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2.
Nature ; 571(7765): E7, 2019 Jul.
Article in English | MEDLINE | ID: mdl-31263274

ABSTRACT

Change history: In this Article, the original affiliation 2 was not applicable and has been removed. In addition, in the Acknowledgements there was a statement missing and an error in a name. These errors have been corrected online.

3.
Nature ; 568(7753): 487-492, 2019 04.
Article in English | MEDLINE | ID: mdl-31019327

ABSTRACT

Carbon and other volatiles in the form of gases, fluids or mineral phases are transported from Earth's surface into the mantle at convergent margins, where the oceanic crust subducts beneath the continental crust. The efficiency of this transfer has profound implications for the nature and scale of geochemical heterogeneities in Earth's deep mantle and shallow crustal reservoirs, as well as Earth's oxidation state. However, the proportions of volatiles released from the forearc and backarc are not well constrained compared to fluxes from the volcanic arc front. Here we use helium and carbon isotope data from deeply sourced springs along two cross-arc transects to show that about 91 per cent of carbon released from the slab and mantle beneath the Costa Rican forearc is sequestered within the crust by calcite deposition. Around an additional three per cent is incorporated into the biomass through microbial chemolithoautotrophy, whereby microbes assimilate inorganic carbon into biomass. We estimate that between 1.2 × 108 and 1.3 × 1010 moles of carbon dioxide per year are released from the slab beneath the forearc, and thus up to about 19 per cent less carbon is being transferred into Earth's deep mantle than previously estimated.


Subject(s)
Carbon Dioxide/analysis , Carbon Sequestration , Geologic Sediments/chemistry , Biomass , Carbon Isotopes , Costa Rica , Geologic Sediments/microbiology , Helium
4.
BMC Biol ; 21(1): 22, 2023 02 03.
Article in English | MEDLINE | ID: mdl-36737727

ABSTRACT

BACKGROUND: Microphthalmia, anophthalmia, and coloboma (MAC) spectrum disease encompasses a group of eye malformations which play a role in childhood visual impairment. Although the predominant cause of eye malformations is known to be heritable in nature, with 80% of cases displaying loss-of-function mutations in the ocular developmental genes OTX2 or SOX2, the genetic abnormalities underlying the remaining cases of MAC are incompletely understood. This study intended to identify the novel genes and pathways required for early eye development. Additionally, pathways involved in eye formation during embryogenesis are also incompletely understood. This study aims to identify the novel genes and pathways required for early eye development through systematic forward screening of the mammalian genome. RESULTS: Query of the International Mouse Phenotyping Consortium (IMPC) database (data release 17.0, August 01, 2022) identified 74 unique knockout lines (genes) with genetically associated eye defects in mouse embryos. The vast majority of eye abnormalities were small or absent eyes, findings most relevant to MAC spectrum disease in humans. A literature search showed that 27 of the 74 lines had previously published knockout mouse models, of which only 15 had ocular defects identified in the original publications. These 12 previously published gene knockouts with no reported ocular abnormalities and the 47 unpublished knockouts with ocular abnormalities identified by the IMPC represent 59 genes not previously associated with early eye development in mice. Of these 59, we identified 19 genes with a reported human eye phenotype. Overall, mining of the IMPC data yielded 40 previously unimplicated genes linked to mammalian eye development. Bioinformatic analysis showed that several of the IMPC genes colocalized to several protein anabolic and pluripotency pathways in early eye development. Of note, our analysis suggests that the serine-glycine pathway producing glycine, a mitochondrial one-carbon donator to folate one-carbon metabolism (FOCM), is essential for eye formation. CONCLUSIONS: Using genome-wide phenotype screening of single-gene knockout mouse lines, STRING analysis, and bioinformatic methods, this study identified genes heretofore unassociated with MAC phenotypes providing models to research novel molecular and cellular mechanisms involved in eye development. These findings have the potential to hasten the diagnosis and treatment of this congenital blinding disease.


Subject(s)
Anophthalmos , Coloboma , Eye Abnormalities , Microphthalmos , Humans , Mice , Animals , Eye Abnormalities/genetics , Anophthalmos/genetics , Microphthalmos/genetics , Coloboma/genetics , Mice, Knockout , Embryonic Development/genetics , Phenotype , Eye , Mammals
5.
Mamm Genome ; 34(2): 180-199, 2023 06.
Article in English | MEDLINE | ID: mdl-37294348

ABSTRACT

Reference ranges provide a powerful tool for diagnostic decision-making in clinical medicine and are enormously valuable for understanding normality in pre-clinical scientific research that uses in vivo models. As yet, there are no published reference ranges for electrocardiography (ECG) in the laboratory mouse. The first mouse-specific reference ranges for the assessment of electrical conduction are reported herein generated from an ECG dataset of unprecedented scale. International Mouse Phenotyping Consortium data from over 26,000 conscious or anesthetized C57BL/6N wildtype control mice were stratified by sex and age to develop robust ECG reference ranges. Interesting findings include that heart rate and key elements from the ECG waveform (RR-, PR-, ST-, QT-interval, QT corrected, and QRS complex) demonstrate minimal sexual dimorphism. As expected, anesthesia induces a decrease in heart rate and was shown for both inhalation (isoflurane) and injectable (tribromoethanol) anesthesia. In the absence of pharmacological, environmental, or genetic challenges, we did not observe major age-related ECG changes in C57BL/6N-inbred mice as the differences in the reference ranges of 12-week-old compared to 62-week-old mice were negligible. The generalizability of the C57BL/6N substrain reference ranges was demonstrated by comparison with ECG data from a wide range of non-IMPC studies. The close overlap in data from a wide range of mouse strains suggests that the C57BL/6N-based reference ranges can be used as a robust and comprehensive indicator of normality. We report a unique ECG reference resource of fundamental importance for any experimental study of cardiac function in mice.


Subject(s)
Electrocardiography , Electrophysiologic Techniques, Cardiac , Mice , Animals , Mice, Inbred C57BL , Mice, Inbred Strains
6.
Environ Sci Technol ; 57(26): 9459-9473, 2023 07 04.
Article in English | MEDLINE | ID: mdl-37327355

ABSTRACT

Carbon capture and storage (CCS) is an important component in many national net-zero strategies. Ensuring that CO2 can be safely and economically stored in geological systems is critical. To date, CCS research has focused on the physiochemical behavior of CO2, yet there has been little consideration of the subsurface microbial impact on CO2 storage. However, recent discoveries have shown that microbial processes (e.g., methanogenesis) can be significant. Importantly, methanogenesis may modify the fluid composition and the fluid dynamics within the storage reservoir. Such changes may subsequently reduce the volume of CO2 that can be stored and change the mobility and future trapping systematics of the evolved supercritical fluid. Here, we review the current knowledge of how microbial methanogenesis could impact CO2 storage, including the potential scale of methanogenesis and the range of geologic settings under which this process operates. We find that methanogenesis is possible in all storage target types; however, the kinetics and energetics of methanogenesis will likely be limited by H2 generation. We expect that the bioavailability of H2 (and thus potential of microbial methanogenesis) will be greatest in depleted hydrocarbon fields and least within saline aquifers. We propose that additional integrated monitoring requirements are needed for CO2 storage to trace any biogeochemical processes including baseline, temporal, and spatial studies. Finally, we suggest areas where further research should be targeted in order to fully understand microbial methanogenesis in CO2 storage sites and its potential impact.


Subject(s)
Carbon Dioxide , Groundwater , Carbon
7.
PLoS Genet ; 16(1): e1008577, 2020 01.
Article in English | MEDLINE | ID: mdl-31929527

ABSTRACT

Circadian systems provide a fitness advantage to organisms by allowing them to adapt to daily changes of environmental cues, such as light/dark cycles. The molecular mechanism underlying the circadian clock has been well characterized. However, how internal circadian clocks are entrained with regular daily light/dark cycles remains unclear. By collecting and analyzing indirect calorimetry (IC) data from more than 2000 wild-type mice available from the International Mouse Phenotyping Consortium (IMPC), we show that the onset time and peak phase of activity and food intake rhythms are reliable parameters for screening defects of circadian misalignment. We developed a machine learning algorithm to quantify these two parameters in our misalignment screen (SyncScreener) with existing datasets and used it to screen 750 mutant mouse lines from five IMPC phenotyping centres. Mutants of five genes (Slc7a11, Rhbdl1, Spop, Ctc1 and Oxtr) were found to be associated with altered patterns of activity or food intake. By further studying the Slc7a11tm1a/tm1a mice, we confirmed its advanced activity phase phenotype in response to a simulated jetlag and skeleton photoperiod stimuli. Disruption of Slc7a11 affected the intercellular communication in the suprachiasmatic nucleus, suggesting a defect in synchronization of clock neurons. Our study has established a systematic phenotype analysis approach that can be used to uncover the mechanism of circadian entrainment in mice.


Subject(s)
Circadian Rhythm/genetics , Amino Acid Transport System y+/genetics , Animals , Machine Learning , Male , Mice , Mice, Inbred C57BL , Mutation , Receptors, Oxytocin/genetics , Repressor Proteins/genetics , Serine Endopeptidases/genetics , Telomere-Binding Proteins/genetics , Ubiquitin-Protein Ligase Complexes/genetics
8.
Mamm Genome ; 33(1): 203-212, 2022 03.
Article in English | MEDLINE | ID: mdl-34313795

ABSTRACT

The Mutant Mouse Resource and Research Center (MMRRC) Program is the pre-eminent public national mutant mouse repository and distribution archive in the USA, serving as a national resource of mutant mice available to the global scientific community for biomedical research. Established more than two decades ago with grants from the National Institutes of Health (NIH), the MMRRC Program supports a Consortium of regionally distributed and dedicated vivaria, laboratories, and offices (Centers) and an Informatics Coordination and Service Center (ICSC) at three academic teaching and research universities and one non-profit genetic research institution. The MMRRC Program accepts the submission of unique, scientifically rigorous, and experimentally valuable genetically altered and other mouse models donated by academic and commercial scientists and organizations for deposition, maintenance, preservation, and dissemination to scientists upon request. The four Centers maintain an archive of nearly 60,000 mutant alleles as live mice, frozen germplasm, and/or embryonic stem (ES) cells. Since its inception, the Centers have fulfilled 13,184 orders for mutant mouse models from 9591 scientists at 6626 institutions around the globe. Centers also provide numerous services that facilitate using mutant mouse models obtained from the MMRRC, including genetic assays, microbiome analysis, analytical phenotyping and pathology, cryorecovery, mouse husbandry, infectious disease surveillance and diagnosis, and disease modeling. The ICSC coordinates activities between the Centers, manages the website (mmrrc.org) and online catalog, and conducts communication, outreach, and education to the research community. Centers preserve, secure, and protect mutant mouse lines in perpetuity, promote rigor and reproducibility in scientific experiments using mice, provide experiential training and consultation in the responsible use of mice in research, and pursue cutting edge technologies to advance biomedical studies using mice to improve human health. Researchers benefit from an expansive list of well-defined mouse models of disease that meet the highest standards of rigor and reproducibility, while donating investigators benefit by having their mouse lines preserved, protected, and distributed in compliance with NIH policies.


Subject(s)
Biomedical Research , Disease Models, Animal , Mice , National Institutes of Health (U.S.) , Animals , Humans , Mice/genetics , Reproducibility of Results , United States
9.
Dev Biol ; 458(2): 141-152, 2020 02 15.
Article in English | MEDLINE | ID: mdl-31634437

ABSTRACT

PURPOSE: The purpose of this study is to determine the effect of Cytoglobin (Cygb) deficiency on Crb1-related retinopathy. The Crb1 cell polarity complex is required for photoreceptor function and survival. Crb1-related retinopathies encompass a broad range of phenotypes which are not completely explained by the variability of Crb1 mutations. Genes thought to modify Crb1 function are therefore important targets of research. The biological function of Cygb involves oxygen delivery, scavenging of reactive oxygen species, and nitric oxide metabolism. However, the relationship of Cygb to diseases involving the Crb1 cell polarity complex is unknown. METHODS: Cygb knockout mice homozygous for the rd8 mutation (Cygb-/-rd8/rd8) were screened for ocular abnormalities and imaged using optical coherence tomography and fundus photography. Electroretinography was performed, as was histology and immunohistochemistry. Quantitative PCR was used to determine the effect of Cygb deficiency on transcription of Crb1 related cell polarity genes. RESULTS: Cygb-/-rd8/rd8 mice develop an abnormal retina with severe lamination abnormalities. The retina undergoes progressive degeneration with the ventral retina more severely affected than the dorsal retina. Cygb expression is in neurons of the retinal ganglion cell layer and inner nuclear layer. Immunohistochemical studies suggest that cell death predominates in the photoreceptors. Electroretinography amplitudes show reduced a- and b-waves, consistent with photoreceptor disease. Cygb deficient retinas had only modest transcriptional perturbations of Crb1-related cell polarity genes. Cygb-/- mice without the rd8 mutation did not exhibit obvious retinal abnormalities. CONCLUSIONS: Cygb is necessary for retinal lamination, maintenance of cell polarity, and photoreceptor survival in rd8 mice. These results are consistent with Cygb as a disease modifying gene in Crb1-related retinopathy. Further studies are necessary to investigate the role of Cygb in the human retina.


Subject(s)
Cytoglobin/genetics , Nerve Tissue Proteins/metabolism , Retinal Degeneration/metabolism , Animals , Cytoglobin/metabolism , Disease Models, Animal , Eye Proteins/genetics , Female , Homozygote , Male , Membrane Proteins/metabolism , Mice , Mice, Inbred C57BL , Mice, Knockout , Mutation , Nerve Tissue Proteins/genetics , Phenotype , Retina/metabolism , Retinal Degeneration/genetics , Retinal Degeneration/physiopathology , Retinal Ganglion Cells/metabolism
10.
Am J Physiol Endocrinol Metab ; 321(1): E47-E62, 2021 07 01.
Article in English | MEDLINE | ID: mdl-33969705

ABSTRACT

Myoglobin (Mb) regulates O2 bioavailability in muscle and heart as the partial pressure of O2 (Po2) drops with increased tissue workload. Globin proteins also modulate cellular NO pools, "scavenging" NO at higher Po2 and converting NO2- to NO as Po2 falls. Myoglobin binding of fatty acids may also signal a role in fat metabolism. Interestingly, Mb is expressed in brown adipose tissue (BAT), but its function is unknown. Herein, we present a new conceptual model that proposes links between BAT thermogenic activation, concurrently reduced Po2, and NO pools regulated by deoxy/oxy-globin toggling and xanthine oxidoreductase (XOR). We describe the effect of Mb knockout (Mb-/-) on BAT phenotype [lipid droplets, mitochondrial markers uncoupling protein 1 (UCP1) and cytochrome C oxidase 4 (Cox4), transcriptomics] in male and female mice fed a high-fat diet (HFD, 45% of energy, ∼13 wk), and examine Mb expression during brown adipocyte differentiation. Interscapular BAT weights did not differ by genotype, but there was a higher prevalence of mid-large sized droplets in Mb-/-. COX4 protein expression was significantly reduced in Mb-/- BAT, and a suite of metabolic/NO/stress/hypoxia transcripts were lower. All of these Mb-/--associated differences were most apparent in females. The new conceptual model, and results derived from Mb-/- mice, suggest a role for Mb in BAT metabolic regulation, in part through sexually dimorphic systems and NO signaling. This possibility requires further validation in light of significant mouse-to-mouse variability of BAT Mb mRNA and protein abundances in wild-type mice and lower expression relative to muscle and heart.NEW & NOTEWORTHY Myoglobin confers the distinct red color to muscle and heart, serving as an oxygen-binding protein in oxidative fibers. Less attention has been paid to brown fat, a thermogenic tissue that also expresses myoglobin. In a mouse knockout model lacking myoglobin, brown fat had larger fat droplets and lower markers of mitochondrial oxidative metabolism, especially in females. Gene expression patterns suggest a role for myoglobin as an oxygen/nitric oxide-sensor that regulates cellular metabolic and signaling pathways.


Subject(s)
Adipose Tissue, Brown/physiology , Myoglobin/physiology , Adipocytes, Brown/physiology , Adipose Tissue, Brown/chemistry , Adipose Tissue, Brown/ultrastructure , Animals , Cell Differentiation , Cells, Cultured , Diet, High-Fat , Electron Transport Complex IV/genetics , Female , Gene Expression , Lipids/analysis , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Mitochondria/physiology , Myoglobin/deficiency , Myoglobin/genetics , Nitric Oxide/metabolism , Oxygen/metabolism , RNA, Messenger/analysis
11.
Am J Physiol Endocrinol Metab ; 321(1): E63-E79, 2021 07 01.
Article in English | MEDLINE | ID: mdl-33969704

ABSTRACT

Myoglobin (Mb) is a regulator of O2 bioavailability in type I muscle and heart, at least when tissue O2 levels drop. Mb also plays a role in regulating cellular nitric oxide (NO) pools. Robust binding of long-chain fatty acids and long-chain acylcarnitines to Mb, and enhanced glucose metabolism in hearts of Mb knockout (KO) mice, suggest additional roles in muscle intermediary metabolism and fuel selection. To evaluate this hypothesis, we measured energy expenditure (EE), respiratory exchange ratio (RER), body weight gain and adiposity, glucose tolerance, and insulin sensitivity in Mb knockout (Mb-/-) and wild-type (WT) mice challenged with a high-fat diet (HFD, 45% of calories). In males (n = 10/genotype) and females (n = 9/genotype) tested at 5-6, 11-12, and 17-18 wk, there were no genotype effects on RER, EE, or food intake. RER and EE during cold (10°C, 72 h), and glucose and insulin tolerance, were not different compared with within-sex WT controls. At ∼18 and ∼19 wk of age, female Mb-/- adiposity was ∼42%-48% higher versus WT females (P = 0.1). Transcriptomics analyses (whole gastrocnemius, soleus) revealed few consistent changes, with the notable exception of a 20% drop in soleus transferrin receptor (Tfrc) mRNA. Capillarity indices were significantly increased in Mb-/-, specifically in Mb-rich soleus and deep gastrocnemius. The results indicate that Mb loss does not have a major impact on whole body glucose homeostasis, EE, RER, or response to a cold challenge in mice. However, the greater adiposity in female Mb-/- mice indicates a sex-specific effect of Mb KO on fat storage and feed efficiency.NEW & NOTEWORTHY The roles of myoglobin remain to be elaborated. We address sexual dimorphism in terms of outcomes in response to the loss of myoglobin in knockout mice and perform, for the first time, a series of comprehensive metabolic studies under conditions in which fat is mobilized (high-fat diet, cold). The results highlight that myoglobin is not necessary and sufficient for maintaining oxidative metabolism and point to alternative roles for this protein in muscle and heart.


Subject(s)
Muscle, Skeletal/metabolism , Myocardium/metabolism , Myoglobin/physiology , Adiposity , Animals , Body Weight , Diet, High-Fat , Energy Metabolism , Fatty Acids/metabolism , Female , Glucose Tolerance Test , Lipid Metabolism , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Muscle, Skeletal/blood supply , Myoglobin/deficiency , Myoglobin/genetics , Oxidation-Reduction , Phenotype , Sex Characteristics
12.
Am J Physiol Endocrinol Metab ; 319(3): E472-E484, 2020 09 01.
Article in English | MEDLINE | ID: mdl-32691631

ABSTRACT

Obesity and its metabolic sequelae are implicated in dysfunction of the somatosensory, sympathetic, and hypothalamic systems. Because these systems contribute to integrative regulation of energy expenditure (EE) and energy intake (EI) in response to ambient temperature (Ta) changes, we hypothesized that diet-induced obesity (DIO) disrupts Ta-associated EE-EI coupling. C57BL/6N male mice were fed a high-fat diet (HFD; 45% kcal) or low-fat diet (LFD; 10% kcal) for ∼9.5 wk; HFD mice were then split into body weight (BWT) quartiles (n = 8 each) to study DIO-low gainers (Q1) versus -high gainers (Q4). EI and indirect calorimetry (IC) were measured over 3 days each at 10°C, 20°C, and 30°C. Responses did not differ between LFD, Q1, and Q4; EI and BWT-adjusted EE increased rapidly when transitioning toward 20°C and 10°C. In all groups, EI at 30°C was not reduced despite lower EE, resulting in positive energy balance and respiratory exchange ratios consistent with increased de novo lipogenesis, energy storage, and relative hyperphagia. We conclude that 1) systems controlling Ta-dependent acute EI/EE coupling remained intact in obese mice and 2) rapid coupling of EI/EE at cooler temperatures is an important adaptation to maintain energy stores and defend body temperature, but less critical at thermoneutrality. A post hoc analysis using digestible EI plus IC-calculated EE suggests that standard IC assumptions for EE calculation require further validation in the setting of DIO. The experimental paradigm provides a platform to query the hypothalamic, somatosensory, and sympathetic mechanisms that drive Ta-associated EI/EE coupling.


Subject(s)
Body Temperature Regulation/physiology , Energy Intake , Energy Metabolism , Obesity/metabolism , Temperature , Adipose Tissue, Brown/metabolism , Animals , Blood Glucose/metabolism , Body Composition , Body Weight , Diet, Fat-Restricted , Diet, High-Fat , Drinking , Insulin/blood , Male , Mice , Mice, Inbred C57BL , Mice, Obese , Obesity/etiology
13.
Appl Environ Microbiol ; 85(14)2019 07 15.
Article in English | MEDLINE | ID: mdl-31076435

ABSTRACT

Glacial retreat is changing biogeochemical cycling in the Arctic, where glacial runoff contributes iron for oceanic shelf primary production. We hypothesize that in Svalbard fjords, microbes catalyze intense iron and sulfur cycling in low-organic-matter sediments. This is because low organic matter limits sulfide generation, allowing iron mobility to the water column instead of precipitation as iron monosulfides. In this study, we tested this with high-depth-resolution 16S rRNA gene libraries in the upper 20 cm at two sites in Van Keulenfjorden, Svalbard. At the site closer to the glaciers, iron-reducing Desulfuromonadales, iron-oxidizing Gallionella and Mariprofundus, and sulfur-oxidizing Thiotrichales and Epsilonproteobacteria were abundant above a 12-cm depth. Below this depth, the relative abundances of sequences for sulfate-reducing Desulfobacteraceae and Desulfobulbaceae increased. At the outer station, the switch from iron-cycling clades to sulfate reducers occurred at shallower depths (∼5 cm), corresponding to higher sulfate reduction rates. Relatively labile organic matter (shown by δ13C and C/N ratios) was more abundant at this outer site, and ordination analysis suggested that this affected microbial community structure in surface sediments. Network analysis revealed more correlations between predicted iron- and sulfur-cycling taxa and with uncultured clades proximal to the glacier. Together, these results suggest that complex microbial communities catalyze redox cycling of iron and sulfur, especially closer to the glacier, where sulfate reduction is limited due to low availability of organic matter. Diminished sulfate reduction in upper sediments enables iron to flux into the overlying water, where it may be transported to the shelf.IMPORTANCE Glacial runoff is a key source of iron for primary production in the Arctic. In the fjords of the Svalbard archipelago, glacial retreat is predicted to stimulate phytoplankton blooms that were previously restricted to outer margins. Decreased sediment delivery and enhanced primary production have been hypothesized to alter sediment biogeochemistry, wherein any free reduced iron that could potentially be delivered to the shelf will instead become buried with sulfide generated through microbial sulfate reduction. We support this hypothesis with sequencing data that showed increases in the relative abundance of sulfate reducing taxa and sulfate reduction rates with increasing distance from the glaciers in Van Keulenfjorden, Svalbard. Community structure was driven by organic geochemistry, suggesting that enhanced input of organic material will stimulate sulfate reduction in interior fjord sediments as glaciers continue to recede.


Subject(s)
Iron/metabolism , Microbiota , Seawater/microbiology , Sulfur/metabolism , Arctic Regions , Climate Change , Estuaries , Geologic Sediments/microbiology , RNA, Bacterial/analysis , RNA, Ribosomal, 16S/analysis , Svalbard
14.
Genome Res ; 25(4): 598-607, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25591789

ABSTRACT

Expression of the bacterial beta-galactosidase reporter gene (lacZ) in the vector used for the Knockout Mouse Project (KOMP) is driven by the endogenous promoter of the target gene. In tissues from KOMP mice, histochemical staining for LacZ enzyme activity can be used to determine gene expression patterns. With this technique, we have produced a comprehensive resource of gene expression using both whole mount (WM) and frozen section (FS) LacZ staining in 313 unique KOMP mutant mouse lines. Of these, ∼ 80% of mutants showed specific staining in one or more tissues, while ∼ 20% showed no specific staining, ∼ 13% had staining in only one tissue, and ∼ 25% had staining in >6 tissues. The highest frequency of specific staining occurred in the brain (∼ 50%), male gonads (42%), and kidney (39%). The WM method was useful for rapidly identifying whole organ and some substructure staining, while the FS method often revealed substructure and cellular staining specificity. Both staining methods had >90% repeatability in biological replicates. Nonspecific LacZ staining occurs in some tissues due to the presence of bacteria or endogenous enzyme activity. However, this can be effectively distinguished from reporter gene activity by the combination of the WM and FS methods. After careful annotation, LacZ staining patterns in a high percentage of mutants revealed a unique structure-function not previously reported for many of these genes. The validation of methods for LacZ staining, annotation, and expression analysis reported here provides unique insights into the function of genes for which little is currently known.


Subject(s)
Gene Expression Regulation/genetics , Genes, Reporter/genetics , Lac Operon/genetics , Promoter Regions, Genetic/genetics , Animals , Atlases as Topic , Female , Gene Expression , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Staining and Labeling , Structure-Activity Relationship
15.
Psychol Med ; 48(4): 578-591, 2018 03.
Article in English | MEDLINE | ID: mdl-28714426

ABSTRACT

BACKGROUND: The study aim was to establish and quantify suicide risk following acute admissions for all major physical illnesses, for confirmatory purposes, from two independent information sources from different countries. METHODS: Record linkage of inpatient and death certificate data for 11 004 389 acute admissions for physical illnesses in England and 713 496 in Wales. The main outcome measure was standardised mortality ratios (SMRs) for suicide at 1 year following discharge from hospital. RESULTS: There were 1781 suicides within 1 year of discharge in England (SMR = 1.7; 95% = 1.6-1.8) and 131 in Wales (SMR = 2.0; 1.7-2.3). Of 48 major physical illnesses that were associated with at least eight suicides in either country, there was high consistent suicide mortality (significant SMR >3) in both countries for constipation (SMR = 4.1 in England, 7.5 in Wales), gastritis (4.4 and 4.9) and upper gastrointestinal bleeding (3.4 and 4.5). There was high suicide mortality in one country for alcoholic liver disease, other liver disease and chronic pancreatitis; for epilepsy and Parkinson's disease; for diabetes, hypoglycaemia and hypo-osmolality & hyponatraemia; and for pneumonia, back pain and urinary tract infections. CONCLUSIONS: There is little or no increased suicide mortality following acute admissions for most physical illnesses. Much of the increased suicide mortality relates to gastrointestinal disorders that are often alcohol related or specific chronic conditions, which may be linked to side effects from certain therapeutic medications. Acute hospital admissions for physical illnesses may therefore provide an opportunity for targeted suicide prevention among people with certain conditions, particularly alcohol related disorders.


Subject(s)
Disease/psychology , Patient Admission/statistics & numerical data , Suicide/statistics & numerical data , Adult , Age Distribution , Aged , Aged, 80 and over , Alcohol-Related Disorders/psychology , Databases, Factual , England/epidemiology , Female , Humans , Logistic Models , Male , Middle Aged , Retrospective Studies , Sex Distribution , Wales/epidemiology
16.
PLoS Biol ; 13(5): e1002151, 2015 May.
Article in English | MEDLINE | ID: mdl-25992600

ABSTRACT

The Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines were developed to address the lack of reproducibility in biomedical animal studies and improve the communication of research findings. While intended to guide the preparation of peer-reviewed manuscripts, the principles of transparent reporting are also fundamental for in vivo databases. Here, we describe the benefits and challenges of applying the guidelines for the International Mouse Phenotyping Consortium (IMPC), whose goal is to produce and phenotype 20,000 knockout mouse strains in a reproducible manner across ten research centres. In addition to ensuring the transparency and reproducibility of the IMPC, the solutions to the challenges of applying the ARRIVE guidelines in the context of IMPC will provide a resource to help guide similar initiatives in the future.


Subject(s)
Animal Experimentation/standards , Databases as Topic , Guidelines as Topic , Phenotype , Animals , Mice
17.
Conserv Genet ; 19(4): 995-1005, 2018.
Article in English | MEDLINE | ID: mdl-30100824

ABSTRACT

The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied.

18.
J Dairy Sci ; 100(5): 3584-3590, 2017 May.
Article in English | MEDLINE | ID: mdl-28237600

ABSTRACT

Chromium (Cr), in the form of Cr propionate, has been permitted for supplementation to cattle diets in the United States at levels up to 0.50 mg of Cr/kg of DM since 2009. Little is known regarding Cr concentrations naturally present in practical feed ingredients. The present study was conducted to determine Cr concentrations in feed ingredients commonly fed to ruminants. Feed ingredients were collected from dairy farms, feed mills, grain bins, and university research farms. Mean Cr concentrations in whole cereal grains ranged from 0.025 mg/kg of DM for oats to 0.041 mg/kg of DM for wheat. Grinding whole samples of corn, soybeans, and wheat through a stainless steel Wiley mill screen greatly increased analyzed Cr concentrations. Harvested forages had greater Cr concentrations than concentrates, and alfalfa hay or haylage had greater Cr concentrations than grass hay or corn silage. Chromium in alfalfa hay or haylage (n = 13) averaged 0.522 mg/kg of DM, with a range of 0.199 to 0.889 mg/kg of DM. Corn silage (n = 21) averaged 0.220 mg of Cr/kg of DM with a range of 0.105 to 0.441 mg of Cr/kg of DM. By-product feeds ranged from 0.040 mg of Cr/kg of DM for cottonseed hulls to 1.222 mg of Cr/kg of DM for beet pulp. Of the feed ingredients analyzed, feed grade phosphate sources had the greatest Cr concentration (135.0 mg/kg). Most ruminant feedstuffs and feed ingredients had less than 0.50 mg of Cr/kg of DM. Much of the analyzed total Cr in feed ingredients appears to be due to Cr contamination from soil or metal contact during harvesting, processing, or both.


Subject(s)
Animal Feed , Chromium , Animals , Cattle , Diet/veterinary , Digestion , Ruminants , Silage , Zea mays
19.
J Intellect Disabil Res ; 61(8): 766-777, 2017 08.
Article in English | MEDLINE | ID: mdl-28593714

ABSTRACT

BACKGROUND: Increasingly, pupils on the autism spectrum are educated in inclusive mainstream classrooms. However, they often experience social isolation and bullying, and raising the awareness of autism in peers has been suggested as a remedy. METHODS: In order to assess autism awareness in peers, autism-related questions were included in two large-scale surveys: the Kids Life and Times survey for 11-year olds and the Young Life and Times survey for 16-year olds; a total of n = 3353 children and young people completed the surveys. RESULTS: Autism awareness was higher for the teenagers (80%) than for the younger children (50%). Many of the children knew someone with autism (50%) and generally reported positive and supportive attitudes. Self-reported prevalence of autism was 3.1% for teenagers and 2.7% for the younger children. Peers recognised bullying as a problem and were willing to help. CONCLUSIONS: Children and young people have good levels of awareness and knowledge about autism and reported positive attitudes towards peers with autism and are willing to help those who are bullied. A higher than expected number of children and young people self-reported being on the autism spectrum. These findings bode well for peer-mediated support strategies for inclusive education.


Subject(s)
Autism Spectrum Disorder , Health Knowledge, Attitudes, Practice , Adolescent , Child , Female , Humans , Male
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