The mouse Gene Expression Database (GXD): 2021 update.

The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental gene expression information. For many years, GXD has collected and integrated data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot, and western blot experiments through curation of the scientific literature and by collaborations with large-scale expression projects. Since our last report in 2019, we have continued to acquire these classical types of expression data; developed a searchable index of RNA-Seq and microarray experiments that allows users to quickly and reliably find specific mouse expression studies in ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) and GEO (https://www.ncbi.nlm.nih.gov/geo/); and expanded GXD to include RNA-Seq data. Uniformly processed RNA-Seq data are imported from the EBI Expression Atlas and then integrated with the other types of expression data in GXD, and with the genetic, functional, phenotypic and disease-related information in Mouse Genome Informatics (MGI). This integration has made the RNA-Seq data accessible via GXD's enhanced searching and filtering capabilities. Further, we have embedded the Morpheus heat map utility into the GXD user interface to provide additional tools for display and analysis of RNA-Seq data, including heat map visualization, sorting, filtering, hierarchical clustering, nearest neighbors analysis and visual enrichment.

The mouse Gene Expression Database (GXD): 2019 update.

The mouse Gene Expression Database (GXD) is an extensive, well-curated community resource freely available at www.informatics.jax.org/expression.shtml. Covering all developmental stages, GXD includes data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments in wild-type and mutant mice. GXD's gene expression information is integrated with the other data in Mouse Genome Informatics and interconnected with other databases, placing these data in the larger biological and biomedical context. Since the last report, the ability of GXD to provide insights into the molecular mechanisms of development and disease has been greatly enhanced by the addition of new data and by the implementation of new web features. These include: improvements to the Differential Gene Expression Data Search, facilitating searches for genes that have been shown to be exclusively expressed in a specified structure and/or developmental stage; an enhanced anatomy browser that now provides access to expression data and phenotype data for a given anatomical structure; direct access to the wild-type gene expression data for the tissues affected in a specific mutant; and a comparison matrix that juxtaposes tissues where a gene is normally expressed against tissues, where mutations in that gene cause abnormalities.

The mouse Gene Expression Database (GXD): 2017 update.

The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental expression information. Through curation of the scientific literature and by collaborations with large-scale expression projects, GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches. At present, GXD includes over 1.5 million expression results and more than 300 000 images, all annotated with detailed and standardized metadata. Since our last report in 2014, we have added a large amount of data, we have enhanced data and database infrastructure, and we have implemented many new search and display features. Interface enhancements include: a new Mouse Developmental Anatomy Browser; interactive tissue-by-developmental stage and tissue-by-gene matrix views; capabilities to filter and sort expression data summaries; a batch search utility; gene-based expression overviews; and links to expression data from other species.

Transcriptomic changes in Echinochloa colona in response to treatment with the herbicide imazamox.

MAIN CONCLUSION: Presented here is the first Echinochloa colona leaf transcriptome. Analysis of gene expression before and after herbicide treatment reveals that E. colona mounts a stress response upon exposure to herbicide. Herbicides are the most frequently used means of controlling weeds. For many herbicides, the target site is known; however, it is considerably less clear how plant gene expression changes in response to herbicide exposure. In this study, changes in gene expression in response to herbicide exposure in imazamox-sensitive (S) and- resistant (R) junglerice (Echinochloa colona L.) biotypes was examined. As no reference genome is available for this weed, a reference leaf transcriptome was generated. Messenger RNA was isolated from imazamox-treated- and untreated R and S plants and the resulting cDNA libraries were sequenced on an Illumina HiSeq2000. The transcriptome was assembled, annotated, and differential gene expression analysis was performed to identify transcripts that were upregulated or downregulated in response to herbicide exposure for both biotypes. Differentially expressed transcripts included transcription factors, protein-modifying enzymes, and enzymes involved in metabolism and signaling. A literature search revealed that members of the families represented in this analysis were known to be involved in abiotic stress response in other plants, suggesting that imazamox exposure induced a stress response. A time course study examining a subset of transcripts showed that expression peaked within 4-12 h and then returned to untreated levels within 48 h of exposure. Testing of plants from two additional biotypes showed a similar change in gene expression 4 h after herbicide exposure compared to the resistant and sensitive biotypes. This study shows that within 48 h junglerice mounts a stress response to imazamox exposure.

The mouse Gene Expression Database (GXD): 2014 update.

The Gene Expression Database (GXD; http://www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental expression information. GXD collects different types of expression data from studies of wild-type and mutant mice, covering all developmental stages and including data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. The data are acquired from the scientific literature and from researchers, including groups doing large-scale expression studies. Integration with the other data in Mouse Genome Informatics (MGI) and interconnections with other databases places GXD's gene expression information in the larger biological and biomedical context. Since the last report, the utility of GXD has been greatly enhanced by the addition of new data and by the implementation of more powerful and versatile search and display features. Web interface enhancements include the capability to search for expression data for genes associated with specific phenotypes and/or human diseases; new, more interactive data summaries; easy downloading of data; direct searches of expression images via associated metadata; and new displays that combine image data and their associated annotations. At present, GXD includes >1.4 million expression results and 250,000 images that are accessible to our search tools.

Involvement of facultative apomixis in inheritance of EPSPS gene amplification in glyphosate-resistant Amaranthus palmeri.

The inheritance of glyphosate resistance in two Amaranthus palmeri populations (R1 and R2) was examined in reciprocal crosses (RC) and second reciprocal crosses (2RC) between glyphosate-resistant (R) and -susceptible (S) parents of this dioecious species. R populations and Female-R × Male-S crosses contain higher 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene copy numbers than the S population. EPSPS expression, EPSPS enzyme activity, EPSPS protein quantity, and level of resistance to glyphosate correlated positively with genomic EPSPS relative copy number. Transfer of resistance was more influenced by the female than the male parent in spite of the fact that the multiple copies of EPSPS are amplified in the nuclear genome. This led us to hypothesize that this perplexing pattern of inheritance may result from apomictic seed production in A. palmeri. We confirmed that reproductively isolated R and S female plants produced seeds, indicating that A. palmeri can produce seeds both sexually and apomictically (facultative apomixis). This apomictic trait accounts for the low copy number inheritance in the Female-S × Male-R offsprings. Apomixis may also enhance the stability of the glyphosate resistance trait in the R populations in the absence of reproductive partners.

Indoor cooking and cleaning as a source of outdoor air pollution in urban environments.

Indoor sources of air pollution, such as from cooking and cleaning, play a key role in indoor gas-phase chemistry. The focus of the impact of these activities on air quality tends to be indoors, with less attention given to the impact on air quality outside buildings. This study uses the INdoor CHEmical Model in Python (INCHEM-Py) and the Advanced Dispersion Modelling System (ADMS) to quantify the impact cooking and cleaning have on indoor and outdoor air quality for an idealised street of houses. INCHEM-Py has been developed to determine the concentrations of 106 indoor volatile organic compounds at the point they leave a building (defined as near-field concentrations). For a simulated 140 m long street with 10 equi-distant houses undertaking cooking and cleaning activities, the maximum downwind concentration of acetaldehyde increases from a background value of 0.1 ppb to 0.9 ppb post-cooking, whilst the maximum downwind chloroform concentrations increase from 1.2 to 6.2 ppt after cleaning. Although emissions to outdoors are higher when cooking and cleaning happen indoors, the contribution of these activities to total UK emissions of volatile organic compounds is low (less than 1%), and comprise about a quarter of those emitted from traffic across the UK. It is important to quantify these emissions, particularly as continued vehicle technology improvements lead to lower direct emissions outdoors, making indoor emissions relatively more important. Understanding how indoor pollution can affect outdoor environments, will allow better mitigation measures to be designed in the future that can take into account all sources of pollution that contribute to human exposure.

Does green mean clean? Volatile organic emissions from regular versus green cleaning products.

Cleaning products emit a range of volatile organic compounds (VOCs), including some which are hazardous or can undergo chemical transformations to generate harmful secondary pollutants. In recent years, "green" cleaners have become increasingly popular, with an implicit assumption that these are better for our health and/or the environment. However, there is no strong evidence to suggest that they are better for indoor air quality compared to regular products. In this study, the VOC composition of 10 regular and 13 green cleaners was examined by headspace analysis. Monoterpenes were the most prevalent VOCs, with average total monoterpene concentrations of 8.6 and 25.0 mg L-1 for regular and green cleaners, respectively. Speciated monoterpene emissions were applied to a detailed chemical model to investigate the indoor air chemistry following a typical cleaning event. Green cleaners generally emitted more monoterpenes than regular cleaners, resulting in larger increases in harmful secondary pollutant concentrations following use, such as formaldehyde (up to 7%) and PAN species (up to 6%). However, emissions of the most reactive monoterpenes (α-terpinene, terpinolene and α-phellandrene), were observed more frequently from regular cleaners, resulting in a disproportionately large impact on the concentrations of radical species and secondary pollutants that were formed after cleaning occurred.

Exploring the effect of region on diversity and composition of weed seedbanks in herbicide-resistant crop systems in the United States.

BACKGROUND: Soil seedbanks have been recognized as one of the crucial components of agricultural ecosystems. However, studies on the shift in structure and biodiversity of soil seedbanks in herbicide-resistant crop systems are limited, and a functional trait perspective of the soil seedbank is often overlooked. RESULTS: A 6 years experiment was conducted to investigate the roles of region, crop system, and weed management strategy on species richness, functional trait diversity, and composition of the weed seedbank. Species richness was different across the interaction of region and crop system, while functional trait diversity only showed difference across regions. Species and functional trait compositions were affected by the interaction of region and crop system. Specifically, the compositional difference among crop systems was mainly determined by the significant heterogeneity of group dispersion. CONCLUSION: Growers and practitioners should consider weed functional traits in developing lasting agricultural management strategies. Long-term weed research should draw attention to the impact of transgenic crop systems and specific management tactics on weed dispersal, functional composition, and resistance evolution of weed species in such agroecosystems. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Changing the paradigm for pesticide resistance management.

Collaborative action on the part of all stakeholders in pest management is essential to effectively address the challenges of pesticide resistance. The US Environmental Protection Agency (EPA), through its Pesticide Program Dialogue Committee, recently posted a report on pesticide resistance management and the role the Agency can play in these efforts. In this Perspective, we commend the Agency for acknowledging these needs, and encourage implementation of the recommendations. We urge all stakeholders to follow the example set by the EPA to engage openly, listen to other stakeholders, and determine their role as part of the broader community that is needed to address the challenges of resistance. Our contention is that pesticide resistance will continue to escalate until all stakeholders evaluate their roles in resistance management and work together as a community to influence effective management. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

A measurement and modelling investigation of the indoor air chemistry following cooking activities.

Domestic cooking is a source of indoor air pollutants, including volatile organic compounds (VOCs), which can impact on indoor air quality. However, the real-time VOC emissions from cooking are not well characterised, and similarly, the resulting secondary chemistry is poorly understood. Here, selected-ion flow-tube mass spectrometry (SIFT-MS) was used to monitor the real-time VOC emissions during the cooking of a scripted chicken and vegetable stir-fry meal, in a room scale, semi-realistic environment. The VOC emissions were dominated by alcohols (70% of total emission), but also contained a range of aldehydes (14%) and terpenes (5%), largely attributable to the heating of oil and the preparation and heating of spices, respectively. The direct cooking-related VOC emissions were then simulated using the Indoor Chemical Model in Python (INCHEM-Py), to investigate the resulting secondary chemistry. Modelling revealed that VOC concentrations were dominated by direct emissions, with only a small contribution from secondary products, though the secondary species were longer lived than the directly emitted species. Following cooking, hydroxyl radical concentrations reduced by 86%, while organic peroxy radical levels increased by over 700%, later forming secondary organic nitrates, peroxyacylnitrates (PANs) and formaldehyde. Monoterpene emissions were shown to drive the formation of secondary formaldehyde, albeit to produce relatively modest concentrations (average of 60 ppt). Sensitivity analysis of the simulation conditions revealed that increasing the outdoor concentrations of ozone and NOx species (2.9× and 9×, respectively) resulted in the greatest increase in secondary product formation indoors (≈400%, 200% and 600% increase in organic nitrates, PANs and formaldehyde production, respectively). Given the fact that climate change is likely to result in increased ozone concentrations in the future, and that increased window-opening in response to rising temperatures is also likely, higher concentrations of indoor oxidants are likely in homes in the future. This work, therefore, suggests that cooking could be a more important source of secondary pollutants indoors in the future.

Understanding the patterns and health impact of indoor air pollutant exposures in Bradford, UK: a study protocol.

INTRODUCTION: Relative to outdoor air pollution, there is little evidence examining the composition and concentrations of indoor air pollution and its associated health impacts. The INGENIOUS project aims to provide the comprehensive understanding of indoor air pollution in UK homes. METHODS AND ANALYSIS: 'Real Home Assessment' is a cross-sectional, multimethod study within INGENIOUS. This study monitors indoor air pollutants over 2 weeks using low-cost sensors placed in three rooms in 300 Born in Bradford (BiB) households. Building audits are completed by researchers, and participants are asked to complete a home survey and a health and behaviour questionnaire, in addition to recording household activities and health symptoms on at least 1 weekday and 1 weekend day. A subsample of 150 households will receive more intensive measurements of volatile organic compound and particulate matter for 3 days. Qualitative interviews conducted with 30 participants will identify key barriers and enablers of effective ventilation practices. Outdoor air pollution is measured in 14 locations across Bradford to explore relationships between indoor and outdoor air quality. Data will be analysed to explore total concentrations of indoor air pollutants, how these vary with building characteristics, and whether they are related to health symptoms. Interviews will be analysed through content and thematic analysis. ETHICS AND DISSEMINATION: Ethical approval has been obtained from the NHS Health Research Authority Yorkshire and the Humber (Bradford Leeds) Research Ethics Committee (22/YH/0288). We will disseminate findings using our websites, social media, publications and conferences. Data will be open access through the BiB, the Open Science Framework and the UK Data Service.

Serum N-Glycomics Stratifies Bacteremic Patients Infected with Different Pathogens.

Bacteremia-i.e., the presence of pathogens in the blood stream-is associated with long-term morbidity and is a potential precursor condition to life-threatening sepsis. Timely detection of bacteremia is therefore critical to reduce patient mortality, but existing methods lack precision, speed, and sensitivity to effectively stratify bacteremic patients. Herein, we tested the potential of quantitative serum N-glycomics performed using porous graphitized carbon liquid chromatography tandem mass spectrometry to stratify bacteremic patients infected with Escherichia coli (n = 11), Staphylococcus aureus (n = 11), Pseudomonas aeruginosa (n = 5), and Streptococcus viridans (n = 5) from healthy donors (n = 39). In total, 62 N-glycan isomers spanning 41 glycan compositions primarily comprising complex-type core fucosylated, bisecting N-acetylglucosamine (GlcNAc), and α2,3-/α2,6-sialylated structures were profiled across all samples using label-free quantitation. Excitingly, unsupervised hierarchical clustering and principal component analysis of the serum N-glycome data accurately separated the patient groups. P. aeruginosa-infected patients displayed prominent N-glycome aberrations involving elevated levels of fucosylation and bisecting GlcNAcylation and reduced sialylation relative to other bacteremic patients. Notably, receiver operating characteristic analyses demonstrated that a single N-glycan isomer could effectively stratify each of the four bacteremic patient groups from the healthy donors (area under the curve 0.93-1.00). Thus, the serum N-glycome represents a new hitherto unexplored class of potential diagnostic markers for bloodstream infections.

Environmental dynamics of hospital microbiome upon transfer from a major hospital to a new facility.

BACKGROUND: Infection control is critical to safe hospital care. However, how bacteria within nosocomial environments relate to space utilisation and occupancy remains poorly understood. Our aim was to characterise the hospital microbiome in the context of the closure of a tertiary hospital and the opening of a new facility. METHODS: Environmental swabs were collected from common and inpatient areas in the old and new hospitals during a 12-month transition period. Microbiota characteristics were determined by 16S rRNA gene sequencing and quantitative (q)PCR. Targeted assays were used to detect Methicillin-resistant Staphylococcus aureus (MRSA) and vanB-positive Vancomycin-Resistant Enterococci (VRE). RESULTS: The transition to full occupancy in the new facility was associated with an increase in bacterial load (inpatient areas, 3 months p = 0.001; common areas, 6 months p = 0.039) and a change in microbiota composition (baseline-12 months, PERMANOVA p = 0.002). These changes were characterised by an increase in human microbiota-associated taxa, including Acinetobacter and Veillonella. Closure of the existing facility was associated with a decrease in bacterial load (p = 0.040). Detection of MRSA did not differ significantly between sites. CONCLUSIONS: Occupancy is a major determinant of bacterial dispersion within hospital environments. Steady-state bacterial levels and microbiota composition provide a basis for assessment of infection control measures.

High prevalence of late relapse and reinfection in prisoners treated for chronic hepatitis C.

BACKGROUND AND AIM: Prisoners have a high prevalence of injection drug use (IDU) and chronic hepatitis C (CHC) infection. Treatment of CHC in these patients is effective; however, their long-term outcomes following treatment are unknown. We determined the durability of a sustained virological response (SVR) in prisoners treated for CHC. METHODS: Patients were treated as part of routine clinical practice with interferon (IFN) and ribavirin. A retrospective review of medical records and a computerized pathology system was performed for clinical and laboratory information. RESULTS: Seventy-four prisoners (70 males, mean age 34 years, IDU in 55%) were evaluable for a SVR over a 12-year period to December 2008; the mean follow-up period was 1243 days. Genotype 1, 2, 3, and 6 infection was present in 18, three, 38 and three patients, respectively; the genotype was unknown in 12. Three out of 52 biopsied had cirrhosis. Standard IFN was administered to 25 (34%; 11 with ribavirin), and 49 received pegylated IFN and ribavirin; one did not complete treatment, and two had breakthrough relapses. The end-of-treatment response was achieved in 57 and SVR in 53; 14 were non-responders. Five male patients, four with unknown genotypes and treated with standard IFN alone, relapsed late (following SVR, 9%). Five patients, all treated with pegylated IFN and ribavirin, were reinfected (one prior to and four following SVR). CONCLUSIONS: Prisoners are often successfully treated for CHC. However, this retrospective study indicates that there is a high (17%) prevalence of late recurrence of viremia that is likely a reflection of reinfection due to ongoing risk-taking behavior.

Pictorial review on the endovascular management of paediatric aortic injuries.

Paediatric aortic trauma is a rare injury which can be fatal if not identified and managed appropriately. Surgical repair remains the gold-standard in moderate to severe aortic injuries. In the last decade however, endovascular treatment has gained popularity in children who have suitable vascular anatomy for intervention and are either not fit for surgery or in whom, endovascular intervention is the only alternative that will make a difference in the clinical outcome. Children pose a unique set of challenges to endovascular therapy. In this article, we aim to illustrate the different endovascular options that are available for the treatment of acute traumatic aortic injury and visceral thromboembolisation through pictorial representation. We will also demonstrate the feasibility and the limitation of this technique.

Mouse Genome Informatics (MGI) Is the International Resource for Information on the Laboratory Mouse.

Mouse Genome Informatics (MGI, http://www.informatics.jax.org/ ) web resources provide free access to meticulously curated information about the laboratory mouse. MGI's primary goal is to help researchers investigate the genetic foundations of human diseases by translating information from mouse phenotypes and disease models studies to human systems. MGI provides comprehensive phenotypes for over 50,000 mutant alleles in mice and provides experimental model descriptions for over 1500 human diseases. Curated data from scientific publications are integrated with those from high-throughput phenotyping and gene expression centers. Data are standardized using defined, hierarchical vocabularies such as the Mammalian Phenotype (MP) Ontology, Mouse Developmental Anatomy and the Gene Ontologies (GO). This chapter introduces you to Gene and Allele Detail pages and provides step-by-step instructions for simple searches and those that take advantage of the breadth of MGI data integration.

Lack of transgene and glyphosate effects on yield, and mineral and amino acid content of glyphosate-resistant soybean.

BACKGROUND: There has been controversy as to whether the glyphosate resistance gene and/or glyphosate applied to glyphosate-resistant (GR) soybean affect the content of cationic minerals (especially Mg, Mn and Fe), yield and amino acid content of GR soybean. A two-year field study (2013 and 2014) examined these questions at sites in Mississippi, USA. RESULTS: There were no effects of glyphosate, the GR transgene or field crop history (for a field with both no history of glyphosate use versus one with a long history of glyphosate use) on grain yield. Furthermore, these factors had no consistent effects on measured mineral (Al, As, Ba, Cd, Ca, Co, Cr, Cs, Cu, Fe, Ga, K, Li, Mg, Mn, Ni, Pb, Rb, Se, Sr, Tl, U, V, Zn) content of leaves or harvested seed. Effects on minerals were small and inconsistent between years, treatments and mineral, and appeared to be random false positives. No notable effects on free or protein amino acids of the seed were measured, although glyphosate and its degradation product, aminomethylphosphonic acid (AMPA), were found in the seed in concentrations consistent with previous studies. CONCLUSIONS: Neither glyphosate nor the GR transgene affect the content of the minerals measured in leaves and seed, harvested seed amino acid composition, or yield of GR soybean. Furthermore, soils with a legacy of GR crops have no effects on these parameters in soybean. © 2017 Society of Chemical Industry.

Searching the Mouse Genome Informatics (MGI) Resources for Information on Mouse Biology from Genotype to Phenotype.

The Mouse Genome Informatics (MGI) resource provides the research community with access to information on the genetics, genomics, and biology of the laboratory mouse. Core data in MGI include gene characterization and function, phenotype and disease model descriptions, DNA and protein sequence data, gene expression data, vertebrate homologies, SNPs, mapping data, and links to other bioinformatics databases. Semantic integration is supported through the use of standardized nomenclature, and through the use of controlled vocabularies such as the mouse Anatomical Dictionary, the Mammalian Phenotype Ontology, and the Gene Ontologies. MGI extracts and organizes data from primary literature. MGI data are shared with and widely displayed from other bioinformatics resources. The database is updated weekly with curated annotations, and regularly adds new datasets and features. This unit provides a guide to using the MGI bioinformatics resource. © 2016 by John Wiley & Sons, Inc.

Benchmark study on glyphosate-resistant cropping systems in the United States. Part 7: Effects of weed management strategy (grower practices versus academic recommendations) on the weed soil seedbank over 6 years.

BACKGROUND: Shifts in weed species composition and richness resulting from near-exclusive reliance on herbicides in glyphosate-resistant (GR) cropping systems has necessitated the implementation of alternative weed management tactics to reduce selection pressures of herbicides. We contrasted the response of the weed soil seedbank to effects of weed management strategy, comparing grower practices with academic recommendations for best management practices (BMPs) over 6 years and across five weed hardiness zones in the US Midwest at sites subject to GR cropping systems. RESULTS: Total weed population density and species richness varied according to cropping system, location and prior year's crop, but less so to weed management strategy. The seedbank population density for 11 of the 14 most frequent weed species was affected by weed management strategy either alone or in an interaction with hardiness zone or year, or both. In only 29% of comparisons was weed population density lower following academic recommendations, and this depended upon prior crop and cropping system. The population density of high-risk weed species was reduced by academic recommendations, but only in two of six years and under continuous GR maize. Overall, the weed population density was decreasing in field halves subject to the BMPs in the academic recommendations relative to grower practices. CONCLUSION: The soil seedbank is slow to respond to academic recommendations to mitigate glyphosate-resistant weeds, but represents a biological legacy that growers need to keep in mind even when management practices reduce emerged field weed population densities.