Biology subjects

Yu, C.-P.

Publications and source records attributed to Yu, C.-P..

6 recordsLinked to original sources

bioRxiv2023

Mass-immigration shapes the antibiotic resistome of wastewater treatment plants

Wastewater treatment plants (WWTPs) are the hotspots for the spread of antibiotic resistance genes (ARGs) into the environment. Nevertheless, a comprehensive assessment of the city-level and short-term daily variations of ARG surveillance is still lacking in WWTPs. Here, 285 ARGs and ten mobile gene elements (MGEs) were monitored in seven WWTPs in Xiamen via high-throughput qPCR (HT-qPCR) for seven days. The average daily load of ARGs to WWTPs was about 1.21 x 1020 copies/d, and a total of 1.44 x 1018 copies/d was discharged to the environment across the entire city. Interestingly, no daily variations were observed in ARG richness, abundance, and community composition. Stochastic processes were the main force determining the assembly of ARG communities, with their relative importance ranked in the order of influent (INF) > effluent (EFF) > activated sludge (AS). Further analyses indicated that bacteria and ARGs from upstream treatment units played an increasingly dominant role in shaping ARG communities in AS and EFF, respectively, suggesting the importance of mass-immigration of bacteria and ARGs from the source on ARG transport in wastewater treatment units. This emphasizes the need to revise the way we mitigate ARG contamination but focus on the source of ARGs in urban wastewater.

microbiology↗

bioRxiv2022

Hydrological dynamics drive the transition of antibiotic resistance genes between particle-attached and free-living lifestyles in a deep freshwater reservoir

Despite the growing awareness of antibiotic resistance genes (ARGs) spreading in the environment, there is a knowledge gap on the fate and transport of ARGs in particle-attached (PA) and free-living (FL) lifestyles in deep freshwater ecosystems experiencing seasonal hydrological changes. Here, we examined the ARG profiles using high-throughput quantitative PCR in PA and FL lifestyles at four seasons representing two hydrological seasons (i.e., vertical mixing and thermal stratification) in the Shuikou Reservoir (SR), Southern China. The results indicated that seasonal hydrological dynamics were critical for influencing ARGs in PA and FL fractions, and the transition of ARGs between the two lifestyles. Although both PA and FL ARG profiles were likely to be shaped by horizontal gene transfer, PA and FL ARGs had different responses to the changes in physico-chemicals (e.g., nutrients and dissolved oxygen) caused by seasonal hydrological dynamics. The particle-associated niche (PAN) index revealed that there were 94 non-conservative ARGs (i.e., no preferences for PA and FL), 23 conservative ARGs that preferred PA lifestyle, and 16 conservative ARGs for FL lifestyle. A sharp decline in the number of conservative ARGs in stratified seasons suggests a hydrological dynamics-dependent transition of ARGs between two lifestyles. Remarkably, the conservative ARGs (in PA or FL lifestyle) were more closely related to bacterial OTUs in their preferred lifestyle compared to their counterpart lifestyle, suggesting a lifestyle-dependent ARG enrichment. Altogether, these findings enhance our understanding of the role of seasonal hydrological changes in the dissemination of ARGs in different size fractions in deep aquatic ecosystems.

ecology↗

bioRxiv2021

Recurrent micropollutant exposure leads to divergent degradation abilities and community succession in a freshwater microbiome

The increasing-volume release of micropollutants into natural surface waters has raised great concern due to their environmental accumulation. Persisting micropollutants can impact multiple generations of organisms, but their microbially-mediated degradation and their influence on community assembly remain understudied. Here, freshwater microbes were treated with several common micropollutants, alone or in combination, and then transferred every 5 days to fresh medium containing the same micropollutants to mimic the repeated exposure of microbes. Metabarcoding of 16S rRNA gene makers was chosen to study the succession of bacterial assemblages following micropollutant exposure. The removal rates of micropollutants were then measured to assess degradation capacity of the associated communities. The degradation of micropollutants did not accelerate over time but altered the microbial community composition. Community assembly was dominated by stochastic processes during early exposure, via random community changes and emergence of seedbanks, and deterministic processes later in the exposure, via advanced community succession. Early exposure stages were characterized by the presence of sensitive microorganisms such as Actinobacteria and Planctomycetes, which were then replaced by more tolerant bacteria such as Bacteroidetes and Gammaproteobacteria. Our findings have important implication for ecological feedback between microbe-micropollutants under anthropogenic climate change scenarios.

ecology↗

bioRxiv2020

GAMYB modulates bHLH142 and is homeostatically regulated by TDR during rice anther tapetal and pollen development

GAMYB, UDT1, TIP2/bHLH142, TDR, and EAT1/DTD are important transcription factors (TFs) that play a crucial role during rice pollen development. This study demonstrates that bHLH142 acts downstream of UDT1 and GAMYB and works as a "hub" in these two pollen pathways. We show that GAMYB modulates bHLH142 expression through specific binding to the MYB motif of bHLH142 promoter during early stage of pollen development; while TDR acts as a transcriptional repressor of the GAMYB modulation of bHLH142 by binding to the E-box close to the MYB motif on the promoter. The up- and down-regulation of TFs highlights the importance that a tight, precise, and coordinated regulation among these TFs is essential for normal pollen development. Most notably, this study illustrates the regulatory pathways of GAMYB and UDT1 that rely on bHLH142 in a direct and an indirect manner, respectively, and function in different tissues with distinct biological functions during pollen development. This study advances our understanding of the molecular mechanisms of rice pollen development. HighlightGAMYB can directly modulate the transactivation of the bHLH142, but the modulation is repressed by TDR to keep the homeostasis of bHLH142 gene expression to ensure normal pollen development.

molecular biology↗

bioRxiv2018

Modeling Attention Control Using A Convolutional Neural Network Designed After The Ventral Visual Pathway

Recently we proposed that people represent object categories using category-consistent features (CCFs), those features that occur both frequently and consistently across a categorys exemplars [70]. Here we designed a Convolutional Neural Network (CNN) after the primate ventral stream (VsNet) and used it to extract CCFs from 68 categories of objects spanning a three-level category hierarchy. We evaluated VsNet against people searching for the same targets from the same 68 categories. Not only did VsNet replicate our previous report of stronger attention guidance to subordinate-level targets, with its more powerful CNN-CCFs it was able to predict attention control to individual target categories-the more CNN-CCFs extracted for a category, the faster gaze was directed to the target. We also probed VsNet to determine where in its network of layers these attention control signals originate. We found that CCFs extracted from VsNets V1 layer contributed most to guiding attention to targets cued at the subordinate (e.g., police car) and basic (e.g., car) levels, but that guidance to superordinate-cued (e.g., vehicle) targets was strongest using CCFs from the CIT+AIT layer. We also identified the image patches eliciting the strongest filter responses from areas V4 and higher and found that they depicted representative parts of an object category (e.g., advertisements appearing on top of taxi cabs). Finally, we found that VsNet better predicted attention control than comparable CNN models, despite having fewer convolutional filters. This work shows that a brain-inspired CNN can predict goal-directed attention control by extracting and using category-consistent features.

neuroscience↗

bioRxiv2017

A mid-level organization of the ventral stream

Human object-selective cortex shows a large-scale organization characterized by the high-level properties of both animacy and object-size. To what extent are these neural responses explained by primitive perceptual features that distinguish animals from objects and big objects from small objects? To address this question, we used a texture synthesis algorithm to create a novel class of stimuli--texforms--which preserve some mid-level texture and form information from objects while rendering them unrecognizable. We found that unrecognizable texforms were sufficient to elicit the large-scale organizations of object-selective cortex along the entire ventral pathway. Further, the structure in the neural patterns elicited by texforms was well predicted by curvature features and by intermediate layers of a deep convolutional neural network, supporting the mid-level nature of the representations. These results provide clear evidence that a substantial portion of ventral stream organization can be accounted for by coarse texture and form information, without requiring explicit recognition of intact objects.\n\nSIGNIFICANCE STATEMENTWhile neural responses to object categories are remarkably systematic across human visual cortex, the nature of these responses been hotly debated for the past 20 years. In this paper, a new class of stimuli (\"texforms\") is used to examine how mid-level features contribute to the large-scale organization of the ventral visual stream. Despite their relatively primitive visual appearance, these unrecognizable texforms elicited the entire large-scale organizations of the ventral stream by animacy and object size. This work demonstrates that much of ventral stream organization can be explained by relatively primitive mid-level features, without requiring explicit recognition of the objects themselves.

neuroscience↗