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Identification of Lipid Droplets in Gut Microbiota [article]

Kai Zhang, Chang Zhou, Ziyun Zhou, Xuehan Li, Zemin Li, Mengwei Zhang, Xuelin Zhang, Congyan Zhang, Taotao Wei, Shuyan Zhang, Pingsheng Liu
2020 bioRxiv   pre-print
Recent research has accumulating evidence to support that gut microbiota can be a newly discovered organ/tissue for humans. Although the functions of gut microbiota have been linked to almost all aspects of human physiological, most findings so far are still either belonged to correlational research or at preliminary stage of causal study due to the complexity of gut microbiota as well as lack of proper tools and methods. Thus, development of new approaches is essential and necessary. Lipid
more » ... let is a cellular organelle governing cell lipid homeostasis that is directly related to human metabolic syndromes. Previously we and other groups found lipid droplets in several bacterial strains. We wonder if gut bacteria have lipid droplets. If so, these bacteria may play key roles to regulate gut lipid content, remove unnecessary lipids and produce useful lipid molecules for host. Here we identified lipid droplet-like structures in freshly isolated bacteria from mouse small and large intestines, as well as mouse and human feces. We also purified and analyzed lipid droplets from a cloned human gut bacterium Streptomyces thermovulgaris. Together, we demonstrate the existence of lipid droplets in gut microbiota and established an approach to study them.
doi:10.1101/2020.05.06.080317 fatcat:qinsuczi4rbgxjdmmilr5mtlda

The lipid droplet: A conserved cellular organelle

Congyan Zhang, Pingsheng Liu
2017 Protein & Cell  
b MINI-REVIEW Congyan Zhang and Pingsheng Liu Figure 1 . 1 The conserved lipid droplet functions of binding and regulating nucleic acids from bacterial to human cells. © The Author(s) 2017.  ...  survival under stress (Zhang et al., 2017) .  ... 
doi:10.1007/s13238-017-0467-6 pmid:28913786 pmcid:PMC5676593 fatcat:gaagnb4ji5dxbmrq36uxcdsvfy

Microorganism lipid droplets and biofuel development

Yingmei Liu, Congyan Zhang, Xipeng Shen, Xuelin Zhang, Simon Cichello, Hongbin Guan, Pingsheng Liu
2013 BMB Reports  
Lipid droplet (LD) is a cellular organelle that stores neutral lipids as a source of energy and carbon. However, recent research has emerged that the organelle is involved in lipid synthesis, transportation, and metabolism, as well as mediating cellular protein storage and degradation. With the exception of multi-cellular organisms, some unicellular microorganisms have been observed to contain LDs. The organelle has been isolated and characterized from numerous organisms. Triacylglycerol (TAG)
more » ... ccumulation in LDs can be in excess of 50% of the dry weight in some microorganisms, and a maximum of 87% in some instances. These microorganisms include eukaryotes such as yeast and green algae as well as prokaryotes such as bacteria. Some organisms obtain carbon from CO2 via photosynthesis, while the majority utilizes carbon from various types of biomass. Therefore, high TAG content generated by utilizing waste or cheap biomass, coupled with an efficient conversion rate, present these organisms as bio-tech 'factories' to produce biodiesel. This review summarizes LD research in these organisms and provides useful information for further LD biological research and microorganism biodiesel development. [BMB Reports 2013; 46(12): 575-581] Invited Mini Review Lipid droplets in microorganisms Yingmei Liu, et al. BMB Reports
doi:10.5483/bmbrep.2013.46.12.271 pmid:24355300 pmcid:PMC4133864 fatcat:vctmc4wuibfmhbj6euylwqjjdm

Lipid Droplet Is an Ancient and Inheritable Organelle in Bacteria [article]

Xiang Chi, Ololade Omolara Ogunsade, Ziyun Zhou, Zemin Li, Xuehan Li, Mengwei Zhang, Fuhang Song, Jun Wang, Mirza Ahmed Hammad, Xuelin Zhang, Shuyan Zhang, Xia Wan (+3 others)
2020 bioRxiv   pre-print
Lipid droplet (LD) is a monolayer phospholipid membrane-bound organelle found in all eukaryotes and several prokaryotes which plays key roles in cellular lipid homeostasis and human health. The origin and evolution of the organelle remains unknown. Here, we report that through screening over 660 bacteria using biophysical and biochemical methods, plus LD isolation and proteomic tool, LDs were identified in most of these microbes, affiliated with five main bacterial phyla. Moreover, LDs were
more » ... identified in E. coli overexpressing lipid synthesis enzymes, indicating that bacteria without detectable LDs possessed the ability of LD biogenesis. The similarity of isolated LDs from representative strains and evolutionary analysis of LD major protein PspA demonstrate that LDs were conserved in bacteria. Furthermore, time-lapse imaging revealed that LDs were inheritable accompanying with bacterial growth and division. Finally, a common ancestor of LD-containing bacteria was predicted to originate 3.19 billion years ago by a phylogenetic analysis. Our findings suggest that LD is a widespread and inheritable organelle from an ancient common ancestor.
doi:10.1101/2020.05.18.103093 fatcat:jn6xglv6tbcizizumhklwjj6je

Electrochemical Energy Storage Properties of High-Porosity Foamed Cement

Changshun Zhou, Qidong Wang, Congyan Zhang
2022 Materials  
(Congyan Zhang); Project administration, C.Z. (Congyan Zhang); Funding acquisition, C.Z. (Congyan Zhang). All authors have read and agreed to the published version of the manuscript.  ... 
doi:10.3390/ma15072459 pmid:35407792 pmcid:PMC8999372 fatcat:j4rfj5p3cvgnfdg5fr73556rni

Tracing Evolutionary Footprints to Identify Novel Gene Functional Linkages

Yong Chen, Li Yang, Yunfeng Ding, Shuyan Zhang, Tong He, Fenglou Mao, Congyan Zhang, Huina Zhang, Chaoxing Huo, Pingsheng Liu, Marc Robinson-Rechavi
2013 PLoS ONE  
Systematic determination of gene function is an essential step in fully understanding the precise contribution of each gene for the proper execution of molecular functions in the cell. Gene functional linkage is defined as to describe the relationship of a group of genes with similar functions. With thousands of genomes sequenced, there arises a great opportunity to utilize gene evolutionary information to identify gene functional linkages. To this end, we established a computational method
more » ... led TRACE) to trace gene footprints through a gene functional network constructed from 341 prokaryotic genomes. TRACE performance was validated and successfully tested to predict enzyme functions as well as components of pathway. A so far undescribed chromosome partitioning-like protein ro03654 of an oleaginous bacteria Rhodococcus sp. RHA1 (RHA1) was predicted and verified experimentally with its deletion mutant showing growth inhibition compared to RHA1 wild type. In addition, four proteins were predicted to act as prokaryotic SNARE-like proteins, and two of them were shown to be localized at the plasma membrane. Thus, we believe that TRACE is an effective new method to infer prokaryotic gene functional linkages by tracing evolutionary events.
doi:10.1371/journal.pone.0066817 pmid:23825567 pmcid:PMC3692504 fatcat:imngrxnt4zeqxi7tqc6qvcefsq

Chromosome-level genome assembly of the humpback puffer, Tetraodon palembangensis

Rui Zhang, Chang Li, Mengjun Yu, Xiaoyun Huang, Mengqi Zhang, Shanshan Liu, Shanshan Pan, Weizhen Xue, Congyan Wang, Chunyan Mao, He Zhang, Guangyi Fan
2021 Gigabyte  
The humpback puffer, Tetraodon palembangensis, is a poisonous freshwater pufferfish species mainly distributed in Southeast Asia (Thailand, Laos, Malaysia and Indonesia). The humpback puffer has many interesting biological features, such as inactivity, tetrodotoxin production and body expansion. Here, we report the first chromosome-level genome assembly of the humpback puffer. The genome size is 362 Mb, with a contig N50 value of ∼1.78 Mb and a scaffold N50 value of ∼15.8 Mb. Based on this
more » ... e assembly, ∼61.5 Mb (18.11%) repeat sequences were identified, 19,925 genes were annotated, and the function of 90.01% of these genes could be predicted. Finally, a phylogenetic tree of ten teleost fish species was constructed. This analysis suggests that the humpback puffer and T. nigroviridis share a common ancestor 18.1 million years ago (MYA), and diverged from T. rubripes 45.8 MYA. The humpback puffer genome will be a valuable genomic resource to illustrate possible mechanisms of tetrodotoxin synthesis and tolerance.
doi:10.46471/gigabyte.17 fatcat:6mvaufsc75e7fanlxaq7i3wp7u

Mechanical and Thermal Properties of Low-Density Al20+xCr20-xMo20-yTi20V20+y Alloys

Uttam Bhandari, Congyan Zhang, Shizhong Yang
2020 Crystals  
To form a sold solution, Zhang et al. [38] proposed that ∆H mix should be −15 ≤ ∆H mix ≤ 5 kJ/mol, while Guo et al. [41] reported that ∆H mix should be −22 ≤ ∆H mix ≤ 7 kJ/mol.  ... 
doi:10.3390/cryst10040278 fatcat:lkaptttlmvabnncqzomazbzqji

Predicting Elastic Constants of Refractory Complex Concentrated Alloys Using Machine Learning Approach

Uttam Bhandari, Hamed Ghadimi, Congyan Zhang, Shizhong Yang, Shengmin Guo
2022 Materials  
Refractory complex concentrated alloys (RCCAs) have drawn increasing attention recently owing to their balanced mechanical properties, including excellent creep resistance, ductility, and oxidation resistance. The mechanical and thermal properties of RCCAs are directly linked with the elastic constants. However, it is time consuming and expensive to obtain the elastic constants of RCCAs with conventional trial-and-error experiments. The elastic constants of RCCAs are predicted using a
more » ... n of density functional theory simulation data and machine learning (ML) algorithms in this study. The elastic constants of several RCCAs are predicted using the random forest regressor, gradient boosting regressor (GBR), and XGBoost regression models. Based on performance metrics R-squared, mean average error and root mean square error, the GBR model was found to be most promising in predicting the elastic constant of RCCAs among the three ML models. Additionally, GBR model accuracy was verified using the other four RHEAs dataset which was never seen by the GBR model, and reasonable agreements between ML prediction and available results were found. The present findings show that the GBR model can be used to predict the elastic constant of new RHEAs more accurately without performing any expensive computational and experimental work.
doi:10.3390/ma15144997 pmid:35888464 pmcid:PMC9323025 fatcat:z4wk7nuyzjaudcdhx7pslsab4i

Bicolor angelfish (Centropyge bicolor) provides the first chromosome-level genome of the Pomacanthidae family

Chunhua Li, Xianwei Yang, Libin Shao, Rui Zhang, Qun Liu, Mengqi Zhang, Shanshan Liu, Shanshan Pan, Weizhen Xue, Congyan Wang, Chunyan Mao, He Zhang (+1 others)
2021 Gigabyte  
The Bicolor Angelfish, Centropyge bicolor, is a tropical coral reef fish. It is named for its striking two-color body. However, a lack of high-quality genomic data means little is known about the genome of this species. Here, we present a chromosome-level C. bicolor genome constructed using Hi-C data. The assembled genome is 650 Mbp in size, with a scaffold N50 value of 4.4 Mbp, and a contig N50 value of 114 Kbp. Protein-coding genes numbering 21,774 were annotated. Our analysis will help
more » ... to choose the most appropriate de novo genome sequencing strategy based on resources and target applications. To the best of our knowledge, this is the first chromosome-level genome for the Pomacanthidae family, which might contribute to further studies exploring coral reef fish evolution, diversity and conservation. Subjects Genetics and Genomics, Evolutionary Biology, Marine Biology DATA DESCRIPTION Background Centropyge bicolor (NCBI:txid109723; FishbaseID: 5454; urn:lsid:marinespecies.org:taxname:211780) (Figure 1 ), also known as the Bicolor, Two-Colored, or Pacific Rock Beauty Angelfish, is a showy coral reef fish commonly distributed in the Indo-Pacific ocean (from East Africa to the Samoan and Phoenix Islands, north to southern Japan, south to New Caledonia; throughout Micronesia). As a member of the Pomacanthidae family, it is similar to those of the Chaetodontidae (Butterflyfishes) but is distinguished by the presence of strong preopercle spines. C. bicolor has clear boundaries between its body colors, so might be a good model in which to study body color development in coral fish [1] . Context Although the availability of genetic, and especially genomic resources, remains limited for the Pomacanthidae family, we assembled the first C. bicolor reference genome. This will provide valuable information for genetic studies of this coral reef fish, and will contribute to studies in body color diversity. With the whole genome sequence of C. bicolor, it might be
doi:10.46471/gigabyte.32 fatcat:odwyp7yxnfdfhcowahznizkd7u

Performance of Carbide Alloy Compounds in Carbon Doped MoNbTaW

Congyan Zhang, Uttam Bhandari, Jialin Lei, Congyuan Zeng, Shengmin Guo, Hyunjoo Choi, Seungjin Nam, Jinyuan Yan, Shizhong Yang, Feng Gao
2021 Crystals  
In this work, the performance of the carbon doped compositionally complex alloy (CCA) MoNbTaW was studied under ambient and high pressure and high temperature conditions. TaC and NbC carbides were formed when a large concentration of carbon was introduced while synthesizing the MoNbTaW alloy. Both FCC carbides and BCC CCA phases were detected in the sample compound at room temperature, in which the BCC phase was believed to have only refractory elements MoNbTaW while FCC carbide came from TaC
more » ... d NbC. Carbides in the carbon doped MoNbTaW alloy were very stable since no phase transition was obtained even under 3.1 GPa and 870 °C by employing the resistor-heating diamond anvil cell (DAC) synchrotron X-ray diffraction technique. Via in situ examination, this study confirms the stability of carbides and MoNbTaW in the carbon doped CCA even under high pressure and high temperature.
doi:10.3390/cryst11091073 fatcat:tsqmbeixrvgvjltfwbgtbesptm

Alterations of Signaling Pathways in Essential Thrombocythemia with Calreticulin Mutation

Wuhan Hui, Wei Zhang, Congyan Liu, Suigui Wan, Wanling Sun, Li Su
2021 Cancer Management and Research  
Zhang and Dr. Fei Ye (Mount Sinai Hospital) for the technical support in PPA experiments.  ... 
doi:10.2147/cmar.s316919 pmid:34393515 pmcid:PMC8357313 fatcat:bkqts42syfgyfkkuwbdvkweley

Deep Learning-Based Hardness Prediction of Novel Refractory High-Entropy Alloys with Experimental Validation

Uttam Bhandari, Congyan Zhang, Congyuan Zeng, Shengmin Guo, Aashish Adhikari, Shizhong Yang
2021 Crystals  
(Congyan Zhang) and S.Y.; methodology, U.B. and A.A; software, U.B; C.Z. (Congyuan Zeng), A.A.; validation, C.Z. (Congyan Zhang), S.G. and S.Y.; formal analysis, C.Z.  ...  (Congyan Zhang); resources, S.Y.; data curation, A.A., and U.B.; writing-original draft preparation, U.B., C.Z.  ... 
doi:10.3390/cryst11010046 fatcat:f22yyuxfbbgzhhprwvxn2y53ri

Bacterial lipid droplets bind to DNA via an intermediary protein that enhances survival under stress

Congyan Zhang, Li Yang, Yunfeng Ding, Yang Wang, Lan Lan, Qin Ma, Xiang Chi, Peng Wei, Yongfang Zhao, Alexander Steinbüchel, Hong Zhang, Pingsheng Liu
2017 Nature Communications  
doi:10.1038/ncomms15979 pmid:28681845 pmcid:PMC5504291 fatcat:c3h5qnjk7vbeles2qbhjnvplpa

Hydroxysteroid dehydrogenase family proteins on lipid droplets through bacteria, C. elegans , and mammals

Yangli Liu, Shimeng Xu, Congyan Zhang, Xiaotong Zhu, Mirza Ahmed Hammad, Xuelin Zhang, Mark Christian, Hong Zhang, Pingsheng Liu
2018 Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids  
The authors thank Peng Zhang, Huimin Na, Kang Xie and Linxiang Qi for genetically technical assistance, Yaqin Deng and Xuejing Ma for assistance of adiposome construction and protein purification, Wenyan  ... 
doi:10.1016/j.bbalip.2018.04.018 pmid:29702244 fatcat:qilbc5dtufex3duffqkgmhbgtu
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