Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows

Multiplexed bimolecular profiling of tissue microenvironment, or spatial omics, can provide deep insight into cellular compositions and interactions in both normal and diseased tissues. Proteome-scale tissue mapping, which aims to unbiasedly visualize all the proteins in whole tissue section or region of interest, has attracted significant interest because it holds great potential to directly reveal diagnostic biomarkers and therapeutic targets. While many approaches are available, however, proteome mapping still exhibits significant technical challenges in both protein coverage and analytical throughput. Since many of these existing challenges are associated with mass spectrometry-based protein identification and quantification, we performed a detailed benchmarking study of three protein quantification methods for spatial proteome mapping, including label-free, TMT-MS2, and TMT-MS3. Our study indicates label-free method provided the deepest coverages of ~3500 proteins at a spatial resolution of 50 μm and the largest quantification dynamic range, while TMT-MS2 method holds great benefit in mapping throughput at >125 pixels per day. The evaluation also indicates both label-free and TMT-MS2 provide robust protein quantifications in terms of identifying differentially abundant proteins and spatially co-variable clusters. In the study of pancreatic islet microenvironment, we demonstrated deep proteome mapping not only enables to identify protein markers specific to different cell types, but more importantly, it also reveals unknown or hidden protein patterns by spatial co-expression analysis.

Spatial top-down proteomics for the functional characterization of human kidney

Background

The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by the human genome. However, the proteome is enigmatic, where alterations in amino acid sequences from polymorphisms and alternative splicing, errors in translation, and post-translational modifications result in a proteome depth estimated at several million unique proteoforms. Recently mass spectrometry has been demonstrated in several landmark efforts mapping the human proteoform landscape in bulk analyses. Herein, we developed an integrated workflow for characterizing proteoforms from human tissue in a spatially resolved manner by coupling laser capture microdissection, nanoliter-scale sample preparation, and mass spectrometry imaging.

Results

Using healthy human kidney sections as the case study, we focused our analyses on the major functional tissue units including glomeruli, tubules, and medullary rays. After laser capture microdissection, these isolated functional tissue units were processed with microPOTS (microdroplet processing in one-pot for trace samples) for sensitive top-down proteomics measurement. This provided a quantitative database of 616 proteoforms that was further leveraged as a library for mass spectrometry imaging with near-cellular spatial resolution over the entire section. Notably, several mitochondrial proteoforms were found to be differentially abundant between glomeruli and convoluted tubules, and further spatial contextualization was provided by mass spectrometry imaging confirming unique differences identified by microPOTS, and further expanding the field-of-view for unique distributions such as enhanced abundance of a truncated form (1-74) of ubiquitin within cortical regions.

Conclusions

We developed an integrated workflow to directly identify proteoforms and reveal their spatial distributions. Where of the 20 differentially abundant proteoforms identified as discriminate between tubules and glomeruli by microPOTS, the vast majority of tubular proteoforms were of mitochondrial origin (8 of 10) where discriminate proteoforms in glomeruli were primarily hemoglobin subunits (9 of 10). These trends were also identified within ion images demonstrating spatially resolved characterization of proteoforms that has the potential to reshape discovery-based proteomics because the proteoforms are the ultimate effector of cellular functions. Applications of this technology have the potential to unravel etiology and pathophysiology of disease states, informing on biologically active proteoforms, which remodel the proteomic landscape in chronic and acute disorders.

Spatial Proteomics toward Subcellular Resolution by Coupling Deep Ultraviolet Laser Ablation with Nanodroplet Sample Preparation

Multiplexed molecular profiling of tissue microenvironments, or spatial omics, can provide critical insights into cellular functions and disease pathology. The coupling of laser microdissection with mass spectrometry-based proteomics has enabled deep and unbiased mapping of >1000 proteins. However, the throughput of laser microdissection is often limited due to tedious two-step procedures, sequential laser cutting, and sample collection. The two-step procedure also hinders the further improvement of spatial resolution to <10 μm as needed for subcellular proteomics. Herein, we developed a high-throughput and high-resolution spatial proteomics platform by seamlessly coupling deep ultraviolet (DUV) laser ablation (LA) with nanoPOTS (Nanodroplet Processing in One pot for Trace Samples)-based sample preparation. We demonstrated the DUV-LA system can quickly isolate and collect tissue samples at a throughput of ∼30 spots/min and a spatial resolution down to 2 μm from a 10 μm thick human pancreas tissue section. To improve sample recovery, we developed a proximity aerosol collection approach by placing DMSO droplets close to LA spots. We demonstrated the DUV-LA-nanoPOTS platform can detect an average of 1312, 1533, and 1966 proteins from ablation spots with diameters of 7, 13, and 19 μm, respectively. In a proof-of-concept study, we isolated and profiled two distinct subcellular regions of the pancreas tissue revealed by hematoxylin and eosin (H&E) staining. Quantitative proteomics revealed proteins specifically enriched to subcellular compartments.

Body composition, gastrointestinal, and reproductive differences between broiler breeders fed using everyday or skip-a-day rearing programs

Broiler breeder feed restriction practices have intensified as broiler feed efficiency has been improved. Skip-a-day (SAD) rearing regimen has controlled breeder growth, although this practice has become questionable for the modern breeder. We compared everyday (ED) and SAD programs and evaluated their impact on pullet growth performance, body composition, gastrointestinal tract development, and reproduction. At d 0, Ross 708 (Aviagen) pullet chicks (n = 1,778) were randomly assigned to 7 floor pens. Three pens were fed using the ED and 4 pens with SAD program through wk 21 using a chain-feeder system. ED and SAD grower diets were formulated to be isonutritious, with the only difference that ED diets had more crude fiber. Pullets (n = 44 per pen) were moved to 16 hen pens by treatment at wk 21 with 3 YP males (Aviagen) in each pen. All birds were fed common laying diets. In addition to BW data, sampled pullets and hens were scanned using dual energy X-ray absorptiometry (DEXA) to obtain body bone density and composition. Hen performance and hatchery metrics were recorded through wk 60. ED birds were heavier with similar nutrient intake from wk 10 to 45 (P ≤ 0.013). Pullet uniformity was unaffected by feeding method (P ≥ 0.443). SAD pullets had less body fat at wk 19 (P = 0.034) compared to ED pullets, likely as a metabolic consequence of intermittent feeding. SAD birds had lower bone density at wk 7, 15, and 19 (P ≤ 0.026). At 4 wk of age, SAD pullets had less intestinal villi goblet cells compared to ED pullets (P ≤ 0.050), possibly explained by the effect that feed removal has on cell migration rates. Overall egg-specific gravity (P = 0.057) and hatch of fertile % (P = 0.088) tended to be higher in eggs from ED hens. Altogether, ED feeding increased young pullet intestinal goblet cells and increased both bone density and body fat at wk 19. ED program improved pullet feed conversion (2.6% less feed) and increased eggshell quality and hatch of fertile.

Coupling microdroplet-based sample preparation, multiplexed isobaric labeling, and nanoflow peptide fractionation for deep proteome profiling of tissue microenvironment

There is increasing interest in developing in-depth proteomic approaches for mapping tissue heterogeneity at a cell-type-specific level to better understand and predict the function of complex biological systems, such as human organs. Existing spatially resolved proteomics technologies cannot provide deep proteome coverages due to limited sensitivity and poor sample recovery. Herein, we seamlessly combined laser capture microdissection with a low-volume sample processing technology that includes a microfluidic device named microPOTS (Microdroplet Processing in One pot for Trace Samples), the multiplexed isobaric labelling, and a nanoflow peptide fractionation approach. The integrated workflow allowed to maximize proteome coverage of laser-isolated tissue samples containing nanogram proteins. We demonstrated the deep spatial proteomics can quantify more than 5,000 unique proteins from a small-sized human pancreatic tissue pixel (∼60,000 µm2) and reveal unique islet microenvironments.

MZA: A Data Conversion Tool to Facilitate Software Development and Artificial Intelligence Research in Multidimensional Mass Spectrometry

Modern mass spectrometry-based workflows employing hybrid instrumentation and orthogonal separations collect multidimensional data, potentially allowing deeper understanding in omics studies through adoption of artificial intelligence methods. However, the large volume of these rich spectra challenges existing data storage and access technologies, therefore precluding informatics advancements. We present MZA (pronounced m-za), the mass-to-charge (m/z) generic data storage and access tool designed to facilitate software development and artificial intelligence research in multidimensional mass spectrometry measurements. Composed of a data conversion tool and a simple file structure based on the HDF5 format, MZA provides easy, cross-platform and cross-programming language access to raw MS-data, enabling fast development of new tools in data science programming languages such as Python and R. The software executable, example MS-data and example Python and R scripts are freely available at https://github.com/PNNL-m-q/mza.

A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics

Effective phosphoproteome of nanoscale sample analysis remains a daunting task, primarily due to significant sample loss associated with non-specific surface adsorption during enrichment of low stoichiometric phosphopeptide. We develop a tandem tip phosphoproteomics sample preparation method that is capable of sample cleanup and enrichment without additional sample transfer, and its integration with our recently developed SOP (Surfactant-assisted One-Pot sample preparation) and iBASIL (improved Boosting to Amplify Signal with Isobaric Labeling) approaches provides a streamlined workflow enabling sensitive, high-throughput nanoscale phosphoproteome measurements. This approach significantly reduces both sample loss and processing time, allowing the identification of >3000 (>9500) phosphopeptides from 1 (10) µg of cell lysate using the label-free method without a spectral library. It also enables precise quantification of ~600 phosphopeptides from 100 sorted cells (single-cell level input for the enriched phosphopeptides) and ~700 phosphopeptides from human spleen tissue voxels with a spatial resolution of 200 µm (equivalent to ~100 cells) in a high-throughput manner. The new workflow opens avenues for phosphoproteome profiling of mass-limited samples at the low nanogram level.

Evaluating Linear Ion Trap for MS3-Based Multiplexed Single-Cell Proteomics

There is a growing demand to develop high-throughput and high-sensitivity mass spectrometry methods for single-cell proteomics. The commonly used isobaric labeling-based multiplexed single-cell proteomics approach suffers from distorted protein quantification due to co-isolated interfering ions during MS/MS fragmentation, also known as ratio compression. We reasoned that the use of MS3-based quantification could mitigate ratio compression and provide better quantification. However, previous studies indicated reduced proteome coverages in the MS3 method, likely due to long duty cycle time and ion losses during multilevel ion selection and fragmentation. Herein, we described an improved MS acquisition method for MS3-based single-cell proteomics by employing a linear ion trap to measure reporter ions. We demonstrated that linear ion trap can increase the proteome coverages for single-cell-level peptides with even higher gain obtained via the MS3 method. The optimized real-time search MS3 method was further applied to study the immune activation of single macrophages. Among a total of 126 single cells studied, over 1200 and 1000 proteins were quantifiable when at least 50 and 75% nonmissing data were required, respectively. Our evaluation also revealed several limitations of the low-resolution ion trap detector for multiplexed single-cell proteomics and suggested experimental solutions to minimize their impacts on single-cell analysis.

An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue

Human disease states are biomolecularly multifaceted and can span across phenotypic states, therefore it is important to understand diseases on all levels, across cell types, and within and across microanatomical tissue compartments. To obtain an accurate and representative view of the molecular landscape within human lungs, this fragile tissue must be inflated and embedded to maintain spatial fidelity of the location of molecules and minimize molecular degradation for molecular imaging experiments. Here, we evaluated agarose inflation and carboxymethyl cellulose embedding media and determined effective tissue preparation protocols for performing bulk and spatial mass spectrometry-based omics measurements. Mass spectrometry imaging methods were optimized to boost the number of annotatable molecules in agarose inflated lung samples. This optimized protocol permitted the observation of unique lipid distributions within several airway regions in the lung tissue block. Laser capture microdissection of these airway regions followed by high-resolution proteomic analysis allowed us to begin linking the lipidome with the proteome in a spatially resolved manner, where we observed proteins with high abundance specifically localized to the airway regions. We also compared our mass spectrometry results to lung tissue samples preserved using two other inflation/embedding media, but we identified several pitfalls with the sample preparation steps using this preservation method. Overall, we demonstrated the versatility of the inflation method, and we can start to reveal how the metabolome, lipidome, and proteome are connected spatially in human lungs and across disease states through a variety of different experiments.

Cell lineage specification and signalling pathway use during development of the lateral plate mesoderm and forelimb mesenchyme

The lateral plate mesoderm (LPM) is a transient tissue that produces a diverse range of differentiated structures, including the limbs. However, the molecular mechanisms that drive early LPM specification and development are poorly understood. In this study, we use single-cell transcriptomics to define the cell-fate decisions directing LPM specification, subdivision and early initiation of the forelimb mesenchyme in chicken embryos. We establish a transcriptional atlas and global cell-cell signalling interactions in progenitor, transitional and mature cell types throughout the developing forelimb field. During LPM subdivision, somatic and splanchnic LPM fate is achieved through activation of lineage-specific gene modules. During the earliest stages of limb initiation, we identify activation of TWIST1 in the somatic LPM as a putative driver of limb bud epithelial-to-mesenchymal transition. Furthermore, we define a new role for BMP signalling during early limb development, revealing that it is necessary for inducing a somatic LPM fate and initiation of limb outgrowth, potentially through activation of TBX5. Together, these findings provide new insights into the mechanisms underlying LPM development, somatic LPM fate choice and early initiation of the vertebrate limb.

Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering

Single-cell proteomics (scProteomics) promises to advance our understanding of cell functions within complex biological systems. However, a major challenge of current methods is their inability to identify and provide accurate quantitative information for low-abundance proteins. Herein, we describe an ion-mobility-enhanced mass spectrometry acquisition and peptide identification method, transferring identification based on FAIMS filtering (TIFF), to improve the sensitivity and accuracy of label-free scProteomics. TIFF extends the ion accumulation times for peptide ions by filtering out singly charged ions. The peptide identities are assigned by a three-dimensional MS1 feature matching approach (retention time, accurate mass, and FAIMS compensation voltage). The TIFF method enabled unbiased proteome analysis to a depth of >1,700 proteins in single HeLa cells, with >1,100 proteins consistently identified. As a demonstration, we applied the TIFF method to obtain temporal proteome profiles of >150 single murine macrophage cells during lipopolysaccharide stimulation and identified time-dependent proteome changes. A record of this paper's transparent peer review process is included in the supplemental information.

High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip

Global quantification of protein abundances in single cells could provide direct information on cellular phenotypes and complement transcriptomics measurements. However, single-cell proteomics is still immature and confronts many technical challenges. Herein we describe a nested nanoPOTS (N2) chip to improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based scProteomics workflow. The N2 chip reduces reaction volume to <30 nL and increases capacity to >240 single cells on a single microchip. The tandem mass tag (TMT) pooling step is simplified by adding a microliter droplet on the nested nanowells to combine labeled single-cell samples. In the analysis of ~100 individual cells from three different cell lines, we demonstrate that the N2 chip-based scProteomics platform can robustly quantify ~1500 proteins and reveal membrane protein markers. Our analyses also reveal low protein abundance variations, suggesting the single-cell proteome profiles are highly stable for the cells cultured under identical conditions.

Survey of coccidia on commercial broiler farms in Colombia: frequency of Eimeria species, anticoccidial sensitivity, and histopathology

Avian coccidiosis continues to be one of the costliest diseases of commercial poultry. Understanding the epidemiology of Eimeria species in poultry flocks and the resistance profile to common anticoccidials is important to design effective disease prevention and control strategies. This study examined litter samples to estimate the prevalence and distribution of Eimeria species among broiler farms in 4 geographic regions of Colombia. A total of 245 litter samples were collected from 194 broiler farms across representative regions of poultry production between March and August 2019. The litter samples were processed for oocysts enumeration and speciation after sporulation. End-point polymerase chain reaction (PCR) analysis was conducted to confirm the presence of Eimeria species. Anticoccidial sensitivity was determined with 160 Ross AP males in 5 treatment groups: noninfected, nonmedicated control (NNC), infected, nonmedicated control (INC), infected salinomycin treated (SAL, dose: 66 ppm), infected diclazuril treated (DIC, dose: 1 ppm), and infected methylbenzocuate-Clopidol treated (MET.CLO, dose: 100 ppm), All birds were orally inoculated with 1 × 106 sporulated oocysts using a 1 mL syringe, except for the NNC- group who received 1ml of water.Eimeria spp. were found in 236 (96.3%) out of 245 individual houses, representing 180 (92.8%) out of 194 farms. Eimeria acervulina was the most prevalent species (35.0%) followed by Eimeria tenella (30.9%), Eimeria maxima (20.4%), and other Eimeria spp. (13.6%). However, mixed species infections were common, with the most prevalent combination being mixtures of E. acervulina, E. maxima, E. tenella, and other species in 31.4% of the Eimeria-positive samples. PCR analysis identified E. acervulina, E. maxima, E. tenella, Eimeria necatrix, Eimeria mitis, and Eimeria praecox with variable prevalence across farms and regions. Anticoccidial sensitivity testing of strains of Eimeria isolated from 1 region, no treatment difference (P > 0.05) was observed in final weight (BW), weight gain (BWG) or feed conversion (FCR). For the global resistance index (GI) classified SAL and MET.CLO as good efficacy (85.79 and 85.49, respectively) and DIC as limited efficacy (74.52%). These results demonstrate the ubiquitous nature of Eimeria spp. and identifies the current state of sensitivity to commonly used anticoccidials in a region of poultry importance for Colombia.

MicroPOTS Analysis of Barrett's Esophageal Cell Line Models Identifies Proteomic Changes after Physiologic and Radiation Stress

Moving from macroscale preparative systems in proteomics to micro- and nanotechnologies offers researchers the ability to deeply profile smaller numbers of cells that are more likely to be encountered in clinical settings. Herein a recently developed microscale proteomic method, microdroplet processing in one pot for trace samples (microPOTS), was employed to identify proteomic changes in ∼200 Barrett’s esophageal cells following physiologic and radiation stress exposure. From this small population of cells, microPOTS confidently identified >1500 protein groups, and achieved a high reproducibility with a Pearson’s correlation coefficient value of R > 0.9 and over 50% protein overlap from replicates. A Barrett’s cell line model treated with either lithocholic acid (LCA) or X-ray had 21 (e.g., ASNS, RALY, FAM120A, UBE2M, IDH1, ESD) and 32 (e.g., GLUL, CALU, SH3BGRL3, S100A9, FKBP3, AGR2) overexpressed proteins, respectively, compared to the untreated set. These results demonstrate the ability of microPOTS to routinely identify and quantify differentially expressed proteins from limited numbers of cells.

The Effect of Different Species of Eimeria with Clostridium perfringens on Performance Parameters and Induction of Clinical Necrotic Enteritis in Broiler Chickens

Necrotic enteritis (NE) is a common disease that causes great economic loss to the broiler industry due to mortality and reduced performance. Although Clostridium perfringens (CP) is a necessary component of this disease, coccidia species are a well-defined predisposing factor that exacerbates the condition. Different Eimeria species have been reported to influence NE to different degrees. In a pair of experiments, six different Eimeria species were evaluated in the presence and absence of C. perfringens. Male broiler chicks were housed in battery cages for the duration of both experiments. Feed conversion, body weight gain, and NE mortality were reported in both experiments. Experiment 1 challenged birds with E. maxima, E. acervulina, E. tenella, E. necatrix, and E. brunetti at day 13 and subsequently inoculated birds with CP on days 18, 19, and 20. In the second experiment, E. maxima, E. acervulina, E. tenella, and E. praecox were inoculated on day 15 and challenged with CP on days 17, 18, 19, 20, 21, and 22 of the experiment. In the first experiment, E. acervulina, E. brunetti, E. maxima, and E. necatrix with the addition of CP all stimulated necrotic enteritis mortality. In the second experiment, E. praecox had minimal impact on performance during the challenge (14-23 days) while E. maxima + CP decreased body weight gain and increased mortality compared to the CP alone control. Eimeria maxima had the highest mortality (21.9%) in this experiment followed by E. acervulina (6.3%). The remaining Eimeria with added CP in the second experiment did not induce NE mortality. While the challenge with CP alone did not induce mortality, feed conversion was increased compared to the unchallenged control group. When using isolated Eimeria species in these experiments, disturbances created by E. brunetti and E. maxima resulted in the most-severe challenges. These experiments highlight the NE risk of these species of Eimeria and give insight into how other species interact with the host in a controlled CP challenge model.

Automated Coupling of Nanodroplet Sample Preparation with Liquid Chromatography-Mass Spectrometry for High-Throughput Single-Cell Proteomics

Single-cell proteomics can provide critical biological insight into the cellular heterogeneity that is masked by bulk-scale analysis. We have developed a nanoPOTS (nanodroplet processing in one pot for trace samples) platform and demonstrated its broad applicability for single-cell proteomics. However, because of nanoliter-scale sample volumes, the nanoPOTS platform is not compatible with automated LC-MS systems, which significantly limits sample throughput and robustness. To address this challenge, we have developed a nanoPOTS autosampler allowing fully automated sample injection from nanowells to LC-MS systems. We also developed a sample drying, extraction, and loading workflow to enable reproducible and reliable sample injection. The sequential analysis of 20 samples containing 10 ng tryptic peptides demonstrated high reproducibility with correlation coefficients of >0.995 between any two samples. The nanoPOTS autosampler can provide analysis throughput of 9.6, 16, and 24 single cells per day using 120, 60, and 30 min LC gradients, respectively. As a demonstration for single-cell proteomics, the autosampler was first applied to profiling protein expression in single MCF10A cells using a label-free approach. At a throughput of 24 single cells per day, an average of 256 proteins was identified from each cell and the number was increased to 731 when the Match Between Runs algorithm of MaxQuant was used. Using a multiplexed isobaric labeling approach (TMT-11plex), ∼77 single cells could be analyzed per day. We analyzed 152 cells from three acute myeloid leukemia cell lines, resulting in a total of 2558 identified proteins with 1465 proteins quantifiable (70% valid values) across the 152 cells. These data showed quantitative single-cell proteomics can cluster cells to distinct groups and reveal functionally distinct differences.

Ocular exposure to infectious laryngotracheitis virus alters leukocyte subsets in the head-associated lymphoid tissues and trachea of 6-week-old White Leghorn chickens

Infectious laryngotracheitis virus (ILTV), an alphaherpesvirus, causes acute respiratory disease primarily infecting the upper respiratory tract and conjunctiva. Administration of live attenuated ILTV vaccines via eye drop, drinking water, or by coarse spray elicits protective mucosal immunity in the head-associated lymphoid tissues (HALT), of which conjunctiva-associated lymphoid tissue (CALT) and the Harderian gland (HG) are important tissue components. The trachea, a non-lymphoid tissue, also receives significant influx of inflammatory cells that dictate the outcome of ILTV infection. The objective of this study was to evaluate leukocyte cellular and phenotypic changes in the CALT, HG and trachea following ocular infection with a virulent ILTV strain. At 1, 3, 5, 7 and 9 days post-infection, CALT, HG, and trachea of 6-week-old specific pathogen free (SPF) chickens ocularly-exposed to vehicle or virulent ILTV strain 63140 were dissociated, the cells enumerated and then phenotyped using flow cytometry. The CALT had the highest viral genomic load, which peaked on day 3. In ILTV-infected birds, the CALT had a decreased percentage of leukocytes. This was reflected by decreased numbers of MHCI⁺MHCII^-, MHCI⁺MHCII^low+, and CD4⁺ cells, while IgM⁺ and MHCI⁺MHCII^High+ expressing cell populations increased. In the HG, the most notable change in cells from ILTV-infected birds was a decrease in IgM expressing cells and histologically, an increase in Mott cells. In summary, an acute, ocular exposure to ILTV strain 63140 in young birds shifts subsets of lymphocyte populations in the CALT and HG with minimal impact on the trachea.

Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform

Top-down proteomics is a powerful tool for characterizing genetic variations and post-translational modifications at intact protein level. However, one significant technical gap of top-down proteomics is the inability to analyze a low amount of biological samples, which limits its access to isolated rare cells, fine needle aspiration biopsies, and tissue substructures. Herein, we developed an ultrasensitive top-down platform by incorporating a microfluidic sample preparation system, termed nanoPOTS (nanodroplet processing in one pot for trace samples), into a top-down proteomic workflow. A unique combination of a nonionic detergent dodecyl-β-d-maltopyranoside (DDM) with urea as protein extraction buffer significantly improved both protein extraction efficiency and sample recovery. We hypothesize that the DDM detergent improves protein recovery by efficiently reducing nonspecific adsorption of intact proteins on container surfaces, while urea serves as a strong denaturant to disrupt noncovalent complexes and release intact proteins for downstream analysis. The nanoPOTS-based top-down platform reproducibly and quantitatively identified ∼170 to ∼620 proteoforms from ∼70 to ∼770 HeLa cells containing ∼10 to ∼115 ng of total protein. A variety of post-translational modifications including acetylation, myristoylation, and iron binding were identified using only less than 800 cells. We anticipate the nanoPOTS top-down proteomics platform will be broadly applicable in biomedical research, particularly where clinical specimens are not available in amounts amenable to standard workflows.

An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics

Mass spectrometry (MS)-based proteomics has great potential for overcoming the limitations of antibody-based immunoassays for antibody-independent, comprehensive, and quantitative proteomic analysis of single cells. Indeed, recent advances in nanoscale sample preparation have enabled effective processing of single cells. In particular, the concept of using boosting/carrier channels in isobaric labeling to increase the sensitivity in MS detection has also been increasingly used for quantitative proteomic analysis of small-sized samples including single cells. However, the full potential of such boosting/carrier approaches has not been significantly explored, nor has the resulting quantitation quality been carefully evaluated. Herein, we have further evaluated and optimized our recent boosting to amplify signal with isobaric labeling (BASIL) approach, originally developed for quantifying phosphorylation in small number of cells, for highly effective analysis of proteins in single cells. This improved BASIL (iBASIL) approach enables reliable quantitative single-cell proteomics analysis with greater proteome coverage by carefully controlling the boosting-to-sample ratio (e.g. in general <100×) and optimizing MS automatic gain control (AGC) and ion injection time settings in MS/MS analysis (e.g. 5E5 and 300 ms, respectively, which is significantly higher than that used in typical bulk analysis). By coupling with a nanodroplet-based single cell preparation (nanoPOTS) platform, iBASIL enabled identification of ∼2500 proteins and precise quantification of ∼1500 proteins in the analysis of 104 FACS-isolated single cells, with the resulting protein profiles robustly clustering the cells from three different acute myeloid leukemia cell lines. This study highlights the importance of carefully evaluating and optimizing the boosting ratios and MS data acquisition conditions for achieving robust, comprehensive proteomic analysis of single cells.

Picoflow Liquid Chromatography-Mass Spectrometry for Ultrasensitive Bottom-Up Proteomics Using 2-μm-i.d. Open Tubular Columns

In many areas of application, key objectives of chemical separation and analysis are to minimize the sample quantity while maximizing the chemical information obtained. Increasing measurement sensitivity is especially critical for proteomics research, especially when processing trace samples and where multiple measurements are desired. A rich collection of technologies has been developed, but the resulting sensitivity remains insufficient for achieving in-depth coverage of proteomic samples as small as single cells. Here, we combine picoliter-scale liquid chromatography (picoLC) with mass spectrometry (MS) to address this issue. The picoLC employs a 2-μm-i.d. open tubular column to reduce the sample input needed to greatly increase the sensitivity achieved using electrospray ionization (ESI) with MS. With this picoLC-MS system, we show that we can identify ∼1000 proteins reliably using only 75 pg of tryptic peptides, representing a 10-100-fold sensitivity improvement compared with the state-of-the-art liquid chromatography (LC) or capillary electrophoresis (CE)-MS methods. PicoLC-MS extends the limit of separation science and is expected to be a powerful tool for single cell proteomics.

Determination of Oxytetracycline/Oxytetracycline Hydrochloride in Animal Feed, Fish Feed, and Veterinary Medicinal Products by Liquid Chromatography with Fluorescence Detection: Collaborative Study

A method for determining oxytetracycline (OTC) in animal feed, fish feed, and veterinary medicinal products at medicated use and contamination levels was collaboratively studied. The method is applicable to the analysis of animal feeds and mineral premixes containing levels 2 mg/kg, and fish feed containing levels 10 mg/kg. Oxytetracycline hydrochloride (OTC.HCl) is extracted from ground feed material in acidmethanol solution using mechanical agitation. After centrifugation for 5 min at 1230 g, an aliquot of the extract is diluted with water and/or acidmethanol so that the concentration of OTC.HCl is approximately the same as that in the working standard, and the solutions contain at least 50 water. Injectable veterinary medicinal materials (also called animal remedy materials) are diluted with water and/or extractant to reach the target concentration. The extracts are filtered and analyzed by reversed-phase liquid chromatography with fluorescence detection with excitation at 390 nm and emission at 512 nm. Twenty-eight test samples of medicated feeds, supplements, and drug premixes, including 4 test samples for trace-level analysis, were sent to 17 collaborators in Canada, The Netherlands, and the United States. Results were received from 11 laboratories. The RSDr values (within-laboratory repeatability) ranged from 1.26 to 9.21; RSDR values (among-laboratory reproducibility) ranged from 2.14 to 12.9, and HorRat values ranged from 0.54 to 3.02. It is recommended that this method be adopted AOAC Official First Action.

Determination of Decoquinate in Animal Feeds by Liquid Chromatography: Collaborative Study

The performance characteristics of a liquid chromatographic (LC) method for the analysis of decoquinate (DEC) in supplements, premixes, and complete animal feeds at medicating and trace levels were collaboratively studied. DEC is extracted from ground feed samples with 1 calcium chloridemethanol solution using mechanical agitation for 90 min. After centrifugation for 5 min and dilution (if necessary), an aliquot of the extract is diluted with water. The diluted extracts are filtered and analyzed by reversed-phase LC with fluorescence detection. Suspect positive trace-level samples are confirmed by using an alternate excitation wavelength. Fourteen test samples of medicated feeds, supplement, and medicated premix, along with 8 test samples for trace-level analysis, were sent to 13 collaborators (one in Canada, 4 in Europe, and 8 in the United States). Test samples were analyzed as blind duplicates. Acceptable results were received from 12 laboratories for the medicated test samples and from 13 laboratories for the trace-level samples. Repeatability relative standard deviation estimates ranged from 1.3 to 5.6. Reproducibility relative standard deviations estimates ranged from 2.8 to 6.1, and HorRat values ranged from 0.22 to 0.74.

An integrative analysis of non-coding regulatory DNA variations associated with autism spectrum disorder

A number of genetic studies have identified rare protein-coding DNA variations associated with autism spectrum disorder (ASD), a neurodevelopmental disorder with significant genetic etiology and heterogeneity. In contrast, the contributions of functional, regulatory genetic variations that occur in the extensive non-protein-coding regions of the genome remain poorly understood. Here we developed a genome-wide analysis to identify the rare single nucleotide variants (SNVs) that occur in non-coding regions and determined the regulatory function and evolutionary conservation of these variants. Using publicly available datasets and computational predictions, we identified SNVs within putative regulatory regions in promoters, transcription factor binding sites, and microRNA genes and their target sites. Overall, we found that the regulatory variants in ASD cases were enriched in ASD-risk genes and genes involved in fetal neurodevelopment. As with previously reported coding mutations, we found an enrichment of the regulatory variants associated with dysregulation of neurodevelopmental and synaptic signaling pathways. Among these were several rare inherited SNVs found in the mature sequence of microRNAs predicted to affect the regulation of ASD-risk genes. We show a paternally inherited miR-873-5p variant with altered binding affinity for several risk-genes including NRXN2 and CNTNAP2 putatively overlay maternally inherited loss-of-function coding variations in NRXN1 and CNTNAP2 to likely increase the genetic liability in an idiopathic ASD case. Our analysis pipeline provides a new resource for identifying loss-of-function regulatory DNA variations that may contribute to the genetic etiology of complex disorders.

Evaluation of encapsulated sodium butyrate with varying releasing times on growth performance and necrotic enteritis mitigation in broilers

This study was conducted to evaluate the effect of an encapsulated sodium butyrate (Na-B) with targeted releasing times on growth performance and mitigating the impact of necrotic enteritis in broilers. Two Na-B (30% of Na-B content) products, CMA (2 h releasing time) and CMP (3 to 4 h releasing time), were evaluated in a necrotic enteritis challenge model. The experiment consisted of 4 Na-B treatments (500 and 1,000 ppm of each product) plus 2 control (non-challenged and challenged). A total of 336 Cobb-Cobb male broilers were placed 8 birds per pen into 7 replicate battery cages. On day 14, birds from challenged treatments were orally gavaged with ∼5,000 oocysts of Eimeria maxima. On day 19, 20, and 21, the challenged birds received 1 mL of 108 cfu/mL Clostridium perfringens. Total pen body weight (BW) and feed weight were assessed on day 14, 21, and 28 for BW gain and mortality-adjusted feed conversion ratio (FCR). On day 21, 3 birds were randomly selected per pen and scored for intestinal lesions. The duodenum and jejunum tissue were collected on day 21 and 28 for quantifying intestinal histology. Results revealed that adding CMA at 500 ppm showed significantly higher cumulative BW gain (P < 0.05) compared to the challenged control from day 1 to 21. Adding CMA at 500 ppm also showed the equivalent cumulative FCR that was comparable to the non-challenged control on day 21. The CMA treatments and CMP at 1,000 ppm treatment showed equivalent BW gain compared to the non-challenge control after an additional 7 d post-challenge on day 28. Both products at 500 or 1,000 ppm had the significantly (P < 0.05) lower intestinal lesion scores compared to the challenged control. However, there was no difference in lesion scores among the Na-B treatments. The Na-B product targeted to release in the anterior intestinal tract shows the beneficial effects on BW gain and feed utilization efficiency in current challenge model. Adding encapsulated Na-B product has the potential to mitigate the impact of necrotic enteritis in broilers.

Parental reactions to weight screening in young children: a randomized controlled trial

BACKGROUND

Parental inability to recognize child overweight and physician reluctance to instigate discussion prevents behaviour change.

OBJECTIVE

To evaluate parental acceptance of child overweight status following screening.

METHODS

Interviewers used motivational interviewing or best practice care to discuss overweight status of 271 young children (BMI ≥ 85^th ) with parents using simple traffic-light BMI charts. Follow-up sessions two weeks later (n = 251, 93%) were coded qualitatively to assess parental reactions to the information (overweight diagnosis) and how it was presented (feedback condition).

RESULTS

Eight-two percent of parents rated the charts positively with few (8-10%) feeling judged. Motivational interviewing parents viewed feedback as more empathetic (relative risk, 95% CI: 4.07, 1.64-10.09), but more uncomfortable (12.2, 1.48-100.1) than best practice care parents. Overall, 65.2% of parents accepted their child was overweight, 22.1% were ambivalent and 12.7% rejected the information. Although motivational interviewing parents were less likely to accept it (OR, 95% CI: 0.49, 0.37-0.64) and more likely to be ambivalent (2.01, 1.17-3.47), the most important predictor of acceptance was a positive experience of feedback (P < 0.001).

CONCLUSIONS

Simple traffic-light charts facilitate discussion of child overweight status with parents. Style of feedback is less relevant than ensuring a positive experience for parents to increase acceptance of the weight information.

An Injectable Reverse Thermal Gel for Minimally Invasive Coverage of Mouse Myelomeningocele

BACKGROUND

Myelomeningocele (MMC) results in lifelong neurologic and functional deficits. Currently, prenatal repair of MMC closes the defect, resulting in a 50% reduction in postnatal ventriculoperitoneal shunting. However, this invasive fetal surgery is associated with significant morbidities to mother and baby. We have pioneered a novel reverse thermal gel (RTG) to cover MMC defects in a minimally invasive manner. Here, we test in-vitro RTG long-term stability in amniotic fluid and in vivo application in the Grainy head-like 3 (Grhl3) mouse MMC model.

MATERIALS AND METHODS

RTG stability in amniotic fluid (in-vitro) was monitored for 6 mo and measured using gel permeation chromatography and solution-gel transition temperature (lower critical solution temperature). E16.5 Grhl3 mouse fetuses were injected with the RTG or saline and harvested on E19.5. Tissue was assessed for RTG coverage of the gross defect and inflammatory response by immunohistochemistry for macrophages.

RESULTS

Polymer backbone molecular weight and lower critical solution temperature remain stable in amniotic fluid after 6 mo. Needle injection over the MMC of Grhl3 fetuses successfully forms a stable gel that covers the entire defect. On harvest, some animals demonstrate >50% RTG coverage. RTG injection is not associated with inflammation.

CONCLUSIONS

Our results demonstrate that the RTG is a promising candidate for a minimally invasive approach to patch MMC. We are now poised to test our RTG patch in the large preclinical ovine model used to evaluate prenatal repair of MMC.

The Role of Fibrinolysis in the Pathogenesis of the Haemorrhagic Syndrome Produced by Virulent Isolates of African Swine Fever Virus

The activity of several proteins involved in fibrinolysis and the morphological changes in the blood vessel walls of pigs infected with highly virulent (Malawi’83) and moderately virulent (Dominican Republic ‘78-DR’78) ASF virus isolates were determined. Pigs infected with the Malawi’83 virus developed an increased fibrinolytic activity due to high plasma levels of tissue-plasminogen activator (t-PA) of 71.3 ± 22.8 IU/ml (mean ± SD), which correlated well with an increased activation of interstitial capillary endothelial cells and high levels of 1150 ± 73.6 nM of fibrin monomer in the circulation. Animals infected with DR’78 virus, in contrast, showed an inhibition of fibrinolysis in the late stages of disease with almost a 5-fold increase of plasminogen activator inhibitor (PAI) activity of 196.0 AU/ml. These results suggest that activation of the fibrinolytic system in pigs infected with the Malawi’83 virus is probably due to increased formation and deposition of fibrin in the circulation, contributing to an increased bleeding tendency and higher mortality. On the contrary, animals infected with DR’78 virus developed an inhibition of fibrinolysis and thus a reduction in bleeding.

Evaluation of encapsulated sodium butyrate on growth performance, energy digestibility, gut development, and Salmonella colonization in broilers

Two experiments were conducted to determine the effect of an encapsulated sodium butyrate (Na-B) with targeted releasing times on broiler performance, energy digestibility, intestinal morphology, and ceca Salmonella colonization. In experiment 1, 3 different Na-B products (CMA, CMP, and CMS) were evaluated following a challenge with a nalidixic acid-resistant Salmonella typhimurium (STNAR). Cobb-Cobb male birds were placed 8 per pen into 6 replicates for each treatment. Treatments included 6 Na-B treatments (500 and 1,000 ppm of each product) plus 2 control (non-challenged and challenged). Birds were orally gavaged with 0.1 mL of 107 cfu/mL STNAR on d 4. Ceca and ileal samples were collected on d 11. In experiment 2, CMA and CMP products were evaluated for a full grow-out period without an external challenge. Cobb-Cobb male birds were distributed among 45 floor pens with 24 birds per pen. Treatments included 4 product treatments (500 and 1,000 ppm of each product) plus one control. Feed intake and pen weight were obtained on d 14, 28, and 42. Experiment 1 showed that CMP at 1,000 ppm had the highest value for BW and BWG on d 4 (P = 0.07). Adding CMA and CMP at 500 ppm increased ileal digestibility energy (IDE) compared to the challenged control (P ≤ 0.05). The Salmonella recovery data indicated that the challenge had a significant but mild impact, since it did not affect the performance variables but did result in a significant increase in log10 cfu/g cecal material between the non-challenged and challenged control (1.42 vs 3.72). Experiment 2 showed that both products improved the villus height in the duodenum on d 21 (P = 0.08) and IDE on d 42, relative to the control (P ≤ 0.05). This study demonstrates that Na-B has the potential to improve growth in broilers at an early age. The beneficial effects on intestinal morphology and IDE are affected not only by dosage level, but also by the product's releasing time.

The effect of increasing risk and challenge in the school playground on physical activity and weight in children: a cluster randomised controlled trial (PLAY)

BACKGROUND

To investigate whether changing the play environment in primary schools to one that includes greater risk and challenge increases physical activity and reduces body mass index (BMI).

SUBJECTS/METHODS

A 2-year cluster randomised controlled trial was undertaken in 16 New Zealand schools (years 1-8). Intervention schools (n=8) redesigned their play environments to encourage imaginative and independent free play by increasing opportunities for risk and challenge (for example, rough-and-tumble play), reducing rules and adding new playground components (for example, loose parts). Control schools (n=8) were asked to not change their play environment. A qualified playworker rated all school play environments at baseline and 1 year. Primary outcomes were moderate-to-vigorous physical activity (7-day accelerometry) and BMI z-score, collected in 840 children at baseline, 1 and 2 years. Data were analysed using generalised estimating equations.

RESULTS

Multiple changes were made to the school play environments resulting in a significant difference in overall play evaluation score between intervention and control schools of 4.50 (95% confidence interval: 1.82 to 7.18, P=0.005), which represents a substantial improvement from baseline values of 19.0 (s.d. 3.2). Overall, schools liked the intervention and reported many benefits, including increased physical activity. However, these beliefs did not translate into significant differences in objectively measured physical activity, either as counts per minute (for example, 35 (-51 to 120) during lunch break) or as minutes of moderate-to-vigorous physical activity (0.4, -1.1 to 2.0). Similarly, no significant differences were observed for BMI, BMI z-score or waist circumference at 1 or 2 years (all P>0.321).

CONCLUSIONS

Altering the school play environment to one that promoted greater risk and challenge for children did not increase physical activity, nor subsequently alter body weight. Although schools embraced the concept of adding risk and challenge in the playground, our findings suggest that children may have been involved in different, rather than additional activities.

Identification of the genomic mutation in Epha4(rb-2J/rb-2J) mice

The EphA4 receptor tyrosine kinase is involved in numerous cell-signalling activities during embryonic development. EphA4 has the ability to bind to both types of ephrin ligands, the ephrinAs and ephrinBs. The C57BL/6J-Epha4rb-2J/GrsrJ strain, denoted Epha4(rb-2J/rb-2J), is a spontaneous mouse mutant that arose at The Jackson Laboratory. These mutants exhibited a synchronous hind limb locomotion defect or "hopping gait" phenotype, which is also characteristic of EphA4 null mice. Genetic complementation experiments suggested that Epha4(rb-2J) corresponds to an allele of EphA4, but details of the genomic defect in this mouse mutant are currently unavailable. We found a single base-pair deletion in exon 9 resulting in a frame shift mutation that subsequently resulted in a premature stop codon. Analysis of the predicted structure of the truncated protein suggests that both the kinase and sterile α motif (SAM) domains are absent. Definitive determination of genotype is needed for experimental studies of mice carrying the Epha4(rb-2J) allele, and we have also developed a method to ease detection of the mutation through RFLP. Eph-ephrin family members are reportedly expressed as numerous isoforms. Hence, delineation of the specific mutation in EphA4 in this strain is important for further functional studies, such as protein-protein interactions, immunostaining and gene compensatory studies, investigating the mechanism underlying the effects of altered function of Eph family of receptor tyrosine kinases on phenotype.

Bioelectrical impedance as a measure of change in body composition in young children

BACKGROUND AND OBJECTIVES

The ability of bioelectrical impedance (BIA) to measure change in body composition in children has rarely been examined.

METHODS

Body composition was estimated by BIA (Tanita BC-418) and dual-energy x-ray absorptiometry (DXA) in 187 children aged 4-8 years at baseline and at 12 months. Change in body composition was compared between the two methods using mixed models.

RESULTS

Estimates of change in fat mass did not differ between BIA and DXA for overweight girls (mean difference between methods, 95% confidence interval: 0.04 kg, -0.19 to 0.28) or boys (0.07 kg, -0.14 to 0.27). BIA was also able to accurately detect change in fat-free mass, with no significant differences between methods (-0.14 kg, -0.10 to 0.38 in girls and -0.07 kg, -0.35 to -0.20 in boys). Change in percentage fat produced similar estimates in both genders (0.18%, -0.82 to 0.46 in girls and 0.38%, -0.37 to 1.13 in boys). BIA/DXA comparisons in normal weight children were also not significantly different, with the exception of percentage fat in girls, where BIA slightly underestimated change compared with DXA (0.7%, 0.02-0.37).

CONCLUSION

BIA performed well as a measure of change in body composition, providing confidence for its use as an outcome measure in children.

Effects of diet mix time and ractopamine hydrochloride on finishing pig growth and carcass performance

Two experiments were completed to determine the effects of diet mix uniformity and ractopamine HCl on finishing pig performance. In Exp. 1, a total of 200 pigs (BW = 90 kg) were used in a 33-d growth assay arranged in a randomized complete block design with 5 pigs/pen and 8 pens/treatment. Treatments were a corn-soybean meal-based control diet mixed for 360 s or the mixed control diet with 10 mg/kg ractopamine added before additional mixing for 0, 30, 120, or 360 s. Chromium was added to the diet and analyzed to determine mix uniformity of the ractopamine. Therefore, this experiment was designed to determine the effects of nutrient utilization from a thoroughly mixed diet with a potentially nonuniform distribution of ractopamine. Pigs fed diets with ractopamine had greater (P < 0.05) ADG, G:F, final BW, HCW, dressing percentage, loin depth, and percentage carcass lean with lower (P = 0.005) 10th rib backfat thickness. Increasing mix time from 0 to 360 s decreased (quadratic, P = 0.001) CV for Cr from 67 to 12% but had no effect on the response to ractopamine for any growth or carcass measurements. In Exp. 2, a total of 160 pigs (BW = 93 kg) were used in a 27-d growth assay arranged in a completely randomized design with 2 pigs/pen and 16 pens/treatment. Treatments were a corn-soybean meal-based control diet mixed for 360 s or the control diet with 10 mg/kg ractopamine mixed for 0, 30, 120, or 360 s. Diet mix uniformity was determined by measuring Cr and using Quantab Cl titrators (low range 0.005 to 0.1% as NaCl; Environmental Test Systems Inc., Elkhart, IN) to measure the concentration of salt. This experiment was designed to determine the combined effects of potentially nonuniform distribution of both nutrients and ractopamine. The use of ractopamine increased (P < 0.05) ADG, G:F, final BW, HCW, dressing percentage, percentage lean, and loin depth. Increasing mix times from 0 to 360 s decreased (quadratic, P = 0.050) CV for salt and Cr from 51 to 12% and 51 to 15%, respectively, with no effect on ADG, ADFI, final BW CV, HCW, dressing percentage, backfat thickness, loin depth, or percentage carcass lean; however, G:F tended to increase (linear, P = 0.07) as mix time increased from 0 to 360 s. In conclusion, increasing mix time of diets from 0 to 360 s did not affect the response of finishing pigs to ractopamine

Epiregulin (EREG) and human V-ATPase (TCIRG1): genetic variation, ethnicity and pulmonary tuberculosis susceptibility in Guinea-Bissau and The Gambia

We analyzed two West African samples (Guinea-Bissau: n=289 cases and 322 controls; The Gambia: n=240 cases and 248 controls) to evaluate single-nucleotide polymorphisms (SNPs) in Epiregulin (EREG) and V-ATPase (T-cell immune regulator 1 (TCIRG1)) using single and multilocus analyses to determine whether previously described associations with pulmonary tuberculosis (PTB) in Vietnamese and Italians would replicate in African populations. We did not detect any significant single locus or haplotype associations in either sample. We also performed exploratory pairwise interaction analyses using Visualization of Statistical Epistasis Networks (ViSEN), a novel method to detect only interactions among multiple variables, to elucidate possible interaction effects between SNPs and demographic factors. Although we found no strong evidence of marginal effects, there were several significant pairwise interactions that were identified in either the Guinea-Bissau or the Gambian samples, two of which replicated across populations. Our results indicate that the effects of EREG and TCIRG1 variants on PTB susceptibility, to the extent that they exist, are dependent on gene-gene interactions in West African populations as detected with ViSEN. In addition, epistatic effects are likely to be influenced by inter- and intra-population differences in genetic or environmental context and/or the mycobacterial lineages causing disease.

HDAC6 contributes to pathological responses of heart and skeletal muscle to chronic angiotensin-II signaling

Little is known about the function of the cytoplasmic histone deacetylase HDAC6 in striated muscle. Here, we addressed the role of HDAC6 in cardiac and skeletal muscle remodeling induced by the peptide hormone angiotensin II (ANG II), which plays a central role in blood pressure control, heart failure, and associated skeletal muscle wasting. Comparable with wild-type (WT) mice, HDAC6 null mice developed cardiac hypertrophy and fibrosis in response to ANG II. However, whereas WT mice developed systolic dysfunction upon treatment with ANG II, cardiac function was maintained in HDAC6 null mice treated with ANG II for up to 8 wk. The cardioprotective effect of HDAC6 deletion was mimicked in WT mice treated with the small molecule HDAC6 inhibitor tubastatin A. HDAC6 null mice also exhibited improved left ventricular function in the setting of pressure overload mediated by transverse aortic constriction. HDAC6 inhibition appeared to preserve systolic function, in part, by enhancing cooperativity of myofibrillar force generation. Finally, we show that HDAC6 null mice are resistant to skeletal muscle wasting mediated by chronic ANG-II signaling. These findings define novel roles for HDAC6 in striated muscle and suggest potential for HDAC6-selective inhibitors for the treatment of cardiac dysfunction and muscle wasting in patients with heart failure.

Exposure of juvenile Leghorn chickens to lead acetate enhances antibiotic resistance in enteric bacterial flora

Heavy metals have been implicated for their ability to increase antibiotic resistance in bacteria collected from polluted waters, independent of antibiotic exposure. Specific-pathogen-free Leghorn chickens were therefore given Pb acetate in the drinking water to expose the enteric bacteria to Pb and to determine if antibiotic resistance changed in these bacteria. Concentrations of Pb used were 0.0, 0.01, 0.1, 1.0, or 10.0 mM; birds given the highest 2 concentrations showed signs of moribundity and dehydration and were removed from the study. Vent culture samples were collected for bacterial cultures on d 0 before Pb exposure, d 7 and 14, and then birds were euthanized by CO2 gas for necropsy on d 14, at which time intestinal contents were also collected for bacterial cultures. Fecal swabs but not intestinal samples from Pb-exposed birds contained isolates that had significantly elevated antibiotic resistance. Some of the isolates contained bacteria that were resistant to up to 20 antibiotics. These results suggest the need for repeated studies in chickens infected with zoonotic pathogens.

The prognostic significance of MRI-detected extramural venous invasion in rectal carcinoma

AIM

To assess whether there is a significant difference in the incidence of patients with metastases of rectal carcinoma at 1 year follow-up between magnetic resonance imaging (MRI)-detected extramural venous invasion (EMVI) and those without.

MATERIALS AND METHODS

A search of our institution's cancer registry revealed 788 patients with rectal carcinoma between January 2007 and April 2012. Those who were initially staged using MRI and computed tomography (CT) chest/abdomen/pelvis, and followed-up with a CT chest/abdomen/pelvis examination at 1 year were included in this retrospective study. Patients with synchronous metastases were excluded, leaving a cohort of 202 cases. Two consultant radiologists reviewed all MRI images and gave a consensus opinion regarding EMVI grade and vessel size involved. All CT images were reviewed for metastases. Results were analysed using chi-squared and Fisher's exact tests.

RESULTS

There were 53 cases (26.2%) of EMVI-positive rectal carcinoma. Of the patients with EMVI, 24.5% developed metastases at 1 year follow-up, compared to 6.7% of those without. There is a significant difference in prognosis between those patients with and those without MRI-detected EMVI (χ(2) = 12.29, p < 0·001). Those with EMVI have a 3.7 times increased relative risk of developing metachronous metastases within 1 year of diagnosis.

CONCLUSION

MRI-detected EMVI-positive rectal carcinomas are associated with an increased risk of metachronous metastases within 1 year of diagnosis. Currently, EMVI status does not directly influence the initial management of rectal carcinoma. This available and potentially prognostic feature could be used to guide treatment pathways to increase disease-free survival.

Class I HDACs regulate angiotensin II-dependent cardiac fibrosis via fibroblasts and circulating fibrocytes

Fibrosis, which is defined as excessive accumulation of fibrous connective tissue, contributes to the pathogenesis of numerous diseases involving diverse organ systems. Cardiac fibrosis predisposes individuals to myocardial ischemia, arrhythmias and sudden death, and is commonly associated with diastolic dysfunction. Histone deacetylase (HDAC) inhibitors block cardiac fibrosis in pre-clinical models of heart failure. However, which HDAC isoforms govern cardiac fibrosis, and the mechanisms by which they do so, remains unclear. Here, we show that selective inhibition of class I HDACs potently suppresses angiotensin II (Ang II)-mediated cardiac fibrosis by targeting two key effector cell populations, cardiac fibroblasts and bone marrow-derived fibrocytes. Class I HDAC inhibition blocks cardiac fibroblast cell cycle progression through derepression of the genes encoding the cyclin-dependent kinase (CDK) inhibitors, p15 and p57. In contrast, class I HDAC inhibitors block agonist-dependent differentiation of fibrocytes through a mechanism involving repression of ERK1/2 signaling. These findings define novel roles for class I HDACs in the control of pathological cardiac fibrosis. Furthermore, since fibrocytes have been implicated in the pathogenesis of a variety of human diseases, including heart, lung and kidney failure, our results suggest broad utility for isoform-selective HDAC inhibitors as anti-fibrotic agents that function, in part, by targeting these circulating mesenchymal cells.

Biomarker interactions are better predictors of spontaneous preterm birth

OBJECTIVE

The objective of this study was to assess the role of biomarker interactions as predictors of spontaneous preterm birth (PTB) using multifactor dimensionality reduction (MDR) analysis. With MDR, a nonparametric, unsupervised, model-free approach, we tested for biomarker interactions within maternal-fetal compartments in 2 racial groups: African Americans (AA) and Caucasians (C).

STUDY DESIGN

A total of 36 biomarkers from maternal plasma (MP), cord plasma (CP), and amniotic fluid (AF) were analyzed from 191 patients. The MDR combined attribute selection, construction, and classification to detect biomarker interactions that were assessed for generality and significance using 10× cross-validation and permutation testing. Selected significant interactive models were replicated with additional samples.

RESULTS

The interactive model containing interleukin (IL)-2, angiopoietin 2 (ANGPT-2), and IL-6 receptor was significant in AA MP. In AA CP, the IL-8 and tumor necrosis factor (TNF) receptor 1 model was significant. In AA AF, the ANGPT-2 and macrophage inflammatory protein 1 alpha model was significant. Replication of the AA MP model using 54 additional AA MP samples confirmed predictability of these biomarkers. In C AF, interaction was observed between ANGPT-2, monocyte chemotactic protein 3, and TNF-α, but no other interactions were significant in C.

CONCLUSIONS

Using MDR, we identified biomarker interactions that are predictors of PTB even in the absence of a main effect with a single biomarker.

The effect of lipoic acid and vitamin E therapies in individuals with the metabolic syndrome

The metabolic syndrome is associated with abnormal glucose and lipid metabolism, insulin resistance, increased oxidative stress and pro-inflammatory activity that increase the risk of type 2 diabetes and cardiovascular disease. The aim of this study was to investigate the effect of treatment with the antioxidant α-lipoic acid (ALA) with or without vitamin E supplementation, on markers of insulin resistance and systemic inflammation and plasma nonesterified fatty acid (NEFA) concentrations in individuals with the metabolic syndrome. In a randomized, double-blind, placebo-controlled trial, subjects with the metabolic syndrome received ALA (600 mg/day, n = 34), vitamin E (100 IU/day, n = 36), both ALA and vitamin E (n = 41), or matching placebo (n = 40) for 1 year. Fasting circulating concentrations of glucose and insulin were measure every 3 months and NEFA, markers of inflammation, adiponectin and vitamin E were measured at 6 monthly intervals. Plasma NEFA concentrations decreased [-10 (-18, 0)%] at a marginal level of significance (p = 0.05) in those who received ALA alone compared with placebo and decreased [-8 (-14, -1)% (95% CI)] significantly (P = 0.02) in participants who were randomised to ALA with and without vitamin E compared with those who did not receive ALA. Fasting glucose, insulin, homeostatic model assessment of insulin resistance, adiponectin, and markers of inflammation did not change significantly during the study. These data suggest that prolonged treatment with ALA may modestly reduce plasma NEFA concentrations but does not alter insulin or glucose levels in individuals with the metabolic syndrome.

Glycaemic responses to glucose and rice in people of Chinese and European ethnicity

AIMS

Diabetes rates are especially high in China. Risk of Type 2 diabetes increases with high intakes of white rice, a staple food of Chinese people. Ethnic differences in postprandial glycaemia have been reported. We compared glycaemic responses to glucose and five rice varieties in people of European and Chinese ethnicity and examined possible determinants of ethnic differences in postprandial glycaemia.

METHODS

Self-identified Chinese (n = 32) and European (n = 31) healthy volunteers attended on eight occasions for studies following ingestion of glucose and jasmine, basmati, brown, Doongara(®) and parboiled rice. In addition to measuring glycaemic response, we investigated physical activity levels, extent of chewing of rice and salivary α-amylase activity to determine whether these measures explained any differences in postprandial glycaemia.

RESULTS

Glycaemic response, measured by incremental area under the glucose curve, was over 60% greater for the five rice varieties (P < 0.001) and 39% greater for glucose (P < 0.004) amongst Chinese compared with Europeans. The calculated glycaemic index was approximately 20% greater for rice varieties other than basmati (P = 0.01 to 0.05). Ethnicity [adjusted risk ratio 1.4 (1.2-1.8) P < 0.001] and rice variety were the only important determinants of incremental area under the glucose curve.

CONCLUSIONS

Glycaemic responses following ingestion of glucose and several rice varieties are appreciably greater in Chinese compared with Europeans, suggesting the need to review recommendations regarding dietary carbohydrate amongst rice-eating populations at high risk of diabetes.

Secular changes in BMI and the associations between risk factors and BMI in children born 29 years apart

What is already known about this subject Factors associated with children's body mass index (BMI) include parents' BMIs, birth weight, maternal smoking, sleep duration and television watching. Few studies have attempted to quantify either changes in the association between risk factors and BMI or the contribution of changes in the risk factors to increases in BMI over a generation. What this study adds The magnitude of the association between most risk factors and children's BMIs has not changed over a 29-year period. Increases in the population level of mothers' body mass index (BMI) explains ~20% of the increase in children's BMI whereas the smaller increase in fathers' BMI contributes only 6%. Maternal smoking, despite the decrease in prevalence, contributes ~17%.

OBJECTIVE

Using two cohorts born 29 years apart in Dunedin, New Zealand we aim to examine changes in risk factors and their associations with body mass index (BMI) at ages 3 and 7 years, and estimate their contribution to the secular changes in BMI at age 7 years.

METHODS

Birth weight and anthropometric measures at ages 3, 5 and 7 years were obtained for 974 participants in the Dunedin Multidisciplinary Health and Development Study (DMHDS), born in 1972-1973, and 241 in the Family Lifestyle, Activity, Movement and Eating Study (FLAME), born in 2001-2002. Information about maternal age, education and smoking in pregnancy, as well as breastfeeding, children's television time and time in bed, was obtained by questionnaire.

RESULTS

The increase in BMI over the 29-year period was 0.84 (95% CI 0.61, 1.06) kg m(-2) at age 7. A 1-unit difference in the mother's BMI was associated with a 0.06 (0.03, 0.08) kg m(-2) difference in offspring in both studies; the 3.4 (2.8, 4.0) kg m(-2) increase in the mothers' BMIs accounts for a change of 0.19 kg m(-2) in the children's BMI. The much smaller generational increase in fathers' BMI (0.7 kg m(-2) ) correspondingly had a more limited effect on change in child BMI over time (0.06 kg m(-2) ). Although smoking in pregnancy decreased by 15% (8, 21) its association with BMI increased from 0.20 (-0.01, 0.42) in the DMHDS cohort to 1.24 (0.76, 1.71) kg m(-2) in the FLAME cohort, contributing 0.18 kg m(-2) to the increase in children's BMI.

CONCLUSIONS

Societal factors such as higher maternal BMI and smoking in pregnancy contribute most to the secular increase in BMI, with changes in behavioural factors, including sleep and television viewing, having little effect in this setting.

What is the effect of peer support on diabetes outcomes in adults? A systematic review

AIM

There is increasing interest in the role that peers may play to support positive health behaviours in diabetes, but there is limited evidence to inform policy and practice. The aim of this study was to systematically review evidence of the impact and effectiveness of peer support in adults living with diabetes.

METHODS

We searched the Cochrane Library, MEDLINE, PubMed, EMBASE and CINHAL for the period 1966-2011, together with reference lists of articles for eligible studies. Data were synthesized in a narrative review.

RESULTS

Twenty-five studies, including fourteen randomized, controlled or comparative trials, met the inclusion criteria. There was considerable heterogeneity in the design, setting, outcomes and measurement tools. Peer support was associated with statistically significant improvements in glycaemic control (three out of 14 trials), blood pressure (one out of four trials), cholesterol (one out of six trials), BMI/weight (two out of seven trials), physical activity (two out of five trials), self-efficacy (two out of three trials), depression (four out of six trials) and perceived social support (two out of two trials). No consistent pattern of effect related to any model of peer support emerged.

CONCLUSIONS

Peer support appears to benefit some adults living with diabetes, but the evidence is too limited and inconsistent to support firm recommendations. There remains a need for further well-designed evaluations of its effectiveness and impact. Key questions remain over its suitability to the needs of particular individuals, populations and settings, how best to implement its specific components and the sustainability of its effects.

Persistent increase of blood lead level and suppression of δ-ALAD activity in northern bobwhite quail orally dosed with even a single 2-mm spent lead shot

Birds that display grit ingestion behavior are potentially at risk of lead (Pb) poisoning from mistaken ingestion of spent Pb shot pellets. The majority of available studies designed to assess such risk have used unspent shot pellets rather than field-obtained spent shot, which is oxidized and otherwise changed by weathering. Available studies also often administered more or heavier shot pellets to a bird than it might be expected to ingest. The current study dosed northern bobwhite quail (Colinus virginianus) weighing 194.6 ± 23.1 g (female birds) and 199.3 ± 12.2 g (male birds) with one to three spent no. 9 Pb shot collected from a skeet range, with particular interest in the toxicity that may occur from ingestion of a single 2-mm, 50 mg shot. An 8 week post-dosing clinical observation period was employed, over which feed consumption, body weight, blood Pb levels, and a battery of blood physiological parameters were made. Weight loss occurred in the birds, including male birds dosed with one Pb pellet. Erythrocyte delta aminolevulinic acid dehydratase (δ-ALAD) levels were decreased for the duration of the study across exposures and to levels associated with injury in wild bird populations. Decreased ALAD was particularly severe in female birds dosed with one Pb pellet and was still 92 % decreased at 8 weeks after dosing. Together, these results suggest that inadvertent ingestion of a single no. 9 Pb shot pellet can adversely affect the health of northern bobwhite quail.