Open Science Practices in Psychiatric Genetics: A Primer

Open science ensures that research is transparently reported and freely accessible for all to assess and collaboratively build on. Psychiatric genetics has led among the health sciences in implementing some open science practices in common study designs, such as replication as part of genome-wide association studies. However, thorough open science implementation guidelines are limited and largely not specific to data, privacy, and research conduct challenges in psychiatric genetics. Here, we present a primer of open science practices, including selection of a research topic with patients/nonacademic collaborators, equitable authorship and citation practices, design of replicable, reproducible studies, preregistrations, open data, and privacy issues. We provide tips for informative figures and inclusive, precise reporting. We discuss considerations in working with nonacademic collaborators and distributing research through preprints, blogs, social media, and accessible lecture materials. Finally, we provide extra resources to support every step of the research process.

Dietary Factors and Hidradenitis Suppurativa

Hidradenitis suppurativa (HS) is a debilitating chronic inflammatory skin condition affecting hair follicles in flexural sites. Obesity is considered to be a risk factor for HS occurrence and thought to be associated with increased severity of HS symptoms. Here, we review the literature examining the impact of dietary factors on HS. Moreover, we propose potential mechanistic links between dietary factors and HS pathogenesis, incorporating evidence from both clinical and basic science studies.

A study of gene expression in the living human brain

A goal of medical research is to determine the molecular basis of human brain health and illness. One way to achieve this goal is through observational studies of gene expression in human brain tissue. Due to the unavailability of brain tissue from living people, most such studies are performed using tissue from postmortem brain donors. An assumption underlying this practice is that gene expression in the postmortem human brain is an accurate representation of gene expression in the living human brain. Here, this assumption - which, until now, had not been adequately tested - is tested by comparing human prefrontal cortex gene expression between 275 living samples and 243 postmortem samples. Expression levels differed significantly for nearly 80% of genes, and a systematic examination of alternative explanations for this observation determined that these differences are not a consequence of cell type composition, RNA quality, postmortem interval, age, medication, morbidity, symptom severity, tissue pathology, sample handling, batch effects, or computational methods utilized. Analyses integrating the data generated for this study with data from earlier landmark studies that used tissue from postmortem brain donors showed that postmortem brain gene expression signatures of neurological and mental illnesses, as well as of normal traits such as aging, may not be accurate representations of these gene expression signatures in the living brain. By using tissue from large cohorts living people, future observational studies of human brain biology have the potential to (1) determine the medical research questions that can be addressed using postmortem tissue as a proxy for living tissue and (2) expand the scope of medical research to include questions about the molecular basis of human brain health and illness that can only be addressed in living people (e.g., "What happens at the molecular level in the brain as a person experiences an emotion?").

Mapping anorexia nervosa genes to clinical phenotypes

BACKGROUND

Anorexia nervosa (AN) is a psychiatric disorder with complex etiology, with a significant portion of disease risk imparted by genetics. Traditional genome-wide association studies (GWAS) produce principal evidence for the association of genetic variants with disease. Transcriptomic imputation (TI) allows for the translation of those variants into regulatory mechanisms, which can then be used to assess the functional outcome of genetically regulated gene expression (GReX) in a broader setting through the use of phenome-wide association studies (pheWASs) in large and diverse clinical biobank populations with electronic health record phenotypes.

METHODS

Here, we applied TI using S-PrediXcan to translate the most recent PGC-ED AN GWAS findings into AN-GReX. For significant genes, we imputed AN-GReX in the Mount Sinai BioMe™ Biobank and performed pheWASs on over 2000 outcomes to test the clinical consequences of aberrant expression of these genes. We performed a secondary analysis to assess the impact of body mass index (BMI) and sex on AN-GReX clinical associations.

RESULTS

Our S-PrediXcan analysis identified 53 genes associated with AN, including what is, to our knowledge, the first-genetic association of AN with the major histocompatibility complex. AN-GReX was associated with autoimmune, metabolic, and gastrointestinal diagnoses in our biobank cohort, as well as measures of cholesterol, medications, substance use, and pain. Additionally, our analyses showed moderation of AN-GReX associations with measures of cholesterol and substance use by BMI, and moderation of AN-GReX associations with celiac disease by sex.

CONCLUSIONS

Our BMI-stratified results provide potential avenues of functional mechanism for AN-genes to investigate further.

Schizophrenia risk conferred by rare protein-truncating variants is conserved across diverse human populations

Schizophrenia (SCZ) is a chronic mental illness and among the most debilitating conditions encountered in medical practice. A recent landmark SCZ study of the protein-coding regions of the genome identified a causal role for ten genes and a concentration of rare variant signals in evolutionarily constrained genes1. This recent study-and most other large-scale human genetics studies-was mainly composed of individuals of European (EUR) ancestry, and the generalizability of the findings in non-EUR populations remains unclear. To address this gap, we designed a custom sequencing panel of 161 genes selected based on the current knowledge of SCZ genetics and sequenced a new cohort of 11,580 SCZ cases and 10,555 controls of diverse ancestries. Replicating earlier work, we found that cases carried a significantly higher burden of rare protein-truncating variants (PTVs) among evolutionarily constrained genes (odds ratio = 1.48; P = 5.4 × 10-6). In meta-analyses with existing datasets totaling up to 35,828 cases and 107,877 controls, this excess burden was largely consistent across five ancestral populations. Two genes (SRRM2 and AKAP11) were newly implicated as SCZ risk genes, and one gene (PCLO) was identified as shared by individuals with SCZ and those with autism. Overall, our results lend robust support to the rare allelic spectrum of the genetic architecture of SCZ being conserved across diverse human populations.

Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae

Post-acute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are debilitating, clinically heterogeneous and of unknown molecular etiology. A transcriptome-wide investigation was performed in 165 acutely infected hospitalized individuals who were followed clinically into the post-acute period. Distinct gene expression signatures of post-acute sequelae were already present in whole blood during acute infection, with innate and adaptive immune cells implicated in different symptoms. Two clusters of sequelae exhibited divergent plasma-cell-associated gene expression patterns. In one cluster, sequelae associated with higher expression of immunoglobulin-related genes in an anti-spike antibody titer-dependent manner. In the other, sequelae associated independently of these titers with lower expression of immunoglobulin-related genes, indicating lower non-specific antibody production in individuals with these sequelae. This relationship between lower total immunoglobulins and sequelae was validated in an external cohort. Altogether, multiple etiologies of post-acute sequelae were already detectable during SARS-CoV-2 infection, directly linking these sequelae with the acute host response to the virus and providing early insights into their development.

Exploring the clinical and genetic associations of adult weight trajectories using electronic health records in a racially diverse biobank: a phenome-wide and polygenic risk study

BACKGROUND

Weight trajectories might reflect individual health status. In this study, we aimed to examine the clinical and genetic associations of adult weight trajectories using electronic health records (EHRs) in the BioMe Biobank.

METHODS

We constructed four weight trajectories based on a-priori definitions of weight changes (5% or 10%) using annual weight in EHRs (stable weight, weight gain, weight loss, and weight cycle); the final weight dataset included 21 487 participants with 162 783 annual weight measures. To confirm accurate assignment of weight trajectories, we manually reviewed weight trajectory plots for 100 random individuals. We then did a hypothesis-free phenome-wide association study (PheWAS) to identify diseases associated with each weight trajectory. Next, we estimated the single-nucleotide polymorphism-based heritability (hSNP2) of weight trajectories using GCTA-GREML, and we did a hypothesis-driven analysis of anorexia nervosa and depression polygenic risk scores (PRS) on these weight trajectories, given both diseases are associated with weight changes. We extended our analyses to the UK Biobank to replicate findings from a patient population to a generally healthy population.

FINDINGS

We found high concordance between manually assigned weight trajectories and those assigned by the algorithm (accuracy ≥98%). Stable weight was consistently associated with lower disease risks among those passing Bonferroni-corrected p value in our PheWAS (p≤4·4 × 10-5). Additionally, we identified an association between depression and weight cycle (odds ratio [OR] 1·42, 95% CI 1·31-1·55, p≤7·7 × 10-16). The adult weight trajectories were heritable (using 5% weight change as the cutoff: hSNP2 of 2·1%, 95% CI 0·9-3·3, for stable weight; 4·1%, 1·4-6·8, for weight gain; 5·5%, 2·8-8·2, for weight loss; and 4·7%, 2·3-7·1%, for weight cycle). Anorexia nervosa PRS was positively associated with weight loss trajectory among individuals without eating disorder diagnoses (OR1SD 1·16, 95% CI 1·07-1·26, per 1 SD higher PRS, p=0·011), and the association was not attenuated by obesity PRS. No association was found between depression PRS and weight trajectories after permutation tests. All main findings were replicated in the UK Biobank (p<0·05).

INTERPRETATION

Our findings suggest the importance of considering weight from a longitudinal aspect for its association with health and highlight a crucial role of weight management during disease development and progression.

FUNDING

Klarman Family Foundation, US National Institute of Mental Health (NIMH).

Altered gene expression and PTSD symptom dimensions in World Trade Center responders

Despite experiencing a significant trauma, only a subset of World Trade Center (WTC) rescue and recovery workers developed posttraumatic stress disorder (PTSD). Identification of biomarkers is critical to the development of targeted interventions for treating disaster responders and potentially preventing the development of PTSD in this population. Analysis of gene expression from these individuals can help in identifying biomarkers of PTSD. We established a well-phenotyped sample of 371 WTC responders, recruited from a longitudinal WTC responder cohort using stratified random sampling, by obtaining blood, self-reported and clinical interview data. Using bulk RNA-sequencing from whole blood, we examined the association between gene expression and WTC-related PTSD symptom severity on (i) highest lifetime Clinician-Administered PTSD Scale (CAPS) score, (ii) past-month CAPS score, and (iii) PTSD symptom dimensions using a 5-factor model of re-experiencing, avoidance, emotional numbing, dysphoric arousal and anxious arousal symptoms. We corrected for sex, age, genotype-derived principal components and surrogate variables. Finally, we performed a meta-analysis with existing PTSD studies (total N = 1016), using case/control status as the predictor and correcting for these variables. We identified 66 genes significantly associated with total highest lifetime CAPS score (FDR-corrected p < 0.05), and 31 genes associated with total past-month CAPS score. Our more granular analyses of PTSD symptom dimensions identified additional genes that did not reach statistical significance in our analyses with total CAPS scores. In particular, we identified 82 genes significantly associated with lifetime anxious arousal symptoms. Several genes significantly associated with multiple PTSD symptom dimensions and total lifetime CAPS score (SERPINA1, RPS6KA1, and STAT3) have been previously associated with PTSD. Geneset enrichment of these findings has identified pathways significant in metabolism, immune signaling, other psychiatric disorders, neurological signaling, and cellular structure. Our meta-analysis revealed 10 genes that reached genome-wide significance, all of which were downregulated in cases compared to controls (CIRBP, TMSB10, FCGRT, CLIC1, RPS6KB2, HNRNPUL1, ALDOA, NACA, ZNF429 and COPE). Additionally, cellular deconvolution highlighted an enrichment in CD4 T cells and eosinophils in responders with PTSD compared to controls. The distinction in significant genes between total lifetime CAPS score and the anxious arousal symptom dimension of PTSD highlights a potential biological difference in the mechanism underlying the heterogeneity of the PTSD phenotype. Future studies should be clear about methods used to analyze PTSD status, as phenotypes based on PTSD symptom dimensions may yield different gene sets than combined CAPS score analysis. Potential biomarkers implicated from our meta-analysis may help improve therapeutic target development for PTSD.

Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains

Chromosomal organization, scaling from the 147 base pair nucleosome to megabase-ranging domains encompassing multiple transcriptional units including heritability loci for psychiatric traits, remains largely unexplored in the human brain. Here, we construct promoter and enhancer enriched nucleosomal histone modification landscapes for adult prefrontal cortex (PFC) from H3-lysine 27 acetylation and H3-lysine 4 trimethylation profiles, generated from (n=739) 388 controls and 351 subjects diagnosed with schizophrenia (SCZ) or bipolar disorder (BD). We mapped thousands of cis-regulatory domains (CRDs), revealing fine-grained, 10⁴-10⁶ bp chromosomal organization, firmly integrated into Hi-C topologically associating domain (TAD) stratification by open/repressive chromosomal environments and nuclear topography. Large clusters of hyperacetylated CRDs were enriched for SCZ heritability, with prominent representation of regulatory sequences governing fetal development and glutamatergic neuron signaling. Therefore, SCZ and BD brains show coordinated dysregulation of risk-associated regulatory sequences assembled into kilo- to megabase-scaling chromosomal domains.

Acute COVID-19 gene-expression profiles show multiple etiologies of long-term sequelae

Two years into the SARS-CoV-2 pandemic, the post-acute sequelae of infection are compounding the global health crisis. Often debilitating, these sequelae are clinically heterogeneous and of unknown molecular etiology. Here, a transcriptome-wide investigation of this new condition was performed in a large cohort of acutely infected patients followed clinically into the post-acute period. Gene expression signatures of post-acute sequelae were already present in whole blood during the acute phase of infection, with both innate and adaptive immune cells involved. Plasma cells stood out as driving at least two distinct clusters of sequelae, one largely dependent on circulating antibodies against the SARS-CoV-2 spike protein and the other antibody-independent. Altogether, multiple etiologies of post-acute sequelae were found concomitant with SARS-CoV-2 infection, directly linking the emergence of these sequelae with the host response to the virus.

Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology

Bipolar disorder is a heritable mental illness with complex etiology. We performed a genome-wide association study of 41,917 bipolar disorder cases and 371,549 controls of European ancestry, which identified 64 associated genomic loci. Bipolar disorder risk alleles were enriched in genes in synaptic signaling pathways and brain-expressed genes, particularly those with high specificity of expression in neurons of the prefrontal cortex and hippocampus. Significant signal enrichment was found in genes encoding targets of antipsychotics, calcium channel blockers, antiepileptics and anesthetics. Integrating expression quantitative trait locus data implicated 15 genes robustly linked to bipolar disorder via gene expression, encoding druggable targets such as HTR6, MCHR1, DCLK3 and FURIN. Analyses of bipolar disorder subtypes indicated high but imperfect genetic correlation between bipolar disorder type I and II and identified additional associated loci. Together, these results advance our understanding of the biological etiology of bipolar disorder, identify novel therapeutic leads and prioritize genes for functional follow-up studies.

The effects of zinc amino acid complex on biomarkers of gut integrity, inflammation, and metabolism in heat-stressed ruminants

Study objectives were to evaluate the effects of replacing 40 mg/kg of dietary Zn from Zn sulfate (ZS) with Zn amino acid complex (ZA; Zinpro Corporation, Eden Prairie, MN) on inflammation and intestinal integrity in heat-stressed and pair-fed (PF) ruminants. Forty Holstein steers (173.6 ± 4.9 kg) were randomly assigned to 1 of 5 dietary-environmental treatments: (1) thermoneutral (TN) ad libitum with 75 mg/kg of dry matter (DM) ZS (ZSCON); (2) TN pair-fed with 75 mg/kg DM ZS (ZSPF); (3) TN pair-fed with 40 mg/kg DM ZA and 35 mg/kg DM ZS (ZAPF); (4) heat stress (HS) ad libitum with 75 mg/kg DM ZS (ZSHS); and (5) HS ad libitum 40 mg/kg DM ZA and 35 mg/kg DM ZS (ZAHS). Before study initiation, calves were fed their respective diets for 21 d. Following the pre-feeding phase, steers were transferred into environmental chambers and were subjected to 2 successive experimental periods. During period 1 (5 d), all steers were fed their respective diets ad libitum and housed in TN conditions (20.2 ± 1.4°C, 30.4 ± 4.3% relative humidity). During period 2 (6 d), ZSHS and ZAHS steers were exposed to cyclical HS conditions (27.1 ± 1.5°C to 35.0 ± 2.9°C, 19.3 ± 3.5% relative humidity), whereas the ZSCON, ZSPF, and ZAPF steers remained in TN conditions and were fed ad libitum or pair-fed relative to their ZSHS and ZAHS counterparts. Overall, steers exposed to HS had markedly increased rectal temperature (0.83°C), respiration rate (26 breaths per min), and skin temperature (8.00°C) relative to TN treatments. Rectal temperature from ZAHS steers was decreased (0.24°C) on d 4 to 6 of HS relative to ZSHS steers. Regardless of diet, HS decreased DMI (18%) relative to ZSCON steers. Circulating glucose from HS and PF steers decreased (16%) relative to ZSCON steers. Heat stress and nutrient restriction increased circulating nonesterified fatty acids 2- and 3-fold, respectively, compared with ZSCON steers. Serum amyloid A increased ~2-fold in PF relative to ZSCON and HS steers. We detected no treatment effect on blood pH; however, ZAHS steers had increased HCO₃ relative to ZSHS. Relative to ZSHS, ZAHS steers had increased jejunum villi height (25%), a tendency for increased ileum villi height (9%), and decreased duodenal villi width (16%). In summary, ZA supplementation has some beneficial effects on thermal indices, intestinal architecture characteristics, and biomarkers of leaky gut in heat-stressed steers, indicative of an ameliorated heat load, and thus may be a nutritional strategy to minimize negative consequences of HS.

Implicit bias of encoded variables: frameworks for addressing structured bias in EHR-GWAS data

The 'discovery' stage of genome-wide association studies required amassing large, homogeneous cohorts. In order to attain clinically useful insights, we must now consider the presentation of disease within our clinics and, by extension, within our medical records. Large-scale use of electronic health record (EHR) data can help to understand phenotypes in a scalable manner, incorporating lifelong and whole-phenome context. However, extending analyses to incorporate EHR and biobank-based analyses will require careful consideration of phenotype definition. Judgements and clinical decisions that occur 'outside' the system inevitably contain some degree of bias and become encoded in EHR data. Any algorithmic approach to phenotypic characterization that assumes non-biased variables will generate compounded biased conclusions. Here, we discuss and illustrate potential biases inherent within EHR analyses, how these may be compounded across time and suggest frameworks for large-scale phenotypic analysis to minimize and uncover encoded bias.

Author Correction: Sampling the host response to SARS-CoV-2 in hospitals under siege

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Functional annotation of rare structural variation in the human brain

Structural variants (SVs) contribute to many disorders, yet, functionally annotating them remains a major challenge. Here, we integrate SVs with RNA-sequencing from human post-mortem brains to quantify their dosage and regulatory effects. We show that genic and regulatory SVs exist at significantly lower frequencies than intergenic SVs. Functional impact of copy number variants (CNVs) stems from both the proportion of genic and regulatory content altered and loss-of-function intolerance of the gene. We train a linear model to predict expression effects of rare CNVs and use it to annotate regulatory disruption of CNVs from 14,891 independent genome-sequenced individuals. Pathogenic deletions implicated in neurodevelopmental disorders show significantly more extreme regulatory disruption scores and if rank ordered would be prioritized higher than using frequency or length alone. This work shows the deleteriousness of regulatory SVs, particularly those altering CTCF sites and provides a simple approach for functionally annotating the regulatory consequences of CNVs.

Characterization of Single Gene Copy Number Variants in Schizophrenia

BACKGROUND

Genetic studies of schizophrenia have implicated numerous risk loci including several copy number variants (CNVs) of large effect and hundreds of loci of small effect. In only a few cases has a specific gene been clearly identified. Rare CNVs affecting a single gene offer a potential avenue to discovering schizophrenia risk genes.

METHODS

CNVs were generated from exome sequencing of 4913 schizophrenia cases and 6188 control subjects from Sweden. We integrated two CNV calling methods (XHMM and ExomeDepth) to expand our set of single-gene CNVs and leveraged two different approaches for validating these variants (quantitative polymerase chain reaction and NanoString).

RESULTS

We found a significant excess of all rare CNVs (deletions: p = .0004, duplications: p = .0006) and single-gene CNVs (deletions: p = .04, duplications: p = .03) in schizophrenia cases compared with control subjects. An expanded set of CNVs generated from integrating multiple approaches showed a significant burden of deletions in 11 of 21 gene sets previously implicated in schizophrenia and across all genes in those sets (p = .008), although no tests survived correction. We performed an extensive validation of all deletions in the significant set of voltage-gated calcium channels among CNVs called from both exome sequencing and genotyping arrays. In total, 4 exonic, single-gene deletions were validated in schizophrenia cases and none in control subjects (p = .039), of which all were identified by exome sequencing.

CONCLUSIONS

These results point to the potential contribution of single-gene CNVs to schizophrenia, indicate that the utility of exome sequencing for CNV calling has yet to be maximized, and note that single-gene CNVs should be included in gene-focused studies using other classes of variation.

Genome-wide association study identifies 30 loci associated with bipolar disorder

Bipolar disorder is a highly heritable psychiatric disorder. We performed a genome-wide association study (GWAS) including 20,352 cases and 31,358 controls of European descent, with follow-up analysis of 822 variants with P < 1 × 10-4 in an additional 9,412 cases and 137,760 controls. Eight of the 19 variants that were genome-wide significant (P < 5 × 10-8) in the discovery GWAS were not genome-wide significant in the combined analysis, consistent with small effect sizes and limited power but also with genetic heterogeneity. In the combined analysis, 30 loci were genome-wide significant, including 20 newly identified loci. The significant loci contain genes encoding ion channels, neurotransmitter transporters and synaptic components. Pathway analysis revealed nine significantly enriched gene sets, including regulation of insulin secretion and endocannabinoid signaling. Bipolar I disorder is strongly genetically correlated with schizophrenia, driven by psychosis, whereas bipolar II disorder is more strongly correlated with major depressive disorder. These findings address key clinical questions and provide potential biological mechanisms for bipolar disorder.

Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome

Risk variants for schizophrenia affect more than 100 genomic loci, yet cell- and tissue-specific roles underlying disease liability remain poorly characterized. We have generated for two cortical areas implicated in psychosis, the dorsolateral prefrontal cortex and anterior cingulate cortex, 157 reference maps from neuronal, neuron-depleted and bulk tissue chromatin for two histone marks associated with active promoters and enhancers, H3-trimethyl-Lys4 (H3K4me3) and H3-acetyl-Lys27 (H3K27ac). Differences between neuronal and neuron-depleted chromatin states were the major axis of variation in histone modification profiles, followed by substantial variability across subjects and cortical areas. Thousands of significant histone quantitative trait loci were identified in neuronal and neuron-depleted samples. Risk variants for schizophrenia, depressive symptoms and neuroticism were significantly over-represented in neuronal H3K4me3 and H3K27ac landscapes. Our Resource, sponsored by PsychENCODE and CommonMind, highlights the critical role of cell-type-specific signatures at regulatory and disease-associated noncoding sequences in the human frontal lobe.

Determining the effects of early gestation in utero heat stress on postnatal fasting heat production and circulating biomarkers associated with metabolism in growing pigs

The study objective was to characterize effects of early gestation in utero heat stress (IUHS) on postnatal fasting heat production (FHP) and blood biomarkers associated with metabolism in growing pigs. Based on previous observation of increased postnatal core body temperature set point in IUHS pigs, we hypothesized that FHP would be altered during postnatal life because of IUHS. Pregnant first-parity gilts were exposed to thermoneutral (TN; = 4; 17.8 ± 0.1°C) or heat stress (HS; = 4; cyclical 28 to 38°C) conditions from d 30 to 60 of gestation. At weaning (21 d of age), 2 median-weight male pigs (1 barrow and 1 boar) were selected from each litter ( = 8 in utero TN [IUTN] and 8 IUHS pigs) and then housed in TN conditions based on age. Blood samples were collected at 8, 9, and 10 wk of age when pigs were in a fed state to analyze thyroxine (T4) and triiodothyronine (T3) concentrations. Pigs were trained to enter an indirect calorimeter from wk 8 through 10 of life and then acclimated over a 24-h period 1 wk prior to testing. At 12 wk of age, pigs were fasted for 24 h, and then indirect calorimetry was performed on individual pigs over a 23-h testing period to determine FHP and the respiratory quotient in 3 intervals (0900 to 1700 h, 1700 to 0000 h, and 0000 to 0800 h). Body weight was determined before and after testing and was similar for all pigs ( = 0.77; 37.0 ± 0.5 kg BW). Data were analyzed using PROC MIXED in SAS 9.4. No boar vs. barrow differences were observed with any analysis. Overall, FHP per kilogram BW was greater ( = 0.03; 12.1%) in IUHS pigs compared with IUTN pigs. Fasting heat production per kilogram BW was greater ( < 0.01; 19.8%) from 0900 to 1700 h compared with 1700 to 0000 h and 0000 to 0800 h and was greater (10.9%) from 1700 to 0000 h compared with 0000 to 0800 h. The RQ did not differ by in utero treatment ( = 0.51; 0.72 ± 0.01); however, the RQ was increased ( < 0.01; 13.0%) from 1700 to 0000 h compared with 0900 to 1700 h and 0000 to 0800 h. No other FHP and RQ differences were detected. Although no in utero treatment differences were observed for T4 ( = 0.11; 52.2 ± 6.2 ng/mL), T3 was greater overall ( = 0.04; 19.5%) in IUHS pigs than in IUTN pigs. In summary, FHP and circulating T3 were increased in IUHS pigs, and this may have implications for postnatal production efficiency in pigs gestated during hot summer months.

Effects of heat stress and insulin sensitizers on pig adipose tissue

Heat stress (HS) negatively impacts several swine production variables, including carcass fat quality and quantity. Pigs reared in HS have more adipose tissue than energetically predicted, explainable, in part, by HS-induced hyperinsulinemia. Study objectives were to evaluate insulin's role in altering fat characteristics during HS via feeding insulin-sensitizing compounds. Forty crossbred barrows (113 ± 9 kg BW) were randomly assigned to one of five environment by diet treatments: 1) thermoneutral (TN) fed ad libitum (TNAL), 2) TN and pair-fed (TNPF), 3) HS fed ad libitum (HSAL), 4) HS fed ad libitum with sterculic oil (SO) supplementation (HSSO; 13 g/d), and 5) HS fed ad libitum with dietary chromium (Cr) supplementation (HSCr; 0.5 mg/d; Kemin Industries, Des Moines, IA). The study consisted of three experimental periods (P). During P0 (2 d), all pigs were exposed to TN conditions (23 ± 3 °C, 68 ± 10% RH) and fed ad libitum. During P1 (7 d), all pigs received their respective dietary supplements, were maintained in TN conditions, and fed ad libitum. During P2 (21 d), HSAL, HSSO, and HSCr pigs were fed ad libitum and exposed to cyclical HS conditions (28 to 33 °C, 58 ± 10% RH). The TNAL and TNPF pigs remained in TN conditions and were fed ad libitum or pair-fed to their HSAL counterparts. Rectal temperature (TR), respiration rate (RR), and skin temperature (TS) were obtained daily at 0600 and 1800 h. At 1800 h, HS exposed pigs had increased TR, RR, and TS relative to TNAL controls (1.13 °C, 48 bpm, and 3.51 °C, respectively; P < 0.01). During wk 2 and 3 of P2, HSSO pigs had increased 1800 h TR relative to HSAL and HSCr (~0.40 and ~0.42 °C, respectively; P ≤ 0.05). Heat stress decreased ADFI and ADG compared to TNAL pigs (2.24 vs. 3.28 and 0.63 vs. 1.09 kg/d, respectively; P < 0.01) and neither variable was affected by SO or Cr supplementation. Heat stress increased or tended to increase moisture content of abdominal (7.7 vs. 5.9%; P = 0.07) and inner s.c. (11.4 vs. 9.8%; P < 0.05) adipose depots compared to TNAL controls. Interestingly, TNPF pigs also had increased adipose tissue moisture content and this was most pronounced in the outer s.c. depot (15.0 vs. 12.2%; P < 0.01) compared to TNAL pigs. Heat stress had little or no effect on fatty acid composition of abdominal, inner, and outer s.c. adipose tissue depots. In summary, the negative effects of HS on fat quality do not appear to be fatty acid composition related, but may be explained by increased adipose tissue moisture content.

Immune responses in hibernating little brown myotis (Myotis lucifugus) with white-nose syndrome

White-nose syndrome (WNS) is a fungal disease responsible for decimating many bat populations in North America. Pseudogymnoascus destructans (Pd), the psychrophilic fungus responsible for WNS, prospers in the winter habitat of many hibernating bat species. The immune response that Pd elicits in bats is not yet fully understood; antibodies are produced in response to infection by Pd, but they may not be protective and indeed may be harmful. To understand how bats respond to infection during hibernation, we studied the effect of Pd inoculation on the survival and gene expression of captive hibernating Myotis lucifugus with varying pre-hibernation antifungal antibody titres. We investigated gene expression through the transcription of selected cytokine genes (Il6, Il17a, Il1b, Il4 and Ifng) associated with inflammatory, Th1, Th2 and Th17 immune responses in wing tissue and lymph nodes. We found no difference in survival between bats with low and high anti-Pd titres, although anti-Pd antibody production during hibernation differed significantly between infected and uninfected bats. Transcription of Il6 and Il17a was higher in the lymph nodes of infected bats compared with uninfected bats. Increased transcription of these cytokines in the lymph node suggests that a pro-inflammatory immune response to WNS is not restricted to infected tissues and occurs during hibernation. The resulting Th17 response may be protective in euthermic bats, but because it may disrupt torpor, it could be detrimental during hibernation.

Large-Scale Identification of Common Trait and Disease Variants Affecting Gene Expression

Genome-wide association studies (GWASs) have identified a multitude of genetic loci involved with traits and diseases. However, it is often unclear which genes are affected in such loci and whether the associated genetic variants lead to increased or decreased gene function. To mitigate this, we integrated associations of common genetic variants in 57 GWASs with 24 studies of expression quantitative trait loci (eQTLs) from a broad range of tissues by using a Mendelian randomization approach. We discovered a total of 3,484 instances of gene-trait-associated changes in expression at a false-discovery rate < 0.05. These genes were often not closest to the genetic variant and were primarily identified in eQTLs derived from pathophysiologically relevant tissues. For instance, genes with expression changes associated with lipid traits were mostly identified in the liver, and those associated with cardiovascular disease were identified in arterial tissue. The affected genes additionally point to biological processes implicated in the interrogated traits, such as the interleukin-27 pathway in rheumatoid arthritis. Further, comparing trait-associated gene expression changes across traits suggests that pleiotropy is a widespread phenomenon and points to specific instances of both agonistic and antagonistic pleiotropy. For instance, expression of SNX19 and ABCB9 is positively correlated with both the risk of schizophrenia and educational attainment. To facilitate interpretation, we provide this lexicon of how common trait-associated genetic variants alter gene expression in various tissues as the online database GWAS2Genes.

Evaluating the behavior, growth performance, immune parameters, and intestinal morphology of weaned piglets after simulated transport and heat stress when antibiotics are eliminated from the diet or replaced with L-glutamine

Study objectives were to evaluate the effects of post-weaning transport during heat stress (HS) and thermoneutral (TN) conditions when dietary antibiotics are removed or replaced with a nutraceutical. Sixty mixed sex piglets from 10 sows ( = 6 piglets/sow) were weaned (18.8 ± 0.8 d of age) and then herded up ramps into 1 of 2 simulated transport trailers in either TN (28.8 ± 0.2°C) or HS (cyclical 32 to 37°C) conditions where they remained for 12 h. During the 12 h of simulated transport, fans were used to simulate air movement through the trailer, feed and water were withheld, and rectal temperature (T) was measured hourly. Following the 12 h simulated transport, piglets were unloaded from the trailer, weighed, and then housed individually in TN conditions [28.5 ± 0.1°C; 29.1 ± 0.1% relative humidity (RH)] and assigned to 1 of 3 dietary treatments balanced by weaning weight, sex, sow, and transport environment. Treatments were dietary antibiotics [A; = 20 piglets; 5.5 ± 0.2 kg BW; chlortetracycline (400 g/ton) + tiamulin (35 g/ton)], no dietary antibiotics (NA; = 20 piglets; 5.6 ± 0.2 kg BW), or 0.20% L-glutamine (GLU; = 20 piglets; 5.6 ± 0.2 kg BW) fed for 14 d. During the diet treatment period, feed intake (FI), BW, and behaviors were monitored daily. At the conclusion of the diet treatment period, all piglets were euthanized and intestinal samples were collected for histology. The T and post-transport BW loss were increased in HS (40.7°C and 0.43 kg, respectively) compared to TN-exposed (39.2°C and 0.27 kg, respectively) piglets during simulated transport. Throughout the 14 d dietary treatment phase, FI was greater overall ( < 0.01; 60.3%) in GLU compared to A and NA pigs, and tended to be greater (37.7%) in A compared to NA pigs. BW was greater overall ( < 0.01; 8.7%) in GLU and A compared to NA pigs, but no differences were detected between A and GLU pigs. Lying behavior was greater ( = 0.05; 11.7%) in NA compared to A and GLU piglets in the first 2 d following simulated transport. The villus height to crypt depth ratio was greater ( < 0.05) in the duodenum (12.1%) and jejunum (12.8%) for A and GLU compared to NA pigs, and greater in the ileum (15.6%) for GLU compared to A and NA pigs. In summary, withholding dietary antibiotics after weaning and transport can negatively affect piglet productivity and measures of intestinal morphology compared to dietary antibiotic administration and L-glutamine provision.

Defective γ-Glutamyl Carboxylase Activity and Bleeding in Rambouillet Sheep

A flock of Rambouillet sheep was examined because of increased lamb mortality caused by ineffective hemostasis at parturition. Neonatal-affected lambs presented with inadequate hemostasis at the umbilicus, pale mucus membranes, and markedly prolonged activated clotting time. Affected lambs had consistently prolonged 1-stage prothrombin times and activated partial thromboplastin times that supported a defect in the common pathway or defects in both the intrinsic and extrinsic pathway of the coagulation cascade. Decreased activity of vitamin K-dependent procoagulant factors II, VII, IX, and X in male and female lambs suggested either a defect of the hepatic enzyme γ-glutamyl carboxylase, or vitamin K1 2,3 epoxide reductase. Affected lamb hepatic γ-glutamyl carboxylase activity was markedly decreased compared with that of age- and sex-matched control lambs, while vitamin K1 2,3 epoxide reductase and glucose-6-phosphatase activities were similar between an affected and normal lamb. Subcutaneous vitamin K1 supplementation did not increase vitamin K-dependent procoagulant factor activities in 3 lambs administered vitamin K1 daily. These data confirm defective γ-glutamyl carboxylase activity as the cause of impaired coagulation of sheep in this flock. This flock represents the only viable animal model of hereditarily defective γ-glutamyl carboxylase activity.

In utero heat stress increases postnatal core body temperature in pigs

In utero heat stress (IUHS) negatively impacts postnatal development, but how it alters future body temperature parameters and energetic metabolism is not well understood. Future body temperature indices and bioenergetic markers were characterized in pigs from differing in utero thermal environments during postnatal thermoneutral (TN) and cyclical heat stress (HS) exposure. First-parity pregnant gilts ( = 13) were exposed to 1 of 4 ambient temperature (T) treatments (HS [cyclic 28°C to 34°C] or TN [cyclic 18°C to 22°C]) applied for the entire gestation (HSHS, TNTN), HS for the first half of gestation (HSTN), or HS for the second half of gestation (TNHS). Twenty-four offspring (23.1 ± 1.2 kg BW; = 6 HSHS, = 6 TNTN, = 6 HSTN, = 6 TNHS) were housed in TN (21.7°C ± 0.7°C) conditions and then exposed to 2 separate but similar HS periods (HS1 = 6 d; HS2 = 6 d; cycling 28°C to 36°C). Core body temperature (T) was assessed every 15 min with implanted temperature recorders. Regardless of in utero treatment, T increased during both HS periods ( = 0.01; 0.58°C). During TN, HS1, and HS2, all IUHS pigs combined had increased T ( = 0.01; 0.36°C, 0.20°C, and 0.16°C, respectively) compared to TNTN controls. Although unaffected by in utero environment, the total plasma thyroxine to triiodothyronine ratio was reduced ( = 0.01) during HS1 and HS2 (39% and 29%, respectively) compared with TN. In summary, pigs from IUHS maintained an increased T compared with TNTN controls regardless of external T, and this thermal differential may have practical implications to developmental biology and animal bioenergetics.

Effects of in utero heat stress on postnatal body composition in pigs: I. Growing phase

Environmentally induced heat stress (HS) negatively influences production variables in agriculturally important species. However, the extent to which HS experienced in utero affects nutrient partitioning during the rapid lean tissue accretion phase of postnatal growth is unknown. Study objectives were to compare future whole-body tissue accretion rates in pigs exposed to differing in utero and postnatal thermal environments when lean tissue deposition is likely maximized. Pregnant sows were exposed to thermoneutral (TN; cyclical 15°C nighttime and 22°C daytime; n = 9) or HS (cyclical 27°C nighttime and 37°C daytime; n = 12) conditions during their entire gestation. Twenty-four offspring from in utero TN (IUTN; n = 6 gilts and 6 barrows; 30.8 ± 0.2 kg BW) and in utero HS (IUHS; n = 6 gilts and 6 barrows; 30.3 ± 0.2 kg BW) were euthanized as an initial slaughter group (ISG). Following the ISG, 48 pigs from IUTN (n = 12 gilts and 12 barrows; 34.1 ± 0.5 kg BW) and IUHS (n = 12 gilts and 12 barrows; 33.3 ± 0.3 kg BW) were exposed to constant HS (34.1 ± 2.4°C) or TN (21.5 ± 2.0°C) conditions until they reached 61.5 ± 0.8 kg BW, at which point they were sacrificed and their whole-body composition was determined. Homogenized carcasses were analyzed for N, crude fat, ash, water, and GE content. Data were analyzed using PROC MIXED in SAS 9.3. Rectal temperature and respiration rate increased (P < 0.01) during postnatal HS compared to TN (39.4 vs. 39.0°C and 94 vs. 49 breaths per minute, respectively). Regardless of in utero environment, postnatal HS reduced (P < 0.01) feed intake (2.06 vs. 2.37 kg/d) and ADG (0.86 vs. 0.98 kg/d) compared to TN conditions. Postnatal HS did not alter water, protein, and ash accretion rates but reduced lipid accretion rates (198 vs. 232 g/d; P < 0.04) compared to TN-reared pigs. In utero environment had no effect on future tissue deposition rates; however, IUHS pigs from the ISG had reduced liver weight (P < 0.04; 17.9%) compared to IUTN controls. In summary, postnatal HS reduced adipose tissue accretion rates, but IUHS did not appear to impact either lean or adipose tissue accretion during this specific growth phase.

Effects of in utero heat stress on postnatal body composition in pigs: II. Finishing phase

The detrimental effects of heat stress (HS) on animal productivity have been well documented. However, whether in utero HS interacts with a future thermal insult to alter tissue deposition during the finishing phase of pig growth is unknown. Study objectives were to compare the subsequent rate and quantity of whole-body tissue accretion in pigs exposed to differing in utero and postnatal thermal environments. Pregnant sows were exposed to thermoneutral (TN; cyclical 15°C nighttime and 22°C daytime; n = 9) or HS (cyclical 27°C nighttime and 37°C daytime; n = 11) conditions during their entire gestation. Twenty-four offspring from in utero TN (IUTN; n = 6 gilts and 6 barrows; 62.4 ± 0.7 kg BW) and in utero HS (IUHS; n = 6 gilts and 6 barrows; 61.9 ± 0.8 kg BW) were euthanized as part of an initial slaughter group (ISG). After the ISG, 48 pigs from IUTN (n = 12 gilts and 12 barrows; 66.1 ± 1.0 kg BW) and IUHS (n = 12 gilts and 12 barrows; 63.4 ± 0.7 kg BW) were exposed to constant HS (34.4 ± 1.8°C) or TN (22.7 ± 2.5°C) conditions until they reached 80.5 ± 1.5 kg BW, at which point they were sacrificed and their whole-body composition was determined. Homogenized carcasses were analyzed for N, crude fat, ash, water, and GE content. Data were analyzed using PROC MIXED in SAS 9.3. Rectal temperature and respiration rate increased during postnatal HS compared to TN (39.6 vs. 39.3°C and 92 vs. 58 breaths per minute, respectively; P < 0.01). Postnatal HS decreased (P < 0.01) feed intake (2.13 vs. 2.65 kg/d) and ADG (0.70 vs. 0.94 kg/d) compared to TN conditions, but neither variable was influenced by in utero environment. Whole-body protein and lipid accretion rates were reduced in HS pigs compared to TN controls (126 vs. 164 g/d and 218 vs. 294 g/d, respectively; P < 0.04). Independent of postnatal environments, IUHS reduced future protein accretion rates (16%; P < 0.01) and tended to increase lipid accretion rates (292 vs. 220 g/d; P < 0.07) compared to IUTN controls. The ratio of lipid to protein accretion rates increased (95%; P < 0.01) in IUHS pigs compared to IUTN controls. In summary, the future hierarchy of tissue accretion is altered by IUHS, and this modified nutrient partitioning favors adipose deposition at the expense of skeletal muscle during this specific phase of growth.

Regional differences in the fescue toxicosis response of Bos taurus cattle

Cattle of the same breed from different regions of the USA may have altered responses to heat stress and fescue toxicosis. Angus steers from Missouri (MO ANG, n = 10, 513.6 ± 13.6 kg BW) and Oklahoma (OK ANG, n = 10, 552.8 ± 12.0 kg BW) were fed a diet containing either endophyte-infected (E+, 30 μg ergovaline/kg BW/day) or endophyte-uninfected (E-, 0 μg ergovaline/kg BW/day) tall fescue seed for 23 days. Diet treatment began on day 2. Animals were maintained at thermoneutrality (TN, 19-22 °C, days 1-8) and then exposed to heat stress (HS, cycling 26-36 °C, days 9-22). On day 23, ambient temperature was returned to TN and used as a recovery day. Feed intake (FI) was measured daily, with rectal and skin temperatures determined six times daily. Feed intake reduction from pretreatment levels was greater (P < 0.01) for E + (13.9 ± 0.9 versus 11.9 ± 0.3 kg/day) compared to E - (12.6 ± 0.9 versus 12.4 ± 0.3 kg/day) steers over the entire TN period, regardless of Angus group. During HS, E + cattle had reduced FI (P < 0.02; 6.9 ± 0.2 versus 8.4 ± 0.2 kg/day) compared to E - animals, independent of region of origin. A greater decrease in FI (P < 0.01) was observed for OK (12.1 ± 0.3 versus 6.2 ± 0.2 kg/day) compared to MO ANG (12.2 ± 0.3 versus 7.9 ± 0.2 kg/day) when ambient temperature was increased from TN to HS. On day 13 and days 15-22, OK ANG (E+) had reduced FI (P < 0.01, -2.21 kg) compared to OK ANG (E-), while there was no effect on MO ANG. From day 12 to day 22 of HS, daily minimum temperatures for ear, rump, and tail skin were less for E + (P < 0.05) when compared with E-treated steers, signifying peripheral vasoconstriction in E + animals. This was supported by reduced shoulder and lower tail temperatures (P < 0.01) for E + compared to E-treated OK ANG on the recovery day. In summary, regional differences in the response to fescue toxicosis exist, with peripheral vasomotor effects becoming most evident when animals are subjected to rapid changes in their environment.

Rapid thinning of Pine Island Glacier in the early Holocene

Pine Island Glacier, a major outlet of the West Antarctic Ice Sheet, has been undergoing rapid thinning and retreat for the past two decades. We demonstrate, using glacial-geological and geochronological data, that Pine Island Glacier (PIG) also experienced rapid thinning during the early Holocene, around 8000 years ago. Cosmogenic (10)Be concentrations in glacially transported rocks show that this thinning was sustained for decades to centuries at an average rate of more than 100 centimeters per year, which is comparable with contemporary thinning rates. The most likely mechanism was a reduction in ice shelf buttressing. Our findings reveal that PIG has experienced rapid thinning at least once in the past and that, once set in motion, rapid ice sheet changes in this region can persist for centuries.

De novo mutations in schizophrenia implicate synaptic networks

Inherited alleles account for most of the genetic risk for schizophrenia. However, new (de novo) mutations, in the form of large chromosomal copy number changes, occur in a small fraction of cases and disproportionally disrupt genes encoding postsynaptic proteins. Here we show that small de novo mutations, affecting one or a few nucleotides, are overrepresented among glutamatergic postsynaptic proteins comprising activity-regulated cytoskeleton-associated protein (ARC) and N-methyl-d-aspartate receptor (NMDAR) complexes. Mutations are additionally enriched in proteins that interact with these complexes to modulate synaptic strength, namely proteins regulating actin filament dynamics and those whose messenger RNAs are targets of fragile X mental retardation protein (FMRP). Genes affected by mutations in schizophrenia overlap those mutated in autism and intellectual disability, as do mutation-enriched synaptic pathways. Aligning our findings with a parallel case-control study, we demonstrate reproducible insights into aetiological mechanisms for schizophrenia and reveal pathophysiology shared with other neurodevelopmental disorders.

Heat stress reduces barrier function and alters intestinal metabolism in growing pigs

High ambient temperature exposure can cause major reductions in intestinal function, pig performance, and, if severe enough, mortality. Therefore, our objective was to examine how acute heat stress (HS) alters growing pig intestinal integrity and metabolism. Individually penned crossbred gilts and barrows (46 ± 6 kg BW) were exposed to either thermal neutral (TN; 21°C; 35 to 50% humidity; n = 8) or HS conditions (35°C; 24 to 43% humidity; n = 8) for 24 h. All pigs had ad libitum access to feed and water. Rectal temperature (Tr), respiration rates (RR), BW, and feed intake (FI) were measured. Pigs were killed after 24 h of environmental exposure and freshly isolated ileum and colon samples were mounted into modified Ussing chambers. Segments were analyzed for glucose and glutamine nutrient transport and barrier integrity [transepithelial electrical resistance (TER) and fluorescein isothiocyanate-labeled dextran transport]. As expected, pigs exposed to HS had an increase in Tr (39.3 vs. 40.9°C; P < 0.01) and RR (52 vs. 119 breaths per minute; P < 0.05). Heat stress decreased FI (53%; P < 0.05) and BW (-2.2 kg; P < 0.05) compared to TN pigs. Compared to TN pigs, mucosal heat shock protein 70 increased (101%; P < 0.05) whereas intestinal integrity was compromised in the HS pigs (ileum and colon TER decreased 52 and 24%, respectively; P < 0.05). Furthermore, serum endotoxin concentrations increased 200% due to HS (P = 0.05). Intestinal glucose transport and blood glucose were elevated due to HS (P < 0.05). However, ileal sucrase and maltase activities decreased in HS pigs (30 and 24%, respectively; P < 0.05). Altogether, these data indicate that high ambient heat loads reduce intestinal integrity and increase circulating endotoxin and stress in pigs. Furthermore, glucose transport and digestive capacity are altered during acute HS.

Cytometric investigations on hemocytes of the American oyster, Crassostrea virginica

Pericardial hemolymph was obtained from American Oysters (Crassostrea virginica) and the hemocytes characterized by flow cytometry. The cells were found to have a broad unimodal size distribution with a median diameter of 7 micrometers. Total protein measured by flow cytometric fluorescence of dansylated cells also revealed a broad unimodal distribution similar to that obtained for size. The proportion of hemocytes in each stage of the cell cycle was measured using DNA-specific DAPI fluorescence. Histograms showed a single peak representing the G(0)/G(1) population. There was no evidence of S or G(2)+M phases of the cell cycle, nor was polyploidy seen. The forward and orthogonal light scatter of fixed hemocytes showed no evidence of sub-populations on the basis of cytoplasmic granularity. Thus, in terms of these parameters, oyster hemocytes appear to represent a single population exhibiting graded cellular differences.

Anterior fusion alone compared with combined anterior and posterior fusion for the treatment of degenerative cervical kyphosis

We evaluated the efficacy of anterior fusion alone compared with combined anterior and posterior fusion for the treatment of degenerative cervical kyphosis. Anterior fusion alone was undertaken in 15 patients (group A) and combined anterior and posterior fusion was carried out in a further 15 (group B). The degree and maintenance of the angle of correction, the incidence of graft subsidence, degeneration at adjacent levels and the rate of fusion were assessed radiologically and clinically and the rate of complications recorded. The mean angle of correction in group B was significantly higher than in group A (p = 0.0009). The mean visual analogue scale and the neck disability index in group B was better than in group A (p = 0.043, 0.0006). The mean operation time and the blood loss in B were greater than in group A (p < 0.0001, 0.037). Pseudarthrosis, subsidence of the cage, and problems related to the hardware were more prevalent in group A than in group B (p = 0.034, 0.025, 0.013). Although the combined procedure resulted in a longer operating time and greater blood loss than with anterior fusion alone, our results suggest that for the treatment of degenerative cervical kyphosis the combined approach leads to better maintenance of sagittal alignment, a higher rate of fusion, a lower incidence of complications and a better clinical outcome.

Salt rejection by a porous glass

Porous glass partly filters dissolved salt from aqueous solutions passed through it under pressure. Rejection of salt can be increased by increase in the pH of the solution or by addition of Th(IV). The filtration seems to accord with a mechanism of salt exclusion characteristic of ion exchangers.

Biocompatible surfactants for water-in-fluorocarbon emulsions

Drops of water-in-fluorocarbon emulsions have great potential for compartmentalizing both in vitro and in vivo biological systems; however, surfactants to stabilize such emulsions are scarce. Here we present a novel class of fluorosurfactants that we synthesize by coupling oligomeric perfluorinated polyethers (PFPE) with polyethyleneglycol (PEG). We demonstrate that these block copolymer surfactants stabilize water-in-fluorocarbon oil emulsions during all necessary steps of a drop-based experiment including drop formation, incubation, and reinjection into a second microfluidic device. Furthermore, we show that aqueous drops stabilized with these surfactants can be used for in vitro translation (IVT), as well as encapsulation and incubation of single cells. The compatability of this emulsion system with both biological systems and polydimethylsiloxane (PDMS) microfluidic devices makes these surfactants ideal for a broad range of high-throughput, drop-based applications.

Bioluminescent virion shells: new tools for quantitation of AAV vector dynamics in cells and live animals

Current technologies for visualizing infectious pathways of viruses rely on fluorescent labeling of capsid proteins by chemical conjugation or genetic manipulation. For noninvasive in vivo imaging of such agents in mammalian tissue, we engineered bioluminescent Gaussia luciferase-tagged Adeno-associated viral (gLuc/AAV) vectors. The enzyme was incorporated into recombinant AAV serotypes 1, 2 and 8 capsids by fusing to the N-terminus of the VP2 capsid subunit to yield bioluminescent virion shells. The gLuc/AAV vectors were used to quantify kinetics of cell-surface-binding by AAV2 capsids in vitro. Bioluminescent virion shells displayed an exponential decrease in luminescent signal following cellular uptake in vitro. A similar trend was observed following intramuscular injection in vivo, although the rate of decline in bioluminescent signal varied markedly between AAV serotypes. gLuc/AAV1 and gLuc/AAV8 vectors displayed rapid decrease in bioluminescent signal to background levels within 30 min, whereas the signal from gLuc/AAV2 vectors persisted for over 2 h. Bioluminescent virion shells might be particularly useful in quantifying dynamics of viral vector uptake in cells and peripheral tissues in live animals.

Regulation of tradeoffs between plant defenses against pathogens with different lifestyles

Plants activate distinct defense responses depending on the lifestyle of the attacker encountered. In these responses, salicylic acid (SA) and jasmonic acid (JA) play important signaling roles. SA induces defense against biotrophic pathogens that feed and reproduce on live host cells, whereas JA activates defense against necrotrophic pathogens that kill host cells for nutrition and reproduction. Cross-talk between these defense signaling pathways has been shown to optimize the response against a single attacker. However, its role in defense against multiple pathogens with distinct lifestyles is unknown. Here we show that infection with biotrophic Pseudomonas syringae, which induces SA-mediated defense, rendered plants more susceptible to the necrotrophic pathogen Alternaria brassicicola by suppression of the JA signaling pathway. This process was partly dependent on the cross-talk modulator NPR1. Surprisingly, this tradeoff was restricted to tissues adjacent to the site of initial infection; A. brassicicola infection in systemic tissue was not affected. Even more surprisingly, tradeoff occurred only with the virulent Pseudomonas strain. Avirulent strains that induced programmed cell death (PCD), an effective plant-resistance mechanism against biotrophs, did not cause suppression of JA-dependent defense. This result might be advantageous to the plant by preventing necrotrophic pathogen growth in tissues undergoing PCD. Our findings show that plants tightly control cross-talk between SA- and JA-dependent defenses in a previously unrecognized spatial and pathogen type-specific fashion. This process allows them to prevent unfavorable signal interactions and maximize their ability to concomitantly fend off multiple pathogens.

Managing aggression in a psychiatric hospital using a behaviour plan: a case study

This paper focuses on the critical role of nursing in implementing a behaviour plan in a psychiatric hospital. The plan was implemented with a 40-year-old man with a long history of aggression towards others and self. The study used a single-subject research design with baseline and intervention phases (AB Design). Data were collected on (1) frequency of incidents of aggression towards others and self; (2) use of restrictive interventions to manage aggression (i.e. restraints, pro re nata medication, 1:1 special observation); and (3) frequency of staff injury. The data show a decrease in frequency of aggression towards others and self, a concurrent reduction in the use of restrictive interventions to manage aggression, and a decrease in incidents of staff injury. The behaviour plan helped staff maintain a safe and therapeutic milieu. The behaviour plan has given the patient an opportunity to learn positive replacement behaviours and skills, and the opportunity eventually to leave the hospital to live in a less restrictive community home.

Truncated gamma-glutamyl carboxylase in rambouillet sheep

A flock of Rambouillet sheep was examined because of increased lamb mortality due to ineffective hemostasis at parturition. Decreased activities of coagulation factors II, VII, IX, and X, and severely reduced hepatic gamma-glutamyl carboxylase activity with adequate vitamin K 2,3 epoxide reductase activity was determined.(1,)(21) Parenteral vitamin K(1) supplementation did not improve vitamin K-dependent coagulation factor activities in 3 affected lambs. Affected lamb gamma-glutamyl carboxylase deoxyribonucleic acid was sequenced, and 4 single nucleotide polymorphisms (SNPs 2-5) of the gamma-glutamyl carboxylase gene were identified. Single nucleotide polymorphism-4 results in an arginine to stop codon (UGA) substitution, which prematurely terminates the peptide at residue 686 (R686Stop). This genotype (GATT/GATT) has a strong association with the coagulopathy observed in clinically affected lambs, P < 0.001. The frequency of SNP-3 in exon 11 (R486H) within the MARC 1.1 database is high in the US sheep population overall. Gamma-glutamyl carboxylase activity in hepatic microsomes from a SNP-3 homozygous lamb lacking the SNP-4 mutation (GACC/GACC) was similar to control sheep homozygous for arginine at 486 and also lacking SNP-4 (TGCC/TGCC), indicating that the R486H does not measurably impact gamma-glutamyl carboxylase activity. The remaining two SNPs (2 and 5) are located within non-coding intron sequences. These 4 SNPs allowed for determining the genotype associated with the observed fatal coagulopathy. Screening for the premature truncation (SNP-4) based on the presence of a Bbv I restriction site in clinically normal lambs but not in the homozygous affected lambs allows for detection of the heterozygous state (GATT/GACC), because carrier animals are clinically normal.

Molecular alterations resulting from frameshift mutations in peripheral myelin protein 22: implications for neuropathy severity

Alterations in peripheral myelin protein 22 (PMP22) expression are associated with a heterogeneous group of hereditary demyelinating peripheral neuropathies. Two mutations at glycine 94, a single guanine insertion or deletion in PMP22, result in different reading frameshifts and, consequently, an extended G94fsX222 or a truncated G94fsX110 protein, respectively. Both of these autosomal dominant mutations alter the second half of PMP22 and yet are linked to clinical phenotypes with distinct severities. The G94fsX222 is associated with hereditary neuropathy with liability to pressure palsies, whereas G94fsX110 causes severe neuropathy diagnosed as Dejerine-Sottas disease or Charcot-Marie-Tooth disease type IA. To investigate the subcellular changes associated with the G94 frameshift mutations, we expressed epitope-tagged forms in primary rat Schwann cells. Biochemical and immunolabeling studies indicate that, unlike the wild-type protein, which is targeted for the plasma membrane, frameshift PMP22s are retained in the cell, prior to reaching the medial Golgi compartment. Similar to Wt-PMP22, both frameshift mutants are targeted for proteasomal degradation and accumulate in detergent-insoluble, ubiquitin-containing aggregates upon inhibition of this pathway. The extended frameshift PMP22 shows the ability to form spontaneous aggregates in the absence of proteasome inhibition. On the other hand, Schwann cells expressing the truncated protein proliferate at a significantly higher rate than Schwann cells expressing the wild-type or the extended PMP22. In summary, these results suggest that a greater potential for PMP22 aggregation is associated with a less severe phenotype, whereas dysregulation of Schwann cell proliferation is linked to severe neuropathy.

Selectable marker-free transgenic barley producing a high level of cellulase (1,4-beta-glucanase) in developing grains

The use of barley grains as bioreactors for high-level production of cellulase (1,4-beta-glucanase) was investigated. A hybrid cellulase gene, cel-hyb1, driven by the rice GluB-1 promoter was expressed specifically in developing endosperm. Codon usage optimisation of cel-hyb1 increased its expression in barley grains 527-fold and led to cellulase production of up to 1.5% of total grain protein. CEL-HYB1 enzyme in barley grains was highly stable during post-harvest storage. Selectable marker gene ( hph) was subsequently eliminated from transgenic lines through segregation of hph from synthetic cel-hyb1 ( syn.cel-hyb1) in T1 progeny, using a binary plasmid containing hph and syn.cel-hyb1 in separate T-DNAs. These data suggest that barley grains can potentially be used for the commercial production of cellulase.