Biology subjects

Su, S.-H.

Publications and source records attributed to Su, S.-H..

5 recordsLinked to original sources

bioRxiv2023

Latitudinal scaling of aggregation with abundance and its consequences for coexistence in species rich forests

The search for simple principles underlying the complex spatial structure and dynamics of plant communities is a long-standing challenge in ecology1-6. In particular, the relationship between the spatial distribution of plants and species coexistence is challenging to resolve in species-rich communities7-9. Analysing the spatial patterns of tree species in 21 large forest plots, we find that rare species tend to be more spatially aggregated than common species, and a latitudinal gradient in the strength of this negative correlations that increases from tropical to temperate forests. Our analysis suggests that latitudinal gradients in animal seed dispersal10 and mycorrhizal associations11,12,13 may jointly generate this intriguing pattern. To assess the consequences of negative aggregation-abundance correlations for species coexistence, we present here a framework to incorporate the observed spatial patterns into population models8 along with an analytical solution for the local extinction risk14 of species invading from low abundances in dependence of spatial structure, demographic parameters, and immigration. For example, the stabilizing effect of the observed spatial patterns reduced the local extinction risk of species when rare almost by a factor of two. Our approach opens up new avenues for integrating observed spatial patterns into mathematical theory, and our findings demonstrate that spatial patterns, such as species aggregation and segregation, can contribute substantially to coexistence in species-rich communities. This underscores the need to understand the interactions between multiple ecological processes and spatial patterns in greater detail.

ecology↗

bioRxiv2022

The Modular μSiM: a Mass Produced, Rapidly Assembled, and Reconfigurable Platform for the Study of Barrier Tissue Models In Vitro

Advanced in vitro tissue chip models can reduce and replace animal experimentation and may eventually support on-chip clinical trials. To realize this potential, however, tissue chip platforms must be both mass-produced and reconfigurable to allow for customized design. To address these unmet needs, we introduce an extension of our {micro}SiM (microdevice featuring a silicon-nitride membrane) platform. The modular {micro}SiM (m-{micro}SiM) uses mass-produced components to enable rapid assembly and reconfiguration by laboratories without knowledge of microfabrication. We demonstrate the utility of the m-{micro}SiM by establishing an hiPSC-derived blood-brain barrier (BBB) in bioengineering and non-engineering, brain barriers focused laboratories. We develop and validate in situ and sampling-based assays of small molecule diffusion as a measure of barrier function. BBB properties show excellent interlaboratory agreement and match expectations from literature, validating the m-{micro}SiM as a platform for barrier models and demonstrating successful dissemination of components and protocols. We then demonstrate the ability to quickly reconfigure the m-{micro}SiM for co-culture and immune cell transmigration studies through addition of accessories and/or quick exchange of components. Because the development of modified components and accessories is easily achieved, custom designs of the m-{micro}SiM should be accessible to any laboratory desiring a barrier-style tissue chip platform.

bioengineering↗

bioRxiv2020

Machine Learning-Based Protein Microarray Digital Assay Analysis

Serial measurement of a large panel of protein biomarkers near the bedside could provide a promising pathway to transform the critical care of acutely ill patients. However, attaining the combination of high sensitivity and multiplexity with a short assay turnaround poses a formidable technological challenge. Here, we developed a rapid, accurate, and highly multiplexed microfluidic digital immunoassay by incorporating machine learning-based autonomous image analysis. The assay achieved 14-plexed biomarker detection at concentrations < 10pg/mL with a sample volume < 10 L, including all processes from sampling to analyzed data delivery within 30 min, while only requiring a 5-min assay incubation. The assay procedure applied both a spatial-spectral microfluidic encoding scheme and an image data analysis algorithm based on machine learning with a convolutional neural network (CNN) for pre-equilibrated single-molecule protein digital counting. This unique approach remarkably reduced errors facing the high-capacity multiplexing of digital immunoassay at low protein concentrations. Longitudinal data obtained for a panel of 14 serum cytokines in human patients receiving chimeric antigen receptor-T (CAR-T) cell therapy manifested the powerful biomarker profiling capability and great potential of the assay for its translation to near-real-time bedside immune status monitoring.

bioengineering↗

bioRxiv2020

Species packing and the latitudinal gradient in local beta-diversity

The decline in species richness at higher latitudes is among the most fundamental patterns in ecology. Whether changes in species composition across space (beta-diversity) contribute to this gradient of overall species richness (gamma-diversity) remains hotly debated. Previous studies that failed to resolve the issue suffered from a well-known tendency for small samples in areas with high gamma-diversity to have inflated measures of beta-diversity. Here, we provide here a novel analytical test, using beta-diversity metrics that correct the gamma-diversity and sampling biases, to compare beta-diversity and species packing across a latitudinal gradient in tree species richness of 21 large forest plots along a large environmental gradient in East Asia. We demonstrate that after accounting for topography and correcting the gamma-diversity bias, tropical forests still have higher beta-diversity than temperate analogs. This suggests that beta-diversity contributes to the latitudinal species richness gradient as a component of gamma-diversity. Moreover, both niche specialization and niche marginality (a measure of niche spacing along an environmental gradient) also increase towards the equator, after controlling for the effect of topographic heterogeneity. This supports the joint importance of tighter species packing and larger niche space in tropical forests while also demonstrating the importance of local processes in controlling beta-diversity.

ecology↗

bioRxiv2020

Deficiency of cyclin-dependent kinase-like 5 causes spontaneous seizures in neonatal mice

Cyclin-dependent kinase-like 5 (CDKL5), an X-linked gene encoding a serine-threonine kinase, is enriched in the mammalian forebrain and critical for neuronal maturation and synaptic function. Mutations in this gene cause CDKL5 deficiency disorder (CDD) that is characterized by early-onset epileptic seizures, autistic behaviors and intellectual disability. Although numerous CDD symptoms have been recapitulated in mouse models, spontaneous seizures have not been reported in mice with CDKL5 deficiency. Here, we present the first systematic study of spontaneous seizures in a mouse model of CDD. Through wireless electroencephalographic (EEG) recording and simultaneous videotaping, we observed epileptiform discharges accompanied with ictal behaviors in pups lacking CDKL5 at a selective time window during the pre-weaning period. The seizure-like patterns of EEG showed robust increase in total number of spike events, the total number and duration of bursts in Cdkl5 null pups compared to wild-type littermate controls at the age of postnatal day 12 (P12). The mutants displayed not only jerky and spasm-like movements during the prolonged bursts of discharges at P12, but also strengthened ictal grasping in both juvenile stage and adulthood. In addition, loss of CDKL5 remarkably reduced the phosphorylation of K+/Cl- co-transporter 2, which may impede GABA-mediated inhibition, in the cortex of P12 mouse pups. Our study reveals previously unidentified phenotypes of early-onset seizures in CDKL5-deficient mice, highlights the translational value of mouse models of CDD and provides a potential molecular target for early diagnosis and treatment for CDD. Significance StatementCyclin-dependent kinase-like 5 (CDKL5) is an X-linked gene encoding a serine-threonine kinase. Mutations in this gene cause CDKL5 deficiency disorder (CDD), a rare disease characterized by developmental delays, autistic behaviors and early-onset epilepsy. Even though many symptoms of CDD patients have been phenocopied in mice, spontaneous seizures are yet to be reported in mouse models of CDD. Here, for the first time, we identified early-onset seizures and ictal behaviors in neonatal pups of CDKL5-deficient mice. Loss of CDKL5 also selectively reduced protein levels of phosphorylated K+/Cl-cotransporter 2 in neonatal cortex of mice. Our study reveals an indispensible role of CDKL5 in regulating neuronal excitability in developing brains and highlights the translational significance of the CDD mouse models.

neuroscience↗