Biology subjects

Hildebrand, M.

Publications and source records attributed to Hildebrand, M..

8 recordsLinked to original sources

bioRxiv2024

Diversity-enhanced canopy space occupation and leaf functional diversity jointly promote overyielding in tropical tree communities

Understanding the mechanisms that drive biodiversity-productivity relationships is critical for guiding forest restoration. Although complementarity among trees in the canopy space has been suggested as a key mechanism for greater productivity in mixed-species tree communities, empirical evidence remains limited. Here, we used data from a tropical tree diversity experiment to disentangle the effects of tree species richness and community functional characteristics (community-weighted mean and functional diversity of leaf traits) on canopy space filling, and how these effects are related to overyielding. We found that canopy space filling was largely explained by species identity effects rather than tree diversity effects. Communities with a high abundance of species with conservative leaf traits were those with most densely packed canopies. Overall, a higher canopy space filling translated into an enhanced wood productivity, with communities associated with a high taxonomic and functional diversity being the most productive. Importantly, most communities (83%) produced more wood volume than the average of their constituent species in monoculture (i.e. most communities overyielded). Our results show that overyielding increased with leaf functional diversity and positive net biodiversity effects on canopy space filling, which mainly arose due to a high taxonomic diversity. These findings suggest that both taxonomic diversity-enhanced canopy space filling and canopy leaf diversity are important drivers for overyielding in mixed-species forests. Consequently, restoration initiatives should promote stands with functionally diverse canopies by selecting tree species with large interspecific differences in leaf nutrition, as well as leaf and branch morphology to optimize carbon capture in young forest stands.

ecology↗

bioRxiv2022

A proton pump enhancing photosynthesis links phagocytosis to marine phytoplankton symbiogenesis

Diatoms, dinoflagellates, and coccolithophorids are the dominant groups of marine eukaryotic phytoplankton collectively responsible for the majority of primary production in the ocean1. These phytoplankton contain additional intracellular membranes around their chloroplasts derived from ancestral engulfment of red microalgae by unicellular heterotrophic eukaryotes that led to secondary endosymbiosis2. This symbiogenesis hypothesis for the origin of modern secondary endosymbiotic phytoplankton is supported by a wealth of palaeontologic, morphologic, and genomic evidence3-6. However, the selectable evolutionary advantage of these membranes and the physiological significance for extant phytoplankton are unknown. We report that the proton-pumping enzyme V-type H+-ATPase (VHA), ubiquitously used in eukaryotic intercellular digestion, is localized around the chloroplasts of centric diatoms and that VHA-activity significantly enhances photosynthesis over a wide range of oceanic irradiances. Similar results in pennate diatoms, dinoflagellates, and coccolithophorids, but not green or red microalgae, imply a mechanism resulting from the co-option of phagocytic VHA activity into a carbon concentrating mechanism that is common to secondary endosymbiotic phytoplankton. Furthermore, analogous VHA-dependent mechanisms in extant photosymbiotic marine invertebrates7-9 provide functional evidence for an adaptive advantage throughout the transition from endosymbiosis to symbiogenesis. Our results suggest that VHA-dependent enhancement of photosynthesis contributes at least 7% of primary production in the ocean, providing an example of a symbiosis-derived evolutionary innovation with global environmental implications.

evolutionary biology↗

bioRxiv2021

Loss-of-function variants in the cardiac Kv11.1 channel as a genetic biomarker for SUDEP

ObjectiveTo compare the frequency and impact on channel function of KCNH2 variants in SUDEP patients with epilepsy controls comprising patients older than 50 years, a group with low SUDEP risk, and establish loss-of-function KCNH2 variants as predictive biomarkers of SUDEP risk. MethodsWe searched for KCNH2 variants with a minor allele frequency of < 5%. Functional analysis in Xenopus laevis oocytes was performed for all KCNH2 variants identified. ResultsKCNH2 variants were found in 11.1% (10/90) of SUDEP individuals compared to 6.0% (20/332) of epilepsy controls (p = 0.11). Loss-of-function KCNH2 variants, defined as causing > 20% reduction in maximal amplitude, were observed in 8.9% (8/90) SUDEP patients compared to 3.3% (11/332) epilepsy controls suggesting about three-fold enrichment (nominal p = 0.04). KCNH2 variants that did not change channel function occurred at a similar frequency in SUDEP (2.2%; 2/90) and epilepsy control (2.7%; 9/332) cohorts (p > 0.99). Rare KCNH2 variants (< 1% allele frequency) associated with greater loss of function and an [~]11-fold enrichment in the SUDEP cohort (nominal p = 0.03). In silico tools were unable to predict the impact of a variant on function highlighting the need for electrophysiological analysis. ConclusionsThese data show that loss-of-function KCNH2 variants are enriched in SUDEP patients and suggest that cardiac mechanisms contribute to SUDEP risk. We propose that genetic screening in combination with functional analysis can identify loss-of-function KCNH2 variants that could act as biomarkers of an individuals SUDEP risk.

neuroscience↗

bioRxiv2020

A plastid antiporter as a bioindicator of Thalassiosira pseudonana resilience

Acidification of the ocean due to high atmospheric CO2 levels may increase the resilience of diatoms causing dramatic shifts in abiotic and biotic cycles with lasting implications on marine ecosystems. Here, we report a potential bioindicator of a shift in the resilience of a coastal and centric model diatom Thalassiosira pseudonana under elevated CO2. Specifically, we have discovered, through EGFP-tagging, a plastid membrane localized putative Na+(K+)/H+ antiporter that is significantly upregulated at > 800 ppm CO2, with a potentially important role in maintaining pH homeostasis. Notably, transcript abundance of this antiporter gene was relatively low and constant over the diel cycle under contemporary CO2 conditions. In future acidified oceanic conditions, dramatic oscillations of >10-fold change between nighttime (high) and daytime (low) in transcript abundances of the antiporter gene were associated with increased resilience of T. pseudonana. By analyzing metatranscriptomic data from the Tara Oceans project, we demonstrate that phylogenetically diverse diatoms express homologs of this antiporter across the globe. We propose that the differential between night- and daytime transcript levels of the antiporter could serve as a bioindicator of a shift in the resilience of diatoms in response to high CO2 conditions in marine environments.

systems biology↗

bioRxiv2020

Transcriptional alterations in opioid use disorder reveal an interplay between neuroinflammation and synaptic remodeling

BackgroundPrevalence rates of opioid use disorder (OUD) have increased dramatically, accompanied by a surge of overdose deaths. While opioid dependence has been extensively studied in preclinical models, an understanding of the biological alterations that occur in the brains of people who chronically use opioids and who are diagnosed with OUD remains limited. To address this limitation, RNA-sequencing (RNA-seq) was conducted on the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc), regions heavily implicated in OUD, from postmortem brains in subjects with OUD. MethodsWe performed RNA-seq on the DLPFC and NAc from unaffected comparison subjects (n=20) and subjects diagnosed with OUD (n=20). Our transcriptomic analyses identified differentially expressed (DE) transcripts and investigated the transcriptional coherence between brain regions using rank-rank hypergeometric ordering (RRHO). Weighted gene co-expression analyses (WGCNA) also identified OUD-specific modules and gene networks. Integrative analyses between DE transcripts and GWAS datasets using linkage disequilibrium score (LDSC) assessed the genetic liability psychiatric-related phenotypes. ResultsRRHO analyses revealed extensive overlap in transcripts between DLPFC and NAc in OUD, primarily relating to synaptic remodeling and neuroinflammation. Identified transcripts were enriched for factors that control pro-inflammatory cytokine-mediated, chondroitin sulfate, and extracellular matrix signaling. Cell-type deconvolution implicated a role for microglia as a critical driver for opioid-induced neuroplasticity. Using LDSC, we discovered genetic liabilities for risky behavior, attention deficit hyperactivity disorder, and depression. ConclusionsOverall, our findings reveal new connections between the brains immune system and opioid dependence in the human brain.

neuroscience↗

bioRxiv2020

Enhanced triacylglycerol (TAG) and protein accumulation in transgenic diatom Thalassiosira pseudonana with altered photosynthetic pigmentation

Microalgal productivity in mass cultures is limited by the inefficiency with which available light energy is utilized. In dense cultures, cells closest to the light source absorb more light energy than they can use and dissipate the excess, while light penetrance into the culture is steeply attenuated. Reducing microalgal light harvesting and/or dissipating capacity per cell may improve total light utilization efficiency in mass cultures. In this study, two transgenic lines of the diatom Thalassiosira pseudonana with altered photosynthetic pigment content are evaluated with respect to photosynthetic parameters, growth, and macromolecule accumulation. In one line, violaxanthin de-epoxidase-like 2 (VDL2) is overexpressed (OE), resulting in a reduction of the diadinoxanthin cycle pigments, which are involved in light energy dissipation (non-photochemical quenching, NPQ), accompanied by a stoichiometric increase in the light-harvesting pigment fucoxanthin. No differences in the maximum potential quantum yield of photosystem II (Fv/Fm) or light-limited photosynthetic rate () were found. However, when adapted to 30 {micro}mol photons m-2 sec-1, the VDL2 OE maximum relative electron transport rate (rETRmax) upon exposure to saturating light intensities was 86-95% of wild type (WT). When adapted to 300 {micro}mol photons m-2 sec-1, VDL2 OE saturated photosynthesis at 62-71% of the light intensity needed to saturate WT (Ek). NPQ was substantially lower at and below 300 {micro}mol photons m-2 sec-1. VDL2 OE accumulated up to 3.4 times as much triacylglycerol (TAG) as WT during exponential growth, and up to twice as much protein. Growth in terms of culture density was up to 7% slower. TAG and protein accumulation inversely correlated with NPQ. The second line evaluated was obtained by using antisense RNA to simultaneously silence or knock down (KD) both LUT1-like (LTL) genes, hypothesized to catalyze an intermediate carotenoid biosynthesis step of converting {beta}-carotene to zeaxanthin. Overall reduction of photosynthetic pigment content without altering the relative abundance of individual pigments resulted. No significant differences in photosynthetic parameters compared to WT were found. LTL KD grew at a rate comparable to WT and accumulated up to 40% more TAG during exponential growth, while protein content was reduced by 11-19%. LTL KD cells were elongated and 5-10% smaller than WT, and cultures contained auxospores, indicating stress that may relate to a cell cycle progression defect.

microbiology↗

bioRxiv2020

Overexpression of Thalassiosira pseudonana violaxanthin de-epoxidase-like 2 (VDL2) increases fucoxanthin while stoichiometrically reducing diadinoxanthin cycle pigment abundance

Despite the ubiquity and ecological importance of diatoms, much remains to be understood about their physiology and metabolism, including their carotenoid biosynthesis pathway. Early carotenoid biosynthesis steps are well-conserved, while the identity of the enzymes that catalyze the later steps and their order remain unclear. Those steps lead to the biosynthesis of the final pathway products: the main accessory light-harvesting pigment fucoxanthin (Fx) and the main photoprotective pigment pool comprised of diadinoxanthin (Ddx) and its reversibly de-epoxidized form diatoxanthin (Dtx). We used sequence comparison to known carotenoid biosynthesis enzymes to identify novel candidates in the diatom Thalassiosira pseudonana. Microarray and RNA-seq data was used to select candidates with transcriptomic responses similar to known carotenoid biosynthesis genes and to create full-length gene models, and we focused on those that encode proteins predicted to be chloroplast-localized. We identified a violaxanthin de-epoxidase-like gene (Thaps3_11707, VDL2) that when overexpressed results in increased Fx abundance while stoichiometrically reducing Ddx+Dtx. Based on transcriptomics, we hypothesize that Thaps3_10233 may also contribute to Fx biosynthesis, in addition to VDL2. Separately using antisense RNA to target VDL2, VDL1, and both LUT1-like copies (hypothesized to catalyze an earlier step in the pathway) simultaneously, reduced the overall cellular photosynthetic pigment content, including chlorophylls, suggesting destabilization of light-harvesting complexes by Fx deficiency. Based on transcriptomic and physiological data, we hypothesize that the two predicted T. pseudonana zeaxanthin epoxidases have distinct functions and that different copies of phytoene synthase and phytoene desaturase may serve to initiate carotenoid biosynthesis in response to different cellular needs. Finally, nine carotene cis/trans isomerase (CRTISO) candidates identified based on sequence identity to known CRTISO proteins were narrowed to two most likely to be part of the T. pseudonana carotenoid biosynthesis pathway based on transcriptomic responses and predicted chloroplast targeting.

microbiology↗

bioRxiv2019

Bionic 3D printed corals

Symbiotic corals have evolved as a highly optimised photon augmentation system leading to space-efficient microalgal growth and photosynthetic quantum efficiencies that approach theoretical limits1-3. Corals are characterized by an elastic animal tissue hosting microalgae and a light scattering calcium carbonate skeleton that maximizes light delivery towards otherwise shaded algal-containing tissues4,5. Rapid light attenuation due to algal self-shading is a key limiting factor for the upscaling of microalgal cultivation6,7. Coral-inspired light management systems could overcome this limitation and facilitate scalable bioenergy and bioproduct generation8,9. Here, we developed 3D printed bionic corals capable of growing various types of microalgae with cell densities approaching 109 cells mL-1, up to 100 times greater than in liquid culture. The hybrid photosynthetic biomaterials are produced with a new 3D bioprinting platform which mimics morphological features of living coral tissue and the underlying skeleton with micron resolution, including their optical and mechanical properties. The programmable synthetic microenvironment thus allows for replicating both structural and functional traits of the coral-algal symbiosis. Our work defines a new class of bionic materials capable of interacting with living organisms, that can be exploited for the design of next generation photobioreactors7 and disruptive approaches for coral reef conservation10.

bioengineering↗