Small intestinal immunopathology and GI-associated antibody formation in hereditary alpha-tryptasemia.

BACKGROUND: Hereditary alpha-tryptasemia (HαT) is characterized by elevated basal serum tryptase due to increased copies of the TPSAB1 gene. Individuals with HαT frequently present with multisystem complaints, including anaphylaxis and seemingly functional gastrointestinal (GI) symptoms. OBJECTIVE: We sought to determine the prevalence of HαT in an irritable bowel syndrome cohort and associated immunologic characteristics that may distinguish patients with HαT from patients without HαT. METHODS: Tryptase genotyping by droplet digital PCR, flow cytometry, cytometry by time-of-flight, immunohistochemistry, and other molecular biology techniques was used. RESULTS: HαT prevalence in a large irritable bowel syndrome cohort was 5% (N = 8/158). Immunophenotyping of HαT PBMCs (N ≥ 27) revealed increased total and class-switched memory B cells. In the small bowel, expansion of tissue mast cells with expression of CD203c, HLA-DR, and FcεRI, higher intestinal epithelial cell pyroptosis, and increased class-switched memory B cells were observed. IgG profiles in sera from individuals with HαT (N = 21) significantly differed from those in individuals with quiescent Crohn disease (N = 20) and non-HαT controls (N = 19), with increased antibodies directed against GI-associated proteins identified in individuals with HαT. CONCLUSIONS: Increased mast cell number and intestinal epithelial cell pyroptosis in the small intestine, and class-switched memory B cells in both the gut and peripheral blood associated with IgG reactive to GI-related proteins, distinguish HαT from functional GI disease. These innate and adaptive immunologic findings identified in association with HαT are suggestive of subclinical intestinal inflammation in symptomatic individuals.

Lipidomic analysis of urinary exosomes from hereditary α-tryptasemia patients and healthy volunteers.

Exosomes are nano-sized vesicles that are involved in various biological processes including cell differentiation, proliferation, signaling, and intercellular communication. Urinary exosomes were isolated from a cohort of hereditary α-tryptasemia (HαT) patients and from healthy volunteers. There was a greater number of exosomes isolated from the urine in the HαT group compared to the control volunteers. Here, we investigated the differences in both lipid classes and lipid species within urinary exosomes of the two groups. Lipids were extracted from urinary exosomes and subjected to liquid chromatography mass spectrometry using a targeted approach. Various molecular species of glycerophospholipids, glycerolipids, and sterols were significantly reduced in HαT patients. Out of a possible 1127 lipids, 521 lipid species were detected, and relative quantities were calculated. Sixty-four lipids were significantly reduced in urinary exosomes of HαT patients compared to controls. All significantly reduced sphingolipids and most of the phospholipids were saturated or mono-unsaturated lipids. These results suggest exosome secretion is augmented in HαT patients and the lipids within these exosomes may be involved in various biological processes. The unique lipid composition of urinary exosomes from HαT patients will contribute to our understanding of the biochemistry of this disease.

A usability assessment of riding lawn-mowing equipment with varying levels of design standards compliance.

The use of riding lawn equipment (RLE) is related to a significant number of accidents every year. To provide basis for product design and enhance user performance and safety, a usability and performance assessment of modern riding lawn-mowing tractor designs and features was conducted in a real-world test environment. Five current commercially available RLEs were tested with response measures including task performance time and accuracy, physiological workload, system usability scores (SUS), and subjective rankings of RLE models. This data was used to identify sensitivity of responses to variations in RLE design features and functionality. The data was also used to assess the validity of new tractor design standard conformance tool, the RLEval methodology. This tool made comprehensive evaluation of RLE models compliance with over 70 specific design standards and was applied by human factors experts. Experiment results revealed sensitivity of all response measures to design differences among the five RLE models, except the objective workload measures. Response measures including task performance, SUSs and subjective rankings showed partial agreement with the RLEval scores. In general, the study results demonstrated a comprehensive experimental methodology for usability and performance evaluations of RLEs as well as merit of using the RLEval as preliminary method to compare design features. Some aspects of the usability experimentation and the RLEval method appear to be complementary.

Dusty Deep Convection in the Mars Year 34 Planet-Encircling Dust Event.

Dusty convection, convective activity powered by radiative heating of dust, is a ubiquitous phenomenon in Mars's atmosphere but is especially deep (that is, impactful on the middle atmosphere) and widespread during planet-encircling dust events (PEDE) that occur every few Mars Years (MY). Yet the relative roles of dusty deep convection and global dynamics, such as the principal meridional overturning cell (PMOC) and the radiative tides, in dust storm development and the vertical transport of dust and water are still unclear. Here, observations from the Mars Climate Sounder on board Mars Reconnaissance Orbiter (MRO-MCS) are used to study dusty deep convection and its impact on middle atmospheric water content during the MY 34 PEDE (commenced June 2018). Additional context is provided by MRO-MCS observations of the MY 28 PEDE (commenced June 2007). This investigation establishes that a few, localized centers of dusty deep convection in the tropics formed in the initial phases of both PEDE simultaneously with a substantial increase in middle atmospheric water content. The growth phase of the MY 34 PEDE was defined by episodic outbreaks of deep convection along the Acidalia and Utopia storm tracks as opposed to less episodic, more longitudinally distributed convective activity during the MY 28 PEDE. The most intense convection during both PEDE was observed in southern/eastern Tharsis, where MRO-MCS observed multiple instances of deep convective clouds transporting dust to altitudes of 70-90 km. These results suggest that Martian PEDE typically contain multiple convectively active mesoscale weather systems.

An Observational Overview of Dusty Deep Convection in Martian Dust Storms.

Deep convection, as used in meteorology, refers to the rapid ascent of air parcels in the Earth's troposphere driven by the buoyancy generated by phase change in water. Deep convection undergirds some of the Earth's most important and violent weather phenomena and is responsible for many aspects of the observed distribution of energy, momentum, and constituents (particularly water) in the Earth's atmosphere. Deep convection driven by buoyancy generated by the radiative heating of atmospheric dust may be similarly important in the atmosphere of Mars but lacks a systematic description. Here we propose a comprehensive framework for this phenomenon of dusty deep convection (DDC) that is supported by energetic calculations and observations of the vertical dust distribution and exemplary dusty deep convective structures within local, regional, and global dust storm activity. In this framework, DDC is distinct from a spectrum of weaker dusty convective activity because DDC originates from pre-existing or concurrently forming mesoscale circulations that generate high surface dust fluxes, oppose large-scale horizontal advective-diffusive processes, and are thus able to maintain higher dust concentrations than typically simulated. DDC takes two distinctive forms. Mesoscale circulations that form near Mars's highest volcanoes in dust storms of all scales can transport dust to the base of the upper atmosphere in as little as two hours. In the second distinctive form, mesoscale circulations at low elevations within regional and global dust storm activity generate freely convecting streamers of dust that are sheared into the middle atmosphere over the diurnal cycle.

Transcriptional and post-transcriptional regulation of PenA ß-lactamase in acquired Burkholderia pseudomallei ß-lactam resistance.

Therapy of Burkholderia pseudomallei acute infections is largely limited to a few ß-lactam antibiotics such as ceftazidime or meropenem. Although relatively rare, resistance emergence during therapy leads to treatment failures with high mortality rates. In the absence of acquired external resistance determinants in B. pseudomallei emergence of ß-lactam resistance is invariably caused by mutational modification of genomically encoded factors. These include the deletion of the ceftazidime target penicillin-binding protein 3 or amino acid changes in the Class A PenA ß-lactamase that expand its substrate spectrum, as well as penA gene duplication and amplification or its overexpression via transcriptional up-regulation. Evidence is presented that penA is co-transcribed with the upstream nlpD1 gene, that the transcriptional terminator for nlpD1 serves as a penA attenuator and that generation of a new promoter immediately upstream of the terminator/attenuator by a conserved G to A transition leads to anti-termination and thus constitutive PenA expression and extended ß-lactam resistance. Further evidence obtained with the extensively ß-lactam resistant clinical isolate Bp1651 shows that in addition to PenA overexpression and structural mutations other adaptive mechanisms contribute to intrinsic and acquired B. pseudomallei ß-lactam resistance.

Effect of physical workload and modality of information presentation on pattern recognition and navigation task performance by high-fit young males.

Many occupations require both physical exertion and cognitive task performance. Knowledge of any interaction between physical demands and modalities of cognitive task information presentation can provide a basis for optimising performance. This study examined the effect of physical exertion and modality of information presentation on pattern recognition and navigation-related information processing. Results indicated males of equivalent high fitness, between the ages of 18 and 34, rely more on visual cues vs auditory or haptic for pattern recognition when exertion level is high. We found that navigation response time was shorter under low and medium exertion levels as compared to high intensity. Navigation accuracy was lower under high level exertion compared to medium and low levels. In general, findings indicated that use of the haptic modality for cognitive task cueing decreased accuracy in pattern recognition responses. Practitioner Summary: An examination was conducted on the effect of physical exertion and information presentation modality in pattern recognition and navigation. In occupations requiring information presentation to workers, who are simultaneously performing a physical task, the visual modality appears most effective under high level exertion while haptic cueing degrades performance.

Development of a single-cell array for large-scale DNA fluorescence in situ hybridization.

DNA fluorescence in situ hybridization (FISH) is a powerful cytogenetic assay, but conventional sample-preparation methods for FISH do not support large-scale high-throughput data acquisition and analysis, which are potentially useful for several biomedical applications. To address this limitation, we have developed a novel FISH sample-preparation method based on generating a centimetre-sized cell array, in which all cells are precisely positioned and separated from their neighbours. This method is simple and capable of patterning nonadherent human cells. We have successfully performed DNA FISH on the single-cell arrays, which facilitates analysis of the FISH results with the FISH-FINDER computer program.

Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia.

Abnormal replication timing has been observed in cancer but no study has comprehensively evaluated this misregulation. We generated genome-wide replication-timing profiles for pediatric leukemias from 17 patients and three cell lines, as well as normal B and T cells. Nonleukemic EBV-transformed lymphoblastoid cell lines displayed highly stable replication-timing profiles that were more similar to normal T cells than to leukemias. Leukemias were more similar to each other than to B and T cells but were considerably more heterogeneous than nonleukemic controls. Some differences were patient specific, while others were found in all leukemic samples, potentially representing early epigenetic events. Differences encompassed large segments of chromosomes and included genes implicated in other types of cancer. Remarkably, differences that distinguished leukemias aligned in register to the boundaries of developmentally regulated replication-timing domains that distinguish normal cell types. Most changes did not coincide with copy-number variation or translocations. However, many of the changes that were associated with translocations in some leukemias were also shared between all leukemic samples independent of the genetic lesion, suggesting that they precede and possibly predispose chromosomes to the translocation. Altogether, our results identify sites of abnormal developmental control of DNA replication in cancer that reveal the significance of replication-timing boundaries to chromosome structure and function and support the replication domain model of replication-timing regulation. They also open new avenues of investigation into the chromosomal basis of cancer and provide a potential novel source of epigenetic cancer biomarkers.

FISH Finder: a high-throughput tool for analyzing FISH images.

MOTIVATION: Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus. Analyzing the data from FISH images is a tedious process that invokes an element of subjectivity. Automated FISH image analysis offers savings in time as well as gaining the benefit of objective data analysis. While several FISH image analysis software tools have been developed, they often use a threshold-based segmentation algorithm for nucleus segmentation. As fluorescence signal intensities can vary significantly from experiment to experiment, from cell to cell, and within a cell, threshold-based segmentation is inflexible and often insufficient for automatic image analysis, leading to additional manual segmentation and potential subjective bias. To overcome these problems, we developed a graphical software tool called FISH Finder to automatically analyze FISH images that vary significantly. By posing the nucleus segmentation as a classification problem, compound Bayesian classifier is employed so that contextual information is utilized, resulting in reliable classification and boundary extraction. This makes it possible to analyze FISH images efficiently and objectively without adjustment of input parameters. Additionally, FISH Finder was designed to analyze the distances between differentially stained FISH probes. AVAILABILITY: FISH Finder is a standalone MATLAB application and platform independent software. The program is freely available from: http://code.google.com/p/fishfinder/downloads/list.

Generating knockout rats by transposon mutagenesis in spermatogonial stem cells.

Disrupting genes in the rat on a genome-wide scale will allow the investigation of many biological processes linked to human health. Here we used transposon-mediated mutagenesis to knock out genes in rat spermatogonial stem cells. Given the capacity of the testis to support spermatogenesis from thousands of transplanted, genetically manipulated spermatogonia, this approach paves a way for high-throughput functional genomic studies in the laboratory rat.