Biology subjects

Grossman, J.

Publications and source records attributed to Grossman, J..

8 recordsLinked to original sources

bioRxiv2026

Managing soil sustainably on small-scale vegetable farms: Lessons learned from high tunnel and open field vegetable production

Small-scale vegetable farms are increasingly important to local food systems, but the soils on these farms are not well understood, particularly in high tunnel production environments. Therefore, this study aimed to 1. Compare soil nutrients and soil health metrics in high tunnels and nearby open fields. 2. Document soil nutrient accumulation on diversified vegetable farms and assess loss potential. 3. Explore the impacts of specific management practices (input use, cover crops, tillage, and soil testing) and farm demographics on a variety of soil health and soil nutrient metrics. Just under half of the high tunnels in this study had soluble salt accumulation, which was associated with higher soil nitrate concentrations. The pH of many high tunnel soils was above the optimal range for crop production, which was correlated with irrigation water alkalinity. Some high tunnel soils had rapid water infiltration rates, with implications for irrigation water management. Both high tunnel and open field soil were rich in nutrients compared with other Minnesota farms. Preliminary assessments suggested risks to surface and groundwater from nutrient runoff and leaching. While farmer experience and more years in vegetable production were negatively associated with soil health metrics, management practices including reduced tillage, organic management, and application of plant-based compost were positively associated with soil health. Cation exchange capacity and permanganate oxidizable carbon did not provide significantly more insight than simply measuring organic matter. Arbuscular mycorrhizal fungal spore counts were inconclusive, but aggregate stability and bulk density were responsive to farmer reported soil management activities. Core ideasO_LIHigh tunnel soil tends to be rich in nutrients and organic matter. They also accumulate soluble salts, likely from excess inputs C_LIO_LIIrrigation water routinely tested high in pH and alkalinity. These factors may explain high soil pH in high tunnels. C_LIO_LISmall-scale vegetable farms often have high concentrations of soil nutrients in both high tunnels and open fields, with potential to cause environmental contamination through leaching and runoff C_LIO_LIVegetable production may be inherently hard on soil health, but conservation practices including reduced tillage, organic management, and use of plant-based composts can improve soil health in these production systems C_LI

ecology↗

bioRxiv2025

Deep profiling of lupus nephritis kidneys reveals dynamic changes in myeloid cells associated with disease progression

ObjectivesLupus nephritis (LN) is a common, potentially fatal manifestation of systemic lupus erythematosus. We aim to gain new insights into the immune responses underlying LN and their relation to the histologic heterogeneity observed in this disease, focusing on myeloid cells. MethodsSingle-cell RNA-sequencing (scRNA-seq) was used to profile dissociated kidney samples from 156 LN patients and 30 healthy individuals. Spatial transcriptomics (ST), utilizing a gene panel designed to capture all myeloid subsets identified in the scRNA-seq data, was applied to kidney samples acquired from 6 LN patients and 2 healthy controls. ResultsWe generated a full catalog of the myeloid subsets found in LN kidneys. Our analyses indicated that an increase in irreversible tissue damage, as measured by the NIH chronicity index (CI), is associated with a gradual switch of the local immune response from one dominated by monocytes and macrophages to one featuring expanded CD4+ T, GZMK+CD8+ T, B and dendritic cells, with a parallel decrease in the interferon response. In proliferative/mixed LN only, the degree of active inflammation correlates with expansion of disease-specific macrophage (DMac) subsets, which later contract as the CI increases. Trajectory analysis of the scRNA-seq data suggested that DMacs arise from both infiltrating monocytes and tissue-resident macrophages; this was supported by the ST data, as well as cell cultures. DMacs are indicated to interact with parietal epithelial cells, promoting the development of glomerulosclerosis. ConclusionsWe suggest a detailed picture of the changes in the kidney immune mechanisms in LN as this disease progresses.

immunology↗

bioRxiv2025

A population-scale atlas of blood and tissue in lupus nephritis

One Sentence SummaryA single-cell atlas of paired blood and tissue samples from Lupus Nephritis patients and healthy controls identified stromal and immune populations within renal tissue, including the scar-associated macrophage populations, which correlate with and may drive renal disease activity. Lupus nephritis (LN), a severe manifestation of Systemic Lupus Erythematosus (SLE), is a heterogeneous disease driven by diverse immune and tissue cell types. We obtained 538K single-cell and 140K single-nuclear profiles from kidney biopsies of 155 LN patients and 30 pre-implantation transplant biopsy controls, along with 325K single-cell blood profiles overlapping many of these patients. We identified key tissue cell types and cell states, and immune cell states; we were able to determine cell states that were tissue specific, and those that were present in the blood. We observed that LN pathological features are significantly associated with cell states using differential gene expression and Covarying Neighborhood Analysis (CNA). These analyses revealed broad changes in cell states associated with irreversible chronic tissue damage. After controlling for the effects of ongoing tissue damage, we observed that expansion of key glomerular and Scar Associated Macrophages (SAMs) populations tracked with increasing inflammatory disease activity. SAMs appear to drive LN fibrosis and, in active disease, infiltrate the glomeruli more than other myeloid cells. These observations strongly support that therapeutic targeting of myeloid populations may offer an as-of-yet unproven strategy to prevent renal inflammation and ongoing kidney damage in LN.

molecular biology↗

bioRxiv2024

Temperature and host plant ecotype drive nitrogen fixation, but not nodule community composition, in hairy

Hairy vetch (Vicia villosa Roth) is a commonly grown cover crop throughout the U.S., which can contribute nitrogen for subsequent cash crops through biological nitrogen fixation (BNF) in association with Rhizobium leguminosarum biovar viciae (Rlv) bacteria. Hairy vetch is one of the few cover crops sufficiently cold-tolerant to over-winter in the Upper Midwestern U.S. However, nitrogen contributions by hairy vetch vary across locations, potentially due to cold impacts on the legume/rhizobia symbiosis. The traditional route to improve BNF in legumes involves selecting superior rhizobia strains to create more effective inoculants to apply at planting, but inoculants often fail to compete and survive in agricultural soils. Instead, this study tested the effects of temperature and host plant ecotype on hairy vetch BNF and Rlv community composition in nodules, with the goal of potentially identifying vetch ecotypes able to select beneficial Rlv strains from the soil community. Four hairy vetch ecotypes trapped Rlv from three Minnesota soils, at warm or cold temperatures. Vetch ecotype was a key driver of BNF and nodule formation under warm and cold conditions. However, temperature and plant ecotype did not drive Rlv community composition in nodules, and Rlv community composition did not affect plant productivity. Taken together, these results suggest that the best strategy to improve BNF at low temperatures in hairy vetch likely depends on breeding for improved biomass accumulation and nitrogen fixation in host plants, rather than focusing on host plant selection of beneficial rhizobia.

plant biology↗

bioRxiv2024

Forest and Biodiversity 2: a tree diversity experiment to understand the consequences of multiple dimensions of diversity and composition for long-term ecosystem function and resilience

O_LIWe introduce a new "low-density" tree diversity experiment at the Cedar Creek Ecosystem Science Reserve in central Minnesota, USA aimed at testing long-term ecosystem consequences of tree diversity and composition. The experiment was designed to provide guidance on forest restoration efforts that will simultaneously advance carbon sequestration goals and contribute to biodiversity conservation and sustainability. C_LIO_LIThe new Forest and Biodiversity (FAB2) experiment uses native tree species in varying levels of species richness, phylogenetic diversity, and functional diversity to test the mechanisms and processes that contribute to forest stability and ecosystem productivity in the face of global change. FAB2 was designed and established in conjunction with a prior experiment (FAB1) in which the same set of twelve species was planted in 16 m2 plots at high density (0.5 m spacing). In addition to lower density plantings (1 m spacing), FAB2 also has larger plots (100 m2 and 400 m2) appropriate for testing long-term ecosystem consequences of species composition and diversity. C_LIO_LIWithin the first six years, mortality in the 400 m2 monoculture plots was significantly higher than in the 100 m2 plots. The highest mortality among any treatments occurred in Tilia americana and Acer negundo monocultures, but mortality for both species decreased with increasing plot diversity. These results highlight the importance of forest diversity in reducing mortality in some species and point to potential mechanisms, including light and drought stress, that cause tree mortality in vulnerable monocultures. The experiment highlights challenges to maintaining monoculture and low-diversity treatments in tree mixture experiments of large extent. C_LIO_LIThe FAB2 experiment provides a long-term platform for discerning the importance of species and lineage effects and of multiple dimensions of diversity in restoring ecosystem functions and services provided by forests. It also provides a platform for improving remote sensing approaches, including Uncrewed Aerial Vehicles (UAVs) equipped with LiDAR, multispectral, and hyperspectral sensors, to complement ground-based monitoring of forest function and diversity. We aim for the experiment to contribute to international efforts to monitor and manage forests in the face of global change. C_LI

ecology↗

bioRxiv2024

Blood immunophenotyping identifies distinct kidney histopathology and outcomes in patients with lupus nephritis

Lupus nephritis (LN) is a frequent manifestation of systemic lupus erythematosus, and fewer than half of patients achieve complete renal response with standard immunosuppressants. Identifying non-invasive, blood-based pathologic immune alterations associated with renal injury could aid therapeutic decisions. Here, we used mass cytometry immunophenotyping of peripheral blood mononuclear cells in 145 patients with biopsy-proven LN and 40 healthy controls to evaluate the heterogeneity of immune activation in patients with LN and to identify correlates of renal parameters and treatment response. Unbiased analysis identified 3 immunologically distinct groups of patients with LN that were associated with different patterns of histopathology, renal cell infiltrates, urine proteomic profiles, and treatment response at one year. Patients with enriched circulating granzyme B+ T cells at baseline showed more severe disease and increased numbers of activated CD8 T cells in the kidney, yet they had the highest likelihood of treatment response. A second group characterized primarily by a high type I interferon signature had a lower likelihood of response to therapy, while a third group appeared immunologically inactive by immunophenotyping at enrollment but with chronic renal injuries. Main immune profiles could be distilled down to 5 simple cytometric parameters that recapitulate several of the associations, highlighting the potential for blood immune profiling to translate to clinically useful non-invasive metrics to assess immune-mediated disease in LN.

immunology↗

bioRxiv2020

Clonal expansion of personalized anti-tumor T cells from circulation using tumor organoid-immune co-cultures

Tumor-specific cytotoxic T cells are effective tools for cancer immunotherapy, but the ability to generate them continues to be a challenge. Furthermore, there are no compelling approaches to empirically identify tumor-targeting T cells and T cell receptors by exploiting the multitude of antigens on tumor cell surfaces. Here, we use patients peripheral blood and autologous tumor organoids to enrich tumor-specific cytotoxic T cells with patient-specific killing mechanisms and a tissue-resident memory phenotype. We further demonstrate that these organoid-primed T (opT) cells undergo several orders of magnitude of clonal expansion and express T cells receptors and check-point proteins unique to each patient. Importantly, transferring the TCRs to heterologous T cells was sufficient to confer tumor recognition in a patient-specific manner. Thus, we report a patient-specific and antigen-agnostic platform for expansion of tumor-targeting T cells and identification of cancer-targeting TCRs from the peripheral blood of pancreatic cancer patients that can be exploited for immunotherapy applications.

cancer biology↗

bioRxiv2019

Pancreatic tumor organoids for modeling in vivo drug response and discovering clinically-actionable biomarkers

Patient-derived models are transforming translational cancer research. It is not clear if the emergence of patient-derived organoid (PDO) models can extend the utility of the widely used patient-derived xenograft (PDX). In addition, the utility of PDO models for serum biomarker discovery is not known. Here, we demonstrate that PDO models recapitulate the genomics, cell biology, glycomics and drug responses observed in PDX models. Furthermore, we demonstrate the applicability of PDO models for identification of N-glycans that are enriched in the glycome of pancreatic ductal adenocarcinoma (PDAC). Surprisingly, among all the glycans observed in PDX and PDOs, a core set of 57 N-glycans represent 50-94% of the relative abundance of all N-glycans detected, suggesting that only a subset of glycans dominate the cell surface landscape in PDAC. In addition, we outline a tumor organoid-based pipeline to identify surface proteins in extracellular vesicles (EV) from media supernatant of PDO cultures. When combined with the affinity-based validation platform, the EV surface proteins discovered in PDOs are effective in differentiating patients with PDAC from those with benign pancreatitis in the clinic, identifying PDO as powerful discovery platform for serum biomarkers. Thus, PDOs extend the utility of the archival collections of PDX models for translational research and function as a powerful platform for identification of clinically-actionable biomarkers in patients blood. Significance statementTumor organoids extend the utility of PDX models as platforms for investigating drug response, glycosylation changes and function as new platforms for discovering blood-based biomarkers

cancer biology↗