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Plants are expected to respond to global environmental change through shifts in functional traits and in their ranges. These shifts could alter productivity and interactions among species or genetic lineages, ultimately leading to changes in distributions and abundance. In particular, cosmopolitan species are predicted to increase growth with decreasing latitude due to differences in climate and temperature. The pattern of changes in growth may vary among genotypes within species, leading to different responses with latitude. To evaluate whether climate can affect geographically distinct genotypes of cosmopolitan invasive species differently, we evaluated the trait responses of two lineages of the common reed, Phragmites australis, to variation in environmental conditions spanning North America’s Atlantic coast. Using three reciprocal transplant common gardens, we tested for the effects of garden location and plant lineage on traits related to biomass production, flowering frequency, leaf morphology, and leaf-level physiology. We found that aboveground biomass, stem density, and flowering frequency responded non-linearly to increasing latitude in one or both lineages. These results suggest that measures of plant traits over narrow latitudinal ranges may not accurately reflect organismal-level responses to global change at broad spatial scales. Given the responses to latitude that we observed in P. australis , we propose that feedbacks between growth and reproductive rate will influence range shifts in these two lineages. Such range shifts could lead to genetic admixtures, subsequently yielding more productive, locally-adapted genotypes.

Background Shotgun proteomics utilizes a database search strategy to compare detected mass spectra to a library of theoretical spectra derived from reference genome information. As such, the robustness of proteomics results is contingent upon the completeness and accuracy of the gene annotation in the reference genome. For animal models of disease where genomic annotation is incomplete, such as non-human primates, proteogenomic methods can improve the detection of proteins by incorporating transcriptional data from RNA-Seq to improve proteomics search databases used for peptide spectral matching. Customized search databases derived from RNA-Seq data are capable of identifying unannotated genetic and splice variants while simultaneously reducing the number of comparisons to only those transcripts actively expressed in the tissue. Results We collected RNA-Seq and proteomic data from 10 vervet monkey liver samples and used the RNA-Seq data to curate sample-specific search databases which were analyzed in the program Morpheus. We compared these results against those from a search database generated from the reference vervet genome. A total of 284 previously unannotated splice junctions were predicted by the RNA-Seq data, 92 of which were confirmed by peptide spectral matches. More than half (53/92) of these unannotated splice variants had orthologs in other non-human primates, suggesting that failure to match these peptides in the reference analyses likely arose from incomplete gene model information. The sample-specific databases also identified 101 unique peptides containing single amino acid substitutions which were missed by the reference database. Because the sample-specific searches were restricted to actively expressed transcripts, the search databases were smaller, more computationally efficient, and identified more peptides at the empirically derived 1 % false discovery rate. Conclusion Proteogenomic approaches are ideally suited to facilitate the discovery and annotation of proteins in less widely studies animal models such as non-human primates. We expect that these approaches will help to improve existing genome annotations of non-human primate species such as vervet.

Recent findings suggest that Hematopoietic Stem Cells (HSC) and progenitors arise simultaneously and independently of each other already in the embryonic aorta-gonad mesonephros region, but it is still unknown how their different features are established. Here, we uncover IκBα ( Nfkbia , the inhibitor of NF-κB) as a critical regulator of HSC proliferation throughout development. IκBα balances retinoic acid signaling levels together with the epigenetic silencer, PRC2, specifically in HSCs. Loss of IκBα decreases proliferation of HSC and induces a dormancy related gene expression signature instead. Also, IκBα deficient HSCs respond with superior activation to in vitro culture and in serial transplantation. At the molecular level, chromatin regions harboring binding motifs for retinoic acid signaling are hypo-methylated for the PRC2 dependent H3K27me3 mark in IκBα deficient HSCs. Overall, we show that the proliferation index in the developing HSCs is regulated by a IκBα-PRC2 axis, which controls retinoic acid signaling. Hematopoietic stem cells are generated during development, though how and when they become dormant long term-HSCs remains unclear. Here they show that retinoic acid receptor levels are regulated by a IκBα-PRC2 axis in HSCs, and that IκBα KO mice have HSCs that are fewer in number, but functionally and molecularly more dormant.

Teleost fishes account for 96% of all fish species and exhibit a spectacular variety of body forms. Teleost lineages range from deep bodied to elongate (e.g., eels, needlefish), laterally compressed (e.g., ribbonfish) to globular (e.g., pufferfish), and include uniquely shaped lineages such as seahorses, flatfishes, and ocean sunfishes. Adaptive body shape convergence within fishes has long been hypothesized but the nature of the relationships between fish form and ecological and environmental variables remain largely unknown at the macroevolutionary scale. To facilitate the investigation of the interacting factors influencing teleost body shape evolution we measured eight functionally relevant linear traits on adult-sized specimens along with specimen mass. Linear measurements of standard length, maximum body depth, maximum fish width, lower jaw length, mouth width, head depth, minimum caudal peduncle depth, and minimum caudal peduncle width were taken in millimeters with calipers, or tape measures for oversized specimens. We measured these traits on a total of 16,523 specimens (1—3 specimens per species) at the Smithsonian National Museum of Natural History and took approximately 7000 person hours of data collection to complete. The data went through a three-step error-checking process to clean and validate the data and then species averages were calculated. We present the complete specimen data set, which encompasses approximately one-fifth of extant teleost species diversity, spanning ~90% of teleost families and ~96% of orders. The species and family names are compatible with the taxonomy used by FishBase and the order information with the phylogenetically informed taxonomy of Betancur-R and colleagues published in 2014. This dataset is licensed under Creative Commons CC0 1.0 Universal (CC0 1.0) but please cite this paper when using the data or a subset of it.

Background Persons involved in the justice system are at high risk for HIV and drug overdose upon release to the community. This manuscript describes a randomized controlled trial of two evidence-based linkage interventions for provision of HIV prevention and treatment and substance use disorder (SUD) services in four high risk communities to assess which is more effective at addressing these needs upon reentry to the community from the justice system. Methods This is a 5-year hybrid type 1 effectiveness-implementation randomized controlled trial that compares two models (Patient Navigation [PN] or Mobile Health Unit [MHU] service delivery) of linking justice-involved individuals to the continuum of community-based HIV and SUD prevention and treatment service cascades of care. A total of 864 justice-involved individuals in four US communities with pre-arrest histories of opioid and/or stimulant use who are living with or at-risk of HIV will be randomized to receive either: (a) PN , wherein patient navigators will link study participants to community-based service providers; or (b) services delivered via an MHU , wherein study participants will be provided integrated HIV prevention/ treatment services and SUD services. The six-month post-release intervention will focus on access to pre-exposure prophylaxis (PrEP) for those without HIV and antiretroviral treatment (ART) for people living with HIV (PLH). Secondary outcomes will examine the continuum of PrEP and HIV care, including: HIV viral load, PrEP/ ART adherence; HIV risk behaviors; HCV testing and linkage to treatment; and sexually transmitted infection incidence and treatment. Additionally, opioid and other substance use disorder diagnoses, prescription, receipt, and retention on medication for opioid use disorder; opioid and stimulant use; and overdose will also be assessed. Primary implementation outcomes include feasibility, acceptability, sustainability, and costs required to implement and sustain the approaches as well as to scale-up in additional communities. Discussion Results from this project will help inform future methods of delivery of prevention, testing, and treatment of HIV, HCV, substance use disorders (particularly for opioids and stimulants), and sexually transmitted infections for justice-involved individuals in the community. Trial registration: Clincialtrials.gov NCT05286879 March 18, 2022.

Climate change is altering the frequency and intensity of extreme weather events. Quantifying ecosystem responses to extreme events at the landscape scale is critical for understanding and responding to climate-driven change but is constrained by limited data availability. Here, we integrated remote sensing with ground-based observations to quantify landscape-scale vegetation damage from an extreme climatic event. We used ground- and satellite-based black mangrove (Avicennia germinans) leaf damage data from the northern Gulf of Mexico (USA and Mexico) to examine the effects of an extreme freeze in a region where black mangroves are expanding their range. The February 2021 event produced coastal temperatures as low as − 10 °C in some areas, exceeding thresholds for A. germinans damage and mortality. We used Sentinel-2 surface reflectance data to assess vegetation greenness before and after the freeze, along with ground-based observations of A. germinans leaf damage. Our results show a negative, nonlinear threshold relationship between A. germinans leaf damage and minimum temperature, with a temperature threshold for leaf damage near − 6 °C. Satellite-based analyses indicate that, at the landscape scale, damage was particularly severe along the central Texas coast, where the freeze event affected > 2000 ha of A. germinans-dominated coastal wetlands. Our analyses highlight the value of pairing remotely sensed data with regional, ground-based observations for quantifying and extrapolating the effects of extreme freeze events on mangroves and other tropical, cold-sensitive plants. The results also demonstrate how extreme freeze events govern the expansion and contraction of mangroves near northern range limits in North America.