Seed dispersal increases local species richness and reduces spatial turnover of tropical tree seedlings

Dispersal is thought to be a key process underlying the high spatial diversity of tropical forests. Just how important dispersal is in structuring plant communities is nevertheless an open question because it is very difficult to isolate dispersal from other processes, and thereby measure its effect. Using a unique situation, the loss of vertebrate seed dispersers on the island of Guam and their presence on the neighboring islands of Saipan and Rota, we quantify the contribution of vertebrate seed dispersal to spatial patterns of diversity of tree seedlings in treefall gaps. The presence of vertebrate seed dispersers approximately doubled seedling species richness within canopy gaps and halved species turnover among gaps. Our study demonstrates that dispersal plays a key role in maintaining local and regional patterns of diversity, and highlights the potential for ongoing declines in vertebrate seed dispersers to profoundly alter tropical forest composition

The CSF in neurosarcoidosis contains consistent clonal expansion of CD8 T cells, but not CD4 T cells

The tissue-specific drivers of neurosarcoidosis remain poorly defined. To identify cerebrospinal fluid (CSF) specific, antigen-driven T and B cell responses, we performed single-cell RNA sequencing of CSF and blood cells from neurosarcoid participants coupled to T and B cell receptor sequencing. In contrast to pulmonary sarcoidosis, which is driven by CD4 T cells, we found CD8 T cell clonal expansion enriched in the neurosarcoid CSF. These CSF-enriched CD8 T cells were composed of two subsets with differential expression of EBI2, CXCR3, and CXCR4. Lastly, our data suggest that IFNγ signaling may distinguish neurosarcoidosis from other neurological disorders

Unfamiliar Territory: Emerging Themes for Ecological Drought Research and Management

Novel forms of drought are emerging globally, due to climate change, shifting teleconnection patterns, expanding human water use, and a history of human influence on the environment that increases the probability of transformational ecological impacts. These costly ecological impacts cascade to human communities, and understanding this changing drought landscape is one of today\u27s grand challenges. By using a modified horizon-scanning approach that integrated scientists, managers, and decision-makers, we identified the emerging issues in ecological drought that represent key challenges to timely and effective responses. Here we review the themes that most urgently need attention, including novel drought conditions, the potential for transformational drought impacts, and the need for anticipatory drought management. This horizon scan and review provides a roadmap to facilitate the research and management innovations that will support forward-looking, co-developed approaches to reduce the risk of drought to our socio-ecological systems during the 21st century. We used a modified horizon-scanning approach that brought together scientists, managers, and decision-makers to identify the emerging issues around the ecological impacts from drought that represent key challenges to effective response. We found three broad themes within ecological drought that need attention, including novel drought conditions, transformational drought impacts, and anticipatory drought management. This horizon scan and integrated review provides a roadmap to inspire the needed research and management innovations to reduce the risk of 21st century droughts

1996 Wild Blueberry CSREES Progress Reports/1996 Wild Blueberry Tax Reports

The 1996 edition of the Wild Blueberry CSREES Progress Reports/Wild Blueberry Tax Reports was prepared for the Maine Wild Blueberry Commission and the University of Maine Wild Blueberry Advisory Committee by researchers at the University of Maine, Orono. Projects in this report include: Wild Blueberry CSREES Progress Reports: 1. Factors affecting the quality of Individually Quick Frozen (IQF) wild blueberries 2. Factors affecting the physical and chemical properties of IQF wild blueberries 3. Preventing the bleeding of blueberry fruit in bakery products 4. Amylase test development 5. Determination of pesticide residue levels in freshly harvested and processed wild blueberries 6. Sustainable pollination of wild blueberry 7. Potential for biological control of insect pests of wild blueberry 8. Effect of desiccation on wild blueberry winter survival and cold temperature tolerance 9. Population variation in low-temperature tolerance of wild blueberry 10. Influence of flower delaying sprays on seasonal variation of low temperature tolerance in wild blueberry 11. Effect of various levels of disbudding on yield of wild blueberry 12. Effect of boron and the polyamine putrescine on wild blueberry fruit set and yield 13. Effect of soil pH on nutrient uptake 14. Phosphorus uptake 15. Correcting boron deficiency 16. Hexazinone groundwater survey 17. Effect of time of fall pruning on growth and productivity of wild blueberries 18. Evaluation of Pronone® spot treatments for control of St. Johnswort, dogbane, bracken fern, witch grass/fall panicum and bunchberry 19. Effect of hexazinone formulation on movement through the soil profile 20. Effect of plant source and density on spread of wild blueberry Wild Blueberry Tax Reports: 21. Control of wild blueberry diseases 22. Control of wild blueberry pest insects 23. Biology and action thresholds of secondary blueberry pest insects 24. Phosphorus/nitrogen fertilizer ratio 25. Effect of surfactant and ammonium sulfate on glyphosate activity 26. Blueberry Extension Education Program Bas

Towards a structurally resolved human protein interaction network

Cellular functions are governed by molecular machines that assemble through protein-protein interactions. Their atomic details are critical to studying their molecular mechanisms. However, fewer than 5% of hundreds of thousands of human protein interactions have been structurally characterized. Here we test the potential and limitations of recent progress in deep-learning methods using AlphaFold2 to predict structures for 65,484 human protein interactions. We show that experiments can orthogonally confirm higher-confidence models. We identify 3,137 high-confidence models, of which 1,371 have no homology to a known structure. We identify interface residues harboring disease mutations, suggesting potential mechanisms for pathogenic variants. Groups of interface phosphorylation sites show patterns of co-regulation across conditions, suggestive of coordinated tuning of multiple protein interactions as signaling responses. Finally, we provide examples of how the predicted binary complexes can be used to build larger assemblies helping to expand our understanding of human cell biology

1993-94 Progress Report

The 1993 edition of the Progress Reports was prepared for the Maine Wild Blueberry Commission and the University of Maine Wild Blueberry Advisory Committee by researchers at the University of Maine, Orono. Projects in this report include: 1. Effects of irrigation on lowbush blueberry yield and quality 2. The Economics of investigating irrigation for lowbush blueberries 3. Phosphorus dose/response curve 4. Winter injury protection by potassium 5. Multiple cropping of wild stands 6. Effect of Boron and Calcium on lowbush blueberry fruit set and yield 7. Comparison of N, NP, and NPK fertilizers to correct nitrogen and phosphorus deficiency 8. Determination of pesticide residue levels in freshly harvested and processed lowbush blueberries 9. Effects of calcium salts and citric acid on the quality of canned lowbush blueberries 10. Investigation of preprocess changes (chemical, microbiological, and/or physical) that can lead to the development of a simple and inexpensive method to measure preprocess berry spoilage 11. The effect of fertilization and irrigation in blueberry fruit quality 12. Pollination Ecology of lowbush blueberry in Maine 13. Current importance of insects in lowbush blueberry fields 14. Application of heat as a method of controlling secondary pest insects on lowbush blueberry: a feasibility study 15. Control of blueberry maggot 16. Control of secondary blueberry pest insects 17. Biology and action thresholds of secondary blueberry pest insects 18. Cold-hardiness of native lowbush blueberry 19. Design, fabrication, and testing of an experimental sterilizer for blueberry fields 20. Canned Product Quality--Heat-resistant molds 21. Sanitation for disease control 22. Evaluation of Velpar® impregnated DAP and Pronone® for weed control 23. Evaluation of postemergence applications of tribenuron methyl for bunchberry control 24. Evaluation of postemergence applications of a tank mix of tribenuron methyl and hexazinone for bunchberry control 25. Thresholds of dogbane and bracken fem by mechanical and chemical control in lowbush blueberry fields 26. Effect of time of application of clopyralid for control of vetch and effect on flowering in lowbush blueberries 27. Effect of time of fall pruning on growth and productivity of blueberries and evaluation of infrared burner to prune blueberries 28. Evaluation of infrared burner for selective seedling weed control 29. Evaluation of pressurized rope wick Wick Master wiper for treating weeds growing above lowbush blueberries 30. Blueberry Extension Education Program Base 31. Blueberry ICM program for Hancock County 32. Composting blueberry processing waste 33. Hexazinone ground water survey 34. Investigations of Lowbush Blueberry Fruit bud Cold-hardiness 35. Design, Fabrication, and Testing of an Experimental Sterilizer for Blueberry Field

Vulnerability to climate change of managed stocks in the California Current large marine ecosystem

Introduction: Understanding how abundance, productivity and distribution of individual species may respond to climate change is a critical first step towards anticipating alterations in marine ecosystem structure and function, as well as developing strategies to adapt to the full range of potential changes. Methods: This study applies the NOAA (National Oceanic and Atmospheric Administration) Fisheries Climate Vulnerability Assessment method to 64 federally-managed species in the California Current Large Marine Ecosystem to assess their vulnerability to climate change, where vulnerability is a function of a species’ exposure to environmental change and its biological sensitivity to a set of environmental conditions, which includes components of its resiliency and adaptive capacity to respond to these new conditions. Results: Overall, two-thirds of the species were judged to have Moderate or greater vulnerability to climate change, and only one species was anticipated to have a positive response. Species classified as Highly or Very Highly vulnerable share one or more characteristics including: 1) having complex life histories that utilize a wide range of freshwater and marine habitats; 2) having habitat specialization, particularly for areas that are likely to experience increased hypoxia; 3) having long lifespans and low population growth rates; and/or 4) being of high commercial value combined with impacts from non-climate stressors such as anthropogenic habitat degradation. Species with Low or Moderate vulnerability are either habitat generalists, occupy deep-water habitats or are highly mobile and likely to shift their ranges. Discussion: As climate-related changes intensify, this work provides key information for both scientists and managers as they address the long-term sustainability of fisheries in the region. This information can inform near-term advice for prioritizing species-level data collection and research on climate impacts, help managers to determine when and where a precautionary approach might be warranted, in harvest or other management decisions, and help identify habitats or life history stages that might be especially effective to protect or restore

Quantifying Missing Heritability at Known GWAS Loci

Recent work has shown that much of the missing heritability of complex traits can be resolved by estimates of heritability explained by all genotyped SNPs. However, it is currently unknown how much heritability is missing due to poor tagging or additional causal variants at known GWAS loci. Here, we use variance components to quantify the heritability explained by all SNPs at known GWAS loci in nine diseases from WTCCC1 and WTCCC2. After accounting for expectation, we observed all SNPs at known GWAS loci to explain 1.29 X more heritability than GWAS-associated SNPs on average (P = 3.3 X 10[superscript -5]). For some diseases, this increase was individually significant:2.07 X for Multiple Sclerosis (MS) (P = 6.5 X 10 [superscript -9]) and for Crohn's Disease (CD) (P = 1.3 X 10[superscript -3]); all analyses of autoimmune diseases excluded the well-studied MHC region. Additionally, we found that GWAS loci from other related traits also explained significant heritability. The union of all autoimmune disease loci explained 7.15 X more MS heritability than known MS SNPs (P 20,000 Rheumatoid Arthritis (RA) samples typed on ImmunoChip, with 2.37 X more heritability from all SNPs at GWAS loci (P = 2.3 X 10[superscript -6]) and more heritability from all autoimmune disease loci (P < 1 X 10[superscript -16]) compared to known RA SNPs (including those identified in this cohort). Our methods adjust for LD between SNPs, which can bias standard estimates of heritability from SNPs even if all causal variants are typed. By comparing adjusted estimates, we hypothesize that the genome-wide distribution of causal variants is enriched for low-frequency alleles, but that causal variants at known GWAS loci are skewed towards common alleles. These findings have important ramifications for fine-mapping study design and our understanding of complex disease architecture.National Institutes of Health (U.S.) (Grant R03HG006731)National Institutes of Health (U.S.) (Fellowship F32GM106584

Fumonisins affect the intestinal microbial homeostasis in broiler chickens, predisposing to necrotic enteritis

Fumonisins (FBs) are mycotoxins produced by Fusarium fungi. This study aimed to investigate the effect of these feed contaminants on the intestinal morphology and microbiota composition, and to evaluate whether FBs predispose broilers to necrotic enteritis. One-day-old broiler chicks were divided into a group fed a control diet, and a group fed a FBs contaminated diet (18.6 mg FB1+ FB2/kg feed). A significant increase in the plasma sphinganine/sphingosine ratio in the FBs-treated group (0.21 +/- 0.016) compared to the control (0.14 +/- 0.014) indicated disturbance of the sphingolipid biosynthesis. Furthermore, villus height and crypt depth of the ileum was significantly reduced by FBs. Denaturing gradient gel electrophoresis showed a shift in the microbiota composition in the ileum in the FBs group compared to the control. A reduced presence of low-GC containing operational taxonomic units in ileal digesta of birds exposed to FBs was demonstrated, and identified as a reduced abundance of Candidatus Savagella and Lactobaccilus spp. Quantification of total Clostridium perfringens in these ileal samples, previous to experimental infection, using cpa gene (alpha toxin) quantification by qPCR showed an increase in C. perfringens in chickens fed a FBs contaminated diet compared to control (7.5 +/- 0.30 versus 6.3 +/- 0.24 log10 copies/g intestinal content). After C. perfringens challenge, a higher percentage of birds developed subclinical necrotic enteritis in the group fed a FBs contaminated diet as compared to the control (44.9 +/- 2.22% versus 29.8 +/- 5.46%)

Initial sequencing and analysis of the human genome

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62798/1/409860a0.pd