Biology subjects

Schuster, R.

Publications and source records attributed to Schuster, R..

17 recordsLinked to original sources

bioRxiv2026

Optimal Conservation Prioritization for Waterfowl and Other Birds in Eastern Canada

Conserving and restoring high-quality habitat is widely recognized as one of the most effective means of supporting migratory and wetland bird populations. To advance this objective at a regional scale, the Eastern Habitat Joint Venture (EHJV) coordinates conservation planning for 22 focal bird species across the eastern provinces of Canada. Optimization approaches to support conservation planning are increasingly common, and can be especially valuable in large areas where resources are limited. We present an optimized geospatial prioritization scheme designed to identify regions of primary importance to species coverage objectives within the EHJV. We apply linear programming methods to species abundance data products to maximize population coverage using an adaptable variable-target approach, whose outputs generalize readily to delivery projects of any budget or coverage goal. Our base results highlight areas of high conservation value for priority waterfowl and non-waterfowl species, and we present additional examples of how region-wide solutions can be subdivided based on jurisdictional boundaries, land ownership, or existing protected status. We also address methodological decision points, with attention to how available species abundance data sources were evaluated and what considerations were involved in formulating the optimization computations. We emphasize possibilities for future work to incorporate additional conservation values, such as carbon storage and flood mitigation, and costs, such as land value, and feasibility.

ecology↗

bioRxiv2025

Bigh3 is essential for pulmonary fibrosis

Transforming growth factor beta (TGF-{beta})-induced gene-human, clone 3 (BIGH3) has been implicated as a biomarker of lung fibrosis. However, it is unknown if BIGH3 plays a functional role in fibrosis pathogenesis. To address this question, we used in silico, in vitro and in vivo approaches. We found that BIGH3/Bigh3 is upregulated in human lung fibrosis and mouse models of pulmonary fibrosis. We next generated a novel Bigh3 knockout (Bigh3-/-) mouse and found that while these animals exhibited lung architecture and immune cellularity that is broadly equivalent to wild-type mice, they were protected from lung fibrosis in response to bleomycin administration. In silico modeling suggested that BIGH3 can bind to integrin alpha v (ITGAV). In vitro co-culture systems revealed that activated human lung fibroblasts can elicit BIGH3 expression from human monocyte-derived macrophages. Last, macrophages elicited collagen expression from lung fibroblasts in a manner that is Bigh3-dependent. Collectively, these data suggest that Bigh3 is a product of fibroblast-macrophage interactions that is essential for the pathogenesis of lung fibrosis, possibly via interactions with ITGAV.

immunology↗

bioRxiv2024

Molecular and Pathological Characterization of Cervicovaginal Specimens Evince Significant Protection Against HPV Infections, Bacterial Vaginosis, and Epithelial Cell Abnormalities by Lactobacillus species

BackgroundBacterial vaginosis (BV) results in dysbiosis in the vaginal microbiome and facilitates secondary human papilloma virus (HPV) infections, which can cause cervical abnormalities. The effects of Lactobacilli on BV-HPV infections and cervicovaginal pathology were investigated. MethodElectronic molecular and cytology laboratory results, and demographic records of 19,105 females screened for BV, HPV, and cervical cancer between August 2021 and April 2023 were collected. After data cleaning and reorganization, 15, 607 sample results were used. The data was subjected to epidemiological, statistical, and machine learning analyses to identify patterns, correlations, associations, and interactive effects of age, State, Lactobacilli, BV-associated pathogens, high-risk HPV (hrHPV) genotypes, BV, and cervical cytology. ResultsThe final dataset comprised of data from anonymized females (n = 15541, 99.57%), males (n = 13, 0.08%) and unknown gender (n = 53, 0.34%) between 14 and 95 years from 32 States and Washington D.C. Most samples were BV positive (n = 8282, 53.07%) and/or NILM (n = 11749) followed by 14.29% ASCUS (n = 2231), 7.14% LSIL (n = 1115), 1.04% RCC (n = 163), 0.53% HSIL (n = 82), 0.39% ASC-H (n = 61), and 0.16% AGC (n = 25). HPV-positive samples had higher BV pathogens and BV-positive diagnosis (between 51.90% and 68.60%) than BV-negative diagnosis. Lactobacillus gasseri (79.75%), Lactobacillus jensenii (82.68%), Lactobacillus crispatus (90.91%) were mostly found in BV-negative and NILM specimens. BV and ECA outcomes were significantly associated with age and State. Statistical, correlation, and machine learning models predictively confirmed these findings. ConclusionL. crispatus, followed by L. gasseri and L. jensenii, significantly maintains a healthy cervicovaginal microbiome by inhibiting harmful bacterial pathogens and high-risk HPV subtypes; L. iners have an opposing or neutral effect. Lay summary/importance/highlightsBacterial vaginosis (BV) and human papillomavirus (HPV) infections mostly occur in sexually active and reproductive-age women, adversely affecting their quality of life and predisposing them to sequelae of reproductive disorders. In this study, the protective effects of Lactobacilli against BV and HPV infections to maintain a healthy cervicovaginal microbiome were investigated. Lactobacillus crispatus, L. gasseri, and L. jensenii were common in clinical specimens that had no or relatively lower concentrations of hrHPV, BV, and cervico-vaginal cell abnormalities and vice versa. This shows how important these Lactobacilli are in maintaining a healthy cervix and vagina. Age and BV were found to be strongly associated with the incidence of HPV infections and epithelial cell abnormalities (ECAs). Some States had higher prevalence of BV and ECAs than others. Co-infection with multiple hrHPV and/or hrHPV-BV pathogens segued into negative health effects; some interactions were beneficial for the microbiome, albeit those were few. This makes multiple HPV genotype infections dangerous.

pathology↗

bioRxiv2024

Soil microbes prefer organic acids over sugars in simulated root exudation

Sugars and organic acids, primary components in plant root exudates, are thought to enhance microbial decomposition of organic matter in the rhizosphere. However, their specific impacts on microbial activity and nutrient mobilisation remain poorly understood. Here, we simulated passive root exudation to investigate the distinct effects of sugars and organic acids on microbial metabolism in the rhizosphere. We released 13C- labelled sugars and/or organic acids via reverse microdialysis into intact meadow and forest soils over 6-hours. We measured substrate-induced microbial respiration, soil organic matter mineralization, metabolite concentrations, and substrate incorporation into lipid-derived fatty acids. Our results reveal a pronounced microbial preference for organic acids over sugars, with organic acids being removed faster from the exudation spot and preferentially respired by microbes. Unlike sugars, organic acids increased concentrations of microbial metabolic byproducts and cations (K, Ca, Mg) near the exudation spot. Our results challenge the prevailing assumption that sugars are the most readily available and rapidly consumed substrates for soil microbes. Microbial preference for organic acids indicates a trade-off between rapid biomass growth and ATP yield. Our findings underscore the significant role of exudate composition in influencing microbial dynamics and nutrient availability, and emphasize the importance of biotic and abiotic feedback mechanisms in the rhizosphere in regulating root exudation.

microbiology↗

bioRxiv2024

An operational framework to map Essential Life Support Areas (ELSAs) for biodiversity, climate, and sustainable development

Almost all countries are making increasingly bold commitments to halt and reverse biodiversity loss, minimise the impacts of climate change, and transition to more sustainable development. The effective achievement of many of these commitments relies on integrated spatial planning frameworks that are adaptable to national circumstances, priorities and capabilities. This need is formally recognized by Target 1 of the Kunming-Montreal Global Biodiversity Framework (GBF), which specifies that all areas should be under such planning. Here, we describe the development and application of an operational framework for national-level integrated spatial planning: Essential Life Support Areas (ELSAs). This framework facilitates the identification of areas that - if protected, restored, or sustainably managed - can support the achievement of national commitments to biodiversity, climate, and sustainable development. The process of mapping ELSAs relies heavily on leadership by national experts and stakeholders and the integration of spatial data using systematic conservation planning tools. We showcase the ELSA process carried out for Ecuador, where the use of real-time scenario analyses enabled diverse stakeholder groups to collaborate to assess national priorities for nature, climate, and sustainable development, view trade-offs and synergies, and arrive at a spatial plan to guide national action. ELSA presented an actionable approach for Ecuador, and 12 other pilot countries, to create a spatial plan aimed at fulfilling their national and international commitments to nature, including to the GBF.

ecology↗

bioRxiv2024

Adversarial learning enables unbiased organism-wide cross-species alignment of single-cell RNA data

Todays single-cell RNA (scRNA) datasets remain siloed, due to significant challenges associated with their integration at scale. Moreover, most scRNA analysis tools that operate at scale leverage supervised techniques that are insufficient for cell-type identification and discovery. Here, we demonstrate that the alignment of scRNA data using unsupervised models is accurate at an organism-wide scale and between species. To do this, we show adversarial training of a deep-learning model we term batch-adversarial single-cell variational inference (BA-scVI) can be employed to align standardized benchmark datasets comprising dozens of scRNA studies spanning tissues in humans and mice. In the aligned space, we analyze cell types that span tissues in both species and find prevalent complement expressing macrophages and fibroblasts. We provide access to the tools presented via an online interface for atlas exploration and reference-based drag-and-drop alignment of new data.

genetics↗

bioRxiv2024

High-throughput proteome profiling with low variation in a multi-center study using dia-PASEF

High throughput proteomics is gaining increasing traction as it facilitates screening of large sample cohorts required in clinical research and systems biology studies. Recent developments in mass spectrometry-based proteomics resulted in improved hardware and software providing deep proteome coverage, robustness, and scale accessible to a wide range of laboratories. Here, we benchmark dia-PASEF, a data-independent acquisition scheme that integrates trapped ion mobility with high scan speed, with a high-resolution time-of-flight mass analyzer (timsTOF HT) for the deep proteome analysis of a human cell line applying short 5-minute gradients. To show intra-and interlaboratory reproducibility, we performed a multi-laboratory study including 11 sites. We demonstrate that on average 7,072 protein groups and 99,835 peptides were identified in human chronic myelogenous leukemia cells on the timsTOF HT with low variation. Our results underline that dia-PASEF data acquisition combined with reproducible chromatography enables high robustness and data consistency across instruments and laboratories, which is a prerequisite for translational biomedical insights.

systems biology↗

bioRxiv2023

Unveiling the benefits and gaps of wild pollinators on nutrition and income

Insect pollinators play a crucial role in global crop production, enhancing fruit and seed yield, improving fruit quality, and increasing crop nutritional value. However, wild pollinator populations worldwide have been experiencing alarming declines. This study investigates the contribution of wild pollinators to nutrition and farmers income in Canada, while examining the spatial distribution of these services. Using publicly available data on crop types, yields, nutrient content, and farm gate values, alongside information on natural habitats, we estimated the benefits of wild pollinators across national agricultural landscapes. Our findings reveal that these pollinators sustain approximately 24.4 million equivalent people each year in terms of nutrition and generate an annual income of nearly CAD$2.8 billion for farmers. However, significant benefit gaps exist due to the lack of nearby pollinator habitats and insufficient pollination of dependent crops on a national scale. Addressing these gaps could provide an additional nutrition supply for nearly 30 million equivalent people and increase farmer income by CAD$3 billion. We discuss how and where efforts focused on preserving and enhancing wild pollinator habitats, promoting sustainable farming practices, and raising awareness among stakeholders are crucial for the long-term viability of wild pollinator populations and the sustainability of agricultural systems. This research underscores the urgent need for a national strategy aimed at safeguarding wild pollinators. Implementing such a strategy would not only contribute to strengthening local economies in the regions highlighted in our work but also ensure the production of nutritionally essential food.

ecology↗

bioRxiv2022

Protected area planning to conserve biodiversity in an uncertain future

Protected areas are a key instrument for conservation. Despite this, they are vulnerable to risks associated with weak governance, land use intensification, and climate change. Using a novel hierarchical optimization approach, we identified priority areas for expanding the global protected area system to explicitly account for such risks whilst maximizing protection of all known terrestrial vertebrate species. We illustrate how reducing exposure to these risks requires expanding the area of the global protected area system by 1.6% while still meeting conservation targets. Incorporating risks from weak governance drove the greatest changes in spatial priorities for protection, while incorporating risks from climate change required the largest increase in global protected area. Conserving wide-ranging species required countries with relatively strong governance to protect more land when bordering nations with comparatively weak governance. Our results underscore the need for cross-jurisdictional coordination and demonstrate how risk can be efficiently incorporated into conservation planning. Article Impact StatementAccounting for governance, land use and climate risks will result in more resilient and effective conservation effort for biodiversity.

ecology↗

bioRxiv2021

Canada's human footprint reveals large intact areas juxtaposed against areas under immense anthropogenic pressure

Efforts are underway in Canada to set aside terrestrial lands for conservation, thereby protecting them from anthropogenic pressures. Here we produce the first Canadian human footprint map to identify intact and modified lands and ecosystems. Our results showed strong spatial variation in pressures across the country, with just 18% of Canada experiencing measurable human pressure. However, some ecosystems are experiencing very high pressure, such as the Great Lakes Plains and Prairies national ecological areas which have over 75% and 56% of their areas, respectively, with a high human footprint. In contrast, the Arctic and Northern Mountains have less than 0.02% and 0.2% under high human footprint. A validation of the final map resulted in a Cohen Kappa statistic of 0.911, signifying an almost perfect agreement between the human footprint and the validation data set. By increasing the number and accuracy of mapped pressures, our map demonstrates much more widespread pressures in Canada than were indicated by previous global mapping efforts, demonstrating the value in specific national data applications. Ecological areas with immense anthropogenic pressure, highlight challenges that may arise when planning for ecologically representative protected areas.

ecology↗

bioRxiv2020

Global critical natural assets

Sustaining the organisms, ecosystems, and processes that underpin human well-being is necessary to achieve sustainable development. Here we identify critical natural assets, natural and semi-natural ecosystems that provide 90% of the total current magnitude of 14 types of natures contributions to people (NCP). Critical natural assets for maintaining local-scale NCP (12 of the 14 NCP mapped) comprise 30% of total global land area and 24% of national territorial waters, while 44% of land area is required for maintaining all NCP (including those that accrue at the global scale, carbon storage and moisture recycling). At least 87% of the worlds population lives in the areas benefiting from critical natural assets for local-scale NCP, while only 16% lives on the lands containing these assets. Critical natural assets also overlap substantially with areas important for biodiversity (covering area requirements for 73% of birds and 66% of mammals) and cultural diversity (representing 96% of global Indigenous and non-migrant languages). Many of the NCP mapped here are left out of international agreements focused on conserving species or mitigating climate change, yet this analysis shows that explicitly prioritizing critical natural assets for NCP could simultaneously advance development, climate, and conservation goals. Crafting policy and investment strategies that protect critical natural assets is essential for sustaining human well-being and securing Earths life support systems.

ecology↗

bioRxiv2020

An improved comprehensive strategy for deep and quantitative N-glycomics based on optimization of sample preparation, isotope-based data quality control and quantification, new N-glycan libraries and new algorithms

Withdrawal statement"The authors have withdrawn their manuscript because the authors need to re-organize the data and writing, meanwhile more experimental evidence from human cellular N-glycome will be added to support their viewpoints. In this preprint, only one human cell line, Acute Promyelocytic Leukemia (APL) cells, was deeply investigated to show the N-glycome landscape. To provide the shared features of human N-glycome, more human cells should be investigated. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author."

biochemistry↗

bioRxiv2020

Only 40% of the world's forests are in good health

Many global environmental agendas, including halting biodiversity loss, reversing land degradation, and limiting climate change, depend upon retaining forests with high ecological integrity, yet the scale and degree of forest modification remains poorly quantified and mapped. By integrating data on observed and inferred human pressures and an index of lost connectivity, we generate the first globally-consistent, continuous index of forest condition as determined by degree of anthropogenic modification. Globally, only 17.4 million km2 of forest (40.5%) have high landscape level integrity (mostly found in Canada, Russia, the Amazon, Central Africa and New Guinea) and only 27% of this area is found in nationally-designated protected areas. Of the forest in protected areas, only 56% has high landscape level integrity. Ambitious policies that prioritize the retention of forest integrity, especially in the most intact areas, are now urgently needed alongside current efforts aimed at halting deforestation and restoring the integrity of forests globally.

ecology↗

bioRxiv2019

Integer linear programming outperforms simulated annealing for solving conservation planning problems

The resources available for conserving biodiversity are limited, and so protected areas need to be established in places that will achieve objectives for minimal cost. Two of the main algorithms for solving systematic conservation planning problems are Simulated Annealing (SA) and Integer linear programming (ILP). Using a case study in British Columbia, Canada, we compare the cost-effectiveness and processing times of SA versus ILP using both commercial and open-source algorithms. Plans for expanding protected area systems based on ILP algorithms were 12 to 30% cheaper than plans using SA. The best ILP solver we examined was on average 1071 times faster than the SA algorithm tested. The performance advantages of ILP solvers were also observed when we aimed for spatially compact solutions by including a boundary penalty. One practical advantage of using ILP over SA is that the analysis does not require calibration, saving even more time. Given the performance of ILP solvers, they can be used to generate conservation plans in real-time during stakeholder meetings and can facilitate rapid sensitivity analysis, and contribute to a more transparent, inclusive, and defensible decision-making process.

ecology↗

bioRxiv2018

Prioritize diversity or declining species? Trade-offs and synergies in spatial planning for the conservation of migratory birds

Stemming biodiversity loss requires strategic conservation guided by well-articulated and achievable targets, whether they be proactive (e.g., protect diverse places) or reactive (e.g., protect threatened species). Both types of targets can be effective, but there are trade-offs, especially for broadly-distributed ecosystems or taxa, such as migratory species, a group for which conservation has been challenged by limited knowledge of distributions throughout the annual cycle. We combined novel spatiotemporal distribution models with population trend data to first examine focal areas for the conservation of Neotropical migratory birds (n=112 species) during the non-breeding period in the Western Hemisphere based on a proactive approach (highest diversity) versus a reactive approach (strongest declines) to conservation. For the focal areas, we then assessed the extent of recent anthropogenic impact, protected area status and projected future changes in land cover using three shared socioeconomic pathways (Sustainability=SSP1, Business-as-usual=SSP2, Regional nationalism=SSP3). Spatial priorities were strikingly different when targeting areas of high species diversity, emphasizing southern Mexico and northern Central America, versus areas with more severe declines across species, emphasizing the Andean cordilleras of South America. Only a fraction of the non-breeding region (1.4%) met targets for diversity and decline, mostly in southern Central America. Current levels of protection were similar for the two targets. Areas prioritized to conserve high species diversity have experienced less recent anthropogenic impact than areas prioritized for decline but are predicted to experience more rapid land conversion to less suitable open, agricultural landscapes in the next three decades under both an SSP1 and SSP2 scenario. Only the SSP3 scenario projected similar conversion rates for the two targets. Our findings indicate how even within taxa, efficient conservation efforts will depend on the careful consideration of desired targets combined with reliable predictions about the locations and types of land cover change under alternative socioeconomic futures.

ecology↗

bioRxiv2018

Biodiversity on Indigenous lands equals that in protected areas

Declines in global biodiversity due to land conversion and habitat loss are driving a \"Sixth Mass Extinction\" and many countries currently fall short of meeting even nominal land protection targets to mitigate this crisis. Here, we quantify the potential contribution of Indigenous lands to biodiversity conservation using case studies of Australia, Brazil and Canada. Indigenous lands in each country are slightly more species rich than existing protected areas and, in Brazil and Canada, support more threatened species than existing protected areas or random sites. These results indicate that Indigenous lands and existing protected areas are similar in biodiversity. Enhanced partnerships between Indigenous communities and federal or state governments could help ameliorate current shortfalls in global biodiversity protection by facilitating protection for native species, helping to stem global biodiversity loss.

ecology↗

bioRxiv2018

Optimizing conservation of migratory species over their full annual cycle in the Western Hemisphere

Limited knowledge of the distribution, abundance, and habitat associations of migratory species introduces uncertainty about the most effective conservation actions. We used Neotropical migratory birds as a model group to evaluate contrasting approaches to land prioritization to support [≥]30% of the global abundances of 117 species throughout the annual cycle in the Western hemisphere. Conservation targets were achieved in 43% less land area in plans based on annual vs. weekly optimizations. Plans agnostic to population structure required comparatively less land area to meet targets, but at the expense of representation. Less land area was also needed to meet conservation targets when human-dominated lands were included rather than excluded from solutions. Our results point to key trade-offs between efforts minimizing the opportunity costs of conservation vs. those ensuring spatiotemporal representation of populations, and demonstrate a novel approach to the conservation of migratory species based on leading-edge abundance models and linear programming to identify portfolios of priority landscapes and inform conservation planners.

ecology↗