagnostic radiography were based on interview and medical records. RESULTS: There was no convincing association between AML risk and ionising radiation exposure from diagnostic imaging procedures, either for AML overall or for any AML subtype. CONCLUSION: The association between diagnostic radiography and AML risk remains uncertain.

A non-coding plastid DNA phylogeny of Asian Begonia (Begoniaceae): evidence for morphological homoplasy and sectional polyphyly.

Maximum likelihood and Bayesian analyses of non-coding plastid DNA sequence data based on a broad sampling of all major Asian Begonia sections (ndhA intron, ndhF-rpl32 spacer, rpl32-trnL spacer, 3977 aligned characters, 84 species) were used to reconstruct the phylogeny of Asian Begonia and to test the monophyly of major Asian Begonia sections. Ovary and fruit characters which are crucial in current sectional circumscriptions were mapped on the phylogeny to assess their utility in infrageneric classifications. The results indicate that the strong systematic emphasis placed on single, homoplasious characters such as undivided placenta lamellae (section Reichenheimia) and fleshy pericarps (section Sphenanthera), and the recognition of sections primarily based on a suite of plesiomorphic characters including three-locular ovaries with axillary, bilamellate placentae and dry, dehiscent pericarps (section Diploclinium), has resulted in the circumscription of several polyphyletic sections. Moreover, sections Platycentrum and Petermannia were recovered as paraphyletic. Because of the homoplasy of systematically important characters, current classifications have a certain diagnostic, but only poor predictive value. The presented phylogeny provides for the first time a reasonably resolved and supported phylogenetic framework for Asian Begonia which has the power to inform future taxonomic, biogeographic and evolutionary studies.

Benefits of a Physician-Scientist-Tailored Curriculum at a Medical Student-Run Free Clinic.

We designed a curriculum to help sustain pre-clinical knowledge for MD/PhD trainees in their graduate training phase while securing regular providers for our student-run free clinic. MD/PhD involvement increased from 1.91 to 2.45 students-per-clinic-day following implementation, and participants affirmed increased preparedness and comfort entering medical school clinical clerkships.

Global patterns and drivers of ecosystem functioning in rivers and riparian zones.

River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.

Strand specificity of mutagenic bypass replication of DNA containing psoralen monoadducts in a human cell extract.

Psoralens are mutagenic compounds of vegetable origin that are used as photosensitizing agents in the treatment of various skin diseases, blood cell cancer, and autoimmune disorders. To study the mechanism of mutagenicity of psoralens in humans, we examined the efficiency and fidelity of simian virus 40 origin-dependent replication in a human cell extract of M13mp2 DNA randomly treated with the psoralen derivative 4'-hydroxymethyl-4,5',8-trimethyl psoralen plus UVA irradiation. Replication of DNA treated with variable amounts of 4'-hydroxymethyl-4,5',8-trimethyl psoralen and a fixed UVA fluence was inhibited in a concentration-dependent manner. However, covalently closed monomer-length circular replication products were observed. Product analysis by renaturing agarose gel electrophoresis after cross-linking with 250- to 280-nm UV light indicated that approximately 1 of 9 psoralen monoadducts was bypassed during in vitro replication. Introduction of product DNA into Escherichia coli to score replication errors in the lacZalpha reporter gene demonstrated that replication of the damaged DNA was more mutagenic than was replication of undamaged DNA. Sequence analysis of lacZ mutants revealed that damage-dependent replication errors were predominantly T.A-->C.G transitions, transversions at C.G base pairs, and deletions of single A.T base pairs, the last occurring most frequently in homopolymeric runs. A comparison of error specificities with two substrates having the replication origin asymmetrically placed on opposite sides of the mutational target suggests that the lagging-strand replication apparatus is less accurate than the leading-strand replication apparatus for psoralen monoadduct-dependent deletion errors. A model is proposed based on the preferential loopout of the monoadducted base from the strand that templates retrograde discontinuous synthesis.

Prior exposure to medical and dental x-rays related to tumors of the parotid gland.

Findings from this population-based study in Los Angeles County suggest, for the first time, that tumors of the parotid gland are related to prior exposure to diagnostic medical and dental radiography. Responses to interviews with 408 patients with a parotid tumor (269 benign tumors and 139 malignant tumors) were compared to responses of 408 neighborhood controls. Cumulative exposure of the parotid gland from diagnostic radiography was associated with a dose-related increase in risk of malignant tumors (P for trend less than .05; relative risk for exposure to greater than or equal to 50 rad = 3.4; 95% confidence interval = 1.02-11.46). Benign tumors showed a weaker positive association, and exposure before age 20 to a major diagnostic examination (full-mouth or panoramic dental radiography or medical radiography to the head) increased risk (relative risk = 1.8; confidence interval = 1.13-2.91). This study also confirmed the association of malignant tumors with prior radiation treatment to the head or neck; 28% of these tumors are attributable to exposure of the parotid gland from diagnostic and therapeutic radiation.

Secular trends in histologic types of lung cancer.

The histology pattern of lung cancer in Los Angeles County was reviewed for a 10-year period, 1972-81. In men, the total lung cancer incidence has been fairly constant, but there has been a shift in the histology pattern with an increase in adenocarcinoma and a decrease in "other" cell type (i.e., carcinoma not otherwise specified, large-cell and undifferentiated tumors). This changing histology pattern may be partly due to changes in diagnostic standards and practices. With the assumption that these changes are comparable in men and women, the "true" annual rate of change was estimated for each lung cancer cell type in women. All lung cancer types have increased in women; of the cell types squamous cell carcinoma, small-cell carcinoma, and adenocarcinoma, small-cell carcinoma showed the largest rate of annual increase and adenocarcinoma, the smallest.

Fidelity of DNA replication by extracts of normal and malignantly transformed human cells.

To test the hypothesis that a mutator phenotype may be associated with carcinogenesis (L. A. Loeb, Cancer Res., 51: 3074-3079, 1991), we have compared the fidelity of double-stranded DNA replication and the efficiency of mismatch repair in extracts from normal diploid and malignantly transformed human cells. Included was a diploid fibroblast strain and its transformed derivative, as well as a second diploid fibroblast strain and HeLa cells. The fidelity of DNA replication by cytoplasmic extracts in the presence of simian virus 40 large tumor antigen (SV40 T-antigen) was measured using a forward mutagenesis assay. The replicated DNA consisted of double-stranded M13 mp2 DNA containing the SV40 origin of replication and the lacZ alpha complementation gene as a target sequence for scoring mutations. T-antigen-dependent replication was detected in all cell extracts, with those from transformed cells having the greatest activity. No differences in replication fidelity were detected between normal and transformed cell extracts. Using a heteroduplex containing a G.G mispair, we also detected mismatch repair activity in the cell extracts, including efficient repair in extracts from malignantly transformed cells. While these data do not eliminate the possibility that a mutator phenotype may be associated with carcinogenesis, they do suggest that genetic instability associated with transformation does not involve reduced fidelity of replication of undamaged DNA or reduced mismatch repair efficiency.

Personal and family history of lung disease as risk factors for adenocarcinoma of the lung.

To identify risk factors for adenocarcinoma of the lung, a population-based case-control study of 336 female cancers of this cell type and an equal number of neighborhood controls was conducted between 1983 and 1986. After adjusting for personal smoking, personal and family histories of lung disease emerged as additional risk factors. A personal history of any lung disease was associated with a 40% increase in risk [smoking adjusted relative risk (SARR) = 1.4, 95% confidence interval (CI) = 1.0, 2.0] with a more marked increase in risk for lung diseases occurring during childhood (SARR = 1.9, 95% CI = 1.2, 3.2) and for tuberculosis (SARR = 10.0, 95% CI = 1.1, 90.1). Family histories of tuberculosis (SARR = 2.0, 95% CI = 1.1, 3.6) and of lung cancer (SARR = 3.9, 95% CI = 2.0, 7.6) were also risk factors for adenocarcinoma of the lung. Increasing risk was observed with decreasing intake of dietary beta-carotene. After adjusting for personal smoking, women in the lowest quartile of intake showed a two-fold increased risk relative to those in the highest quartile of intake (P = 0.003). There were also some suggestive differences between cases and controls in their reproductive history and hormone use.