Early, nonlethal ploidy and genome size quantification using confocal microscopy in zebrafish embryos.

Ploidy transitions through whole genome duplication have shaped evolution by allowing the sub- and neo-functionalization of redundant copies of highly conserved genes to express novel traits. The nuclear:cytoplasmic (n:c) ratio is maintained in polyploid vertebrates resulting in larger cells, but body size is maintained by a concomitant reduction in cell number. Ploidy can be manipulated easily in most teleosts, and the zebrafish, already well established as a model system for biomedical research, is therefore an excellent system in which to study the effects of increased cell size and reduced cell numbers in polyploids on development and physiology. Here we describe a novel technique using confocal microscopy to measure genome size and determine ploidy non-lethally at 48 h post-fertilization (hpf) in transgenic zebrafish expressing fluorescent histones. Volumetric analysis of myofiber nuclei using open-source software can reliably distinguish diploids and triploids from a mixed-ploidy pool of embryos for subsequent experimentation. We present an example of this by comparing heart rate between confirmed diploid and triploid embryos at 54 hpf.

Adiponectin GWAS loci harboring extensive allelic heterogeneity exhibit distinct molecular consequences.

Loci identified in genome-wide association studies (GWAS) can include multiple distinct association signals. We sought to identify the molecular basis of multiple association signals for adiponectin, a hormone involved in glucose regulation secreted almost exclusively from adipose tissue, identified in the Metabolic Syndrome in Men (METSIM) study. With GWAS data for 9,262 men, four loci were significantly associated with adiponectin: ADIPOQ, CDH13, IRS1, and PBRM1. We performed stepwise conditional analyses to identify distinct association signals, a subset of which are also nearly independent (lead variant pairwise r2<0.01). Two loci exhibited allelic heterogeneity, ADIPOQ and CDH13. Of seven association signals at the ADIPOQ locus, two signals colocalized with adipose tissue expression quantitative trait loci (eQTLs) for three transcripts: trait-increasing alleles at one signal were associated with increased ADIPOQ and LINC02043, while trait-increasing alleles at the other signal were associated with decreased ADIPOQ-AS1. In reporter assays, adiponectin-increasing alleles at two signals showed corresponding directions of effect on transcriptional activity. Putative mechanisms for the seven ADIPOQ signals include a missense variant (ADIPOQ G90S), a splice variant, a promoter variant, and four enhancer variants. Of two association signals at the CDH13 locus, the first signal consisted of promoter variants, including the lead adipose tissue eQTL variant for CDH13, while a second signal included a distal intron 1 enhancer variant that showed ~2-fold allelic differences in transcriptional reporter activity. Fine-mapping and experimental validation demonstrated that multiple, distinct association signals at these loci can influence multiple transcripts through multiple molecular mechanisms.

Enhancer deletion and allelic effects define a regulatory molecular mechanism at the VLDLR cholesterol GWAS locus.

Total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) are heritable risk factors for cardiovascular disease, yet the molecular mechanisms underlying the majority of blood lipid-associated genome-wide association studies signals remain elusive. One association signal is located in intron 3 of VLDLR; rs3780181-A is a risk allele associated (P ≤ 2 × 10-9) with increased TC and LDL-C. We investigated variants, genes and mechanisms underlying this association signal. We used a functional genetic approach to show that the intronic region spanning rs3780181 exhibited 1.6-7.6-fold enhancer activity in human HepG2 hepatocyte, THP-1 monocyte and Simpson-Golabi-Behmel Syndrome (SGBS) preadipocyte cells and that the rs3780181-A risk allele showed significantly less enhancer activity compared with the G allele, consistent with the direction of an expression quantitative trait locus in liver. In addition, rs3780181 alleles showed differential binding to multiple nuclear proteins, including stronger IRF2 binding to the rs3780181 G allele. We used a CRISPR-cas9 approach to delete 475 and 663 bp of the putative enhancer element in HEK293T kidney cells; compared to expression of mock-edited cell lines, the homozygous enhancer deletion cell lines showed 1.2-fold significantly (P < 0.04) decreased expression of VLDLR, as well as 1.5-fold decreased expression of SMARCA2, located 388 kb away. Together, these results identify an enhancer of VLDLR expression and suggest that altered binding of one or more factors bound to rs3780181 alleles decreases enhancer activity and reduces at least VLDLR expression, leading to increased TC and LDL-C.

Identification and functional analysis of glycemic trait loci in the China Health and Nutrition Survey.

To identify genetic contributions to type 2 diabetes (T2D) and related glycemic traits (fasting glucose, fasting insulin, and HbA1c), we conducted genome-wide association analyses (GWAS) in up to 7,178 Chinese subjects from nine provinces in the China Health and Nutrition Survey (CHNS). We examined patterns of population structure within CHNS and found that allele frequencies differed across provinces, consistent with genetic drift and population substructure. We further validated 32 previously described T2D- and glycemic trait-loci, including G6PC2 and SIX3-SIX2 associated with fasting glucose. At G6PC2, we replicated a known fasting glucose-associated variant (rs34177044) and identified a second signal (rs2232326), a low-frequency (4%), probably damaging missense variant (S324P). A variant within the lead fasting glucose-associated signal at SIX3-SIX2 co-localized with pancreatic islet expression quantitative trait loci (eQTL) for SIX3, SIX2, and three noncoding transcripts. To identify variants functionally responsible for the fasting glucose association at SIX3-SIX2, we tested five candidate variants for allelic differences in regulatory function. The rs12712928-C allele, associated with higher fasting glucose and lower transcript expression level, showed lower transcriptional activity in reporter assays and increased binding to GABP compared to the rs12712928-G, suggesting that rs12712928-C contributes to elevated fasting glucose levels by disrupting an islet enhancer, resulting in reduced gene expression. Taken together, these analyses identified multiple loci associated with glycemic traits across China, and suggest a regulatory mechanism at the SIX3-SIX2 fasting glucose GWAS locus.

Identification of seven novel loci associated with amino acid levels using single-variant and gene-based tests in 8545 Finnish men from the METSIM study.

Comprehensive metabolite profiling captures many highly heritable traits, including amino acid levels, which are potentially sensitive biomarkers for disease pathogenesis. To better understand the contribution of genetic variation to amino acid levels, we performed single variant and gene-based tests of association between nine serum amino acids (alanine, glutamine, glycine, histidine, isoleucine, leucine, phenylalanine, tyrosine, and valine) and 16.6 million genotyped and imputed variants in 8545 non-diabetic Finnish men from the METabolic Syndrome In Men (METSIM) study with replication in Northern Finland Birth Cohort (NFBC1966). We identified five novel loci associated with amino acid levels (P = < 5×10-8): LOC157273/PPP1R3B with glycine (rs9987289, P = 2.3×10-26); ZFHX3 (chr16:73326579, minor allele frequency (MAF) = 0.42%, P = 3.6×10-9), LIPC (rs10468017, P = 1.5×10-8), and WWOX (rs9937914, P = 3.8×10-8) with alanine; and TRIB1 with tyrosine (rs28601761, P = 8×10-9). Gene-based tests identified two novel genes harboring missense variants of MAF <1% that show aggregate association with amino acid levels: PYCR1 with glycine (Pgene = 1.5×10-6) and BCAT2 with valine (Pgene = 7.4×10-7); neither gene was implicated by single variant association tests. These findings are among the first applications of gene-based tests to identify new loci for amino acid levels. In addition to the seven novel gene associations, we identified five independent signals at established amino acid loci, including two rare variant signals at GLDC (rs138640017, MAF=0.95%, Pconditional = 5.8×10-40) with glycine levels and HAL (rs141635447, MAF = 0.46%, Pconditional = 9.4×10-11) with histidine levels. Examination of all single variant association results in our data revealed a strong inverse relationship between effect size and MAF (Ptrend<0.001). These novel signals provide further insight into the molecular mechanisms of amino acid metabolism and potentially, their perturbations in disease.

Common, low-frequency, and rare genetic variants associated with lipoprotein subclasses and triglyceride measures in Finnish men from the METSIM study.

Lipid and lipoprotein subclasses are associated with metabolic and cardiovascular diseases, yet the genetic contributions to variability in subclass traits are not fully understood. We conducted single-variant and gene-based association tests between 15.1M variants from genome-wide and exome array and imputed genotypes and 72 lipid and lipoprotein traits in 8,372 Finns. After accounting for 885 variants at 157 previously identified lipid loci, we identified five novel signals near established loci at HIF3A, ADAMTS3, PLTP, LCAT, and LIPG. Four of the signals were identified with a low-frequency (0.005

Alterations to chromatin in intestinal macrophages link IL-10 deficiency to inappropriate inflammatory responses.

Intestinal macrophages (IMs) are uniquely programmed to tolerate exposure to bacteria without mounting potent inflammatory responses. The cytokine IL-10 maintains the macrophage anti-inflammatory response such that loss of IL-10 results in chronic intestinal inflammation. To investigate how IL-10-deficiency alters IM programming and bacterial tolerance, we studied changes in chromatin accessibility in response to bacteria in macrophages from two distinct niches, the intestine and bone-marrow, from both wild-type and IL-10-deficient (Il10(-/-) ) mice. We identified chromatin accessibility changes associated with bacterial exposure and IL-10 deficiency in both bone marrow derived macrophages and IMs. Surprisingly, Il10(-/-) IMs adopted chromatin and gene expression patterns characteristic of an inflammatory response, even in the absence of bacteria. Further, when recombinant IL-10 was added to Il10(-/-) cells, it could not revert the chromatin landscape to a normal state. Our results demonstrate that IL-10 deficiency results in stable chromatin alterations in macrophages, even in the absence of bacteria. This supports a model in which IL-10-deficiency leads to chromatin alterations that contribute to a loss of IM tolerance to bacteria, which is a primary initiating event in chronic intestinal inflammation.

Genome-wide Association Study of Platelet Count Identifies Ancestry-Specific Loci in Hispanic/Latino Americans.

Platelets play an essential role in hemostasis and thrombosis. We performed a genome-wide association study of platelet count in 12,491 participants of the Hispanic Community Health Study/Study of Latinos by using a mixed-model method that accounts for admixture and family relationships. We discovered and replicated associations with five genes (ACTN1, ETV7, GABBR1-MOG, MEF2C, and ZBTB9-BAK1). Our strongest association was with Amerindian-specific variant rs117672662 (p value = 1.16 × 10(-28)) in ACTN1, a gene implicated in congenital macrothrombocytopenia. rs117672662 exhibited allelic differences in transcriptional activity and protein binding in hematopoietic cells. Our results underscore the value of diverse populations to extend insights into the allelic architecture of complex traits.

Global patterns of abundance, diversity and community structure of the Aminicenantes (candidate phylum OP8).

We investigated the global patterns of abundance, diversity, and community structure of members of the Aminicenantes (candidate phylum OP8). Our aim was to identify the putative ecological role(s) played by members of this poorly characterized bacterial lineages in various ecosystems. Analysis of near full-length 16S rRNA genes identified four classes and eight orders within the Aminicenantes. Within 3,134 datasets comprising ∼1.8 billion high throughput-generated partial 16S rRNA genes, 47,351 Aminicenantes-affiliated sequences were identified in 913 datasets. The Aminicenantes exhibited the highest relative abundance in hydrocarbon-impacted environments, followed by marine habitats (especially hydrothermal vents and coral-associated microbiome samples), and aquatic, non-marine habitats (especially in terrestrial springs and groundwater samples). While the overall abundance of the Aminicenantes was higher in low oxygen tension as well as non-saline and low salinity habitats, it was encountered in a wide range of oxygen tension, salinities, and temperatures. Analysis of the community structure of the Aminicenantes showed distinct patterns across various datasets that appear to be, mostly, driven by habitat variations rather than prevalent environmental parameters. We argue that the detection of the Aminicenantes across environmental extremes and the observed distinct community structure patterns reflect a high level of intraphylum metabolic diversity and adaptive capabilities that enable its survival and growth in a wide range of habitats and environmental conditions.

Bacterial communities associated with production facilities of two newly drilled thermogenic natural gas wells in the Barnett Shale (Texas, USA).

We monitored the bacterial communities in the gas-water separator and water storage tank of two newly drilled natural gas wells in the Barnett Shale in north central Texas, using a 16S rRNA gene pyrosequencing approach over a period of 6 months. Overall, the communities were composed mainly of moderately halophilic and halotolerant members of the phyla Firmicutes and Proteobacteria (classes Βeta-, Gamma-, and Epsilonproteobacteria) in both wells at all sampling times and locations. Many of the observed lineages were encountered in prior investigations of microbial communities from various fossil fluid formations and production facilities. In all of the samples, multiple H(2)S-producing lineages were encountered; belonging to the sulfate- and sulfur-reducing class Deltaproteobacteria, order Clostridiales, and phylum Synergistetes, as well as the thiosulfate-reducing order Halanaerobiales. The bacterial communities from the separator and tank samples bore little resemblance to the bacterial communities in the drilling mud and hydraulic-fracture waters that were used to drill these wells, suggesting the in situ development of the unique bacterial communities in such well components was in response to the prevalent geochemical conditions present. Conversely, comparison of the bacterial communities on temporal and spatial scales suggested the establishment of a core microbial community in each sampled location. The results provide the first overview of bacterial dynamics and colonization patterns in newly drilled, thermogenic natural gas wells and highlights patterns of spatial and temporal variability observed in bacterial communities in natural gas production facilities.

Influence of the drilling mud formulation process on the bacterial communities in thermogenic natural gas wells of the Barnett Shale.

The Barnett Shale in north central Texas contains natural gas generated by high temperatures (120 to 150°C) during the Mississippian Period (300 to 350 million years ago). In spite of the thermogenic origin of this gas, biogenic sulfide production and microbiologically induced corrosion have been observed at several natural gas wells in this formation. It was hypothesized that microorganisms in drilling muds were responsible for these deleterious effects. Here we collected drilling water and drilling mud samples from seven wells in the Barnett Shale during the drilling process. Using quantitative real-time PCR and microbial enumerations, we show that the addition of mud components to drilling water increased total bacterial numbers, as well as the numbers of culturable aerobic heterotrophs, acid producers, and sulfate reducers. The addition of sterile drilling muds to microcosms that contained drilling water stimulated sulfide production. Pyrosequencing-based phylogenetic surveys of the microbial communities in drilling waters and drilling muds showed a marked transition from typical freshwater communities to less diverse communities dominated by Firmicutes and Gammaproteobacteria. The community shifts observed reflected changes in temperature, pH, oxygen availability, and concentrations of sulfate, sulfonate, and carbon additives associated with the mud formulation process. Finally, several of the phylotypes observed in drilling muds belonged to lineages that were thought to be indigenous to marine and terrestrial fossil fuel formations. Our results suggest a possible alternative exogenous origin of such phylotypes via enrichment and introduction to oil and natural gas reservoirs during the drilling process.

Assessment of the diversity, abundance, and ecological distribution of members of candidate division SR1 reveals a high level of phylogenetic diversity but limited morphotypic diversity.

We used a combination of 16S rRNA gene clone library surveys, quantitative PCR (qPCR) analysis, and fluorescent in situ hybridization to investigate the diversity, abundance, and distribution of members of candidate division SR1 in multiple habitats. Using SR1-specific 16S rRNA gene primers, we identified multiple novel SR1 lineages in four different anaerobic environments: sediments from Zodletone Spring, a sulfide- and sulfur-rich spring in southwestern Oklahoma; inner layers of microbial mats obtained from Sperm Pool, a high-temperature, low-pH pool (55 degrees C, pH 2.5) in Yellowstone National Park; fresh bovine ruminal contents; and anaerobic freshwater pond sediments (Duck Pond) in Norman, Oklahoma. qPCR analysis indicated that SR1 members constitute a small fraction (<0.01%) of the microbial communities in Duck Pond and ruminal samples but constitute a significant fraction (11.6 and 48.7%) of the total number of bacterial 16S rRNA genes in Zodletone Spring and the inner layers of Sperm Pool microbial mat samples, respectively. By using SR1-specific fluorescent probes, filamentous cells were identified as the sole SR1 morphotype in all environments examined, with the exception of Sperm Pool, where a second bacillus morphotype was also identified. Using a full-cycle 16S rRNA approach, we show that each of these two morphotypes corresponds to a specific phylogenetic lineage identified in the Sperm Pool clone library. This work greatly expands the intralineage phylogenetic diversity within candidate division SR1 and provides valuable quantification and visualization tools that could be used for investigating the ecological roles, dynamics, and genomics of this as-yet-uncultured bacterial phylum.

Novelty and uniqueness patterns of rare members of the soil biosphere.

Soil bacterial communities typically exhibit a distribution pattern in which most bacterial species are present in low abundance. Due to the relatively small size of most culture-independent sequencing surveys, a detailed phylogenetic analysis of rare members of the community is lacking. To gain access to the rarely sampled soil biosphere, we analyzed a data set of 13,001 near-full-length 16S rRNA gene clones derived from an undisturbed tall grass prairie soil in central Oklahoma. Rare members of the soil bacterial community (empirically defined at two different abundance cutoffs) represented 18.1 to 37.1% of the total number of clones in the data set and were, on average, less similar to their closest relatives in public databases when compared to more abundant members of the community. Detailed phylogenetic analyses indicated that members of the soil rare biosphere either belonged to novel bacterial lineages (members of five novel bacterial phyla identified in the data set, as well as members of multiple novel lineages within previously described phyla or candidate phyla), to lineages that are prevalent in other environments but rarely encountered in soil, or were close relatives to more abundant taxa in the data set. While a fraction of the rare community was closely related to more abundant taxonomic groups in the data set, a significant portion of the rare biosphere represented evolutionarily distinct lineages at various taxonomic cutoffs. We reason that these novelty and uniqueness patterns provide clues regarding the origins and potential ecological roles of members of the soil's rare biosphere.

The time course and determinants of blood pressure within the first 48 h after ischemic stroke.

BACKGROUND AND PURPOSE: Previous research suggests that blood pressure falls acutely after ischemic stroke. We aimed to further characterize this fall with a statistical technique that allows the application of regression techniques to serial blood pressure outcome data. METHODS: In a prospectively recruited ischemic stroke cohort, systolic (SBP) and diastolic (DBP) blood pressure was recorded every 4 h until 48 h after stroke. Potential determinants of blood pressure, including stroke severity and acute infection, were also recorded. Mixed effects models were used to model serial blood pressure measurements over time, adjusted for significant determinants. RESULTS: In 156 patients, SBP and DBP fell by 14.9 mm Hg (95% CI 6.2-22.6 mm Hg) and 6.2 mm Hg (95% CI 1.4-10.6 mm Hg), respectively, over the first 48 h after stroke. SBP was higher in patients with premorbid hypertension, a previous history of stroke or TIA, current alcohol use, increasing age, stroke of mild to moderate severity (NIHSS 3-13) and in patients treated with antihypertensives. SBP was lower in smokers. There was a progressive rise in SBP in patients with acute infection. No factors other than time were associated with DBP. CONCLUSIONS: The use of mixed effects models has identified a linear SBP and DBP fall over the first 48 h after stroke. The timing and magnitude of this fall should be accounted for in the design of future prognostic and intervention studies.

The time course and determinants of temperature within the first 48 h after ischaemic stroke.

BACKGROUND AND PURPOSE: Previous research has attempted to analyze the relationship between post-stroke hyperthermia and prognosis. These analyses have been hindered by a lack of information about the time course and determinants of temperature change after stroke. METHODS: Serial temperatures were measured until 48 h after ischaemic stroke in a prospectively recruited cohort. Potential determinants of temperature, including stroke severity [measured using the National Institutes of Health Stroke Scale (NIHSS)], infection and paracetamol use were recorded. Mixed-effects models were used to model serial temperature measurements over time, adjusted for significant determinants. RESULTS: In 155 patients the mean temperature rose from 36.5 degrees C at the time of stroke to 36.7 degrees C approximately 36 h later. The factors with significant multivariable associations with serial temperatures were: first- and second-order time components, infection, paracetamol administration and the interaction between stroke severity (NIHSS > or =6) and time (all p < 0.1). Patients with admission NIHSS > or =6 had a mean temperature rise of 0.35 degrees C during the first 36 h after stroke, compared with a rise of 0.17 degrees C in those with NIHSS < or =5. CONCLUSIONS: Temperature spontaneously rises during the first 36 h after stroke, particularly after severer stroke and in the presence of infection.

Circadian blood pressure variation after acute stroke.

We aimed to characterise the patterns of circadian blood pressure (BP) variation after acute stroke and determine whether any relationship exists between these patterns and stroke outcome. BP was recorded manually every 4 h for 48 h following acute stroke. Patients were classified according to the percentage fall in mean systolic BP (SBP) at night compared to during the day as: dippers (fall > or = 10-<20%); extreme dippers (> or = 20%); non-dippers (> or = 0-<10%); and reverse dippers (<0%, that is, a rise in mean nocturnal SBP compared to mean daytime SBP). One hundred and seventy-three stroke patients were included in the study (83 men, 90 women; mean age 74.3 years). Four patients (2.3%) were extreme dippers, 25 (14.5%) dippers, 80 (46.2%) non-dippers and 64 (36.9%) reverse dippers. There was a non-significant trend in the proportion of patients who were dead or dependent at 3 months in the extreme dipper (p=0.59) and reverse dipper (p=0.35) groups. Non-dipping and reverse-dipping were relatively common patterns of circadian BP variation seen in acute stroke patients. These patterns were not clearly associated with outcome.

The effect of admission physiological variables on 30 day outcome after stroke.

INTRODUCTION: Potentially modifiable physiological variables may influence stroke prognosis but their independence from modifiable factors remains unclear. METHODS: Admission physiological measures (blood pressure, heart rate, temperature and blood glucose) and other unmodifiable factors were recorded from patients presenting within 48 hours of stroke. These variables were compared with the outcomes of death and death or dependency at 30 days in multivariate statistical models. RESULTS: In the 186 patients included in the study, age, atrial fibrillation and the National Institutes of Health Stroke Score were identified as unmodifiable factors independently associated with death and death or dependency. After adjusting for these factors, none of the physiological variables were independently associated with death, while only diastolic blood pressure (DBP) > or = 90 mmHg was associated with death or dependency at 30 days (p = 0.02). CONCLUSIONS: Except for elevated DBP, we found no independent associations between admission physiology and outcome at 30 days in an unselected stroke cohort. Future studies should look for associations in subgroups, or by analysing serial changes in physiology during the early post-stroke period.

Impact of premorbid undernutrition on outcome in stroke patients.

BACKGROUND AND PURPOSE: To assess the prevalence of premorbid undernutrition and its impact on outcomes 1 month after stroke. METHODS: The study recruited from consecutive stroke admissions during a 10-month period. Premorbid nutritional status (using the subjective global assessment [SGA]), premorbid functioning (modified Rankin scale [MRS]), and stroke severity (National Institutes of Health Stroke Scale [NIHSS] score) were assessed at admission. The associations between premorbid nutritional status, poor outcome (defined as MRS > or =3), and mortality were examined before and after adjustment for confounding variables, including age, gender, stroke risk factors, stroke severity, and admission serum albumin. RESULTS: Thirty of 185 patients were assessed as having undernutrition at admission. Significant unadjusted associations were observed between undernutrition and poor outcome (odds ratio [OR], 3.4; 95% CI, 1.3 to 8.7; P=0.01), and mortality (OR, 3.1, 95% CI, 1.3 to 7.7; P=0.02) at 1 month. NIHSS, age, and premorbid MRS were also significantly associated with poor outcomes. After adjustment for these factors, the effect size of associations remained important but not significant (poor outcome: OR, 2.4; 95% CI, 0.7 to 9.0, P=0.18; mortality: OR, 3.2; 95% CI, 1.0 to 10.4, P=0.05). CONCLUSIONS: Premorbid undernutrition, as assessed using the SGA, appears to be an independent predictor of poor stroke outcome. Stroke prevention strategies should target undernutrition in the population at risk for stroke to improve outcomes.