Microorganisms serve important functions within numerous eukaryotic host organisms. An understanding of the variation in the plant niche-level microbiome, from rhizosphere soils to plant canopies, is ...imperative to gain a better understanding of how both the structural and functional processes of microbiomes impact the health of the overall plant holobiome. Using Populus trees as a model ecosystem, we characterized the archaeal/bacterial and fungal microbiome across 30 different tissue-level niches within replicated Populus deltoides and hybrid Populus trichocarpa × deltoides individuals using 16S and ITS2 rRNA gene analyses.
Our analyses indicate that archaeal/bacterial and fungal microbiomes varied primarily across broader plant habitat classes (leaves, stems, roots, soils) regardless of plant genotype, except for fungal communities within leaf niches, which were greatly impacted by the host genotype. Differences between tree genotypes are evident in the elevated presence of two potential fungal pathogens, Marssonina brunnea and Septoria sp., on hybrid P. trichocarpa × deltoides trees which may in turn be contributing to divergence in overall microbiome composition. Archaeal/bacterial diversity increased from leaves, to stem, to root, and to soil habitats, whereas fungal diversity was the greatest in stems and soils.
This study provides a holistic understanding of microbiome structure within a bioenergy relevant plant host, one of the most complete niche-level analyses of any plant. As such, it constitutes a detailed atlas or map for further hypothesis testing on the significance of individual microbial taxa within specific niches and habitats of Populus and a baseline for comparisons to other plant species.
Abstract
Marine bivalves are important components of ecosystems and exploited by humans for food across the world, but the intrinsic vulnerability of exploited bivalve species to global changes is ...poorly known. Here, we expand the list of shallow-marine bivalves known to be exploited worldwide, with 720 exploited bivalve species added beyond the 81 in the United Nations FAO Production Database, and investigate their diversity, distribution and extinction vulnerability using a metric based on ecological traits and evolutionary history. The added species shift the richness hotspot of exploited species from the northeast Atlantic to the west Pacific, with 55% of bivalve families being exploited, concentrated mostly in two major clades but all major body plans. We find that exploited species tend to be larger in size, occur in shallower waters, and have larger geographic and thermal ranges—the last two traits are known to confer extinction-resistance in marine bivalves. However, exploited bivalve species in certain regions such as the tropical east Atlantic and the temperate northeast and southeast Pacific, are among those with high intrinsic vulnerability and are a large fraction of regional faunal diversity. Our results pinpoint regional faunas and specific taxa of likely concern for management and conservation.
The rising prevalence of childhood obesity has been postulated as an explanation for the increasing rate of individuals diagnosed with type 1 diabetes (T1D). In this study, we use Mendelian ...randomization (MR) to provide evidence that childhood body size has an effect on T1D risk (OR = 2.05 per change in body size category, 95% CI = 1.20 to 3.50, P = 0.008), which remains after accounting for body size at birth and during adulthood using multivariable MR (OR = 2.32, 95% CI = 1.21 to 4.42, P = 0.013). We validate this direct effect of childhood body size using data from a large-scale T1D meta-analysis based on n = 15,573 cases and n = 158,408 controls (OR = 1.94, 95% CI = 1.21 to 3.12, P = 0.006). We also provide evidence that childhood body size influences risk of asthma, eczema and hypothyroidism, although multivariable MR suggested that these effects are mediated by body size in later life. Our findings support a causal role for higher childhood body size on risk of being diagnosed with T1D, whereas its influence on the other immune-associated diseases is likely explained by a long-term effect of remaining overweight for many years over the lifecourse.
Abstract Purpose Few transgender youth eligible for gender-affirming treatments actually receive them. Multidisciplinary gender clinics improve access and care coordination but are rare. Although ...experts support use of pubertal blockers and cross-sex hormones for youth who meet criteria, these are uncommonly offered. This study's aim was to understand barriers that transgender youth and their caregivers face in accessing gender-affirming health care. Methods Transgender youth (age 14–22 years) and caregivers of transgender youth were recruited from Seattle-based clinics, and readerships from a blog and support group listserv. Through individual interviews, focus groups, or an online survey, participants described their experiences accessing gender-affirming health care. We then used theoretical thematic analysis to analyze data. Results Sixty-five participants (15 youth, 50 caregivers) described barriers spanning six themes: (1) few accessible pediatric providers are trained in gender-affirming health care; (2) lack of consistently applied protocols; (3) inconsistent use of chosen name/pronoun; (4) uncoordinated care and gatekeeping; (5) limited/delayed access to pubertal blockers and cross-sex hormones; and (6) insurance exclusions. Conclusions This is the first study aimed at understanding perceived barriers to care among transgender youth and their caregivers. Themed barriers to care led to the following recommendations: (1) mandatory training on gender-affirming health care and cultural humility for providers/staff; (2) development of protocols for the care of young transgender patients, as well as roadmaps for families; (3) asking and recording of chosen name/pronoun; (4) increased number of multidisciplinary gender clinics; (5) providing cross-sex hormones at an age that permits peer-congruent development; and (6) designating a navigator for transgender patients in clinics.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Aims/hypothesis
Given the potential shared aetiology between type 1 and type 2 diabetes, we aimed to identify any genetic regions associated with both diseases. For associations where there is a ...shared signal and the allele that increases risk to one disease also increases risk to the other, inference about shared aetiology could be made, with the potential to develop therapeutic strategies to treat or prevent both diseases simultaneously. Alternatively, if a genetic signal co-localises with divergent effect directions, it could provide valuable biological insight into how the association affects the two diseases differently.
Methods
Using publicly available type 2 diabetes summary statistics from a genome-wide association study (GWAS) meta-analysis of European ancestry individuals (74,124 cases and 824,006 controls) and type 1 diabetes GWAS summary statistics from a meta-analysis of studies on individuals from the UK and Sardinia (7467 cases and 10,218 controls), we identified all regions of 0.5 Mb that contained variants associated with both diseases (false discovery rate <0.01). In each region, we performed forward stepwise logistic regression to identify independent association signals, then examined co-localisation of each type 1 diabetes signal with each type 2 diabetes signal using
coloc
. Any association with a co-localisation posterior probability of ≥0.9 was considered a genuine shared association with both diseases.
Results
Of the 81 association signals from 42 genetic regions that showed association with both type 1 and type 2 diabetes, four association signals co-localised between both diseases (posterior probability ≥0.9): (1) chromosome 16q23.1, near
CTRB1
/
BCAR1
, which has been previously identified; (2) chromosome 11p15.5, near the
INS
gene; (3) chromosome 4p16.3, near
TMEM129
and (4) chromosome 1p31.3, near
PGM1
. In each of these regions, the effect of genetic variants on type 1 diabetes was in the opposite direction to the effect on type 2 diabetes. Use of additional datasets also supported the previously identified co-localisation on chromosome 9p24.2, near the
GLIS3
gene, in this case with a concordant direction of effect.
Conclusions/interpretation
Four of five association signals that co-localise between type 1 diabetes and type 2 diabetes are in opposite directions, suggesting a complex genetic relationship between the two diseases.
Graphical abstract
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Identifying relationships between variables in ecological systems is challenging due to the large number of interacting factors. One system studied in detail is avian reproduction, where molecular ...analyses have revealed dramatic variation in rates of extra-pair paternity-the frequency with which broods contain individuals sired by different males. Despite the attention the topic has received, identification of ecological predictors of the observed variation remains elusive. In this study we evaluate how structural equation modeling-which allows for simultaneous estimation of covariation between all variables in a model-can help identify significant relationships between ecological variables and extra-pair paternity. We estimated the correlation of eight different variables using data from 36 species of passerines by including them in six different models of varying complexity. We recover strong support for species with lower rates of male care having higher rates of extra-pair paternity. Our results also suggest that testes size, range size, and longevity all potentially have a relationship with rates of extra-pair paternity; however, interpretation of this result is more challenging. More generally, these results demonstrate the utility of applying structural equation modeling to understanding correlations among interacting variables in complex biological systems.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The start of the Palaeocene/Eocene thermal maximum-a period of exceptional global warming about 55 million years ago-is marked by a prominent negative carbon isotope excursion that reflects a massive ...input of 13C-depleted ('light') carbon to the ocean-atmosphere system. It is often assumed that this carbon injection initiated the rapid increase in global surface temperatures and environmental change that characterize the climate perturbation, but the exact sequence of events remains uncertain. Here we present chemical and biotic records of environmental change across the Palaeocene/Eocene boundary from two sediment sections in New Jersey that have high sediment accumulation rates. We show that the onsets of environmental change (as recorded by the abundant occurrence ('acme') of the dinoflagellate cyst Apectodinium) and of surface-ocean warming (as evidenced by the palaeothermometer TEX86) preceded the light carbon injection by several thousand years. The onset of the Apectodinium acme also precedes the carbon isotope excursion in sections from the southwest Pacific Ocean and the North Sea, indicating that the early onset of environmental change was not confined to the New Jersey shelf. The lag of ∼3,000 years between the onset of warming in New Jersey shelf waters and the carbon isotope excursion is consistent with the hypothesis that bottom water warming caused the injection of 13C-depleted carbon by triggering the dissociation of submarine methane hydrates, but the cause of the early warming remains uncertain.
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DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Non-coding genetic variants that influence gene transcription in pancreatic islets play a major role in the susceptibility to type 2 diabetes (T2D), and likely also contribute to type 1 diabetes ...(T1D) risk. For many loci, however, the mechanisms through which non-coding variants influence diabetes susceptibility are unknown.
We examine splicing QTLs (sQTLs) in pancreatic islets from 399 human donors and observe that common genetic variation has a widespread influence on the splicing of genes with established roles in islet biology and diabetes. In parallel, we profile expression QTLs (eQTLs) and use transcriptome-wide association as well as genetic co-localization studies to assign islet sQTLs or eQTLs to T2D and T1D susceptibility signals, many of which lack candidate effector genes. This analysis reveals biologically plausible mechanisms, including the association of T2D with an sQTL that creates a nonsense isoform in ERO1B, a regulator of ER-stress and proinsulin biosynthesis. The expanded list of T2D risk effector genes reveals overrepresented pathways, including regulators of G-protein-mediated cAMP production. The analysis of sQTLs also reveals candidate effector genes for T1D susceptibility such as DCLRE1B, a senescence regulator, and lncRNA MEG3.
These data expose widespread effects of common genetic variants on RNA splicing in pancreatic islets. The results support a role for splicing variation in diabetes susceptibility, and offer a new set of genetic targets with potential therapeutic benefit.
Genetics of the human face Crouch, Daniel J. M.; Winney, Bruce; Koppen, Willem P. ...
Proceedings of the National Academy of Sciences - PNAS,
01/2018, Volume:
115, Issue:
4
Journal Article
Peer reviewed
Open access
To discover specific variants with relatively large effects on the human face, we have devised an approach to identifying facial features with high heritability. This is based on using twin data to ...estimate the additive genetic value of each point on a face, as provided by a 3D camera system. In addition, we have used the ethnic difference between East Asian and European faces as a further source of face genetic variation. We use principal components (PCs) analysis to provide a fine definition of the surface features of human faces around the eyes and of the profile, and chose upper and lower 10% extremes of the most heritable PCs for looking for genetic associations. Using this strategy for the analysis of 3D images of 1,832 unique volunteers from the well-characterized People of the British Isles study and 1,567 unique twin images from the TwinsUK cohort, together with genetic data for 500,000 SNPs, we have identified three specific genetic variants with notable effects on facial profiles and eyes.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
We present a new multiproxy (TEX86, δ18O and Mg/Ca), marine temperature history for Canterbury Basin, eastern New Zealand, that extends from middle Paleocene to middle Eocene, including the ...Paleocene–Eocene thermal maximum (PETM) and early Eocene climatic optimum (EECO). In light of concerns that proxy-based sea surface temperature (SST) estimates are untenably warm for the southwest Pacific during the Eocene, we review the assumptions that underlie the proxies and develop a preliminary paleo-calibration for TEX86 that is based on four multiproxy Eocene records that represent an SST range of 15–34°C. For the southwest Pacific Paleogene, we show that TEX86L exhibits the best fit with the Eocene paleo-calibration. SSTs derived from related proxies (TEX86H, 1/TEX86) exhibit a systematic warm bias that increases as TEX86 values decrease (a warm bias of 4–7°C where TEX86<0.7). The TEX86L proxy indicates that southwest Pacific SST increased by ∼10°C from middle Paleocene to early Eocene, with SST maxima of 26–28°C (tropical) during the PETM and EECO and an SST minimum of 13–16°C (cool–warm temperate) at the middle/late Paleocene transition (58.7Ma). The base of the EECO is poorly defined in these records but the top is well-defined in Canterbury Basin by a 2–5°C decrease in SST and bottom water temperature (BWT) in the latest early Eocene (49.3Ma); BWT falls from a maximum of 18–20°C in the EECO to 12–14°C in the middle Eocene. Overall, cooler temperatures are recorded in the mid-Waipara section, which may reflect a deeper (∼500m water depth) and less neritic depositional setting compared with Hampden and ODP 1172 (∼200m water depth). The high SSTs and BWTs inferred for the PETM and EECO can be reconciled with Eocene coupled climate model results if the proxies are biased towards seasonal maxima and the likely effect of a proto-East Australian Current is taken into account.
► A revised multiproxy marine temperature record from middle Paleocene to middle Eocene, Southwest Pacific Ocean. ► Paleo-calibration of GDGT-based SST proxies supports use of TEX86L for southern high-latitude Paleogene records. ► Peak sea surface temperatures (SSTs) during the PETM and EECO of 25–28°C. ► Minimum SSTs during the late Paleocene of 13–15°C.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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