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It has been widely reported that isoprene emissions from the Arctic ecosystem have a strong temperature response. Here we identify sedges ( Carex spp. and Eriophorum spp.) as key contributors to this high sensitivity using plant chamber experiments. We observe that sedges exhibit a markedly stronger temperature response compared to that of other isoprene emitters and predictions by the widely accepted isoprene emission model, the Model of Emissions of Gases and Aerosols from Nature (MEGAN). MEGAN is able to reproduce eddy-covariance flux observations at three high-latitude sites by integrating our findings. Furthermore, the omission of the strong temperature responses of Arctic isoprene emitters causes a 20% underestimation of isoprene emissions for the high-latitude regions of the Northern Hemisphere during 2000-2009 in the Community Land Model with the MEGAN scheme. We also find that the existing model had underestimated the long-term trend of isoprene emissions from 1960 to 2009 by 55% for the high-latitude regions. The authors identify that sedges in the Arctic have a different isoprene temperature response than other temperate plants, and this finding explains the high temperature sensitivity of isoprene emissions from Arctic terrestrial ecosystems.

Warming climate in the Arctic is leading to an increase in isoprene emission from ecosystems. We assessed the influence of temperature on isoprene emission from Arctic willows with laboratory and field measurements. Our findings indicate that the hourly temperature response curve of Salix spp., the dominant isoprene emitting shrub in the Arctic, aligns with that of temperate plants. In contrast, the isoprene capacity of willows exhibited a more substantial than expected response to the mean ambient temperature of the previous day, which is much stronger than the daily temperature response predicted by the current version of the Model of Emissions of Gases and Aerosols from Nature (MEGAN). With a modified algorithm from this study, MEGAN predicts 66% higher isoprene emissions for Arctic willows during an Arctic heatwave. However, despite these findings, we are still unable to fully explain the high temperature sensitivity of isoprene emissions from high latitude ecosystems. Plain Language Summary Isoprene plays an important role in atmospheric chemistry and climate. As the climate warms, ecosystems release more isoprene into the air due to higher temperatures and changes in plant species composition. The Arctic is a hotspot for climate change. In this study, we investigated how temperature affects isoprene emissions from Arctic willow shrubs by conducting experiments in both the lab and the field. Our results show that the response of Salix spp. (willows) in the Arctic react to short‐term temperature changes is similar to plants in temperate regions. Interestingly, the amount of isoprene that willows release responds strongly to the average temperature of the previous day. This response is much stronger than predicted by models. Considering the insights from our study, isoprene emissions from Arctic willows are much higher during Arctic heatwaves than previously thought. This study can help us understand how isoprene from Arctic willows will affect atmospheric composition and climate and contribute to corresponding feedbacks on the local climate. Key Points The hourly temperature response curve of Arctic Salix spp. is similar to temperate plants and is well represented by the Model of Emissions of Gases and Aerosols from Nature (MEGAN) model The isoprene capacity of willows exhibited a pronounced response to the mean temperature of the previous day MEGAN predicts a 66% higher isoprene emission for Arctic willows during an Arctic heatwave after incorporating the findings of this study

The genome of the carnivorous bladderwort plant Utricularia gibba is described here; despite having undergone at least three rounds of whole-genome duplication, its genome is unusually small and virtually devoid of intergenic DNA. Tiny bladderwort genome sequenced Bladderworts are carnivorous plants found in fresh water and damp soil, where they feed on minute prey such as protozoa and rotifers. They lack clearly distinguishable roots, leaves or stems but produce tiny orchid-like flowers. The genome of one of these plants, Utricularia gibba , has now been sequence and analysed. The genome is unusually small (at 82 megabases), in part due to the near absence of intergenic DNA, but it encodes a typical number of genes for a plant and is sufficient to regulate the development and reproduction of a complex organism. Though Although remaining small, the genome has undergone at least three rounds of whole-genome duplication since common ancestry with tomato ( Solanum ) and grape ( Viti s). It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation 1 . However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba . Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato ( Solanum ) and grape ( Vitis ). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism.

Background Group 1 pulmonary arterial hypertension (PAH) is a rare disease with high mortality despite recent therapeutic advances. Pathogenic remodeling of pulmonary arterioles leads to increased pulmonary pressures, right ventricular hypertrophy, and heart failure. Mutations in bone morphogenetic protein receptor type 2 and other risk genes predispose to disease, but the vast majority of non-familial cases remain genetically undefined. Methods To identify new risk genes, we performed exome sequencing in a large cohort from the National Biological Sample and Data Repository for PAH (PAH Biobank, n  = 2572). We then carried out rare deleterious variant identification followed by case-control gene-based association analyses. To control for population structure, only unrelated European cases ( n  = 1832) and controls ( n  = 12,771) were used in association tests. Empirical p values were determined by permutation analyses, and the threshold for significance defined by Bonferroni’s correction for multiple testing. Results Tissue kallikrein 1 ( KLK1 ) and gamma glutamyl carboxylase ( GGCX ) were identified as new candidate risk genes for idiopathic PAH (IPAH) with genome-wide significance. We note that variant carriers had later mean age of onset and relatively moderate disease phenotypes compared to bone morphogenetic receptor type 2 variant carriers. We also confirmed the genome-wide association of recently reported growth differentiation factor ( GDF2 ) with IPAH and further implicate T-box 4 ( TBX4 ) with child-onset PAH. Conclusions We report robust association of novel genes KLK1 and GGCX with IPAH, accounting for ~ 0.4% and 0.9% of PAH Biobank cases, respectively. Both genes play important roles in vascular hemodynamics and inflammation but have not been implicated in PAH previously. These data suggest new genes, pathogenic mechanisms, and therapeutic targets for this lethal vasculopathy.

Background Pulmonary arterial hypertension (PAH) is a rare disease characterized by distinctive changes in pulmonary arterioles that lead to progressive pulmonary arterial pressures, right-sided heart failure, and a high mortality rate. Up to 30% of adult and 75% of pediatric PAH cases are associated with congenital heart disease (PAH-CHD), and the underlying etiology is largely unknown. There are no known major risk genes for PAH-CHD. Methods To identify novel genetic causes of PAH-CHD, we performed whole exome sequencing in 256 PAH-CHD patients. We performed a case-control gene-based association test of rare deleterious variants using 7509 gnomAD whole genome sequencing population controls. We then screened a separate cohort of 413 idiopathic and familial PAH patients without CHD for rare deleterious variants in the top association gene. Results We identified SOX17 as a novel candidate risk gene ( p  = 5.5e−7). SOX17 is highly constrained and encodes a transcription factor involved in Wnt/β-catenin and Notch signaling during development. We estimate that rare deleterious variants contribute to approximately 3.2% of PAH-CHD cases. The coding variants identified include likely gene-disrupting (LGD) and deleterious missense, with most of the missense variants occurring in a highly conserved HMG-box protein domain. We further observed an enrichment of rare deleterious variants in putative targets of SOX17, many of which are highly expressed in developing heart and pulmonary vasculature. In the cohort of PAH without CHD, rare deleterious variants of SOX17 were observed in 0.7% of cases. Conclusions These data strongly implicate SOX17 as a new risk gene contributing to PAH-CHD as well as idiopathic/familial PAH. Replication in other PAH cohorts and further characterization of the clinical phenotype will be important to confirm the precise role of SOX17 and better estimate the contribution of genes regulated by SOX17.

Background Pulmonary arterial hypertension (PAH) is a lethal vasculopathy characterized by pathogenic remodeling of pulmonary arterioles leading to increased pulmonary pressures, right ventricular hypertrophy, and heart failure. PAH can be associated with other diseases (APAH: connective tissue diseases, congenital heart disease, and others) but often the etiology is idiopathic (IPAH). Mutations in bone morphogenetic protein receptor 2 ( BMPR2 ) are the cause of most heritable cases but the vast majority of other cases are genetically undefined. Methods To identify new risk genes, we utilized an international consortium of 4241 PAH cases with exome or genome sequencing data from the National Biological Sample and Data Repository for PAH, Columbia University Irving Medical Center, and the UK NIHR BioResource – Rare Diseases Study. The strength of this combined cohort is a doubling of the number of IPAH cases compared to either national cohort alone. We identified protein-coding variants and performed rare variant association analyses in unrelated participants of European ancestry, including 1647 IPAH cases and 18,819 controls. We also analyzed de novo variants in 124 pediatric trios enriched for IPAH and APAH-CHD. Results Seven genes with rare deleterious variants were associated with IPAH with false discovery rate smaller than 0.1: three known genes ( BMPR2 , GDF2 , and TBX4 ), two recently identified candidate genes ( SOX17 , KDR ), and two new candidate genes (fibulin 2, FBLN2 ; platelet-derived growth factor D, PDGFD ). The new genes were identified based solely on rare deleterious missense variants, a variant type that could not be adequately assessed in either cohort alone. The candidate genes exhibit expression patterns in lung and heart similar to that of known PAH risk genes, and most variants occur in conserved protein domains. For pediatric PAH, predicted deleterious de novo variants exhibited a significant burden compared to the background mutation rate (2.45×, p = 2.5e−5). At least eight novel pediatric candidate genes carrying de novo variants have plausible roles in lung/heart development. Conclusions Rare variant analysis of a large international consortium identified two new candidate genes— FBLN2 and PDGFD . The new genes have known functions in vasculogenesis and remodeling. Trio analysis predicted that ~ 15% of pediatric IPAH may be explained by de novo variants.

Solid tumors are characterized by regions of low oxygen tension (OT), which play a central role in tumor progression and resistance to therapy. Low OT affects mitochondrial function and for the cells to survive, mitochondria must functionally adapt to low OT to maintain the cellular bioenergetics. In this study, a novel experimental approach was developed to examine the real-time bioenergetic changes in breast cancer cells (BCCs) during adaptation to OT (from 20% to <1% oxygen) using sensitive extracellular flux technology. Oxygen was gradually removed from the medium, and the bioenergetics of metastatic BCCs (MDA-MB-231 and MCF10CA clones) was compared with non-tumorigenic (MCF10A) cells. BCCs, but not MCF10A, rapidly responded to low OT by stabilizing HIF-1α and increasing HIF-1α responsive gene expression and glucose uptake. BCCs also increased extracellular acidification rate (ECAR), which was markedly lower in MCF10A. Interestingly, BCCs exhibited a biphasic response in basal respiration as the OT was reduced from 20% to <1%. The initial stimulation of oxygen consumption is found to be due to increased mitochondrial respiration. This effect was HIF-1α-dependent, as silencing HIF-1α abolished the biphasic response. During hypoxia and reoxygenation, BCCs also maintained oxygen consumption rates at specific OT; however, HIF-1α silenced BCC were less responsive to changes in OT. Our results suggest that HIF-1α provides a high degree of bioenergetic flexibility under different OT which may confer an adaptive advantage for BCC survival in the tumor microenvironment and during invasion and metastasis. This study thus provides direct evidence for the cross-talk between HIF-1α and mitochondria during adaptation to low OT by BCCs and may be useful in identifying novel therapeutic agents that target the bioenergetics of BCCs in response to low OT.

Background The complex interspersed pattern of segmental duplications in humans is responsible for rearrangements associated with neurodevelopmental disease, including the emergence of novel genes important in human brain evolution. We investigate the evolution of LCR16a, a putative driver of this phenomenon that encodes one of the most rapidly evolving human–ape gene families, nuclear pore interacting protein ( NPIP ). Results Comparative analysis shows that LCR16a has independently expanded in five primate lineages over the last 35 million years of primate evolution. The expansions are associated with independent lineage-specific segmental duplications flanking LCR16a leading to the emergence of large interspersed duplication blocks at non-orthologous chromosomal locations in each primate lineage. The intron-exon structure of the NPIP gene family has changed dramatically throughout primate evolution with different branches showing characteristic gene models yet maintaining an open reading frame. In the African ape lineage, we detect signatures of positive selection that occurred after a transition to more ubiquitous expression among great ape tissues when compared to Old World and New World monkeys. Mouse transgenic experiments from baboon and human genomic loci confirm these expression differences and suggest that the broader ape expression pattern arose due to mutational changes that emerged in cis. Conclusions LCR16a promotes serial interspersed duplications and creates hotspots of genomic instability that appear to be an ancient property of primate genomes. Dramatic changes to NPIP gene structure and altered tissue expression preceded major bouts of positive selection in the African ape lineage, suggestive of a gene undergoing strong adaptive evolution.

Inflammatory bowel disease (IBD), clinically defined as Crohn’s disease (CD), ulcerative colitis (UC), or IBD-unclassified, results in chronic inflammation of the gastrointestinal tract in genetically susceptible hosts. Pediatric onset IBD represents ≥ 25% of all IBD diagnoses and often presents with intestinal stricturing, perianal disease, and failed response to conventional treatments. NOD2 was the first and is the most replicated locus associated with adult IBD, to date. However, its role in pediatric onset IBD is not well understood. We performed whole-exome sequencing on a cohort of 1,183 patients with pediatric onset IBD (ages 0–18.5 years). We identified 92 probands with biallelic rare and low frequency NOD2 variants accounting for approximately 8% of our cohort, suggesting a Mendelian inheritance pattern of disease. Additionally, we investigated the contribution of recessive inheritance of NOD2 alleles in adult IBD patients from a large clinical population cohort. We found that recessive inheritance of NOD2 variants explains ~ 7% of cases in this adult IBD cohort, including ~ 10% of CD cases, confirming the observations from our pediatric IBD cohort. Exploration of EHR data showed that several of these adult IBD patients obtained their initial IBD diagnosis before 18 years of age, consistent with early onset disease. While it has been previously reported that carriers of more than one NOD2 risk alleles have increased susceptibility to Crohn’s Disease (CD), our data formally demonstrate that recessive inheritance of NOD2 alleles is a mechanistic driver of early onset IBD, specifically CD, likely due to loss of NOD2 protein function. Collectively, our findings show that recessive inheritance of rare and low frequency deleterious NOD2 variants account for 7–10% of CD cases and implicate NOD2 as a Mendelian disease gene for early onset Crohn’s Disease.