Papers by Chengcheng ZHOU [0707Q2]
Frontiers in Plant Science, Nov 24, 2022
Introduction: Quercus acutissima is an economic and ecological tree species often used for affore... more Introduction: Quercus acutissima is an economic and ecological tree species often used for afforestation of arid and semi-arid lands and is considered as an excellent tree for soil and water conservation. Methods: Here, we combined PacBio long reads, Hi-C, and Illumina short reads to assemble Q. acutissima genome. Results: We generated a 957.1 Mb genome with a contig N50 of 1.2 Mb and scaffold N50 of 77.0 Mb. The repetitive sequences constituted 55.63% of the genome, among which long terminal repeats were the majority and accounted for 23.07% of the genome. Ab initio, homology-based and RNA sequencebased gene prediction identified 29,889 protein-coding genes, of which 82.6% could be functionally annotated. Phylogenetic analysis showed that Q. acutissima and Q. variabilis were differentiated around 3.6 million years ago, and showed no evidence of species-specific whole genome duplication. Conclusion: The assembled and annotated high-quality Q. acutissima genome not only promises to accelerate the species molecular biology studies and breeding, but also promotes genome level evolutionary studies.
BMC Neuroscience, Dec 16, 2022
Background: Succinic semialdehyde dehydrogenase deficiency (SSADH-D) is an autosomal recessive ga... more Background: Succinic semialdehyde dehydrogenase deficiency (SSADH-D) is an autosomal recessive gamma-aminobutyric acid (GABA) metabolism disorder that can arise due to ALDH5A1 mutations, resulting in severe, progressive, untreatable neurodegeneration. SSADH-D is primarily studied using simplified models, such as HEK293 cells overexpressing genes of interest, but such overexpression can result in protein aggregation or pathway saturation that may not be representative of actual underlying disease phenotypes. Methods: We used a CRISPR/Cas9 approach to generate human iPSC cell lines bearing ALDH5A1 mutations. Through screening, two different mutant cell lines, NM_001080.3: c.727_735del (p.L243_S245del) and NM_001080.3: c.730_738del (p.A244_Q246del), were obtained. We induced iPSCs to neural stem cells and analyzed the characteristics of ALDH5A1 mutations in stem cells. Results: The human iPSC and NSC cell lines presented typical stem cell-like morphology. We found changes in ALDH5A1 expression and GABA accumulation in the different cell lines. In addition, by analyzing the cDNA between the wild-type and the mutant cell lines, we found that the mutant cell lines had a splicing variant. Conclusions: iPSCs represent a promising in vitro model for SSADH-D that can be used to study early central nervous system developmental alterations and pathogenic mechanisms.
International Journal of Molecular Sciences, Jul 2, 2021
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
arXiv (Cornell University), Dec 9, 2010
In this paper, a 3 × 3-matrix representation of Birman-Wenzl-Murakami(BWM) algebra has been prese... more In this paper, a 3 × 3-matrix representation of Birman-Wenzl-Murakami(BWM) algebra has been presented. Based on which, unitary matrices A(θ, ϕ1, ϕ2) and B(θ, ϕ1, ϕ2) are generated via Yang-Baxterization approach. A Hamiltonian is constructed from the unitary B(θ, ϕ) matrix. Then we study Berry phase of the Yang-Baxter system, and obtain the relationship between topological parameter and Berry phase.
arXiv (Cornell University), Apr 1, 2009
A method of constructing Temperley-Lieb algebras(TLA) representations has been introduced in [Xue... more A method of constructing Temperley-Lieb algebras(TLA) representations has been introduced in [Xue et.al arXiv:0903.3711]. Using this method, we can obtain another series of n 2 × n 2 matrices U which satisfy the TLA with the single loop d = √ n. Specifically, we present a 9 × 9 matrix U with d = √ 3. Via Yang-Baxterization approach, we obtain a unitaryȒ(θ, ϕ1, ϕ2)-matrix, a solution of the Yang-Baxter Equation. This 9 × 9 Yang-Baxter matrix is universal for quantum computing.
Brain Sciences
Neuropathic pain (NP) is a chronic and intractable disease that is widely present in the general ... more Neuropathic pain (NP) is a chronic and intractable disease that is widely present in the general population. It causes painful behavior and even mood changes such as anxiety and depression by altering the metabolism of substances. However, there have been limited metabolomics studies conducted in relation to neuropathic pain. Therefore, in this study, the effects of NP on metabolites in serum and the dorsal root ganglion (DRG) were investigated using a non-targeted metabolomics approach detected by gas chromatography–mass spectrometry (GC-MS) and liquid chromatography–mass spectrometry (LC-MS) to uncover differential metabolites and affected metabolic pathways associated with NP. Sixty mice were divided into the following two groups: a chronic constriction injury (CCI) of the sciatic nerve group and a sham group (n = 30, each). After 7 days of CCI modeling, the metabolite profiles of serum and the DRG were analyzed using GC/LC-MS for both the CCI and sham groups of mice. Multivariat...
Chemosensors
Gram-negative bacteria are difficult to kill due to their complex cell envelope, including the ou... more Gram-negative bacteria are difficult to kill due to their complex cell envelope, including the outer membrane (OM) and cytoplasmic membrane (CM). To monitor the membranolytic action of antimicrobials on Gram-negative bacteria would facilitate the development of effective antimicrobials. In this paper, an aggregation-induced emission luminogen (AIEgen) with microenvironment-sensitive properties was employed to indicate the interaction of antimicrobials with the OM and CM of Gram-negative bacteria. The damaged extent of OM and CM caused by antimicrobials with the change of dosage and incubation time can be visually captured based on the variation of two emission colors of IQ-Cm responding to OM-defective (green) and CM-disruptive bacteria (orange). Meanwhile, the activity assessment of antimicrobials can be easily realized within 1~2 h based on the distinct response of IQ-Cm to live and dead E. coli, which is much faster than the agar plate culture. This probe may shed light on the un...
Background: Succinic semialdehyde dehydrogenase deficiency (SSADH-D) is an autosomal recessive ga... more Background: Succinic semialdehyde dehydrogenase deficiency (SSADH-D) is an autosomal recessive gamma-aminobutyric acid (GABA) metabolism disorder that can arise due to ALDH5A1 mutations, resulting in severe, progressive, untreatable neurodegeneration. The SSADH-D is primarily studied using simplified model symptoms such as HEK293 cells overexpressing genes of interest, but such overexpression can result in protein aggregation or pathway saturation that may not be representative of actual underlying disease phenotypes. Methods: We utilized a CRISPR/Cas9 approach to generate human iPSC cell lines bearing ALDH5A1 mutations. Through screening, two different mutant cell lines, namely NM_001080.3: c.727_735del (p.L243_S245del) and NM_001080.3: c.730_738del (p.A244_Q246del) were obtained. Then, we induced iPSCs to neural stem cells and analyzed the characteristics of ALDH5A1 mutations in stem cells. Results: The hiPSC and NSC cell lines presented typical stem cell-like morphology. We found...
Background: Quercus acutissima is an economic and ecological tree species often used for afforest... more Background: Quercus acutissima is an economic and ecological tree species often used for afforestation of arid and semi-arid lands and is considered an excellent tree species for soil and water conservation. However, the Q. acutissima genome sequencing and assembly have not been reported, which limiting molecular biology studies and breeding progress in Q. acutissima.Results: We generated a 956.9 Mb genome with a contig N50 of 1,203,427 bp and 53,304 annotated genes. Meanwhile, the assembled contigs (1,507) assigned to a total of 12 chromosomes. The BUSCO database evaluation accounted for 98.0% of the genome size and the genome heterozygous rate was 0.25%. Repetitive sequences constituted 57.13% of the assembled genome, the most abundant one was long terminal repeats (7.18% of the genome). Phylogenetic analysis showed that Q. acutissima and Fagus sylvatica were differentiated around 54.2 million years ago (Mya), and Q. sober was differentiated around 4.4 Mya. Conclusion: We sequence...
Scientific Reports, 2021
In this paper, we investigate the Yangian relations of Heisenberg spin chain systems. Firstly, we... more In this paper, we investigate the Yangian relations of Heisenberg spin chain systems. Firstly, we consider the closed XXZ spin chain model, through the Heisenberg spin XXZ model, we found the Hamiltonians for one kind system of three adjacent partial particles interaction systems. The model’s constitution rules of energy levels and energy states which expand from the few-particle system to multi-particle system have good regularity. In this system, we found Yangian’s law and illustrate it through graphs. Secondly, we further consider the closed XXZ spin chain’s generalization of other three neighboring particles interaction systems from few-particle system to multi-particle system. Finally, we also discussed the laws of the three adjacent particles system of some models, they are the XXZ model with twist boundary condition, the open XXZ spin chain model and the XXZ model containing the next neighbor. In addition, not only XXZ model, XXX model, XY model and Ising model, but the relev...
Proceedings of the 29th ACM International Conference on Multimedia, 2021
Video super-resolution (VSR) and video frame interpolation (VFI) are interdependent for enhancing... more Video super-resolution (VSR) and video frame interpolation (VFI) are interdependent for enhancing videos of low resolution and low frame rate. However, most studies treat VSR and temporal VFI as independent tasks. In this work, we design a spatial-temporal superresolution network based on exploring the interaction between VSR and VFI. The main idea is to improve the middle frame of VFI by the super-resolution (SR) frames and feature maps from VSR. In the meantime, VFI also provides extra information for VSR and thus, through interacting, the SR of consecutive frames of the original video can also be improved by the feedback from the generated middle frame. Drawing on this, our approach leverages a simple interaction of VSR and VFI and achieves state-of-the-art performance on various datasets. Due to such a simple strategy, our approach is universally applicable to any existing VSR or VFI networks for effectively improving their video enhancement performance.
Sensors, 2019
The progress of science and technology and the expansion of the Internet of Things make the infor... more The progress of science and technology and the expansion of the Internet of Things make the information transmission between communication infrastructure and wireless sensors become more and more convenient. For the power-limited wireless sensors, the life time can be extended through the energy-harvesting technique. Additionally, wireless sensors can use the unauthored spectrum resource to complete certain information transmission tasks based on cognitive radio. Harvesting enough energy from the environments, the wireless sensors, works as the second users (SUs) can lease spectrum resource from the primary user (PU) to finish their task and bring additional transmission cost to themselves. To minimize the overall cost of SUs and to maximize the spectrum profit of the PU during the information transmission period, we formulated a differential game model to solve the resource allocation problem in the cognitive radio wireless sensor networks with energy harvesting, considering the SU...
Stem Cells International, 2020
The establishment of human-induced pluripotent stem cell (iPSC) models from sporadic Alzheimer’s ... more The establishment of human-induced pluripotent stem cell (iPSC) models from sporadic Alzheimer’s disease (sAD) patients is necessary and could potentially benefit research into disease etiology and therapeutic strategies. However, the development of sAD iPSC models is still limited due to the multifactorial nature of the disease. Here, we extracted peripheral blood mononuclear cells (PBMCs) from a patient with sAD and induced them into iPSC by introducing the Sendai virus expressing Oct3/4, Sox2, c-Myc, and Klf4, which were subsequently induced into neural cells to build the cell model of AD. Using alkaline phosphatase staining, immunofluorescence staining, karyotype analysis, reverse transcription-polymerase chain reaction (RT-PCR), and teratoma formation in vitro, we demonstrated that the iPSC derived from PMBCs (PBMC-iPSC) had a normal karyotype and potential to differentiate into three embryonic layers. Immunofluorescence staining and quantitative real-time polymerase chain reac...
Medicinal Plant Research, 2020
To reveal the sequence characteristics of MoTPS gene of Morinda officinalis and its expression pa... more To reveal the sequence characteristics of MoTPS gene of Morinda officinalis and its expression pattern under auxin (IAA) treatment. The coding sequence of three MoTPS genes were obtained by RT-PCR, they were named separately MoTPS1, MoTPS2 and MoTPS3. Gene sequence analysis showed that the full-length sequence of three MoTPS genes were separately 2 841 bp, 2 126 bp and 2 144 bp, and contained separately 2 481 bp, 1 668 bp and 1 943 bp open reading frame (ORF), encoding separately 826, 555 and 640 amino acids. The sequence analysis results showed that proteins encoded by three MoTPS genes were hydrophilic unstable protein and amino acid sequences of three genes contained terpenoid specific aspartic acid (DDxxD) enrichment motif, RxR conservative motif, and terpenoid class I superfamily domain. Homology analysis showed that amino acid sequences of three MoTPS genes were similar to TPS gene matched in Coffea Arabica, and these plants belonged to Rubiaceae. Phylogenetic tree analysis showed that MoTPS1 belongs to TPS-f subfamily, but MoTPS2 and MoTPS3 belong to TPS-d subfamily. Among the three MoTPS genes, MoTPS3 gene was screened for promoter isolation，the length of 5 'end promoter sequence was 739 bp, including a variety of regulatory elements related to light response, stress response and hormone response, such as G-box, Sp1, P-box, TGA-element etc. Fluorescence quantitative PCR analysis showed that the expression of three MoTPS genes were stable and tissue-specific in roots, shoots and leaves. the relative expression levels of three MoTPS genes were significantly up-regulated after IAA treatment. Therefore, this study has speculated that three MoTPS genes are involved in the synthesis of terpenoid secondary metabolites in root of Morinda officinalis and auxin IAA was predicted to play important role in the regulation of MoTPS gene expression.
Translational Cancer Research, 2020
Background: Melanoma is one of the most lethal cancers in China, and the genomic landscape of mel... more Background: Melanoma is one of the most lethal cancers in China, and the genomic landscape of melanoma in the Asian population is different from Caucasians. Methods: To better understand the genomic profile of distinct kinds of melanomas in China, we used an NGS platform to analysis of 62 melanomas from the southeast coast of China. Results: The recurrently mutated genes are BRAF (29%), RAS (29%), CTNNB1 (11.3%), KIT (9.7%) and NF1 (8.1%) in the whole group. Among the different types of melanoma, cutaneous melanoma has a high frequency of BRAF mutation (70.6%), NRAS (57.1%) is the top one gene found in the mucosal group. For acral melanoma, except for the RAS family, CTNNB1 mutation (13.2%) first found to be frequently mutated in our cohort and patients with CTNNB1 activating mutation. These results may be related to a more reduced response to immunotherapy, according to the earlier report. Conclusions: Our study profiled the mutational landscape of melanoma in patients from the southeast coast of China. In addition to the most frequently mutated genes (BRAF, RAS, KIT) reported in other studies, we found some new recurrent gene mutations, such as CTNNB1 mutation in acral melanoma, that had not been reported in other studies.
Wireless Communications and Mobile Computing, 2020
The last few years have seen the great potential of artificial intelligence (AI) technology to ef... more The last few years have seen the great potential of artificial intelligence (AI) technology to efficiently and effectively deal with an incredible deluge of data generated by the Internet of Things (IoT) devices. If all the massive data is transferred to the cloud for intelligent processing, it not only brings considerable challenges to the network bandwidth but also cannot meet the needs of AI applications that require fast and real-time response. Therefore, to achieve this requirement, mobile or multiaccess edge computing (MEC) is receiving a substantial amount of interest, and its importance is gradually becoming more prominent. However, with the emerging of edge intelligence, AI also suffers from several tremendous security threats in AI model training, AI model inference, and private data. This paper provides three novel defense strategies to tackle malicious attacks in three aspects. First of all, we introduce a cloud-edge collaborative antiattack scheme to realize a reliable ...
Background Sarcandra glabra is an evergreen and traditional Chinese herb, having medicinal signif... more Background Sarcandra glabra is an evergreen and traditional Chinese herb, having medicinal significance as anti-oxidant, anti-bacterial, anti-inflammatory, and anti-tumor. Recently, China has initiated to establish cultivation of this plant in greenhouse under artificial light-emitting diodes (LED). However, little is known regarding the effects of the different LED lights on plant growth, accumulation pattern of secondary metabolites, and the molecular mechanism of Sarcandra glabra. Results Compared to white light (WL), the red light (RL) increased the height and decreased the stem diameter and leaf area, while blue light (BL) suppressed the height and leaf area. According to our transcriptome profiling, some differentially expressed genes (DEGs) were enriched in the phenylpropanoid biosynthesis. We identified 46 unigenes encoding for almost all known enzymes involved in phenylpropanoid biosynthesis, while the expression level of RNA-seq and qPCR were largely consistent. Meanwhile,...
Journal of Clinical Laboratory Analysis, 2019
ObjectiveTo detect the levels of signal transducer and activator of transcription 4 (STAT4) and s... more ObjectiveTo detect the levels of signal transducer and activator of transcription 4 (STAT4) and soluble endoglin (sEng) in preeclampsia patients and analyze the diagnostic values of STAT4 and sEng in preeclampsia.MethodsFifty‐four pregnant women with preeclampsia from October 2017 to June 2018 were included in this study. Twenty‐eight matched healthy pregnant women were set as the control group. The general clinical characteristics were measured. Serum STAT4 and sEng were detected by ELISA. Correlation between STAT4 and sEng, and their diagnostic value in preeclampsia were analyzed.ResultsCompared with control, the prothrombin time in preeclampsia was significantly lower, while the mean arterial pressure, 24‐hour urine protein, serum creatinine, fibrinogen, and ALT were significantly higher. The circulating levels of STAT4 and sEng were significantly increased in the preeclampsia. The serum levels of STAT4 and sEng in preeclampsia were positively correlated. For the diagnosis of pre...
ACS Applied Bio Materials, 2018
Gemini-type peptide amphiphiles 12-(Lys) n-12 (n = 2, 4, and 6) with different lysine spacer leng... more Gemini-type peptide amphiphiles 12-(Lys) n-12 (n = 2, 4, and 6) with different lysine spacer lengths have been established and exhibit excellent antibacterial activities. By varying the lysine number in the spacer, the distinct aggregates with zero ∼ three dimentional structures (fibers, short rods and spherical aggregates) are formed. These different length/diameter ratios of aggregates have great effects on the antibacterial activities and cytotoxicity. 12-(Lys) 2-12 has a relatively higher MIC value and shows toxicity toward mammalian cells just above its MIC value, while 12-(Lys) 4-12 and 12-(Lys) 6-12 have lower MIC values and no cytotoxicity even at 5 times MIC values.
Nature communications, Jan 20, 2017
Proteins can readily assemble into rigid, crystalline and functional structures such as viral cap... more Proteins can readily assemble into rigid, crystalline and functional structures such as viral capsids and bacterial compartments. Despite ongoing advances, it is still a fundamental challenge to design and synthesize protein-mimetic molecules to form crystalline structures. Here we report the lattice self-assembly of cyclodextrin complexes into a variety of capsid-like structures such as lamellae, helical tubes and hollow rhombic dodecahedra. The dodecahedral morphology has not hitherto been observed in self-assembly systems. The tubes can spontaneously encapsulate colloidal particles and liposomes. The dodecahedra and tubes are respectively comparable to and much larger than the largest known virus. In particular, the resemblance to protein assemblies is not limited to morphology but extends to structural rigidity and crystallinity-a well-defined, 2D rhombic lattice of molecular arrangement is strikingly universal for all the observed structures. We propose a simple design rule for...
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Papers by Chengcheng ZHOU [0707Q2]