Biology subjects

Ho, H.-C.

Publications and source records attributed to Ho, H.-C..

8 recordsLinked to original sources

bioRxiv2026

Convergent evolution of extreme snout elongation in deep-sea fishes reveals constrained trajectories

Phenotypic extremes are scattered across the Tree of Life, suggesting that evolutionary constraints often limit their emergence. Yet striking departures from standard body plans, such as elongate snouts, have evolved convergently across deep time. We investigate extreme morphologies in two distantly related deep-sea fish clades: spikefishes (pufferfish relatives) and snipefishes (seahorse relatives). Using spikefishes as a study system, including all 24 living and fossil species, we integrated genome-wide phylogenomic data with a fossil and extant morphological character matrix, skull shape and dentition analyses from 64 CT scans, phenotypic and divergence matrices from >200 X-rays, functional manipulations of freshly collected and cleared-and-stained specimens, and formal convergence test across 300 percomorph species. We show that snout elongation evolved independently twice within spikefishes, reaching intermediate and extreme conditions along one predictable, ordered trajectory of additive skeletal rearrangements. Snout bones form a highly integrated, semi-autonomous module that channels evolutionary change along intrinsic lines of least resistance, coinciding with accelerated cranial evolution and expanded morphospaces in a clade with enhanced cranial mobility. Snipefishes converge on the same body plan through largely non-homologous elements and distinct linkage mechanics, except for near-identical vomer convergence. Extreme morphologies can emerge when phenotypic integration aligns with functional innovation, guiding evolution along repeatable trajectories.

evolutionary biology↗

bioRxiv2026

Investigating the skin response of Striped Catfish to acute ammonia stress reveals a potential exosome-based ammonia excretion system

Ammonia can rapidly accumulate in intensive aquaculture and pose serious threats to fish health. Fish skin functions as a vital immune-related organ and a significant surface barrier against ammonia; however, little is known about the skins response and to acute ammonia stress. In this study, Striped catfish were exposed to a half-lethal concentration of ammonia to evaluate skin responses. We found generalized inflammation in the liver, spleen, and skin. However, the skin tissue showed subtle signs of damage, with tissue ammonia concentration accumulating and then decreasing. Further transcriptomic analysis of skin gene function suggested a hypothesized ammonia regulation occurring within cell compartments. Cellular examination by transmission electron microscopy further showed that accumulated exosome-suspecting vesicles near the epithelial surface were associated with ammonia regulation during acute ammonia stress. Using a newly established Striped catfish skin epithelial cell line, along with an exosome inhibitor, confirms the presence of exosome vesicles and their role in ammonia excretion. In conclusion, acute ammonia stress induces inflammation in Striped catfish skin, while active ammonia excretion via exosomes may alleviate ammonia accumulation, thereby maintaining skin tissue integrity. This study explores Striped catfish skin responses to acute ammonia stress and highlights a newly identified mechanism of ammonia regulation in the skin. HighlightsO_LIFish skin can regulate ammonia concentrations and stress. C_LIO_LIExosomal vesicles are involved in the excretion of ammonia from the skin. C_LI

immunology↗

bioRxiv2022

The structure of Lepidoptera-plant interaction networks across clades, life stages, and environmental gradients

AimIntegrate biogeographic and ecological knowledge to understand the spatial-structural patterns of plant-insect interaction networks at the landscape scale. LocationThe 36,000 km2 German state of Baden-Wurttemberg, Central Europe. MethodsWe integrated extensive data of Lepidoptera-plant occurrences and interactions to inferentially construct local interaction networks across Baden-Wurttemberg, considering in total 3148 plant and 980 Lepidoptera species, covering butterflies, Noctuid moths, Geometrid moths and Bombycoid moths. We quantified clade- and life-stage-specific network structures and related these features to GIS-informed environmental conditions, thereby revealing the spatial (environmental) patterns and potential drivers of networks structural variation across the landscape. ResultsSpanning the same environmental gradients, Lepidoptera clades and life stages can form various interaction structures with food plants and exhibit distinct spatial-structural patterns. For all major Lepidopteran groups, except Geometrid moths, potential diet across life stages tended to broaden toward low-elevation farmlands. The larval and adult networks of butterflies became less modular with farmland coverage; the same for adult Noctuid moths, but the inverse for adult Geometrid moths. With increasing elevation, the larval and adult networks of Noctuid moths became less and more modular, respectively, whereas Geometrid adult networks became more modular. While the adult dietary niche of butterflies was more overlapped at low elevation, those of Noctuid and Geometrid moths further associated with land cover and were more overlapped toward low- and high-elevation farmlands, respectively. Main conclusionsEnvironmental factors and biotic interactions together shape ecological communities. By particularly accounting for species-interaction contexts, we revealed the spatial-structural patterns of Lepidoptera-plant networks along geo-climate and land-cover gradients, where the shaping mechanisms likely include both evolutionary (e.g., resource-consumer co-evolution) and ecological (e.g., competitive exclusion) processes and are specific to Lepidopteras clade or life stage. Such biogeographical structural patterns provide ecological and conservation implications at both species and community levels, and can indicate the potential response of Lepidoptera-plant communities to environmental changes.

ecology↗

bioRxiv2021

Blue and green food webs respond differently to elevation and land use

While aquatic (blue) and terrestrial (green) food webs are parts of the same landscape, it remains unclear whether they respond similarly to shared environmental gradients. We use empirical community data from hundreds of sites across Switzerland, and show that blue and green food webs have different structural and ecological properties along elevation as a temperature proxy, and among various land-use types. Specifically, in green food webs, their modular structure increases with elevation and the overlap of consumers diet niche decreases, while the opposite pattern is observed in blue food webs. Such differences between blue and green food webs are particularly pronounced in farmland-dominated habitats, indicating that anthropogenic habitat modification moderates the climatic effects on food webs but differently in blue versus green systems. These findings indicate general structural differences between blue and green food webs and suggest their potential divergent future alterations through land use or climatic changes.

ecology↗

bioRxiv2021

Less is worse than none: ineffective adaptive foraging can destabilise food webs

O_LIConsumers can potentially adjust their diet in response to changing resource abundances, thereby achieving better foraging payoffs. Although previous work has explored how such adaptive foraging scales up to determine the structure and dynamics of food webs, consumers may not be able to perform perfect diet adjustment due to sensory or cognitive limitations. Whether the effectiveness of consumers diet adjustment alters food-web consequences remains unclear. C_LIO_LIHere, we study how adaptive foraging, specifically the effectiveness (i.e. rate) with which consumers adjust their diet, influences the structure, dynamics, and overall species persistence in synthetic food webs. C_LIO_LIWe model metabolically-constrained optimal foraging as the mechanistic basis of adaptive diet adjustment and ensuing population dynamics within food webs. We compare food-web dynamical outcomes among simulations sharing initial states but differing in the effectiveness of diet adjustment. C_LIO_LIWe show that adaptive diet adjustment generally makes food-web structure resilient to species loss. Effective diet adjustment that maintains optimal foraging in the face of changing resource abundances facilitates species persistence in the community, particularly reducing the extinction of top consumers. However, a greater proportion of intermediate consumers goes extinct as optimal foraging becomes less-effective and, unexpectedly, slow diet adjustment leads to higher extinction rates than no diet adjustment at all. Therefore, food-web responses cannot be predicted from species responses in isolation, as even less-effective adaptive foraging benefits individual species (better than non-adaptive) but can harm species persistence in the food web as a whole (worse than non-adaptive). C_LIO_LIWhether adaptive foraging helps or harms species coexistence has been contradictory in literature Our finding that it can stabilise or destabilise the food web depending on how effectively it is performed help reconcile this conflict. Inspired by our simulations, we deduce that there may exist a positive association between consumers body size and adaptive-foraging effectiveness in the real world. We also infer that such effectiveness may be higher when consumers cognise complete information about their resources, or when trophic interactions are driven more by general traits than by specific trait-matching. We thereby suggest testable hypotheses on species persistence and food-web structure for future research, in both theoretical and empirical systems. C_LI

ecology↗

bioRxiv2021

Spatio-temporal patterns of multi-trophic biodiversity and food-web characteristics across a river catchment

Accurate characterisation of ecological communities with respect to their biodiversity and food-web structure is essential for conservation. However, combined empirical study of biodiversity and multi-trophic food-webs at a large spatial and temporal resolution has been prohibited by the lack of appropriate access to such data from natural systems. Here, we assessed biodiversity and food-web characteristics across a 700 km2 riverine network over seasons using environmental DNA. We found contrasting biodiversity patterns between major taxonomic groups; local richness showed seasonally dependent and statistically significant increases and decreases towards downstream positions within the catchment for fish and bacteria respectively, while invertebrate richness remained unchanged with increased downstream position. The local food-webs, formed by these taxonomic groups, also showed a variation in their structure, such as link density and nestedness, to both space and time, yet these patterns did not necessarily mirror those of biodiversity and functional feeding characteristics. In order to conserve species diversity as well as their functional trophic integrity of communities, patterns of biodiversity and food-web characteristics must thus be jointly studied, as our results suggest that they are not directly scalable to each other even at the same spatial and temporal scales.

ecology↗

bioRxiv2020

Dihydroceramide desaturase directs the switch between exosome production and autophagy for neuronal maintenance

Exosomes are important for cell-cell communication. Deficiencies in the human dihydroceramide desaturase gene, DEGS1, increase the dihydroceramide-to-ceramide ratio and causes hypomyelinating leukodystrophy. However, the disease mechanism remains unknown. Here, we developed an in vivo assay with spatially controlled expression of exosome markers in Drosophila eye imaginal discs and showed that the level and activity of the DEGS1 ortholog, ifc, correlated with exosome production. Knocking out ifc decreased the density of the exosome precursor intraluminal vesicles (ILVs) in the multivesicular endosomes and reduced the number of exosomes released. While ifc overexpression and autophagy inhibition both enhanced exosome production, combining the two had no additive effect. Moreover, DEGS1 activity was sufficient to drive ILV formation in vitro. Together, DEGS1/Ifc controls the dihydroceramide-to-ceramide ration and enhances exosome secretion by promoting ILV formation and preventing the autophagic degradation of MVEs. These findings provide a potential cause for the neuropathy associated with DEGS1-deficient mutations. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/376046v3_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@c7479corg.highwire.dtl.DTLVardef@12e7f46org.highwire.dtl.DTLVardef@1a5e7f0org.highwire.dtl.DTLVardef@11e7f08_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIAn in vivo system was developed for observing exosome production in Drosophila. C_LIO_LIDihydroceramide desaturase (DEGS1/Ifc) promotes exosome production by two means. C_LIO_LIIfc drives membrane invagination to promote the formation of intraluminal vesicles. C_LIO_LIIfc inhibits autophagic degradation of MVEs and increases exosome release. C_LI eTOC BlurbThe level and activity of dihydroceramide desaturase (human DEGS1 and Drosophila Ifc) correlate with exosome production. Wu et al. show that DEGS1 drives the formation of intraluminal vesicles in vivo and in vitro. Overexpressing Ifc inhibits autophagy and reduces the degradation of multivesicular endosomes, thus increases exosome release.

cell biology↗

bioRxiv2018

Interspecies malate-pyruvate shuttle drives amino acid exchange in organohalide-respiring microbial communities

Most microorganisms in the biosphere live in communities and develop coordinated metabolisms via trading metabolites. In this study, we sought to deconstruct the metabolic interdependency in organohalide-respiring microbial communities enriched with Dehalobacter restrictus (Dhb), using a complementary approach of computational metabolic modeling and experimental validation. Dhb possesses a complete set of genes for amino acid biosynthesis yet requires amino acid supplementation. We reconciled this discrepancy using Flux Balance Analysis with consideration for cofactor availability, enzyme promiscuity, and shared protein expression patterns of several Dhb strains. Experimentally, 13C incorporation assays, growth assays, and metabolite analysis of strain PER-K23 cultures were performed to validate the model predictions. The model resolved that Dhbs amino acid dependency results from restricted NADPH regeneration and diagnosed that malate supplementation can replenish intracellular NADPH using malic enzyme. Interestingly, we observed unexpected export of glutamate and pyruvate in parallel to malate consumption in the strain PER-K23 cultures. Further experiments on Dhb-enriched consortium ACT-3 suggested an interspecies malate-pyruvate shuttle between Dhb and a glutamate-auxotrophic Bacteroides sp., reminiscent of the mitochondrial malate shunt pathway in eukaryotic cells. Altogether, this study reveals that redox constraints and metabolic complementarity are important driving forces for amino acid exchange in anaerobic microbial communities.

microbiology↗