Biology subjects

Jia, G.

Publications and source records attributed to Jia, G..

8 recordsLinked to original sources

bioRxiv2018

Multiple isotopic models using various kinetic fractionation coefficients to estimate δ18O of leaf water

Investigation of{delta} 18O of leaf water may improve our understanding of the evapotranspiration partitioning and material exchange between the inside and outside of leaves. In this study,{delta} 18O of bulk leaf water ({delta}L,b) was estimated by both isotopic-steady-state (ISS) and non-steady-state (NSS) assumptions considering the Peclet effect. Specifically, we carefully modified kinetic fractionation coefficients (k). The results showed that the Peclet effect is required to predict{delta} L,b. On the diel time scale, both NSS assumption + Peclet effect (NSS + P) and ISS assumption + Peclet effect (ISS + P) using modified k (k-modified) for{delta} L,b showed a good agreement with observed{delta} L,b (p > 0.05). When using previously proposed k, however, both NSS + P and ISS + P were not reliable estimators of{delta} L,b (p < 0.05). On a longer time scale (days), estimates of daily mean{delta} L,b from ISS + P outperformed the estimates from NSS + P when using the same k values. Also, the employment of k-modified improved model performance in predicting daily mean{delta} L,b compared to the use of previously proposed k. Clearly, special care must be taken concerning k when using isotopic models to estimate{delta} L,b.\n\nHighlightFor hourly and daily mean data sets, the employment of modified kinetic fractionation coefficients significantly improved model performance for{delta} 18O of bulk leaf water.

ecology↗

bioRxiv2018

Water stress and CO2 concentration interactions affect carbon isotope signatures of leaf and phloem organic matter

Investigation of {delta}13C of leaf and twig phloem water-soluble organic material (WSOM) is a promising approach for analysis of the effects of environmental factors on plant performance. In this study, orthogonal treatments of three CO2 concentrations (Ca) x five soil water contents (SWC) were conducted using Platycladus orientalis saplings to investigate the interaction of water stress and CO2 concentration on {delta}13C of leaf and twig phloem WSOM. Under the lowest SWC, the {delta}13C of leaf and twig phloem WSOM had the most positive values at any Ca and their values decreased as Ca increased. However, at improved soil water conditions, the greatest values of {delta}13C of leaf and twig phloem WSOM were mostly observed at C600. In addition, a more significant relationship between SWC and {delta}13C of twig phloem WSOM than that between SWC and {delta}13C of leaf WSOM demonstrated that {delta}13C of twig phloem WSOM is a more sensitive indicator of SWC. Twig phloem WSOM was generally 13C-depleted compared with leaf WSOM for potential post-photosynthetic fractionation, and the 13C discrimination from leaves to twig phloem was insensitive to the interaction between SWC and Ca. Clearly, interacting effects play a more important role in photosynthetic fractionation than in post-photosynthetic fractionation.\n\nHighlightThe {delta}13C of leaf and twig phloem WSOM exhibited the most positive values at C400x35%-45% FC.\n\nPost-photosynthetic fractionation from leaf to twig was not be impacted by the interacting effects.

ecology↗

bioRxiv2017

Variations in δ13C of different plant organs: implications for post-photosynthetic fractionation

Compared to photosynthetic fractionation, the mechanism of post-photosynthetic carbon isotope fractionation is not well understood. The aim of this study was to investigate post-photosynthetic fractionation in both above and below ground tissues and to evaluate potential hypotheses explaining differences in carbon isotope composition ({delta}13C) among different plant organs, which can provide valuable insights into plant physiology. The results revealed that there is no significant day-night difference in{delta} 13C of twig phloem water soluble organic materials (WSOM), which could be explained by the unrestricted exchange of triose-phosphates between the chloroplast and cytoplasm and a time lag for carbohydrate exportation. Further, we found that{delta} 13C of twig phloem WSOM is more sensitive to plant water status than leaf WSOM. Analysis of{delta} 13C in different plant organs showed that the greatest 13C enrichment was recorded in stem phloem. Divergences in{delta} 13C of phloem WSOM among different plant organs were not likely to be explained by respiratory fractionation or time lag and were ascribed to transport of carbohydrates across organ boundaries and metabolic processes. Our study demonstrated that post-photosynthesis fractionation could not be ascribed to a single, unifying hypotheses; instead, it is the result of multiple processes.\n\nHighlight{delta}13C of twig phloem water soluble organic materials varied no clear diel pattern. In the leaf-twig-stem-root sequence, the greatest 13C enrichment was recorded in stem phloem.

ecology↗

bioRxiv2017

Single-cell transcriptional regulations and accessible chromatin landscape of cell fate decisions in early heart development

Formation and segregation of the cell lineages forming the vertebrate heart have been studied extensively by genetic cell tracing techniques and by analysis of single marker gene expression both in embryos and differentiating ES cells. However, the underlying gene regulatory networks driving cell fate transitions during early cardiogenesis is only partially understood, in part due to limited cell numbers and substantial cellular heterogeneity within the early embryo. Here, we comprehensively characterized cardiac progenitor cells (CPC) marked by Nkx2-5 and Isl1 expression from embryonic days E7.5 to E9.5 using single-cell RNA sequencing. By leveraging on cell-to-cell heterogeneity, we identified different previously unknown cardiac sub-populations. Reconstruction of the developmental trajectory revealed that Isl1+ CPC represent a transitional cell population maintaining a prolonged multipotent state, whereas extended expression of Nkx-2.5 commits CPC to a unidirectional cardiomyocyte fate. Correlation-based analysis of cells in the unstable multipotent state uncovered underlying gene regulatory networks associated with differentiation. Furthermore, we show that CPC fate transitions are associated with distinct open chromatin states, which critically depend on Isl1 for accessibility of enhancers. In contrast, forced expression of Nkx2-5 eliminated multipotency of Isl1+ cells and established a unidirectional cardiomyocyte fate. Our data provides a transcriptional map for early cardiogenic events at single-cell resolution and establishes a general model of transcriptional and epigenetic regulations during cardiac progenitor cell fate decisions.

developmental biology↗

bioRxiv2017

Impairment of zebrafish reproduction upon exposure to TDCPP

TDCPP is one of the most common organophosphate flame retardant, which has been widely used in many products. It has been detected in the environment and biota; however, its potential affect to the wildlife and human health remains largely unknown. In this study, we aimed to investigate the effect of long-term exposure to TDCPP on fish reproduction. Zebrafish eggs were treated with various concentration of TDCPP (0, 1, 10 and 100 g/L) from 1 day post-fertilization (hpf) to 6 months. The fecundity of female fish was significantly decreased as indicated by reduced embryos production. The egg quality was decreased and the malformation rates were increased in the F1 generation. Taken together, long-term exposure to TDCPP affects the reproduction of zebrafish.

pharmacology and toxicology↗

bioRxiv2017

DNA 5-Hydroxymethylcytosines from Cell-free Circulating DNA as Diagnostic Biomarkers for Human Cancers

DNA modifications such as 5-methylcytosines (5mC) and 5-hydroxymethylcytosines (5hmC) are epigenetic marks known to affect global gene expression in mammals(1, 2). Given their prevalence in the human genome, close correlation with gene expression, and high chemical stability, these DNA epigenetic marks could serve as ideal biomarkers for cancer diagnosis. Taking advantage of a highly sensitive and selective chemical labeling technology(3), we report here genome-wide 5hmC profiling in circulating cell-free DNA (cfDNA) and in genomic DNA of paired tumor/adjacent tissues collected from a cohort of 90 healthy individuals and 260 patients recently diagnosed with colorectal, gastric, pancreatic, liver, or thyroid cancer. 5hmC was mainly distributed in transcriptionally active regions coincident with open chromatin and permissive histone modifications. Robust cancer-associated 5hmC signatures in cfDNA were identified with specificity for different cancers. 5hmC-based biomarkers of circulating cfDNA demonstrated highly accurate predictive value for patients with colorectal and gastric cancers versus healthy controls, superior to conventional biomarkers, and comparable to 5hmC biomarkers from tissue biopsies. This new strategy could lead to the development of effective blood-based, minimally-invasive cancer diagnosis and prognosis approaches.

cancer biology↗

bioRxiv2017

Universal Microfluidic System for Analysis and Control of Cell Dynamics

Dynamical control of the cellular microenvironment is highly desired for quantitative studies of stem cells and immune signaling. Here, we present an automated microfluidic system for high-throughput culture, differentiation and analysis of a wide range of cells in precisely defined dynamic microenvironments recapitulating cellular niches. This system delivers complex, time-varying biochemical signals to 1,500 independently programmable cultures containing either single cells, 2-D populations, or 3-D organoids, and dynamically stimulates adherent or non-adherent cells while tracking and retrieving them for end-point analysis. Using this system, we investigated the signaling landscape of neural stem cell differentiation under combinatorial and dynamic stimulation with growth factors. Experimental and computational analyses identified \"cellular logic rules\" for stem cell differentiation, and demonstrated the importance of signaling sequence and timing in brain development. This universal platform greatly enhances capabilities of microfluidic cell culture, allows dissection of previously hidden aspects of cellular dynamics, and enables accelerated biological discovery.

bioengineering↗

bioRxiv2017

The acute toxicity of Oxydemeton-methyl in zebrafish

Oxydemeton-methyl, is an organothiophosphate insecticide, which is widely used in agricultural and urban pest controls. It exists in the environment and a large amount bioaccumulation in the wildlife due to its strong water solubility and mobility. Although its potentially harmful effect on animals and humans, few studies have focused on the oxydemeton-methyl pollution in the environment. Zebrafish have been used for many years to valuate the pollution status of water and toxicity of chemicals. In the present study, we aimed to investigate the effect of oxydemeton-methyl on the expression level of liver microsomal cytochrome P450, on the activity of NADPH-P450 reductase and reactive oxygen species (ROS) generation in zebrafish. Adult male and female zebrafish were treated with different concentration of oxydemeton-methyl (10, 50, 100 M) for 5, 10, 20 and 30 days. We found that the oxydemeton-methyl exposure significantly increased the P450 levels and the activity of NAPDH-P450 reductase. ROS generation and the DNA damage were augmented in a dose-dependent manner in the zebrafish. These results indicated that oxydemeton-methyl is able to induce strong oxidative stress and hence highly toxic to the zebrafish.

pharmacology and toxicology↗