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Introduction: Bottom ash (BA) constitutes a significant by-product obtained during the incineration of municipal solid waste in waste-to-energy (WtE) plants. BA is a heterogeneous material made of different fractions, glass, minerals, metals, and unburned residual organic matter. Due to the non-hazardous nature of the unburned material, BA can be effectively recycled, becoming a valuable resource. However, BA displays a high content of potentially toxic elements (PTEs) within its finer grain size. The presence of these elements raises concerns regarding the potential toxicity associated with BA.Materials and methods: The release of PTEs in the smaller fraction (0.063–0.2 mm; 0.3–0.5 mm; 2–4 mm; bulk

Metals are essential in our daily lives and have a finite supply, being simultaneously contaminants of concern. The current carbon emissions and environmental impact of mining are untenable. We need to reclaim metals sustainably from secondary resources, like waste. Biotechnology can be applied in metal recovery from waste streams like fly ashes and bottom ashes of municipal solid waste incineration (MSWI). They represent substantial substance flows, with roughly 46 million tons of MSWI ashes produced annually globally, equivalent in elemental richness to low-grade ores for metal recovery. Next-generation methods for resource recovery, as in particular bioleaching, give the opportunity to recover critical materials and metals, appropriately purified for noble applications, in waste treatment chains inspired by circular economy thinking. In this critical review, we can identify three main lines of discussion: (1) MSWI material characterization and related environmental issues; (2) currently available processes for recycling and metal recovery; and (3) microbially assisted processes for potential recycling and metal recovery. Research trends are chiefly oriented to the potential exploitation of bioprocesses in the industry. Biotechnology for resource recovery shows increasing effectiveness especially downstream the production chains, i.e., in the waste management sector. Therefore, this critical discussion will help assessing the industrial potential of biotechnology for urban mining of municipal, post-combustion waste., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The inter-element relationships and the forms in which metals exist strongly influence their mobility and, in turn, have a signature on the environment and human health. Located in the northern Apennines within the Emilia-Romagna region, the Ridracoli artificial lake is one of Italy's most important reservoirs that provides drinking water for about one million people. This work characterized the reservoir sediments by ICP-MS after aqua regia digestion (ARD), comparing the limits by law to assess environmental compliance and XRF data from the same sample-set taken as total concentrations. The Degree of Extraction (DE) from pseudo-total concentrations of ARD analysis allows assessing elements mobility and the associated environmental risk. Principal Component Analysis (PCA) on the obtained data helped to investigate inter-element relationships better; for example, we observed carbonate-sourced sediments, many trace elements (e.g., Ni, Zn) linked to FeMn oxyhydroxides, the importance of the grain size in elements distribution, and the central role of the organic matter in element partitioning. In addition, a Sequential Extraction Procedure (SEP) was applied to the sediment samples to understand the partitioning of many analytes, including Potentially Harmful Elements (PHE) such as Fe, Mn, Cu, Cr, Ni, Pb, and Zn. The results indicated that the most easily mobilized forms were predominant in the area near the dam, in correspondence to sediments affected by the formation of a seasonal anoxic layer., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Trace Metals (TMs: Pb, Zn, Cu, Cr, Cd, and Ni), major elements (Al and Fe) and radionuclides ( 210 Pb/ 137 Cs) investigations on EL-C01 sediment core provides new information on sedimentary regime and anthropogenic impacts during the last 175 years in the Po river prodelta area. The results allow to identify some TMs/Al peak in the upper part of the core, likely related to the major flood events of the Po river during the XXth century. Sediments deposited after the year 1900 exhibit a gradual increase of some TMs concentrations compared to pre-industrial era values. In particular, Pb, Zn, and Cu high contents are detected after the World War II and during the "Italian Economic Miracle" period. The decrease of heavy metal (Zn and Pb) contents from the second half of the 1980s is probably the effect of the Italian Law 319/76 and anti-pollution environmental policies concerning industrial and urban emitters., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Background: Tumor mutational burden (TMB) measurements aid in identifying patients who are likely to benefit from immunotherapy; however, there is empirical variability across panel assays and factors contributing to this variability have not been comprehensively investigated. Identifying sources of variability can help facilitate comparability across different panel assays, which may aid in broader adoption of panel assays and development of clinical applications., Materials and Methods: Twenty-nine tumor samples and 10 human-derived cell lines were processed and distributed to 16 laboratories; each used their own bioinformatics pipelines to calculate TMB and compare to whole exome results. Additionally, theoretical positive percent agreement (PPA) and negative percent agreement (NPA) of TMB were estimated. The impact of filtering pathogenic and germline variants on TMB estimates was assessed. Calibration curves specific to each panel assay were developed to facilitate translation of panel TMB values to whole exome sequencing (WES) TMB values., Results: Panel sizes >667 Kb are necessary to maintain adequate PPA and NPA for calling TMB high versus TMB low across the range of cut-offs used in practice. Failure to filter out pathogenic variants when estimating panel TMB resulted in overestimating TMB relative to WES for all assays. Filtering out potential germline variants at >0% population minor allele frequency resulted in the strongest correlation to WES TMB. Application of a calibration approach derived from The Cancer Genome Atlas data, tailored to each panel assay, reduced the spread of panel TMB values around the WES TMB as reflected in lower root mean squared error (RMSE) for 26/29 (90%) of the clinical samples., Conclusions: Estimation of TMB varies across different panels, with panel size, gene content, and bioinformatics pipelines contributing to empirical variability. Statistical calibration can achieve more consistent results across panels and allows for comparison of TMB values across various panel assays. To promote reproducibility and comparability across assays, a software tool was developed and made publicly available., Competing Interests: Disclosure XZW is an employee of EMD Serono Research and Development Institute. JN, DF, and ESS are all employees of Foundation Medicine, and ESS is a shareholder in Roche. VF and LKB are employees of Neogenomics and stockholders in NeoGenomics Inc. S-JC and J-HC are employees of ACT Genomics and stockholder in ACT Genomics. JB is employed with BMS, shareholder in BMS, and a shareholder in Johnson & Johnson. JC and SP are employed by OmniSeq, Inc. and hold restricted stock in OmniSeq, Inc. DC and WT are employed with Thermo Fisher Scientific and stockholder in Thermo Fisher Scientific. KE is an employee of Intermountain Genome Diagnostics. GG is employed by BMS and a stockholder in BMS. VRG and R. Samara are employed with QIAGEN. LAK and KCV are employed with Personal Genome Diagnostics. PS is employed by Caris Life Sciences. AS serves on advisory boards and/or receives speech honoraria from AIGnostics, Bayer, Thermo Fisher, Illumina, Astra Zeneca, Novartis, Pfizer, Roche, Seattle Genetics, MSD, BMS, Takeda, Janssen, and Eli-Lily; and research funding from: Chugai and Bristol Myers Squibb. MB is employed by LGC SeraCare. VW is employed with Q Squared Solutions. JCB and MX are employed by AstraZeneca. JCB is employed and holds shares of AstraZeneca. KM and CZ are employees of Illumina Inc and stockholders in Illumina Inc. HM and GP are employees and shareholders in Biodesix Inc. MDH has stock and other ownership interests in Shattuck Labs, Immunai, and Arcus Biosciences; reports honoraria from AstraZeneca and Bristol Myers Squibb; has a consulting or advisory role with Bristol Myers Squibb, Merck, Genentech/Roche, AstraZeneca, Nektar, Syndax, Mirati Therapeutics, Shattuck Labs, Immunai, Blueprint Medicines, Achilles Therapeutics, and Arcus Biosciences; receives research funding from Bristol Myers Squibb (Inst); has patents, royalties, and other intellectual property [a patent has been filed by Memorial Sloan Kettering (PCT/US2015/062208) for the use of TMB for prediction of immunotherapy efficacy, which is licensed to Personal Genome Diagnostics]; and receives travel and accommodation expense reimbursement from AstraZeneca, Bristol Myers Squibb, and Eli Lilly. All other authors have declared no conflicts of interest., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: There has recently been growing interest in the roles of inflammation in contributing to the development of anxiety in people with immune-mediated inflammatory diseases (IMID). Patient-reported outcome measures can facilitate the assessment of physical and psychological functioning. The National Institutes of Health (NIH)'s Patient-Reported Outcomes Measurement Information System (PROMIS®) is a set of Patient-Reported Outcomes (PROs) that cover physical appearance, mental health, and social health. The PROMIS has been built through an Item Response Theory approach (IRT), a model-based measurement in which trait level estimates depend on both persons' responses and on the properties of the items that were administered. The aim of this study is to test the psychometric properties of an Italian custom four-item Short Form of the PROMIS Anxiety item bank in a cohort of outpatients with IMIDs., Methods: We selected four items from the Italian standard Short Form Anxiety 8a and administered them to consecutive outpatients affected by Inflammatory Bowel disease ( n = 246), rheumatological ( n = 100) and dermatological ( n = 43) diseases, and healthy volunteers ( n = 280). Data was analyzed through an Item Response Theory (IRT) analysis in order to evaluate the psychometric properties of the Italian adaptation of the PROMIS anxiety short form., Results: Taken together, Confirmatory Factor Analysis and Exploratory Factor analysis suggest that the unidimensionality assumption of the instrument holds. The instrument has excellent reliability from a Classical Theory of Test (CTT) standpoint (Cronbach's α = 0.93, McDonald's ω = 0.92). The 2PL Graded Response Model (GRM) model provided showed a better goodness of fit as compared to the 1PL GRM model, and local independence assumption appears to be met overall. We did not find signs of differential item functioning (DIF) for age and gender, but evidence for uniform (but not non-uniform) DIF was found in three out of four items for the patient vs . control group. Analysis of the test reliability curve suggested that the instrument is most reliable for higher levels of the latent trait of anxiety. The groups of patients exhibited higher levels of anxiety as compared to the control group ( p s < 0.001, Bonferroni-corrected). The groups of patients were not different between themselves ( p = 1, Bonferroni-corrected). T-scores based on estimated latent trait and raw scores were highly correlated (Pearson's r = 0.98) and led to similar results., Discussion: The Italian custom four-item short form from the PROMIS anxiety form 8a shows acceptable psychometric properties both from a CTT and an IRT standpoint. The Test Reliability Curve shows that this instrument is mostly informative for people with higher levels of anxiety, making it particularly suitable for clinical populations such as IMID patients., Competing Interests: Marco Tullio Liuzza is an Academic Editor for PeerJ., (© 2021 Liuzza et al.)

The sea area around Dajin Island in the Pearl River Estuary is the second-largest habitat in China for the Indo-Pacific humpback dolphin (Sousa Chinensis). However, the rapid economic development of this area brings potential threats to the aquatic ecology around Dajin Island. Real-time monitoring and evaluation of the ecological health of the sea area are urgent. In this study, band ratio and single-band inversion algorithms were performed to obtain Chlorophyll-a (Chl-a) and Suspended Sediment Concentration (SSC), relying on both Compact Airborne Spectrographic Imager (CASI) and Moderate resolution Imaging Spectrometer (MODIS) images. The CASI/Chl-a with high spatial resolution was adopted to assess the eutrophication status, while the dissolved organic carbon (DOC) concentration and chromophoric dissolved organic matter (CDOM) optical properties were used to derive the material composition and sources. The results suggest that the study area is under a low to medium eutrophication state with evenly distributed low Chl-a concentration. However, higher Chl-a is observed in the outer estuary with MODIS/Chl-a. The relatively high DOC concentration, especially in the north, where aquaculture is practiced, and near the estuary's main axis, i.e., east Dajin Island, indicates that the eutrophication state might be underestimated using satellite chlorophyll alone. CDOM optical properties indicated that terrestrial materials are the DOC's primary material sources, but the DOC derived from fishery aquaculture cannot be ignored. The low Chl-a concentration is likely due to the turbulent hydrodynamic regime caused by jet flow and reciprocating flow in this marine area. Comprehensive observation, including the assessment of different technological platforms, is suggested for the aquatic environment.

Mechatronic and soft robotics are taking inspiration from the animal kingdom to create new high-performance robots. Here, we focused on marine biomimetic research and used innovative bibliographic statistics tools, to highlight established and emerging knowledge domains. A total of 6980 scientific publications retrieved from the Scopus database (1950-2020), evidencing a sharp research increase in 2003-2004. Clustering analysis of countries collaborations showed two major Asian-North America and European clusters. Three significant areas appeared: (i) energy provision, whose advancement mainly relies on microbial fuel cells, (ii) biomaterials for not yet fully operational soft-robotic solutions; and finally (iii), design and control, chiefly oriented to locomotor designs. In this scenario, marine biomimicking robotics still lacks solutions for the long-lasting energy provision, which presently hinders operation autonomy. In the research environment, identifying natural processes by which living organisms obtain energy is thus urgent to sustain energy-demanding tasks while, at the same time, the natural designs must increasingly inform to optimize energy consumption.

The discharge of toxic elements from tailings soils in the aquatic environments occurs chiefly in the presence of indigenous bacteria. The biotic components may interact in the opposite direction, leading to the formation of a passivation layer, which can inhibit the solubility of the elements. In this work, the influence of jarosite on the bio-immobilization of toxic elements was studied by native bacteria. In batch experiments, the bio-immobilization of heavy metals by an inhibitory layer was examined in the different aquatic media using pure cultures of Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans. A variety of analyses also investigated the mechanisms of metals bio-immobilization. Among different tests, the highest metal solubility yielded 99% Mn, 91% Cr, 95% Fe, and 78% Cu using A. ferrooxidans in 9KFe medium after ten days. After 22 days, these percentages decreased down to 30% Mn and about 20% Cr, Fe, and Cu, likely due to metal immobilization by biogenic jarosite. The formation of jarosite was confirmed by an electron probe micro-analyzer (EPMA), X-ray diffraction (XRD), and scanning electron microscope (SEM). The mechanisms of metal bio-immobilization by biogenic jarosite from tailings soil confirmed three main steps: 1) the dissolution of metal sulfides in the presence of Acidithiobacillus bacteria; 2) the nucleation of jarosite on the surface of sulfide minerals; 3) the co-precipitation of dissolved elements with jarosite during the bio-immobilization process, demonstrated by a structural study for jarosite. Covering the surface of soils by the jarosite provided a stable compound in the acidic environment of mine-waste., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Municipal solid waste incineration (MSWI) is one of the leading technologies for municipal solid waste (MSW) treatment in Europe. Incineration bottom ash (IBA) is the main solid residue from MSWI, and its annual European production is about 20 million tons. The composition of IBA depends on the composition of the incinerated waste; therefore, it may contain significant amounts of ferrous and non-ferrous (NFe) metals as well as glass that can be recovered. Technologies for NFe metals recovery have emerged in IBA treatment since the 1990s and became common practice in many developed countries. Although the principles and used apparatus are nearly the same in all treatment trains, the differences in technological approaches to recovery of valuable components from IBA - with a special focus on NFe metals recovery - are summarized in this paper., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

This paper reports supplementary information to "Understanding room-temperature magnetic properties of anthropogenic ashes from municipal solid waste incineration to assess potential impacts and resources" [1]. The sample-set is composed of 47 samples of bottom (BA) and fly (FA) ashes from Municipal Solid Waste Incineration (MSWI), including eight magnetic extracts of selected BA and FA materials. The sampling relies on a simple random sampling strategy at four different MSWI sites in Northern Italy [2]. X-Ray Fluorescence (XRF) analysis on pressed powder pellets, microscopic observations on thin sections and stubs, and magnetic analysis were carried out. Various magnetic measurements are presented: the magnetic susceptibility measured at two different frequencies (0.47 and 4.7 kHz); the mass-specific susceptibility of ARM (χ ARM ), expressed in m 3 /kg, calculated after mass-normalization and bias DC field correction; experiments for isothermal remanent magnetization (IRM) experimented were also conducted. The latter measurement allowed the calculation of additional parameters, such as the coercivity of remanence (B 0cr ) and the S-ratio [3]. The IRM acquired in a field of 1.0 T was regarded as the saturation IRM (SIRM). Mass-specific magnetic susceptibility (χ) was calculated by dividing the volume susceptibility by the sample mass. Finally, hysteresis loops and backfield curves at room temperature were measured on selected samples and are available. Data can be reused as groundwork information in future studies on MSWI residues. It would be essential to produce new data on geochemical and magnetic characteristics of MSWI residues to assure good coverage of data for enhanced sustainability of these heterogeneous streams of anthropogenic materials. This combination of methods will contribute to paving the way for quick and reliable resource assessment as well as to promote environmental sustainability., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financialrelationships that could be construed as a potential conflict of interest., (© 2020 The Authors.)

Bioleaching (or microbial leaching) is a biohydrometallurgical technology that can be applied for metal recovery from anthropogenic waste streams. In particular, fly ashes and bottom ashes of municipal solid waste incineration (MSWI) can be used as a target material for biomining. Globally, approximately 46 million tonnes of MSWI ashes are produced annually. Currently landfilled or used as aggregate, these contain large amounts of marketable metals, equivalent to low-grade ores. There is opportunity to recover critical materials as the circular economy demands, using mesophile, moderately thermophile, and extremophile microorganisms for bioleaching. A Strengths, Weaknesses, Opportunities and Threats (SWOT) analysis was developed to assess the potential of this biotechnology to recover critical metals from MSWI wastes. Bioleaching has potential as a sustainable technology for resource recovery and enhanced waste management. However, stakeholders can only reap the full benefits of bioleaching by addressing both the technical engineering challenges and regulatory requirements needed to realise and integrated approach to resource use., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Hydrocarbon seepage is overlooked in the marine environment, mostly due to the lack of high-resolution exploration data. This contribution is about the set-up of a relocatable and cost-effective monitoring system, which was tested on two seepages in the Central Adriatic Sea. The two case studies are an oil spill at a water depth of 10 m and scattered biogenic methane seeps at a water depth of 84 m. Gas plumes in the water column were detected with a multibeam system, tightened to sub-seafloor seismic reflection data. Dissolved benthic fluxes of nutrients, metals and Dissolved Inorganic Carbon (DIC) were measured by in situ deployment of a benthic chamber, which was used also for the first time to collect water samples for hydrocarbons characterization. In addition, the concentration of polycyclic aromatic hydrocarbons, as well as major and trace elements were analyzed to provide an estimate of hydrocarbon contamination in the surrounding sediment and to make further inferences on the petroleum system.

Background: Tumor mutational burden (TMB), defined as the number of somatic mutations per megabase of interrogated genomic sequence, demonstrates predictive biomarker potential for the identification of patients with cancer most likely to respond to immune checkpoint inhibitors. TMB is optimally calculated by whole exome sequencing (WES), but next-generation sequencing targeted panels provide TMB estimates in a time-effective and cost-effective manner. However, differences in panel size and gene coverage, in addition to the underlying bioinformatics pipelines, are known drivers of variability in TMB estimates across laboratories. By directly comparing panel-based TMB estimates from participating laboratories, this study aims to characterize the theoretical variability of panel-based TMB estimates, and provides guidelines on TMB reporting, analytic validation requirements and reference standard alignment in order to maintain consistency of TMB estimation across platforms., Methods: Eleven laboratories used WES data from The Cancer Genome Atlas Multi-Center Mutation calling in Multiple Cancers (MC3) samples and calculated TMB from the subset of the exome restricted to the genes covered by their targeted panel using their own bioinformatics pipeline (panel TMB). A reference TMB value was calculated from the entire exome using a uniform bioinformatics pipeline all members agreed on (WES TMB). Linear regression analyses were performed to investigate the relationship between WES and panel TMB for all 32 cancer types combined and separately. Variability in panel TMB values at various WES TMB values was also quantified using 95% prediction limits., Results: Study results demonstrated that variability within and between panel TMB values increases as the WES TMB values increase. For each panel, prediction limits based on linear regression analyses that modeled panel TMB as a function of WES TMB were calculated and found to approximately capture the intended 95% of observed panel TMB values. Certain cancer types, such as uterine, bladder and colon cancers exhibited greater variability in panel TMB values, compared with lung and head and neck cancers., Conclusions: Increasing uptake of TMB as a predictive biomarker in the clinic creates an urgent need to bring stakeholders together to agree on the harmonization of key aspects of panel-based TMB estimation, such as the standardization of TMB reporting, standardization of analytical validation studies and the alignment of panel-based TMB values with a reference standard. These harmonization efforts should improve consistency and reliability of panel TMB estimates and aid in clinical decision-making., Competing Interests: Competing interests: DF: employment with Foundation Medicine and stockholder in Roche. VF: employment with NeoGenomics Inc and stockholder in NeoGenomics Inc. S-JC: employment with ACT Genomics and stockholder in ACT Genomics. JRW: founder and owner of Resphira Biosciences and paid consultant to PGDx. PW: employment with Illumina and stockholder in Illumina. JB: employment with Bristol-Myers Squibb, shareholder in Bristol-Myers Squibb and shareholder in Johnson & Johnson. JCB: employment with AstraZeneca Pharmaceuticals and stocks in AstraZeneca Pharmaceuticals. RC: employment with Thermo Fisher Scientific. WSC: employment with Caris Life Sciences. JHC: employment with ACT Genomics. DC: employment with Thermo Fisher Scientific and stockholder in Thermo Fisher Scientific. JSD: employment with Personal Genome Diagnostics. VG: employment with QIAGEN. MH: received research funding from Bristol-Myers Squibb; is paid a consultant to Merck, Bristol-Myers Squibb, AstraZeneca, Genentech/Roche, Janssen, Nektar, Syndax, Mirati and Shattuck Labs; has received travel support/honoraria from AztraZeneca and BMS and a patent has been filed by MSK related to the use of tumor mutation burden to predict response to immunotherapy (PCT/US2015/062208), which has received licensing fees from PGDx. EH: employment with Guardant Health Inc and stockholder in Guardant Health Inc. YL: employment with Foundation Medicine while engaged in the research project (March 2019). Currently, an employee of Thrive Sciences, Inc and stockholder of Thrive Sciences, Inc. AP: employment with QIAGEN. KJQ: employment with Guardant Health Inc and stockholder in Guardant Health Inc. NR: NR and Memorial Sloan Kettering Cancer Center have a patent filing (PCT/US2015/062208) for the use of tumor mutation burden and HLA for prediction of immunotherapy efficacy, which is licensed to Personal Genome Diagnostics. NR is a founder, shareholder and serves on the scientific advisory board of Gritstone Oncology. NR has also consulted for AbbVie, AstraZeneca, BMS, EMD Sorono, Genentech, GSK, Janssen, Lilly, Merck, Novartis, Pfizer, Regeneron. HT: employment with Caris Life Sciences. CW: employment with Bristol-Myers Squibb, shareholder in Bristol-Myers Squibb ad shareholder in Johnson & Johnson. MX: employment with AstraZeneca Pharmaceuticals. CZ: employment with Illumina and stockholder in Illumina. AS: advisory board and/or speech honoraria from: Bayer, BMS, MSD, Novartis, AstraZeneca, Roche, Seattle Genomics, Illumina, Thermo Fisher, Takeda. Research funding from: Chugai, BMS., (© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

The continuous presence of toxic elements in the aquatic environments around mine tailings occurs due to bioleaching or chemical extraction promoted by the mining operations. Biogenic passivation treatment of tailings dams can be a new environment-friendly technique to inhibit the solubility of heavy metals. In spite of current bioleaching researches, we tried to minimize the mobility of the trace elements in the laboratory scale through the formation of a passivation layer in the presence of a mixed culture of Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans. The X-ray diffraction (XRD) and scanning electron microscope (SEM) represented the jarosite generation as an inhibitory layer on the mineral surfaces of the tested materials. More detailed observations on electron probe micro-analyzer (EPMA) showed the co-precipitation of metals with the passivation layer. Thereby, the passivation layer demonstrates potential in elements immobilization which, in turn, can be optimized in the natural systems. Our working hypothesis was to exploit and optimize the formation of the passivation layer to maximize the immobilization of heavy metals (e.g., Cu, Cr). The optimization process of bioleaching experiments using indigenous bacteria caused a reduced solubility for Cu (from around 20% to 4.5%) and Cr (from around 30% to 10.6%) and the formation of 6.5 gr passivation layer. The analyses finally represented the high efficiency of the passivation technique to minimize metals bioleaching in comparison to earlier studies., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Inflammatory bowel disease (IBD) is characterized by alterations in the intestinal microbiota and altered immune responses to gut microbiota. Evidence is accumulating that IBD is influenced by not only commensal bacteria but also commensal fungi. We characterized fungi directly associated with the intestinal mucosa in healthy people and Crohn's disease patients and identified fungi specifically abundant in patients. One of these, the common skin resident fungus Malassezia restricta, is also linked to the presence of an IBD-associated polymorphism in the gene for CARD9, a signaling adaptor important for anti-fungal defense. M. restricta elicits innate inflammatory responses largely through CARD9 and is recognized by Crohn's disease patient anti-fungal antibodies. This yeast elicits strong inflammatory cytokine production from innate cells harboring the IBD-linked polymorphism in CARD9 and exacerbates colitis via CARD9 in mouse models of disease. Collectively, these results suggest that targeting specific commensal fungi may be a therapeutic strategy for IBD., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Steel slag is a major by-product of the steel industry and a potential resource of technology critical elements. For this study, a basic oxygen furnace (BOF) steel slag was tested for bacterial leaching and recovery of aluminium (Al), chromium (Cr), and vanadium (V). Mixed acidophilic bacteria were adapted to the steel slag up to 5% (w/v). In the batch tests, Al, Cr, and V were bioleached significantly more from steel slag than in control treatments. No statistical difference was observed arising from the duration of the leaching (3 vs 6 d) in the batch tests. Al and Cr concentrations in the leachate were higher for the smaller particle size of the steel slag (<75 μm), but no difference was observed for V. In the column tests, no statistical difference was found for pH, Al, Cr and V between the live culture (one-step bioleaching) and the supernatant (two-step bioleaching). The results show that the culture supernatant can be effectively used in an upscaled industrial application for metal recovery. If bioleaching is used in the 170-250 million tonnes of steel slag produced per year globally, significant recoveries of metals (100% of Al, 84% of Cr and 8% of V) can be achieved, depending on the slag composition. The removal and recovery percentages of metals from the leachate with Amberlite ® IRA-400 are relatively modest (<67% and <5%, respectively), due to the high concentration of competing ions (SO 4 2- , PO 4 3- ) in the culture medium. Other ion exchange resins can be better suited for the leachate or methods such as selective precipitation could improve the performance of the resin. Further research is needed to minimise interference and maximise metal recovery., (Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Environmental policies in the European Union focus on the prevention of hazardous waste and aim to mitigate its impact on human health and ecosystems. However, progress is promoting a shift in perspective from environmental impacts to resource recovery. Municipal solid waste incineration (MSWI) has been increasing in developed countries, thus the amount of air pollution control residues (APCr) and fly ashes (FA) have followed the same upward trend. APCr from MSWI is classified as hazardous waste in the List of Waste (LoW) and as an absolute entry (19 01 07*), but FA may be classified as a mirror entry (19 0 13*/19 01 14). These properties arise mainly from their content in soluble salts, potentially toxic metals, trace organic pollutants and high pH in contact with water. Since these residues have been mostly disposed of in underground and landfills, other possibilities must be investigated to recover secondary raw materials and products. According to the literature, four additional routes of recovery have been found: detoxification (e.g. washing), product manufacturing (e.g. ceramic products and cement), practical applications (e.g. CO 2 sequestration) and recovery of materials (e.g. Zn and salts). This work aims to identify the best available technologies for material recovery in order to avoid landfill solutions. Within this scope, six case studies are presented and discussed: recycling in lightweight aggregates, glass-ceramics, cement, recovery of zinc, rare metals and salts. Finally, future perspectives are provided to advance understanding of this anthropogenic waste as a source of resources, yet tied to safeguards for the environment., (Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.)

During their production, management, and landfilling, bottom (BA) and fly (FA) ashes from municipal solid waste incineration may liberate Fe-bearing, ultrafine particles and easily enter different environmental sinks of the biosphere. We aim to explore a collection of BA and FA samples from Italian incinerators to probe magnetic mineralogy and the fraction of harmful superparamagnetic (SP) nanoparticles (d<30nm). X-ray diffraction, electron microscopy observation, temperature- and frequency-dependent magnetometry, and Mossbauer analysis are performed. The integration of information from our rock magnetic and non-magnetic techniques leads us to conclude that the dominant magnetic carrier in our samples is magnetite and its intermediate/impure forms, while sulphides (i.e., monoclinic pyrrhotite) are important ancillary magnetic phases. The SP fraction fluxing from the BA and FA outputs of a single incinerator is detected and estimated in 10 3 tons/year. This work stresses the need to calibrate the current technologies towards a safer management of combustion ashes and certainly to inform the environmental impact assessment by using a combination of different methods., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Background: The role of MET amplification in lung cancer, particularly in relation to checkpoint inhibition and EGFR WT, has not been fully explored. In this study, we correlated PD-L1 expression with MET amplification and EGFR , KRAS , or TP53 mutation in primary lung cancer., Methods: In this retrospective study, tissue collected from 471 various tumors, including 397 lung cancers, was tested for MET amplification by FISH with a MET /centromere probe. PD-L1 expression was evaluated using clone SP142 and standard immunohistochemistry, and TP53 , KRAS , and EGFR mutations were tested using next generation sequencing., Results: Our results revealed that PD-L1 expression in non-small cell lung cancer is inversely correlated with EGFR mutation (P=0.0003), and positively correlated with TP53 mutation (P=0.0001) and MET amplification (P=0.004). Patients with TP53 mutations had significantly higher MET amplification (P=0.007), and were more likely (P=0.0002) to be EGFR wild type. There was no correlation between KRAS mutation and overall PD-L1 expression, but significant positive correlation between PD-L1 expression and KRAS with TP53 co-mutation (P=0.0002). A cut-off for the ratio of MET : centromere signal was determined as 1.5%, and 4% of lung cancer patients were identified as MET amplified., Conclusions: This data suggests that in lung cancer both MET and TP53 play direct roles in regulating PD-L1 opposing EGFR . Moreover, KRAS and TP53 co-mutation may cooperate to drive PD-L1 expression in lung cancer. Adding MET or TP53 inhibitors to checkpoint inhibitors may be an attractive combination therapy in patients with lung cancer and MET amplification., Competing Interests: CONFLICTS OF INTEREST Maher Albitar, Wanlong Ma, Vincent Funari, Forrest Blocker, and Sally Agersborg are employed and own stocks in NeoGenomics.

The transcriptional regulator Blimp1 plays crucial roles in controlling terminal differentiation in several lineages. In T cells, Blimp1 is expressed in both effector (Teff) and regulatory (Treg) cells, and mice with T cell-specific deletion of Blimp1 (Blimp1CKO mice) spontaneously develop severe intestinal inflammation, indicating a crucial role for Blimp1 in T cell homeostasis regulation. Blimp1 has been shown to function as a direct activator of the Il10 gene and although its requirement for IL10 expression has been demonstrated in both Treg and Teff cells under inflammatory conditions, the intrinsic requirement of Blimp1 for homeostatic maintenance of these T cell subsets had not been investigated. Using mice with Foxp3 + Treg-cell specific deletion of Blimp1 and other approaches, here we show that Foxp3 + Treg cell-intrinsic expression of Blimp1 is required to control Treg and Teff cells homeostasis but, unexpectedly, it is dispensable to prevent development of severe spontaneous intestinal inflammation. In addition, we show that Blimp1 controls common and unique aspects of Treg and Teff cell function by differentially regulating gene expression in these T cell subsets. These findings document previously unappreciated aspects of Blimp1's role in T cell biology and shed light on the intricate mechanisms regulating Treg and Teff cell function.

Dysregulation of MST1/STK4, a key kinase component of the Hippo-YAP pathway, is linked to the etiology of many cancers with poor prognosis. However, how STK4 restricts the emergence of aggressive cancer remains elusive. Here, we investigated the effects of STK4, primarily localized in the cytoplasm, lipid raft, and nucleus, on cell growth and gene expression in aggressive prostate cancer. We demonstrated that lipid raft and nuclear STK4 had superior suppressive effects on cell growth in vitro and in vivo compared with cytoplasmic STK4. Using RNA sequencing and bioinformatics analysis, we identified several differentially expressed (DE) genes that responded to ectopic STK4 in all three subcellular compartments. We noted that the number of DE genes observed in lipid raft and nuclear STK4 cells were much greater than cytoplasmic STK4. Our functional annotation clustering showed that these DE genes were commonly associated with oncogenic pathways such as AR, PI3K/AKT, BMP/SMAD, GPCR, WNT, and RAS as well as unique pathways such as JAK/STAT, which emerged only in nuclear STK4 cells. These findings indicate that MST1/STK4/Hippo signaling restricts aggressive tumor cell growth by intersecting with multiple molecular pathways, suggesting that targeting of the STK4/Hippo pathway may have important therapeutic implications for cancer.

Glucose is considered the primary energy source for all cells, and some cancers are addicted to glucose. Here, we investigated the functional consequences of chronic glucose deprivation in serous ovarian cancer cells. We found that cells resistant to glucose starvation (glucose-restricted cells) demonstrated increased metabolic plasticity that was dependent on NNMT (Nicotinamide N-methyltransferase) expression. We further show that ZEB1 induced NNMT, rendered cells resistant to glucose deprivation and recapitulated metabolic adaptations and mesenchymal gene expression observed in glucose-restricted cells. NNMT depletion reversed metabolic plasticity in glucose-restricted cells and prevented de novo formation of glucose-restricted colonies. In addition to its role in glucose independence, we found that NNMT was required for other ZEB1-induced phenotypes, such as increased migration. NNMT protein levels were also elevated in metastatic and recurrent tumors compared to matched primary carcinomas, while normal ovary and fallopian tube tissue had no detectable NNMT expression. Our studies define a novel ZEB1/NNMT signaling axis, which elicits mesenchymal gene expression, as well as phenotypic and metabolic plasticity in ovarian cancer cells upon chronic glucose starvation. Understanding the causes of cancer cell plasticity is crucial for the development of therapeutic strategies to counter intratumoral heterogeneity, acquired drug resistance and recurrence in high-grade serous ovarian cancer (HGSC).

Bio- and hydrometallurgical experimental setups at 2-l reactor scale for the processing of fly ash from municipal waste incinerators were explored. We aimed to compare chemical H 2 SO 4 leaching and bioleaching; the latter involved the use of H 2 SO 4 and a mixed culture of acidophilic bacteria. The leaching yields of several elements, including some of those considered as critical (Mg, Co, Ce, Cr, Ga, Nb, Nd, Sb and Sm), are provided. At the end of the experiments, both leaching methods resulted in comparable yields for Mg and Zn (>90%), Al and Mn (>85%), Cr (∼65%), Ga (∼60%), and Ce (∼50%). Chemical leaching showed the best yields for Cu (95%), Fe (91%), and Ni (93%), whereas bioleaching was effective for Nd (76%), Pb (59%), and Co (55%). The two leaching methods generated solids of different quality with respect to the original material as we removed and significantly reduced the metals amounts, and enriched solutions where metals can be recovered for example as mixed salts for further treatment. Compared to chemical leaching the bioleaching halved the use of H 2 SO 4 , i.e., a part of agent costs, as a likely consequence of bio-produced acid and improved metal solubility., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Osmium release from Municipal Solid Waste Incinerators (MSWI), even if acknowledged to occur at least over the last fifteen years, remains overlooked in the majority of recent studies. We present the osmium concentration and (187)Os/(188)Os isotopic measurements of different kinds of bottom and fly ash samples from MSWI plants and reference materials of incinerator fly ash (BCR176 and BCR176R). The analysis of the unknown ash samples shows a relatively wide range of (187)Os/(188)Os ratios (0.24-0.70) and Os concentrations (from 0.026 ng/g to 1.65 ng/g). Osmium concentrations and isotopic signatures differ from those of other known Os sources, either natural or manmade, suggesting a mixture of both contributions in the MSWI feedstock material. Furthermore, the comparison between the BCR176 and the renewed BCR176R indicates a decrease in Os concentration of one order of magnitude over the years (from 1 to 0.1 ng/g) due to improved recycling efficiency of Os-bearing waste. The estimated annual amount of Os from a typical incinerator (using average Os values and MSWI mass balance) is 13.4 g/a. The osmium potentially released from MSWI smokestacks is predicted to be from 16 to 38 ng Os/m(2)/a, considering a medium size country having 50 MSWI facilities; therefore much higher than the naturally transported osmium from continental dust in the atmosphere (about 1 pg Os/m(2)/a). MSWI systems are considered one of the best options for municipal solid waste management in industrialised countries, but their contribution to the Os budget can be significant., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Bottom and fly ashes from Municipal Solid Waste Incinerators (MSWI) are hazardous products that present concern for their safe management. An attractive option to reduce their impact both on the environment and the financial commitment is turning MSWI ashes into secondary raw materials. In this study we present the REE content and distribution of bottom and fly ashes from MSWI after a highly effective digestion method and samples analysis by ICP-MS. The chondrite-normalised REE patterns of MSWI bottom and fly ash are comparable with that of crustal averages, suggesting a main geogenic source. Deviations from typical crustal pattern (e.g., Eu, Tb) disclose a contribution of likely anthropogenic provenance. The correlation with major elements indicates possible sources for REE and facilitates a preliminary resource assessment. Moreover, magnetic susceptibility measurements can be a useful prospecting method in urban ores made of MSWI ashes. The relationship between REE and some influencing parameters (e.g., Pricing Influence Factor) emphasises the importance of MSWI ash as alternative source of REE and the need of further efforts for REE recovery and purification from low concentrations but high flows waste., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Purpose: Children with Hirschsprung disease (HD) who have a history of enterocolitis (HAEC) have a shift in colonic microbiota, many of which are necessary for short chain fatty acid (SCFA) production. As SCFAs play a critical role in colonic mucosal preservation, we hypothesized that fecal SCFA composition is altered in children with HAEC., Methods: A multicenter study enrolled 18 HD children, abstracting for history of feeding, antibiotic/probiotic use, and enterocolitis symptoms. HAEC status was determined per Pastor et al. criteria (12). Fresh feces were collected for microbial community analysis via 16S sequencing as well as SCFA analysis by gas chromatography-mass spectrometry., Results: Nine patients had a history of HAEC, and nine had never had HAEC. Fecal samples from HAEC children showed a 4-fold decline in total SCFA concentration vs. non-HAEC HD patients. We then compared the relative composition of individual SCFAs and found reduced acetate and increased butyrate in HAEC children. Finally, we measured relative abundance of SCFA-producing fecal microbiota. Interestingly, 10 of 12 butyrate-producing genera as well as 3 of 4 acetate-producing genera demonstrated multi-fold expansion., Conclusion: Children with HAEC history have reduced fecal SCFAs and altered SCFA profile. These findings suggest a complex interplay between the colonic metabolome and changes in microbiota, which may influence the pathogenesis of HAEC., (Copyright © 2016. Published by Elsevier Inc.)

Expression of genes associated with inflammation was analyzed during differentiation of human pluripotent stem cells (PSCs) to hepatic cells. Messenger RNA transcript profiles of differentiated endoderm (day 5), hepatoblast (day 15) and hepatocyte-like cells (day 21) were obtained by RNA sequencing analysis. When compared to endoderm cells an immature cell type, the hepatic cells (days 15 and 21) had significantly higher expression of acute phase protein genes including complement factors, coagulation factors, serum amyloid A and serpins. Furthermore, hepatic phase of cells expressed proinflammatory cytokines IL18 and IL32 as well as cytokine receptors IL18R1, IL1R1, IL1RAP, IL2RG, IL6R, IL6ST and IL10RB. These cells also produced CCL14, CCL15, and CXCL- 1, 2, 3, 16 and 17 chemokines. Endoderm cells had higher levels of chemokine receptors, CXCR4 and CXCR7, than that of hepatic cells. Sirtuin family of genes involved in aging, inflammation and metabolism were differentially regulated in endoderm and hepatic phase cells. Ligands and receptors of the tumor necrosis factor (TNF) family as well as downstream signaling factors TRAF2, TRAF4, FADD, NFKB1 and NFKBIB were differentially expressed during hepatic differentiation.

The incineration of municipal solid wastes is an important part of the waste management system along with recycling and waste disposal, and the solid residues produced after the thermal process have received attention for environmental concerns and the recovery of valuable metals. This study focuses on the Critical Raw Materials (CRM) content in solid residues from two Italian municipal waste incinerator (MSWI) plants. We sampled untreated bottom ash and fly ash residues, i.e. the two main outputs of common grate-furnace incinerators, and determined their total elemental composition with sensitive analytical techniques such as XRF and ICP-MS. After the removal of a few coarse metallic objects from bottom ashes, the corresponding ICP solutions were obtained using strong digestion methods, to ensure the dissolution of the most refractory components that could host significant amounts of precious metals and CRM. The integration of accurate chemical data with a substance flow analysis, which takes into account the mass balance and uncertainties assessment, indicates that bottom and fly ashes can be considered as a low concentration stream of precious and high-tech metals. The magnesium, copper, antimony and zinc contents are close to the corresponding values of a low-grade ore. The distribution of the elements flow between bottom and fly ash, and within different grain size fractions of bottom ash, is appraised. Most elements are enriched in the bottom ash flow, especially in the fine grained fractions. However, the calculated transfer coefficients indicate that Sb and Zn strongly partition into the fly ashes. The comparison with available studies indicates that the CRM concentrations in the untreated solid residues are comparable with those residues that undergo post-treatment beneficiations, e.g. separation between ferrous and non-ferrous fractions. The suggested separate collection of "fresh" bottom ash, which could be processed for further mineral upgrading, can constitute an attractive option of the waste management system, when physical-mechanical devices are not available or could not be implemented in old MSWI systems. The suggested procedure may lead to the improvement of recovery efficiency up to 83% for CRM and 94% for other valuable metals., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Unlabelled: Human pluripotent stem cells (hPSCs) are now being used for both disease modeling and cell therapy; however, efficient homologous recombination (HR) is often crucial to develop isogenic control or reporter lines. We showed that limited low-dose irradiation (LDI) using either γ-ray or x-ray exposure (0.4 Gy) significantly enhanced HR frequency, possibly through induction of DNA repair/recombination machinery including ataxia-telangiectasia mutated, histone H2A.X and RAD51 proteins. LDI could also increase HR efficiency by more than 30-fold when combined with the targeting tools zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats. Whole-exome sequencing confirmed that the LDI administered to hPSCs did not induce gross genomic alterations or affect cellular viability. Irradiated and targeted lines were karyotypically normal and made all differentiated lineages that continued to express green fluorescent protein targeted at the AAVS1 locus. This simple method allows higher throughput of new, targeted hPSC lines that are crucial to expand the use of disease modeling and to develop novel avenues of cell therapy., Significance: The simple and relevant technique described in this report uses a low level of radiation to increase desired gene modifications in human pluripotent stem cells by an order of magnitude. This higher efficiency permits greater throughput with reduced time and cost. The low level of radiation also greatly increased the recombination frequency when combined with developed engineered nucleases. Critically, the radiation did not lead to increases in DNA mutations or to reductions in overall cellular viability. This novel technique enables not only the rapid production of disease models using human stem cells but also the possibility of treating genetically based diseases by correcting patient-derived cells., (©AlphaMed Press.)

Pluripotent stem cells are being actively studied as a cell source for regenerating damaged liver. For long-term survival of engrafting cells in the body, not only do the cells have to execute liver-specific function but also withstand the physical strains and invading pathogens. The cellular innate immune system orchestrated by the interferon (IFN) pathway provides the first line of defense against pathogens. The objective of this study is to assess the innate immune function as well as to systematically profile the IFN-induced genes during hepatic differentiation of pluripotent stem cells. To address this objective, we derived endodermal cells (day 5 post-differentiation), hepatoblast (day 15) and hepatocyte-like cells (day 21) from human embryonic stem cells (hESCs). Day 5, 15 and 21 cells were stimulated with IFN-α and subjected to IFN pathway analysis. Transcriptome analysis was carried out by RNA sequencing. The results showed that the IFN-α treatment activated STAT-JAK pathway in differentiating cells. Transcriptome analysis indicated stage specific expression of classical and non-classical IFN-stimulated genes (ISGs). Subsequent validation confirmed the expression of novel ISGs including RASGRP3, CLMP and TRANK1 by differentiated hepatic cells upon IFN treatment. Hepatitis C virus replication in hESC-derived hepatic cells induced the expression of ISGs--LAMP3, ETV7, RASGRP3, and TRANK1. The hESC-derived hepatic cells contain intact innate system and can recognize invading pathogens. Besides assessing the tissue-specific functions for cell therapy applications, it may also be important to test the innate immune function of engrafting cells to ensure adequate defense against infections and improve graft survival., (Copyright © 2015. Published by Elsevier B.V.)

High-grade serous ovarian cancers (HGSOC) are genomically complex, heterogeneous cancers with a high mortality rate, due to acquired chemoresistance and lack of targeted therapy options. Cyclin-dependent kinase inhibitors (CDKi) target the retinoblastoma (RB) signaling network, and have been successfully incorporated into treatment regimens for breast and other cancers. Here, we have compared mechanisms of response and resistance to three CDKi that target either CDK4/6 or CDK2 and abrogate E2F target gene expression. We identify CCNE1 gain and RB1 loss as mechanisms of resistance to CDK4/6 inhibition, whereas receptor tyrosine kinase (RTK) and RAS signaling is associated with CDK2 inhibitor resistance. Mechanistically, we show that ETS factors are mediators of RTK/RAS signaling that cooperate with E2F in cell cycle progression. Consequently, CDK2 inhibition sensitizes cyclin E1-driven but not RAS-driven ovarian cancer cells to platinum-based chemotherapy. In summary, this study outlines a rational approach for incorporating CDKi into treatment regimens for HGSOC.

Background: Compared with the standard qPCR, nanoliter-scale qPCR can use smaller quantities of RNA and increase throughput. The TaqMan™ OpenArray® NT Cycler System was assessed for use with degraded RNA from formalin-fixed paraffin-embedded (FFPE) tumors., Results: Expression of candidate prognostic genes was quantified using the OpenArray platform and matching fresh frozen and FFPE patient renal cell carcinomas. Reverse transcription, with gene-specific reverse transcription and preamplification, optimized the percentage of detectable transcripts. When using high quality RNA from fresh frozen tumors, the OpenArray platform identified 30 prognostic genes. However, when using RNA from FFPE tumors, only 13 prognostic genes were identified, but this increased to 33 with addition of preamplification., Conclusion: The OpenArray platform can be optimized to quantify gene expressions from FFPE tumors.

De novo somatic mutations in focal areas are well documented in diseases such as neoplasia but are rarely reported in malformation of the developing brain. Hemimegalencephaly (HME) is characterized by overgrowth of either one of the two cerebral hemispheres. The molecular etiology of HME remains a mystery. The intractable epilepsy that is associated with HME can be relieved by the surgical treatment hemispherectomy, allowing sampling of diseased tissue. Exome sequencing and mass spectrometry analysis in paired brain-blood samples from individuals with HME (n = 20 cases) identified de novo somatic mutations in 30% of affected individuals in the PIK3CA, AKT3 and MTOR genes. A recurrent PIK3CA c.1633G>A mutation was found in four separate cases. Identified mutations were present in 8-40% of sequenced alleles in various brain regions and were associated with increased neuronal S6 protein phosphorylation in the brains of affected individuals, indicating aberrant activation of mammalian target of rapamycin (mTOR) signaling. Thus HME is probably a genetically mosaic disease caused by gain of function in phosphatidylinositol 3-kinase (PI3K)-AKT3-mTOR signaling.

Background: Establishing the genetic basis of phenotypes such as skeletal dysplasia in model organisms can provide insights into biologic processes and their role in human disease., Methods: We screened mutagenized mice and observed a neonatal lethal skeletal dysplasia with an autosomal recessive pattern of inheritance. Through genetic mapping and positional cloning, we identified the causative mutation., Results: Affected mice had a nonsense mutation in the thyroid hormone receptor interactor 11 gene (Trip11), which encodes the Golgi microtubule-associated protein 210 (GMAP-210); the affected mice lacked this protein. Golgi architecture was disturbed in multiple tissues, including cartilage. Skeletal development was severely impaired, with chondrocytes showing swelling and stress in the endoplasmic reticulum, abnormal cellular differentiation, and increased cell death. Golgi-mediated glycosylation events were altered in fibroblasts and chondrocytes lacking GMAP-210, and these chondrocytes had intracellular accumulation of perlecan, an extracellular matrix protein, but not of type II collagen or aggrecan, two other extracellular matrix proteins. The similarities between the skeletal and cellular phenotypes in these mice and those in patients with achondrogenesis type 1A, a neonatal lethal form of skeletal dysplasia in humans, suggested that achondrogenesis type 1A may be caused by GMAP-210 deficiency. Sequence analysis revealed loss-of-function mutations in the 10 unrelated patients with achondrogenesis type 1A whom we studied., Conclusions: GMAP-210 is required for the efficient glycosylation and cellular transport of multiple proteins. The identification of a mutation affecting GMAP-210 in mice, and then in humans, as the cause of a lethal skeletal dysplasia underscores the value of screening for abnormal phenotypes in model organisms and identifying the causative mutations., (2010 Massachusetts Medical Society)