Biology subjects

Kothari, S.

Publications and source records attributed to Kothari, S..

10 recordsLinked to original sources

bioRxiv2024

Self-pruning in tree crowns is influenced by functional strategies and neighborhood interactions

As canopy closure causes forest stands to face increasing light limitation, trees lower branches begin to die back. This process, called self-pruning, defines a crowns base and depth and shapes the structure of entire stands. Self-pruning is often thought to occur after shading causes individual branches to transition from net carbon sources to sinks. Under this explanation, we would expect resource-conservative and shade-tolerant species to initiate self-pruning under deeper shade because their branches need less light to maintain a positive carbon balance. However, the notion that branches are fully autonomous may be complicated by correlative inhibition, in which plants preferentially allocate resources towards sunlit branches. Consistent with this idea, we predicted that within species, trees with sunlit tops would initiate self-pruning at a higher light threshold. Lastly, we predicted that plot-level diversity in self-pruning strategies would correlate with productivity and total crown volume. We tested these predictions in an experiment where 12 temperate tree species were planted in plots of varying diversity and composition. We measured characteristics of crown size and position as well as the light level at the crown base (denoted Lbase), which we took as an estimate of the light threshold of self-pruning. As we predicted, more shade-tolerant and resource-conservative species self-pruned at a deeper level of shade (lower Lbase). In addition, most species had higher Lbase when they had more light at the crown top, suggestive of correlative inhibition. With respect to their neighbors traits, though, conservative and acquisitive species showed contrary patterns of plasticity: conservative species had lower Lbase around conservative neighbors, while acquisitive species had lower Lbase around acquisitive neighbors. However, all species declined in crown depth when they grew alongside larger, more acquisitive neighbors. As predicted, plots with a greater interspecific diversity of Lbase had greater basal area and crown volume. Using simulations, we showed that plasticity in crown depth between monocultures and mixtures strengthened the relationship with crown volume, primarily due to competitive release experienced by acquisitive species. By placing shade-induced self-pruning in a comparative context, we clarify how forest function emerges from competition for light between individual trees.

ecology↗

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↗

bioRxiv2023

Rapid estimates of leaf litter chemistry using reflectance spectroscopy

Measuring the chemical traits of leaf litter is important for understanding plants roles in nutrient cycles, including through nutrient resorption and litter decomposition, but conventional leaf trait measurements are often destructive and labor-intensive. Here, we develop and evaluate the performance of partial least-squares regression (PLSR) models that use reflectance spectra of intact or ground leaves to estimate leaf litter traits, including carbon and nitrogen concentration, carbon fractions, and leaf mass per area (LMA). Our analyses included more than 300 samples of senesced foliage from 11 species of temperate trees, including needleleaf and broadleaf species. Across all samples, we could predict each trait with moderate-to-high accuracy from both intact-leaf litter spectra (validation R2 = 0.543-0.941; %RMSE = 7.49-18.5) and ground-leaf litter spectra (validation R2 = 0.491-0.946; %RMSE = 7.00-19.5). Notably intact-leaf spectra yielded better predictions of LMA. Our results support the feasibility of building models to estimate multiple chemical traits from leaf litter of a range of species. In particular, the success of intact-leaf spectral models allows non-destructive trait estimation in a matter of seconds, which could enable researchers to measure the same leaves over time in studies of nutrient resorption.

ecology↗

bioRxiv2023

Impact of Memory T Cells on SARS-COV-2 Vaccine Response in Hematopoietic Stem Cell Transplant

During the COVID-19 pandemic, hematopoietic stem cell transplant (HSCT) recipients faced an elevated mortality rate from SARS-CoV-2 infection, ranging between 10-40%. The SARS-CoV-2 mRNA vaccines are important tools in preventing severe disease, yet their efficacy in the post-transplant setting remains unclear, especially in patients subjected to myeloablative chemotherapy and immunosuppression. We evaluated the humoral and adaptive immune responses to the SARS-CoV-2 mRNA vaccination series in 42 HSCT recipients and 5 healthy controls. Peripheral blood mononuclear nuclear cells and serum were prospectively collected before and after each dose of the SARS-CoV-2 vaccine. Post-vaccination responses were assessed by measuring anti-spike IgG and nucleocapsid titers, and antigen specific T cell activity, before and after vaccination. In order to examine mechanisms behind a lack of response, pre-and post-vaccine samples were selected based on humoral and cellular responses for single-cell RNA sequencing with TCR and BCR sequencing. Our observations revealed that while all participants eventually mounted a humoral response, transplant recipients had defects in memory T cell populations that were associated with an absence of T cell response, some of which could be detected pre-vaccination.

immunology↗

bioRxiv2023

Targeted engagement of β-catenin-Ikaros complexes in refractory B-cell malignancies

In most cell types, nuclear {beta}-catenin functions as prominent oncogenic driver and pairs with TCF7-family factors for transcriptional activation of MYC. Surprisingly, B-lymphoid malignancies not only lacked expression and activating lesions of {beta}-catenin but critically depended on GSK3{beta} for effective {beta}-catenin degradation. Our interactome studies in B-lymphoid tumors revealed that {beta}-catenin formed repressive complexes with lymphoid-specific Ikaros factors at the expense of TCF7. Instead of MYC-activation, {beta}-catenin was essential to enable Ikaros-mediated recruitment of nucleosome remodeling and deacetylation (NuRD) complexes for transcriptional repression of MYC. To leverage this previously unrecognized vulnerability of B-cell-specific repressive {beta}-catenin-Ikaros-complexes in refractory B-cell malignancies, we examined GSK3{beta} small molecule inhibitors to subvert {beta}-catenin degradation. Clinically approved GSK3{beta}-inhibitors that achieved favorable safety prof les at micromolar concentrations in clinical trials for neurological disorders and solid tumors were effective at low nanomolar concentrations in B-cell malignancies, induced massive accumulation of {beta}-catenin, repression of MYC and acute cell death. Preclinical in vivo treatment experiments in patient-derived xenografts validated small molecule GSK3{beta}-inhibitors for targeted engagement of lymphoid-specific {beta}-catenin-Ikaros complexes as a novel strategy to overcome conventional mechanisms of drug-resistance in refractory malignancies. HIGHLIGHTSO_LIUnlike other cell lineages, B-cells express nuclear {beta}-catenin protein at low baseline levels and depend on GSK3{beta} for its degradation. C_LIO_LIIn B-cells, {beta}-catenin forms unique complexes with lymphoid-specific Ikaros factors and is required for Ikaros-mediated tumor suppression and assembly of repressive NuRD complexes. C_LIO_LICRISPR-based knockin mutation of a single Ikaros-binding motif in a lymphoid MYC superenhancer region reversed {beta}-catenin-dependent Myc repression and induction of cell death. C_LIO_LIThe discovery of GSK3{beta}-dependent degradation of {beta}-catenin as unique B-lymphoid vulnerability provides a rationale to repurpose clinically approved GSK3{beta}-inhibitors for the treatment of refractory B-cell malignancies. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/532152v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1b70e4dorg.highwire.dtl.DTLVardef@10bfcc8org.highwire.dtl.DTLVardef@b10eorg.highwire.dtl.DTLVardef@1683a3e_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIAbundant nuclear {beta}-catenin C_LIO_LI{beta}-catenin pairs with TCF7 factors for transcriptional activation of MYC C_LIO_LIB-cells rely on efficient degradation of {beta}-catenin by GSK3{beta} C_LIO_LIB-cell-specific expression of Ikaros factors C_LI Unique vulnerability in B-cell tumors: O_LIGSK3{beta}-inhibitors induce nuclear accumulation of {beta}-catenin. C_LIO_LI{beta}-catenin pairs with B-cell-specific Ikaros factors for transcriptional repression of MYC C_LI

cancer biology↗

bioRxiv2022

Microfluidic immuno-serology assay revealed a limited diversity of protection against COVID-19 in patients with altered immunity

The immune response to SARS-CoV-2 for patients with altered immunity such as hematologic malignancies and autoimmune disease may differ substantially from that in general population. These patients remain at high risk despite wide-spread adoption of vaccination. It is critical to examine the differences at the systems level between the general population and the patients with altered immunity in terms of immunologic and serological responses to COVID-19 infection and vaccination. Here, we developed a novel microfluidic chip for high-plex immuno-serological assay to simultaneously measure up to 50 plasma or serum samples for up to 50 soluble markers including 35 plasma proteins, 11 anti-spike/RBD IgG antibodies spanning all major variants, and controls. Our assay demonstrated the quintuplicate test in a single run with high throughput, low sample volume input, high reproducibility and high accuracy. It was applied to the measurement of 1,012 blood samples including in-depth analysis of sera from 127 patients and 21 healthy donors over multiple time points, either with acute COVID infection or vaccination. The protein association matrix analysis revealed distinct immune mediator protein modules that exhibited a reduced degree of diversity in protein-protein cooperation in patients with hematologic malignancies and patients with autoimmune disorders receiving B cell depletion therapy. Serological analysis identified that COVID infected patients with hematologic malignancies display impaired anti-RBD antibody response despite high level of anti-spike IgG, which could be associated with limited clonotype diversity and functional deficiency in B cells and was further confirmed by single-cell BCR and transcriptome sequencing. These findings underscore the importance to individualize immunization strategy for these high-risk patients and provide an informative tool to monitor their responses at the systems level.

bioengineering↗

bioRxiv2022

Predicting leaf traits across functional groups using reflectance spectroscopy

O_LIPlant ecologists use functional traits to describe how plants respond to and influence their environment. Reflectance spectroscopy can provide rapid, non-destructive estimates of leaf traits, but it remains unclear whether general trait-spectra models can yield accurate estimates across functional groups and ecosystems. C_LIO_LIWe measured leaf spectra and 22 structural and chemical traits for nearly 2000 samples from 104 species. These samples span a large share of known trait variation and represent several functional groups and ecosystems. We used partial least-squares regression (PLSR) to build empirical models for estimating traits from spectra. C_LIO_LIWithin the dataset, our PLSR models predicted traits like leaf mass per area (LMA) and leaf dry matter content (LDMC) with high accuracy (R2>0.85; %RMSE<10). Models for most chemical traits, including pigments, carbon fractions, and major nutrients, showed intermediate accuracy (R2=0.55-0.85; %RMSE=12.7-19.1). Micronutrients such as Cu and Fe showed the poorest accuracy. In validation on external datasets, models for traits like LMA and LDMC performed relatively well, while carbon fractions showed steep declines in accuracy. C_LIO_LIWe provide models that produce fast, reliable estimates of several widely used functional traits from leaf reflectance spectra. Our results reinforce the potential uses of spectroscopy in monitoring plant function around the world. C_LI

ecology↗

bioRxiv2021

Reflectance spectroscopy allows rapid, accurate, and non-destructive estimates of functional traits from pressed leaves

O_LIMore than ever, ecologists seek to employ herbarium collections to estimate plant functional traits from the past and across biomes. However, many trait measurements are destructive, which may preclude their use on valuable specimens. Researchers increasingly use reflectance spectroscopy to estimate traits from fresh or ground leaves, and to delimit or identify taxa. Here, we extend this body of work to non-destructive measurements on pressed, intact leaves, like those in herbarium collections. C_LIO_LIUsing 618 samples from 68 species, we used partial least-squares regression to build models linking pressed-leaf reflectance spectra to a broad suite of traits, including leaf mass per area (LMA), leaf dry matter content (LDMC), equivalent water thickness, carbon fractions, pigments, and twelve elements. We compared these models to those trained on fresh- or ground-leaf spectra of the same samples. C_LIO_LIOur pressed-leaf models were best at estimating LMA (R2 = 0.932; %RMSE = 6.56), C (R2 = 0.855; %RMSE = 9.03), and cellulose (R2 = 0.803; %RMSE = 12.2), followed by water-related traits, certain nutrients (Ca, Mg, N, and P), other carbon fractions, and pigments (all R2 = 0.514-0.790; %RMSE = 12.8-19.6). Remaining elements were predicted poorly (R2 < 0.5, %RMSE > 20). For most chemical traits, pressed-leaf models performed better than fresh-leaf models, but worse than ground-leaf models. Pressed-leaf models were worse than fresh-leaf models for estimating LMA and LDMC, but better than ground-leaf models for LMA. Finally, in a subset of samples, we used partial least-squares discriminant analysis to classify specimens among 10 species with near-perfect accuracy (>97%) from pressed- and ground-leaf spectra, and slightly lower accuracy (>93%) from fresh-leaf spectra. C_LIO_LIThese results show that applying spectroscopy to pressed leaves is a promising way to estimate leaf functional traits and identify species without destructive analysis. Pressed-leaf spectra might combine advantages of fresh and ground leaves: like fresh leaves, they retain some of the spectral expression of leaf structure; but like ground leaves, they circumvent the masking effect of water absorption. Our study has far-reaching implications for capturing the wide range of functional and taxonomic information in the worlds preserved plant collections. C_LI

ecology↗

bioRxiv2020

Spectral niches reveal taxonomic identity and complementarity in plant communities

Reflectance spectra provide integrative measures of plant phenotypes by capturing chemical, morphological, anatomical and architectural trait information. Here we investigate the linkages between plant spectral variation, spectral and resource-use complementarity that contribute to ecosystem productivity. In both a prairie grassland and a forest diversity experiment, we delineated N-dimensional hypervolumes using either wavelength-bands of reflectance spectra or foliar traits. First, we compared the hypervolume fraction unique to each species in either spectral or trait space with increasing dimensionality. Then, we investigated the association between the spectral space occupied by individual plants and their growth, as well as the spectral space occupied by plant communities and ecosystem productivity. We show that species are better distinguished in spectral space than in trait space, providing a conceptual basis for identifying plant taxa spectrally. In addition, the spectral space occupied by individuals increased with plant growth, and the spectral space occupied by plant communities increased with ecosystem productivity. Furthermore, ecosystem productivity was better explained by inter-individual spectral complementarity than by the large spectral space occupied by productive individuals. Our results indicate that spectral hypervolumes of plants can reflect ecological strategies that shape community composition and ecosystem function, and that spectral complementarity can reveal resource-use complementarity.

ecology↗

bioRxiv2019

Throwing shade: Physiological responses to light explain competition and facilitation in a tree diversity experiment

O_LIEcologists often invoke interspecific facilitation to help explain positive biodiversity-ecosystem function relationships in plant communities, but seldom test how it occurs. One mechanism through which one species may facilitate another is by ameliorating abiotic stress. Physiological experiments show that a chronic excess of light can cause stress that depresses carbon assimilation. If shading by a plants neighbors reduces light stress enough, it may facilitate that plants growth. If light is instead most often a limiting factor for photosynthesis, shading may have an adverse, competitive effect. C_LIO_LIIn a temperate tree diversity experiment, we measured stem growth rates and photosynthetic physiology in broadleaf trees across a gradient of light availability imposed by their neighbors. At the extremes, trees experienced nearly full sun (monoculture), or were shaded by nearby fast-growing conifers (shaded biculture). C_LIO_LIMost species had slower growth rates with larger neighbors, implying a net competitive effect. On the other hand, the two most shade-tolerant species (Tilia americana and Acer negundo) and the most shade-intolerant one (Betula papyrifera) had faster stem growth rates with larger neighbors. The two most shade-tolerant species had large increases in photoinhibition (reduced dark-acclimated Fv/Fm) across the gradient of increasing light availability, which suggests they are more vulnerable to chronic light stress. While most species had lower carbon assimilation rates in the shaded biculture treatment, T. americana had rates up to 25% higher. T. americana also dropped its leaves 3-4 weeks earlier in monocultures, curtailing its growing season. We conclude that although large neighbors can cause light limitation in shade-intolerant species, they can also increase growth through abiotic stress amelioration in shade-tolerant species. Finally, in shade-intolerant B. papyrifera, we find a pattern of stem elongation in trees with larger neighbors, which may suggest that a shade avoidance response accounts for the apparent positive trend in stem volume. C_LIO_LISynthesis: Both positive and negative species interactions in our experiment can be explained in large part by the photosynthetic responses of trees to the light environment created by their neighbors. We show that photosynthetic physiology can help explain the species interactions that underlie biodiversity-ecosystem function relationships. The insights that ecologists gain by searching for such physiological mechanisms may help us forecast species interactions under environmental change. C_LI

ecology↗