254 research outputs found
Fasting and time of day independently modulate circadian rhythm relevant gene expression in adipose and skin tissue
Full text linkAbstract Background Intermittent fasting and time-restricted diets are associated with lower risk biomarkers for cardio-metabolic disease. The shared mechanisms underpinning the similar physiological response to these events is not established, but circadian rhythm could be involved. Here we investigated the transcriptional response to fasting in a large cross-sectional study of adipose and skin tissue from healthy volunteers (N = 625) controlling for confounders of circadian rhythm: time of day and season. Results We identified 367 genes in adipose and 79 in skin whose expression levels were associated (FDR < 5%) with hours of fasting conditionally independent of time of day and season, with 19 genes common to both tissues. Among these genes, we replicated 38 in human, 157 in non-human studies, and 178 are novel associations. Fasting-responsive genes were enriched for regulation of and response to circadian rhythm. We identified 99 genes in adipose and 54 genes in skin whose expression was associated to time of day; these genes were also enriched for circadian rhythm processes. In genes associated to both exposures the effect of time of day was stronger and in an opposite direction to that of hours fasted. We also investigated the relationship between fasting and genetic regulation of gene expression, including GxE eQTL analysis to identify personal responses to fasting. Conclusion This study robustly implicates circadian rhythm genes in the response to hours fasting independently of time of day, seasonality, age and BMI. We identified tissue-shared and tissue-specific differences in the transcriptional response to fasting in a large sample of healthy volunteers
The Seashell Development Model
Full text linkSmall and new organizations (SNOs) of any nature face similar challenges in a contemporary context defined by the blurring of lines between the private, public and academic sectors and an economy where knowledge is the most valuable currency. The liability of smallness asserts that small organizations fail because of weaknesses in management, infrastructure and capacity, while the liability of newness asserts that new organizations fail because of weaknesses in trust, credibility and support. The Seashell Development Model provides an integrated framework that directly addresses the liabilities of smallness and newness in this contemporary context.
The creation of the Seashell Model comprised a synthesis of the most recent research and well established theories in the disciplines of: networking; collaboration; donor, investor and corporate sponsor behavior; fundraising; collaborative innovation and swarm creativity; knowledge flow and knowledge management; capacity building; Triple Helix engagement, partnership building and boundary spanning; leadership theory, charisma-building and semantic translation; team theory; goal setting theory; information dissemination; change management, and collaborative inquiry.
At the 2017 United Nations ECOSOC partnership forum, the importance of private-public partnerships and capacity building dominated diplomatic dialogue. The Seashell Development Model hinges on the power of human relationships to transcend the disintegrating boundaries between sectors. It provides a comprehensive framework from the inception of the organization to the courtship of higher level investors, donors and corporate sponsors, allowing SNOs of any nature to leverage the intellectual and human capital of their networks to succeed in this dynamic contemporary context
Name Suppression until Conviction: An argument in support of a return to s 45B of the Criminal Justice Act 1954
No full textA cornerstone of New Zealand’s justice system is the principle of “open justice”. The courts are open to the public and the media is free to report on proceedings. The by product of this is the presumption against name suppression being granted, particularly in the criminal jurisdiction. This however was not always the case and for ten months between September 1975 and July 1976 blanket suppression of an accused’s name and identifying particulars until conviction, was a reality.
This paper argues that a return to legislation of that kind is warranted particularly in light of the changing media landscape which includes instantatneous media reporting and the permanent effect of the internet. This author concludes that a return to liberal name suppression laws would not equate to an unjustified limitation on the freedom of expression, nor would it erode the principle of open justice
Name Suppression until Conviction: An argument in support of a return to s 45B of the Criminal Justice Act 1954
No full textA cornerstone of New Zealand’s justice system is the principle of “open justice”. The courts are open to the public and the media is free to report on proceedings. The by product of this is the presumption against name suppression being granted, particularly in the criminal jurisdiction. This however was not always the case and for ten months between September 1975 and July 1976 blanket suppression of an accused’s name and identifying particulars until conviction, was a reality.
This paper argues that a return to legislation of that kind is warranted particularly in light of the changing media landscape which includes instantatneous media reporting and the permanent effect of the internet. This author concludes that a return to liberal name suppression laws would not equate to an unjustified limitation on the freedom of expression, nor would it erode the principle of open justice
Cell-type heterogeneity in adipose tissue is associated with complex traits and reveals disease-relevant cell-specific eQTLs
Full text linkAdipose tissue is an important endocrine organ with a role in many cardiometabolic diseases. It is comprised of a heterogeneous collection of cell-types which can differentially impact disease phenotypes. Cellular heterogeneity can also confound ‘omic analyses, but is rarely taken into account in analysis of solid-tissue transcriptomes. Here, we investigate cell-type heterogeneity in two population-level subcutaneous adipose tissue RNA-seq datasets (TwinsUK, N =766 and GTEx, N=326) by estimating the relative proportions of four distinct cell types (adipocytes, macrophages, CD4+ t-cells and Micro-Vascular Endothelial Cells). We find significant cellular heterogeneity within and between the TwinsUK and GTEx adipose datasets. We find that adipose cell-type composition is heritable and confirm the positive association between adipose-resident macrophage proportion and obesity (BMI), but find a stronger BMI-independent association with DXA-derived body-fat distribution traits. We benchmark the impact of adipose tissue cell-composition on a range of standard analyses, including phenotype-gene expression association, co-expression networks and cis-eQTL discovery. Our results indicate that it is critical to account for cell-type composition when combining adipose transcriptome datasets, in co-expression analysis and in differential expression analysis with obesity-related traits. We applied Gene expression by Cell Type Proportion interaction models (G × Cell) to identify 26 cell-type specific eQTLs in 20 genes, including 4 autoimmune disease GWAS loci. These results identify cell-specific eQTLs and demonstrate the potential of in-silico deconvolution of bulk tissue to identify cell-type restricted regulatory variants. <br/
City life does not change a small mammal community composition
No full textRimbach R, Heinze K, Poorthuis L, Petit J, Dammhahn M. City life does not change a small mammal community composition. WILDLIFE RESEARCH. 2025;52(5): WR24196.Context Urbanization is a global phenomenon with profound forms of land-use change. Urban areas are characterized by habitat fragmentation and replacement of natural habitat by human-made structures, which alter environmental conditions such as natural resources, light and noise levels, and ambient temperature. Animal communities respond to urbanization in various ways, often showing shifts towards generalist species and declines in species richness. However, mixed results are found in the literature, with neutral or even positive effects on species diversity.Aims Our goal was to investigate whether community composition, species diversity and evenness of terrestrial small mammals vary with increasing levels of urbanization, approximated as impervious surface cover and human population density.Methods We conducted a camera trap survey in 33 gardens in the city of M & uuml;nster, Germany, and its surroundings. We recorded a total of 25,982 photos with animals (excluding pets). For analysis, we included only photos of the same species captured at least 60 s apart, resulting in a final dataset of 7090 photos.Key results Eight taxa were recorded, with Apodemus spp. dominating (72.6%). The probability of occurrence of all species was not affected by increasing impervious surface cover. We found that community composition, species diversity and evenness do not vary with changing impervious surface cover or human population density. Although associations among species were mostly neutral, trends included a positive association between Myodes glareolus and Crocidura spp., and negative associations between Apodemus spp. and Crocidura spp., and Rattus norvegicus and Sciurus vulgaris.Conclusions Our results suggest that composition, species diversity and evenness of this small mammal community are not affected by the two measures of degree of urbanization, impervious surface cover and human population density. The small mammal community of M & uuml;nster is likely to be the result of generalist species expressing high phenotypic plasticity to bypass the urban filters explaining our overall neutral results.Implications Urban gardens can harbor a small mammal community as diverse as gardens outside of the city, highlighting the importance of these green areas in the urban matrix. Further studies will be needed to address whether our findings are generalizable to multiple cities in Europe
A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
Full text linkAbstract
The sequence of Ciona savignyi was determined using a whole-genome shotgun strategy, but a high degree of polymorphism resulted in a fractured assembly wherein allelic sequences from the same genomic region assembled separately. We designed a multistep strategy to generate a nonredundant reference sequence from the original assembly by reconstructing and aligning the two 'haplomes' (haploid genomes). In the resultant 174 megabase reference sequence, each locus is represented once, misassemblies are corrected, and contiguity and continuity are dramatically improved
Nuclear Genetic Regulation of the Human Mitochondrial Transcriptome
Full text linkMitochondria play important roles in cellular processes and disease, yet little is known about how the transcriptional regime of the mitochondrial genome varies across individuals and tissues. By analyzing >11,000 RNA-sequencing libraries across 36 tissue/cell types, we find considerable variation in mitochondrial-encoded gene expression along the mitochondrial transcriptome, across tissues and between individuals, highlighting the importance of cell-type specific and post-transcriptional processes in shaping mitochondrial-encoded RNA levels. Using whole-genome genetic data we identify 64 nuclear loci associated with expression levels of 14 genes encoded in the mitochondrial genome, including missense variants within genes involved in mitochondrial function (TBRG4, MTPAP and LONP1), implicating genetic mechanisms that act in trans across the two genomes. We replicate ~21% of associations with independent tissue-matched datasets and find genetic variants linked to these nuclear loci that are associated with cardio-metabolic phenotypes and Vitiligo, supporting a potential role for variable mitochondrial-encoded gene expression in complex disease
Cell-type heterogeneity in adipose tissue is associated with complex traits and reveals disease-relevant cell-specific eQTLs
No full textAbstractAdipose tissue is comprised of a heterogeneous collection of cell-types which can differentially impact disease phenotypes. We investigated cell-type heterogeneity in two population-level subcutaneous adipose tissue RNAseq datasets (TwinsUK, N =766 and GTEx, N=326). We find that adipose cell-type composition is heritable and confirm the positive association between macrophage proportion and obesity (BMI), but find a stronger BMI-independent association with DXA-derived body-fat distribution traits. Cellular heterogeneity can confound ‘omic analyses, but is rarely taken into account in analysis of solid-tissue transcriptomes. We benchmark the impact of adipose tissue cell-composition on a range of standard analyses, including phenotypegene expression association, co-expression networks and cis-eQTL discovery. We applied G x Cell Type Proportion interaction models to identify 26 cell-type specific eQTLs in 20 genes, including 4 autoimmune disease GWAS loci, demonstrating the potential of in silico deconvolution of bulk tissue to identify cell-type restricted regulatory variants.</jats:p
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