Search

Spindle cell and pleomorphic lipoma constitute a spectrum of lipomatous lesions with characteristic clinical, morphologic, immunohistochemical, and molecular features. Multiple variants have been previously described including vascular, fibrous, plexiform, and those with significantly less fat termed “low-fat” and “fat-free” by Folpe. Cytogenetically, spindle cell lipomas frequently display monoallelic loss of 13q14 region, an abnormality also found in cellular angiofibroma and mammary-type myofibroblastoma. Pseudoangiomatous spindle cell lipoma, originally described by Fletcher et al in 1994, is a rare variant within the spindle cell/pleomorphic lipoma spectrum, with less than 20 published cases. It consists of an admixture of spindle cells, “ropey” collagen, variable amounts of mature fat, and irregular, branching slit-like vascular spaces. The authors present a case of a 1-cm subcutaneous lesion excised from the neck of a 70-year-old man with classic histologic and immunohistochemical features of “low-fat” pseudoangiomatous spindle cell lipoma. Fluorescence in situ hybridization demonstrated a loss of 13q14 region, a characteristic presumed cytogenetic finding of spindle cell lipoma, which has been previously unconfirmed in this variant.

ABSTRACTMycoplasma pneumoniaeis a leading cause of community-acquired pneumonia (CAP) across patient populations of all ages. We have developed a loop-mediated isothermal amplification (LAMP) assay that enables rapid, low-cost detection of M. pneumoniaefrom nucleic acid extracts and directly from various respiratory specimen types. The assay implements calcein to facilitate simple visual readout of positive results in approximately 1 h, making it ideal for use in primary care facilities and resource-poor settings. The analytical sensitivity of the assay was determined to be 100 fg by testing serial dilutions of target DNA ranging from 1 ng to 1 fg per reaction, and no cross-reactivity was observed against 17 other Mycoplasmaspecies, 27 common respiratory agents, or human DNA. We demonstrated the utility of this assay by testing nucleic acid extracts (n= 252) and unextracted respiratory specimens (n= 72) collected during M. pneumoniaeoutbreaks and sporadic cases occurring in the United States from February 2010 to January 2014. The sensitivity of the LAMP assay was 88.5% tested on extracted nucleic acid and 82.1% evaluated on unextracted clinical specimens compared to a validated real-time PCR test. Further optimization and improvements to this method may lead to the availability of a rapid, cost-efficient laboratory test for M. pneumoniaedetection that is more widely available to primary care facilities, ultimately facilitating prompt detection and appropriate responses to potential M. pneumoniaeoutbreaks and clusters within the community.

Compact Reconnaissance Imaging Spectrometer for Mars hyperspectral (1.0–2.65?µm) along-track oversampled observations covering Victoria, Santa Maria, Endeavour, and Ada craters were processed to 6?m/pixel and used in combination with Opportunity observations to detect and map hydrated Mg and Ca sulfate minerals in the Burns formation. The strongest spectral absorption features were found to be associated with outcrops that are relatively young and fresh (Ada) or preferentially scoured of dust, soil, and coatings by prevailing winds. At Victoria and Santa Maria, the scoured areas are on the southeastern rims and walls, opposite to the sides where wind-blown sands extend out of the craters. At Endeavour, the deepest absorptions are in Botany Bay, a subdued and buried rim segment that exhibits high thermal inertias, extensive outcrops, and is interpreted to be a region of enhanced wind scour extending up and out of the crater. Ada, Victoria, and Santa Maria outcrops expose the upper portion of the preserved Burns formation and show spectral evidence for the presence of kieserite. In contrast, gypsum is pervasive spectrally in the Botany Bay exposures. Gypsum, a relatively insoluble evaporative mineral, is interpreted to have formed close to the contact with the Noachian crust as rising groundwaters brought brines close to and onto the surface, either as a direct precipitate or during later diagenesis. The presence of kieserite at the top of the section is hypothesized to reflect precipitation from evaporatively concentrated brines or dehydration of polyhydrated sulfates, in both scenarios as the aqueous environment evolved to very arid conditions. Hydrated Mg and Ca sulfate Burns formation minerals mapped with MRO and MER data

We assimilate atmospheric temperatures from the Emirates Mars Infrared Spectrometer on board the Emirates Mars Mission (EMM) into the Mars Planetary Climate Model at the start of EMM's early science phase (Mars Year 36 Ls= 57.34–92.90°). Mars data assimilation benefits significantly from EMM's unique near‐hemispheric observations, frequent repeated observations of the same location, and full diurnal cycle coverage. Our analysis verifies well against in‐sample temperature observations, and is 1–3 K warmer than Mars Climate Sounder observations. We identify a warm front in concurrent Emirates eXploration Imager observations by correlating an elongated water ice cloud with temperatures and winds in the analysis; the analysis winds are consistent with its observed motion. We also calculate the full horizontal wind diurnal cycle; the zonal flow is weaker and the meridional circulation is stronger than simulating the same time period using the model alone. The Emirates Mars Mission (EMM) promises advances in our understanding of Mars' atmosphere similar to when geostationary satellites first observed Earth. Data assimilation is a process where we combine observations with an atmospheric simulation. Using it to study Mars will benefit from EMM's observations of the whole of one side of the planet, frequent repeated observations of the same location, and observations of the full day‐night cycle. We combined observations of Mars atmospheric temperatures with our model over 79 Martian days at the start of EMM's main study period. We were able to demonstrate what is possible with EMM that has not been possible before. In particular, we found a long water ice cloud near the north pole in separate visible and ultraviolet images made by EMM. By comparing the motion and structure of this cloud with our results, we found that this “warm front” also appears in our results, and we were able to deduce properties of the front that were not observed. We were also able to deduce how Martian winds change over the course of the day and night, by making use of EMM's temperature observations over the full day‐night period. We assimilate atmospheric temperature profiles from Emirates Mars Mission‐Emirates Mars InfraRed Spectrometer (EMM‐EMIRS) over a 79‐sol period in Mars Year 36 shortly before northern summer solsticeEMIRS’ near‐hemispheric spatial coverage is used to analyze complete weather systems; we deduce the structure and motion of a warm frontThe horizontal wind diurnal cycle is retrieved by assimilation based on EMM‐EMIRS’ extended local time coverage of atmospheric temperatures We assimilate atmospheric temperature profiles from Emirates Mars Mission‐Emirates Mars InfraRed Spectrometer (EMM‐EMIRS) over a 79‐sol period in Mars Year 36 shortly before northern summer solstice EMIRS’ near‐hemispheric spatial coverage is used to analyze complete weather systems; we deduce the structure and motion of a warm front The horizontal wind diurnal cycle is retrieved by assimilation based on EMM‐EMIRS’ extended local time coverage of atmospheric temperatures

The Emirates Mars Mission (EMM) science phase began in Martian Year 36, solar longitude 49, which is outside of the classical Mars dust storm season. EMM observed a distinct dust cloud at northern mid‐to‐high latitudes on 10 September 2021 (Martian Year 36, solar longitude 97). The dust cloud is an arc‐shaped dust storm, typically observed at the northern polar cap edge. This type of non‐season dust storm is a well‐known phenomenon, but this particular case is interesting because the dust cloud has frontal structure. A large atmospheric front is unusual in this location and season. Moreover, EMM's unique observational coverage adds value to this observation. EMM provided a sequence of four camera images, which are separated by just 2–3 hr. The dust cloud showed very little motion over 7–8 hr, that is, it is quasi‐stationary. We discuss relevant dynamical processes, supported by a consistency check with the Mars Climate Database. The Emirates Mars Mission (EMM) officially started its science observations on 23 May 2021. We saw some, but not many dust storms until end of 2021. That is because Mars has a dust storm season and a non‐dust‐storm‐season, and EMM arrived during the latter. On 10 September 2021, EMM observed an arc‐shaped dust storm close to the northern polar cap. This type of non‐season dust storm is well‐known. What makes this observation interesting is that the dust storm is also a weather front. A large atmospheric front is unusual for this location and time during the Martian year. Moreover, it is unique how EMM observed this dust storm. EMM took a camera image every 2–3 hr, giving four dust cloud images in total. The dust cloud showed very little motion over 7–8 hr. We discuss how the motion of air masses in the Mars atmosphere may have caused the observed dust storm. The discussion is supported by wind and temperature data from the Mars Climate Database. We study a sequence of four Emirates Mars Mission images, showing a frontal dust cloud on 10 September 2021 (solar longitude 97)The dust cloud extends from the Chasma Boreale of the northern polar cap to the midlatitudes; it shows very little movement for 7–8 hrLarge atmospheric fronts are unusual in this location and season; we discuss dynamical processes, supported by the Mars Climate Database We study a sequence of four Emirates Mars Mission images, showing a frontal dust cloud on 10 September 2021 (solar longitude 97) The dust cloud extends from the Chasma Boreale of the northern polar cap to the midlatitudes; it shows very little movement for 7–8 hr Large atmospheric fronts are unusual in this location and season; we discuss dynamical processes, supported by the Mars Climate Database

Observations by the Emirates eXploration Imager (EXI) on‐board the Emirates Mars Mission are used to characterize the diurnal, seasonal, and spatial behavior of aphelion cloud belt during Mars Year 36 LS∼ 30°–190°. Building from previous work with the Mars Color Imager (MARCI) onboard the Mars Reconnaissance Orbiter, we retrieve water ice extinction optical depth (τice) with an uncertainty ±0.0232 (excluding particle size effects). We connect EXI and MARCI using radiance and τice. Zonal and meridional diurnal trends are analyzed over 6–18 hr Local True Solar Time. The retrievals show large morning‐evening asymmetries about a minimum near 12 hr. The latitudinal distributions in early morning are extensive and particularly striking near mid‐summer. Comparisons to the Mars Planetary Climate Model show reasonable agreement with basic diurnal behavior, but noticeable departures include too much water ice in early morning, the general latitudinal extent, and behavior at smaller scales like the volcanoes and other topographically distinct features. Water ice clouds have important roles in the Martian atmosphere because they can influence weather and act as probes of important weather and climate processes. Using the camera on‐board the Emirates Mars Mission, water ice clouds are studied for the first time throughout the Martian day and year at scales of 10–20 km around the planet. We study a key cloud structure called the aphelion cloud belt (ACB) that encircles the planet at low latitudes during the northern hemisphere spring and summer seasons. Using the camera images from this period, we examine how the ACB structure changes from morning through evening and throughout these two seasons. We developed a computer program that converts the brightness of a pixel into a measure of the cloud thickness. We find that the ACB clouds are much thicker and wide‐spread in the early morning compared to other times of day; and are much more extant across the planet in the morning, particularly in mid‐summer. We also compare to weather prediction programs and find important differences that will help scientists improve Mars weather forecasts for future research and missions. The Emirates eXploration Imager is used to retrieve ice extinction optical depth in Mars Year 36 during solar longitudes 30–190°Diurnal trends of the aphelion cloud belt are examined between 6 and 18 hr using both zonal and meridional maps, revealing new behaviorComparisons to the Mars Planetary Climate Model show reasonable agreement with broad structure, but important differences are noted The Emirates eXploration Imager is used to retrieve ice extinction optical depth in Mars Year 36 during solar longitudes 30–190° Diurnal trends of the aphelion cloud belt are examined between 6 and 18 hr using both zonal and meridional maps, revealing new behavior Comparisons to the Mars Planetary Climate Model show reasonable agreement with broad structure, but important differences are noted

Observations by several cameras on the Perseverance rover showed a 22° scattering halo around the Sun over several hours during northern midsummer (solar longitude 142°). Such a halo has not previously been seen beyond Earth. The halo occurred during the aphelion cloud belt season and the cloudiest time yet observed from the Perseverance site. The halo required crystalline water‐ice cloud particles in the form of hexagonal columns large enough for refraction to be significant, at least 11 μm in diameter and length. From a possible 40–50 km altitude, and over the 3.3 hr duration of the halo, particles could have fallen 3–12 km, causing downward transport of water and dust. Halo‐forming clouds are likely rare due to the high supersaturation of water that is required but may be more common in northern subtropical regions during northern midsummer. A scattering halo, or bright ring around the Sun, was seen in pictures taken by cameras on the Perseverance rover. Such halos are commonly seen in ice clouds on Earth but have never before been seen on Mars. When the halo was seen, on 15 December 2021, the rover was within a period of unusually cloudy weather near the end of a season known for water‐ice clouds in northern tropical areas such as the rover's site in Jezero crater. The appearance and size of the halo showed that the clouds were made of water‐ice crystals shaped like hexagonal columns. The crystals were likely larger than those in most water‐ice clouds on Mars, which allowed the halo to form. A 22°‐radius halo around the Sun was imaged for over 3 hr by cameras on the Perseverance rover on MarsSuch a halo is diagnostic of scattering by large, hexagonal water‐ice crystals and has not previously been seen beyond EarthThe halo implies that high supersaturation of water may be more common in late summer in the northern subtropics than elsewhere A 22°‐radius halo around the Sun was imaged for over 3 hr by cameras on the Perseverance rover on Mars Such a halo is diagnostic of scattering by large, hexagonal water‐ice crystals and has not previously been seen beyond Earth The halo implies that high supersaturation of water may be more common in late summer in the northern subtropics than elsewhere

The mucosal microbiota lives in close proximity with the intestinal epithelium and may interact more directly with the host immune system than the luminal/fecal bacteria. The availability of nutrients in the mucus layer of the epithelium is also very different from the gut lumen environment. Inferred metagenomic analysis for microbial function of the mucosal microbiota is possible by PICRUSt. We recently found that by using this approach, actively inflamed tissue of ulcerative colitis (UC) patients have mucosal communities enriched for genes involved in lipid and amino acid metabolism, and reduced for carbohydrate and nucleotide metabolism. Here, we find that the same bacterial taxa (e.g. Acinetobacter) and predicted microbial pathways enriched in actively inflamed colitis tissue are also enriched in the mucosa of subjects undergoing routine screening colonoscopies, when compared with paired samples of luminal/fecal bacteria. These results suggest that the mucosa of healthy individuals may be a reservoir of aerotolerant microbial communities expanded during colitis.

Habitat selection by mammalian carnivores may be driven by prey availability, physical characteristics of the habitat, and landscape context. However, the cues used by carnivores to select habitat are often unclear. We examined the seasonal diet of American mink Neovison visonand determined if the abundance of a primary prey, crayfish, was an important driver of habitat use during summer in an agricultural landscape in Illinois. We also evaluated effects of stream size, water depth, riparian buffer width, and urbanization on occupancy of stream segments by mink. We collected mink scats during three seasons and tested for seasonal differences in the percentage of occurrence and volume percentage of prey classes in the diet of mink. Crayfish remains were the dominant component of mink scats during summer. In summer 2012, we performed occupancy surveys for mink and concurrently measured crayfish densities and habitat features in 59 stream segments. Site occupancy by mink was related positively to presence of local areas with high crayfish concentrations (hotspots) instead of local habitat characteristics that might indicate high prey densities. Mink also were associated negatively with degree of urbanization and stream size. Our study highlights the effectiveness of integrating data on diets and occupancy modeling to obtain insights on cues used by carnivores to select habitat.

ABSTRACTAn outbreak at a university in Georgia was identified after 83 cases of probable pneumonia were reported among students. Respiratory specimens were obtained from 21 students for the outbreak investigation. The TaqMan array card (TAC), a quantitative PCR (qPCR)-based multipathogen detection technology, was used to initially identify Mycoplasma pneumoniaeas the causative agent in this outbreak. TAC demonstrated 100% diagnostic specificity and sensitivity compared to those of the multiplex qPCR assay for this agent. All M. pneumoniaespecimens (n= 12) and isolates (n= 10) were found through genetic analysis to be susceptible to macrolide antibiotics. The strain diversity of M. pneumoniaeassociated with this outbreak setting was identified using a variety of molecular typing procedures, resulting in two P1 genotypes (types 1 [60%] and 2 [40%]) and seven different multilocus variable-number tandem-repeat analysis (MLVA) profiles. Continued molecular typing of this organism, particularly during outbreaks, may enhance the current understanding of the epidemiology of M. pneumoniaeand may ultimately lead to a more effective public health response.

Diurnal analyses of water ice cloud optical depths retrieved from thermal infrared spectra by the Emirates Mars Infrared Spectrometer showed changing cloud abundance throughout the Martian day. Observations began with the start of the Emirates Mars Mission science phase near the beginning of aphelion‐season in Mars Year 36 and included the prominent aphelion cloud belt (ACB) and orographic clouds in the vicinity of volcanoes. A midday minimum with higher morning and afternoon optical depths was typical for the ACB, though with considerable spatial variability in this diurnal pattern. Clouds near volcanoes reached a minimum before local noon and tended to increase in abundance throughout the afternoon. Comparisons against the Laboratoire de Météorologie Dynamiqueglobal circulation model showed analogous spatial patterns in the diurnal signal, which suggested thermal tides and topographic effects to be the predominant drivers of ACB variability, while more localized circulations affected volcano clouds. Observations from the Emirates Mars Infrared Spectrometer onboard the Emirates Mars Mission (EMM) spacecraft were used to measure the abundance of clouds in the Martian atmosphere and investigate how they changed throughout the day. Due to the unique nature of EMM's high orbit, the observations provided by EMIRS cover all times of day and provide more detailed information about how clouds change as compared to many previous missions. In these results we present information about this daytime cloud variability for different regions on Mars. A prominent region of clouds that is commonly observed near the equator during Mars' cold season—known as the aphelion cloud belt—was observed to reach a minimum near midday, with more clouds typically observed in both the morning and afternoon. Distinct differences were found in clouds observed near volcanoes, which tended to reach a minimum before local noon and increase throughout the afternoon. These results add detail to our understanding of cloud behavior and help us to validate computer models of the Martian atmosphere. Infrared spectra from the Emirates Mars Infrared Spectrometer were used to obtain water ice cloud optical depths throughout the dayThe aphelion cloud belt had a midday minimum with higher optical depths in the morning and afternoonOrographic clouds near volcanoes were observed to increase throughout the afternoon Infrared spectra from the Emirates Mars Infrared Spectrometer were used to obtain water ice cloud optical depths throughout the day The aphelion cloud belt had a midday minimum with higher optical depths in the morning and afternoon Orographic clouds near volcanoes were observed to increase throughout the afternoon

Thermal infrared spectra taken by the Emirates Mars Infrared Spectrometer (EMIRS) on‐board the Emirates Mars Mission (EMM) spacecraft are well suited for the retrieval of surface temperatures, the atmospheric temperature profile from the surface to ∼40 km, and the column abundance of dust aerosols, water ice clouds, and water vapor. A constrained linear inversion retrieval routine that includes multiple scattering has been developed and optimized for this purpose. Here, we present a brief overview of the retrieval algorithm and first atmospheric science results from observations taken by EMIRS over the first Earth year of EMM Science Phase operations. These retrievals show extensive water ice clouds, typical for the aphelion season of these observations, and the expected north polar summer maximum and subsequent equatorward transport of water vapor is well documented. An unusually strong and early regional dust storm and its associated thermal response were also observed. Data returned from the Emirates Mars Infrared Spectrometer (EMIRS) have been used to characterize the atmosphere of Mars. These data allow estimates of atmospheric temperature as a function of height, the amount of dust and water ice clouds in the atmosphere, and the abundance of water vapor. In this work we describe the process for estimating these quantities and we give a brief overview of our first results. The results show that Mars was relatively cool, relatively cloudy, but with little dust. This was expected given the season on Mars that was observed. More surprising was the observation of a dust storm that occurred earlier in the Martian year than usual. Thermal infrared spectra of Mars taken by the Emirates Mars Infrared Spectrometer have been used to characterize the atmospheric stateThese aphelion season observations show the expected relatively cool atmosphere with prominent water ice clouds and generally little dustThe initiation and evolution of a regional dust storm that occurred unusually early in the season was observed Thermal infrared spectra of Mars taken by the Emirates Mars Infrared Spectrometer have been used to characterize the atmospheric state These aphelion season observations show the expected relatively cool atmosphere with prominent water ice clouds and generally little dust The initiation and evolution of a regional dust storm that occurred unusually early in the season was observed

The Nadir and Occultation for MArs Discovery (NOMAD)/UV‐visible (UVIS) spectrometer on the ExoMars Trace Gas Orbiter provided observations of ozone (O3) and water vapor in the global dust storm of 2018. Here we show in detail, using advanced data filtering and chemical modeling, how Martian O3in the middle atmosphere was destroyed during the dust storm. In data taken exactly 1 year later when no dust storm occurred, the normal situation had been reestablished. The model simulates how water vapor is transported to high altitudes and latitudes in the storm, where it photolyzes to form odd hydrogen species that catalyze O3. O3destruction is simulated at all latitudes and up to 100 km, except near the surface where it increases. The simulations also predict a strong increase in the photochemical production of atomic hydrogen in the middle atmosphere, consistent with the enhanced hydrogen escape observed in the upper atmosphere during global dust storms. Global dust storms are rare but impactful events on Mars, occurring about once in a decade. Previous investigations found how water vapor is redistributed throughout the entire atmosphere in a dust storm. Photolysis of water vapor by sunlight produces highly reactive species that destroy ozone (O3). Here we present O3measurements taken by the NOMAD/UVIS instrument on the ExoMars Trace Gas Orbiter in the 2018 global dust storm. After advanced data filtering, they demonstrate how O3in the middle atmosphere was much reduced compared to one Mars year later when no dust storm occurred. 3D atmospheric model simulations of atmospheric chemistry in the global dust storm confirm this planet‐wide O3destruction, and help to understand the involved processes. The simulations also predict a strong increase in production of atomic hydrogen in the middle atmosphere, that can explain the observed increased hydrogen atmospheric escape during global dust storms. NOMAD ozone (O3) data filtering during the 2018 global dust storm shows strong O3destruction compared to one year later with no dust storm3D simulations of atmospheric chemistry in the 2018 global dust storm are presented to understand impact on odd hydrogen and odd oxygenThe model confirms middle‐atmospheric O3destruction in the dust storm and predicts increased photochemical production of hydrogen NOMAD ozone (O3) data filtering during the 2018 global dust storm shows strong O3destruction compared to one year later with no dust storm 3D simulations of atmospheric chemistry in the 2018 global dust storm are presented to understand impact on odd hydrogen and odd oxygen The model confirms middle‐atmospheric O3destruction in the dust storm and predicts increased photochemical production of hydrogen

ABSTRACTMacrolide-resistant Mycoplasma pneumoniaeis an increasing problem worldwide but is not well documented in the United States. We report a cluster of macrolide-resistant M. pneumoniaecases among a mother and two daughters.

Microarray methodologies, to include array comparative genomic hybridization and single-nucleotide polymorphism–based arrays, are innovative methods that provide genomic data. These data should be correlated with the results from the standard methods, chromosome and/or fluorescence in situhybridization, to ascertain and characterize the genomic aberrations of neoplastic disorders, both liquid and solid tumors. Over the past several decades, standard methods have led to an accumulation of genetic information specific to many neoplasms. This specificity is now used for the diagnosis and classification of neoplasms. Cooperative studies have revealed numerous correlations between particular genetic aberrations and therapeutic outcomes. Molecular investigation of chromosomal abnormalities identified by standard methods has led to discovery of genes, and gene function and dysfunction. This knowledge has led to improved therapeutics and, in some disorders, targeted therapies. Data gained from the higher-resolution microarray methodologies will enhance our knowledge of the genomics of specific disorders, leading to more effective therapeutic strategies. To assist clinical laboratories in validation of the methods, their consistent use, and interpretation and reporting of results from these microarray methodologies, the American College of Medical Genetics and Genomics has developed the following professional standard and guidelines.

SUMMARY By definition, autism spectrum disorder (ASD) emerges early in life. Core clinical symptoms generally appear after a childs first birthday, and most children receive a diagnosis by the age of 4 years. This relatively narrow window of birth to age of onset affords the opportunity to chart the neurodevelopmental processes that give rise to ASD. Although much remains unknown, magnetic resonance brain imaging studies centered around the emergence of the disorder have yielded important clues about its pathogenesis. Prominent findings include evidence of increased cortical gray and white matter volumes, increased amygdala volumes, aberrant structural and functional connectivity, and atypical neurodevelopmental trajectories. Findings to date suggest a disrupted pattern of early brain development during an interval typically characterized by dramatic experience-dependent neurobehavioral development. Developmentally informed neuroimaging studies of ASD have the potential to improve our knowledge pertaining to etiology and early intervention.

ABSTRACTIn this study, we evaluated a recently developed multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) method for the molecular typing of Mycoplasma pneumoniae. The method is based on GeneScan analysis of five VNTR loci throughout the genome which define a specific genotype based on the number of tandem repeats within each locus. A retrospective analysis of 154 M. pneumoniaeclinical isolates collected over the last 50 years and a limited (n= 4) number of M. pneumoniae-positive primary specimens acquired by the CDC was performed using MLVA. Eighteen distinct VNTR types were identified, including two previously unidentified VNTR types. Isolates from several M. pneumoniaecommunity outbreaks within the United States were also analyzed to examine clonality of a specific MLVA type. Observed in vitrovariability of the Mpn1 VNTR locus prompted further analysis, which showed multiple insertions or deletions of tandem repeats within this locus for a number of specimens and isolates. To our knowledge, this is the first report showing variation within the Mpn1 locus, thus affecting precise and reliable classification using the current MLVA typing system. The superior discriminatory capability of MLVA provides a powerful tool for greater resolution of M. pneumoniaestrains and could be useful during outbreaks and epidemiological investigations.

In many macroorganisms, the ultimate source of potent biologically active natural products has remained elusive due to an inability to identify and culture the producing symbiotic microorganisms. As a model system for developing a meta-omic approach to identify and characterize natural product pathways from invertebrate-derived microbial consortia, we chose to investigate the ET-743 (Yondelis) biosynthetic pathway. This molecule is an approved anticancer agent obtained in low abundance (10–4–10–5% w/w) from the tunicate Ecteinascidia turbinataand is generated in suitable quantities for clinical use by a lengthy semisynthetic process. On the basis of structural similarities to three bacterial secondary metabolites, we hypothesized that ET-743 is the product of a marine bacterial symbiont. Using metagenomic sequencing of total DNA from the tunicate/microbial consortium, we targeted and assembled a 35 kb contig containing 25 genes that comprise the core of the NRPS biosynthetic pathway for this valuable anticancer agent. Rigorous sequence analysis based on codon usage of two large unlinked contigs suggests that Candidatus Endoecteinascidia frumentensisproduces the ET-743 metabolite. Subsequent metaproteomic analysis confirmed expression of three key biosynthetic proteins. Moreover, the predicted activity of an enzyme for assembly of the tetrahydroisoquinoline core of ET-743 was verified in vitro. This work provides a foundation for direct production of the drug and new analogues through metabolic engineering. We expect that the interdisciplinary approach described is applicable to diverse host–symbiont systems that generate valuable natural products for drug discovery and development.

Purpose: To evaluate the feasibility of administering a newly established proficiency test offered through the College of American Pathologists and the American College of Medical Genetics for genomic copy number assessment by microarray analysis, and to determine the reproducibility and concordance among laboratory results from this test.Methods: Surveys were designed through the Cytogenetic Resource Committee of the two colleges to assess the ability of testing laboratories to process DNA samples provided and interpret results. Supplemental questions were asked with each Survey to determine laboratory practice trends.Results: Twelve DNA specimens, representing 2 pilot and 10 Survey challenges, were distributed to as many as 74 different laboratories, yielding 493 individual responses. The mean consensus for matching result interpretations was 95.7%. Responses to supplemental questions indicate that the number of laboratories offering this testing is increasing, methods for analysis and evaluation are becoming standardized, and array platforms used are increasing in probe density.Conclusion: The College of American Pathologists/American College of Medical Genetics proficiency testing program for copy number assessment by cytogenomic microarray is a successful and efficient mechanism for assessing interlaboratory reproducibility. This will provide laboratories the opportunity to evaluate their performance and assure overall accuracy of patient results. The high level of concordance in laboratory responses across all testing platforms by multiple facilities highlights the robustness of this technology.

Genomic copy number microarrays have significantly increased the diagnostic yield over a karyotype for clinically significant imbalances in individuals with developmental delay, intellectual disability, multiple congenital anomalies, and autism, and they are now accepted as a first tier diagnostic test for these indications. As it is not feasible to validate microarray technology that targets the entire genome in the same manner as an assay that targets a specific gene or syndromic region, a new paradigm of validation and regulation is needed to regulate this important diagnostic technology. We suggest that these microarray platforms be evaluated and manufacturers regulated for the ability to accurately measure copy number gains or losses in DNA (analytical validation) and that the subsequent interpretation of the findings and assignment of clinical significance be determined by medical professionals with appropriate training and certification. To this end, the American College of Medical Genetics, as the professional organization of board-certified clinical laboratory geneticists, herein outlines recommendations for the design and performance expectations for clinical genomic copy number microarrays and associated software intended for use in the postnatal setting for detection of constitutional abnormalities.

Electron transfer through gas-phase ion–ion reactions has led to the widespread application of electron-based techniques once only capable in ion trapping mass spectrometers. Although any mass analyzer can, in theory, be coupled to an ion–ion reaction device (typically a 3-D ion trap), some systems of interest exceed the capabilities of most mass spectrometers. This case is particularly true in the structural characterization of glycosaminoglycan (GAG) oligosaccharides. To adequately characterize highly sulfated GAGs or oligosaccharides above the tetrasaccharide level, a high-resolution mass analyzer is required. To extend previous efforts on an ion trap mass spectrometer, negative electron transfer dissociation coupled with a Fourier transform ion cyclotron resonance mass spectrometer has been applied to increasingly sulfated heparan sulfate and heparin tetrasaccharides as well as a dermatan sulfate octasaccharide. Results similar to those obtained by electron detachment dissociation are observed.

Numerous marine-derived pyrrole−imidazole alkaloids (PIAs), ostensibly derived from the simple precursor oroidin, 1a, have been reported and have garnered intense synthetic interest due to their complex structures and in some cases biological activity; however very little is known regarding their biosynthesis. We describe a concise synthesis of 7-15N-oroidin (1d) from urocanic acid and a direct method for measurement of 15N incorporation by pulse labeling and analysis by 1D 1H−15N HSQC NMR and FTMS. Using a mock pulse labeling experiment, we estimate the limit of detection (LOD) for incorporation of newly biosynthesized PIA by 1D 1H−15N HSQC to be 0.96 μg equivalent of 15N-oroidin (2.4 nmole) in a background of 1500 μg of unlabeled oroidin (about 1 part per 1600). 7-15N-Oroidin will find utility in biosynthetic feeding experiments with live sponges to provide direct information to clarify the pathways leading to more complex pyrrole−imidazole alkaloids.

ABSTRACTDefinitive identification of Brucellaspecies remains a challenge due to the high degree of genetic homology shared within the genus. We report the development of a molecular technique which utilizes real-time PCR followed by high-resolution melt (HRM) curve analysis to reliably type members of this genus. Using a panel of seven primer sets, we tested 153 Brucellaspp. isolates with >99% accuracy compared to traditional techniques. This assay provides a useful diagnostic tool that can rapidly type Brucellaisolates and has the potential to detect novel species. This approach may also prove helpful for clinical, epidemiological and veterinary investigations.

Turner syndrome is a disorder that has distinct clinical features and has karyotypic aberrations with loss of critical regions of the X chromosome. Several clinical guidelines on the diagnosis and management of patients with Turner syndrome have been published, but there is relatively little on the laboratory aspects associated with this disorder. This disease-specific laboratory guideline provides laboratory guidance for the diagnosis/study of patients with Turner syndrome and its variants. Because the diagnosis of Turner syndrome involves both a clinical and laboratory component, both sets of guidelines are required for the provision of optimal care for patients with Turner syndrome.

ABSTRACTMycoplasma pneumoniaeis a leading cause of community-acquired pneumonia. Although two genetically distinct types of M. pneumoniaeare known, variants of each also exist. We used a real-time PCR high-resolution melt genotyping assay to identify clinical variants which may provide greater insight into the genetic distribution of M. pneumoniaestrains.

Mycoplasma pneumoniae is a leading cause of community-acquired pneumonia. Although two genetically distinct types of M. pneumoniae are known, variants of each also exist. We used a real-time PCR high-resolution melt genotyping assay to identify clinical variants which may provide greater insight into the genetic distribution of M. pneumoniae strains.

The vertical opacity structure of the martian atmosphere is important for understanding the distribution of ice (water and carbon dioxide) and dust. We present a new data set of extinction opacity profiles from the NOMAD/UVIS spectrometer aboard the ExoMars Trace Gas Orbiter, covering one and a half Mars Years (MY) including the MY 34 Global Dust Storm and several regional dust storms. We discuss specific mesospheric cloud features and compare with existing literature and a Mars Global Climate Model (MGCM) run with data assimilation. Mesospheric opacity features, interpreted to be water ice, were present during the global and regional dust events and correlate with an elevated hygropause in the MGCM, providing evidence that regional dust storms can boost transport of vapor to mesospheric altitudes (with potential implications for atmospheric escape). The season of the dust storms also had an apparent impact on the resulting lifetime of the cloud features, with events earlier in the dusty season correlating with longer‐lasting mesospheric cloud layers. Mesospheric opacity features were also present during the dusty season even in the absence of regional dust storms, and interpreted to be water ice based on previous literature. The assimilated MGCM temperature structure agreed well with the UVIS opacities, but the MGCM opacity field struggled to reproduce mesospheric ice features, suggesting a need for further development of water ice parameterizations. The UVIS opacity data set offers opportunities for further research into the vertical aerosol structure of the martian atmosphere, and for validation of how this is represented in numerical models. The martian atmosphere contains several kinds of aerosol, including dust, water ice, and carbon dioxide ice. The NOMAD/UVIS spectrometer aboard the ExoMars Trace Gas orbiter is able to measure the opacity of the atmosphere at different heights by looking through the atmosphere at the Sun, and these opacities provide information on the vertical aerosol distribution. We present a new data set of these opacities for one and a half Mars Years, a period including one Global Dust Storm and several smaller regional‐scale dust storms. By comparing with a martian climate model and previous work we discuss some noteable features in the UVIS data. We see the presence of high‐altitude water ice clouds associated with the Global Dust Storm and several regional dust storms, and find that the lifetime of these cloud layers seems to depend on the seasonal timing of the relevant dust event. These layers also correlate with an elevated higher‐altitude water vapor presence, showing that large dust storms boost the upwards transport of water vapor; this could enhance atmospheric escape of hydrogen. The model temperature structure is consistent with the UVIS results, but the model aerosol field shows a need for improvement in its representation of high‐altitude water ice. Mesospheric water ice clouds were present in ExoMars/UVIS opacity profiles during a global and three regional dust stormsMesospheric water ice correlated with elevated hygropause, showing storms boost vertical water transport with hydrogen escape implicationsPerihelion season mesospheric water ice was also present even in the absence of global/regional dust storm activity Mesospheric water ice clouds were present in ExoMars/UVIS opacity profiles during a global and three regional dust storms Mesospheric water ice correlated with elevated hygropause, showing storms boost vertical water transport with hydrogen escape implications Perihelion season mesospheric water ice was also present even in the absence of global/regional dust storm activity

The structural analysis of sulfated carbohydrates such as glycosaminoglycans (GAGs) has been a long-standing challenge for the field of mass spectrometry. The dissociation of sulfated carbohydrates by collisionally-activated dissociation (CAD) or infrared multiphoton dissociation (IRMPD), which activate ions via vibrational excitation, typically result in few cleavages and abundant SO3loss for highly sulfated GAGs such as heparin and heparan sulfate, hampering efforts to determine sites of modification. The recent application of electron activation techniques, specifically electron capture dissociation (ECD) and electron detachment dissociation (EDD), provides a marked improvement for the mass spectrometry characterization of GAGs. In this work, we compare ECD, EDD and IRMPD for the dissociation of the highly sulfated carbohydrate sucrose octasulfate (SOS). Both positive and negative multiply-charged ions are investigated. ECD, EDD and IRMPD of SOS produce abundant and reproducible fragmentation. The product ions produced by ECD are quite different than those produced by IRMPD of SOS positive ions, suggesting different dissociation mechanisms as a result of electronic versus vibrational excitation. The product ions produced by EDD and IRMPD of SOS negative ions also differ from each other. Evidence for SO3rearrangement exists in the negative ion IRMPD data, complicating the assignment of product ions.

Viralload (VL) assessment of cytomegalovirus (CMV) by real-time PCR is an important tool for diagnosing and monitoring CMV viremia in patients with compromised immune systems. We report results from a sample exchange organized by members of the Association for Molecular Pathology that compared PCR results from 23 laboratories; 22 such laboratories used a laboratory-developed real-time PCR assay and one laboratory used a competitive PCR assay. The samples sent to each laboratory were comprised of a dilution panel of CMV virion-derived reference materials that ranged from 0 to 500,000 copies/ml. Accuracy, linearity, and intralaboratory precision were established for the different laboratory-developed assays. Overall, PCR results were linear for each laboratory (R20.97 in all but two). While 13 laboratories showed no significant quantitative assay bias, 10 laboratories reported VLs that were significantly different compared with expected values (bias range, −0.82 to 1.4 logs). The intralaboratory precision [mean coefficient of variance of 2% to 5% (log-scale)] suggested that changes in VLs of less than 3- to fivefold may not be significantly different. There was no significant association between laboratory-specific technical variables (PCR platform, calibrator, extraction method) and assay linearity or accuracy. These data suggested that, within each laboratory, relative VL values were linear, but additional method standardization and a CMV DNA reference standard are needed to allow laboratories to achieve comparable numeric results.

ABSTRACTHuman infection with Chlamydophila(Chlamydia) psittacican lead to psittacosis, a disease that occasionally results in severe pneumonia and other medical complications. C. psittaciis currently grouped into seven avian genotypes: A through F and E/B. Serological testing, outer membrane protein A (ompA) gene sequencing, and restriction fragment length polymorphism analysis are currently used for distinguishing these genotypes. Although accurate, these methods are time-consuming and require multiple confirmatory tests. By targeting the ompAgene, a real-time PCR assay has been developed to rapidly detect and genotype C. psittaciby light-upon-extension chemistry and high-resolution melt analysis. Using this assay, we screened 169 animal specimens; 98 were positive for C. psittaci(71.4% genotype A, 3.1% genotype B, 4.1% genotype E, and 21.4% unable to be typed). This test may provide insight into the distribution of each genotype among specific hosts and provide epidemiological and epizootiological data in human and mammalian/avian cases. This diagnostic assay may also have veterinary applications during chlamydial outbreaks, particularly with respect to identifying the sources and tracking the movements of a particular genotype when multiple animal facilities are affected.

ABSTRACTMycoplasma pneumoniaeis a significant cause of community-acquired pneumonia, which is often empirically treated with macrolides or azalides such as erythromycin or azithromycin. Recent studies have discovered the existence of macrolide-resistant strains within the population that have been mapped to mutations within the domain V region of the 23S rRNA gene. Currently, identification of these resistant strains relies on time-consuming and labor-intensive procedures such as restriction fragment length polymorphism, MIC studies, and sequence analysis. The current study reports two distinct real-time PCR assays that can detect the A2063G or A2064G base mutation (A2058G or A2059G by Escherichia colinumbering) conferring macrolide resistance. By subjecting the amplicon of the targeted domain V region of the 23S rRNA gene to a high-resolution melt curve analysis, macrolide-resistant strains can quickly be separated from susceptible strains. Utilizing this method, we screened 100 clinical isolates and found 5 strains to possess mutations conferring resistance. These findings were concordant with both sequencing and MIC data. This procedure was also used successfully to identify both susceptible and resistant genotypes in 23 patient specimens. These patient specimens tested positive for the presence of M. pneumoniaeby a separate real-time PCR assay, although the bacteria could not be isolated by culture. This is the first report of a real-time PCR assay capable of detecting the dominant mutations that confer macrolide resistance on M. pneumoniae, and these assays may have utility in detecting resistant strains of other infectious agents. These assays may also allow for clinicians to select appropriate treatment options more rapidly and may provide a convenient method to conduct surveillance for genetic mutations conferring antibiotic resistance.

The fundamental nuclear enzyme DNA topoisomerase I (topo I), cleaves the double-stranded DNA molecule at preferred sequences within its recognition/binding sites. We have recently reported that when cells incorporate halogenated nucleosides analogues of thymidine into DNA, it interferes with normal chromosome segregation, as shown by an extraordinarily high yield of endoreduplication, and results in a protection against DNA breakage induced by the topo II poison m-AMSA [F. Cortés, N. Pastor, S. Mateos, I. Domínguez, The nature of DNA plays a role in chromosome segregation: endoreduplication in halogen-substituted chromosomes, DNA Repair 2 (2003) 719–726; G. Cantero, S. Mateos, N. Pastor; F. Cortés, Halogen substitution of DNA protects from poisoning of topoisomerase II that results in DNA double-strand breaks (DSBs), DNA Repair 5 (2006) 667–674]. In the present investigation, we have assessed whether the presence of halogenated nucleosides in DNA diminishes the frequency of interaction of topo I with DNA and thus the frequency with which the stabilisation of cleavage complexes by the topo I poison camptothecin (CPT) takes place, in such a way that it protects from chromosome breakage and sister-chromatid exchange. This protective effect is shown to parallel a loss in halogen-substituted cells of the otherwise CPT-increased catalytic activity bound to DNA.

In today's world, learning is not confined to a classroom, school or college, and is an essential part of everyday lives and continues throughout life. New technologies have created additional avenues and enhancements for learning. Creating environments that embrace communities, celebrate cultural differences, nurture and hone practical and advanced skills, and encourage innovation and collaboration is the implicit challenge in designing 21st century education facilities. [ABSTRACT FROM AUTHOR]

Fluorescence in situhybridization (FISH) provides an important adjunct to conventional cytogenetics and molecular studies in the evaluation of chromosome abnormalities associated with hematologic malignancies. FISH employs DNA probes and methods that are generally not Food and Drug Administration-approved, and therefore, their use as analyte-specific reagents involves unique pre- and postanalytical requirements. We provide an overview of the technical parameters influencing a reliable FISH result and encourage laboratories to adopt specific procedures and policies in implementing metaphase and interphase FISH testing. A rigorous technologist training program relative to specific types of probes is detailed, as well as guidance for consistent interpretation of findings, including typical and atypical abnormal results. Details are provided on commonly used dual-fusion, extra signal, and break-apart probes, correct FISH nomenclature in the reporting of results, and the use of FISH in relation to other laboratory testing in the ongoing monitoring of disease. This article provides laboratory directors detailed guidance to be used in conjunction with existing regulations to successfully implement a FISH testing program or to assess current practices, allowing for optimal clinical testing for patient care.

Idiopathic usual interstitial pneumonia/idiopathic pulmonary fibrosis (UIP/IPF) and asbestosis represent progressive and often fatal pulmonary fibrous disorders, whereas cryptogenic organizing pneumonia (COP), desquamative interstitial pneumonia (DIP), and respiratory bronchiolitis-interstitial lung disease (RB-ILD) usually are reversible or nonprogressive conditions. Prostaglandin E2 (PGE2) inhibits fibroblast proliferation and myofibroblast transition, its production depending on cyclooxygenase-2 (COX-2). In patients with UIP/IPF, levels of PGE2 and COX-2 are reduced in fibroblasts, and levels of PGE2 in bronchioalveolar lavage fluid may be lowered. We analyzed the immunohistochemical expression of COX-2 in UIP/IPF, asbestosis, COP, DIP, and RB-ILD. Our results show that the metaplastic epithelium in UIP/IPF, asbestosis, and COP is widely COX-2+, whereas COX-2 positivity is scant in DIP and RB-ILD. The mesenchymal cells remained negative. Our results suggest that irrespective of the underlying disease, lung injury that causes extensive fibrosis induces wide expression of COX-2 in the regenerating metaplastic epithelium.

A 28-year-old Caucasian female with no personal or family history of cystic fibrosis (CF) presented for preconception counseling and screening. Cystic fibrosis transmembrane conductance regulator (CFTR) mutation analysis using the Inno-LiPa CFTR assay revealed lack of hybridization for both the wild-type and mutant oligonucleotides for 3120+1GA. This region was sequenced, and an apparent homozygous 3120GA mutation was detected. Additional testing revealed an abnormal sweat chloride (77 mmol/L). Review of systems was essentially unremarkable with an absence of sinus symptoms, occasional nonproductive cough, and no features of malabsorption. Physical examination, chest X-ray, and pulmonary function tests were within normal limits. Only two other patients (siblings) with homozygous 3120GA mutations have been reported (http://www.genet.sickkids.on.ca/cftr/). Both siblings had pancreatic insufficiency, mild pulmonary symptoms, and abnormal sweat chloride levels. Our findings suggest that a homozygous mutation of a GA conversion at 3120 is associated with abnormal CFTR function and either a mild form of CF or no overt symptoms of disease, emphasizing the difficulties in assigning genotype/phenotype correlation.