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  1. Article ; Online: Protocol for Bulk-ATAC sequencing in head and neck squamous cell carcinoma

    Nana Chen / Manik Vohra / Srinivas Vinod Saladi

    STAR Protocols, Vol 4, Iss 2, Pp 102233- (2023)

    2023  

    Abstract: Summary: The transposase-accessible chromatin using sequencing (ATAC-seq) offers a simplified approach to detect chromatin changes in cancer cells after genetic intervention and drug treatment. Here, we present an optimized ATAC-seq protocol to elucidate ...

    Abstract Summary: The transposase-accessible chromatin using sequencing (ATAC-seq) offers a simplified approach to detect chromatin changes in cancer cells after genetic intervention and drug treatment. Here, we present an optimized ATAC-seq protocol to elucidate chromatin accessibility changes at the epigenetic level in head and neck squamous cell carcinoma cells. We describe steps for cell lysate preparation, transposition, and tagmentation, followed by library amplification and purification. We then detail next-generation sequencing and data analysis.For complete details on the use and execution of this protocol, please refer to Buenrostro et al.,1 Chen et al.,2 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
    Keywords Cancer ; Genomics ; Molecular Biology ; Sequencing ; Science (General) ; Q1-390
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Supply chain resource scheduling optimization of e-commerce enterprises in international trade based on mobile edge computing

    Qingxia Dong / Nana Chen / Shuai Wang

    PeerJ Computer Science, Vol 9, p e

    2023  Volume 1407

    Abstract: The cross-border e-commerce supply chain network (CBESCN) has extensive geographical coverage, trade barriers and complexity of cross-border logistics issues, which makes its construction and development face many challenges. This article focuses on ... ...

    Abstract The cross-border e-commerce supply chain network (CBESCN) has extensive geographical coverage, trade barriers and complexity of cross-border logistics issues, which makes its construction and development face many challenges. This article focuses on solving the operation optimisation problem of CBESCN under the background of the Internet of Things. A genetic algorithm constructed and solved the resource scheduling model of the supply chain of e-commerce enterprises in international trade. In addition, the mobile edge computing (MEC) optimisation scheme based on partial computation unloading is involved. The initial offload ratio is set and supply chain resources are allocated, then the remaining computing resources are distributed according to the server’s computing power. Finally, the offload is optimised according to the resource allocation. The experimental results show that time delay and cost adjustment strategies can improve the CBE supply chain’s comprehensive ability. The supply chain optimisation scheme proposed in this article can effectively use supply chain resources according to the requirements of computing tasks to reduce the total delay of task execution and the consumption of node computing.
    Keywords MEC ; International trade ; Supply chain ; Resource scheduling ; Electronic computers. Computer science ; QA75.5-76.95
    Subject code 380
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher PeerJ Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Identification and frequency analysis of drought–flood abrupt alternation events using a daily-scale standardized weighted average of the precipitation index

    Wan Zhou / Dedi Liu / Jiayu Zhang / Sainan Jiang / Shuying Xing / Junde Wang / Yufei Cheng / Nana Chen

    Frontiers in Environmental Science, Vol

    2023  Volume 11

    Abstract: Drought–flood abrupt alternation (DFAA), which is defined as the rapid transition between drought and flood in a short period, amplifies the negative impacts of individual drought or flood. DFAA is divided into drought to flood (DTF) and flood to drought ...

    Abstract Drought–flood abrupt alternation (DFAA), which is defined as the rapid transition between drought and flood in a short period, amplifies the negative impacts of individual drought or flood. DFAA is divided into drought to flood (DTF) and flood to drought (FTD) according to the sequences of drought and flood. Previous studies of identifying DFAA events have mostly been conducted over a long timescale (e.g., over a month), leading to inaccurate identification or omissions of DFAA events. In addition, frequency analysis of DTF and FTD events, which is vital for the design of hydraulic structures and water supply systems, has rarely been studied. This study establishes an identification method for DFAA events based on a daily-scale standardized weighted average of the precipitation index (SWAP) and conducts frequency analysis of DTF and FTD events based on copula theory. The Han River Basin (HRB), China, a crucial area for water resource management, was selected as the study area. Our findings disclose that DFAA events occurred less frequently with larger intensities and durations between 1961 and 2020. The temporal trends of DTF and FTD events varied similarly, while the number of DTF events were less than that of FTD events, indicating that FTD is the main performance of DFAA in HRB. In addition, the identification processes of DFAA events at the Wuhan station were analyzed in detail and proved that SWAP is an effective index for capturing the change of precipitation and accurately depicting the occurrences of droughts and floods. Furthermore, drought intensity (DI) and flood intensity (FI) were selected for bivariate frequency analysis. An OR case was defined as DI ≥ di or FI ≥ fi, while an AND case was defined as DI ≥ di and FI ≥ fi. The results of frequency analysis showed that joint return periods (JRPs) of DFAA events under the OR case are basically equal in three sub-basins, meaning a similar occurrence of probability of drought–flood disaster. JRPs under the AND case increased from the upper and middle ...
    Keywords drought–flood abrupt alternation ; SWAP ; identification ; frequency analysis ; copula theory ; Han River Basin ; Environmental sciences ; GE1-350
    Subject code 550
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Transcriptomics analysis reveals the effect of Broussonetia papyrifera L. fermented feed on meat quality traits in fattening lamb

    Xuejiao An / Shengwei Zhang / Taotao Li / Nana Chen / Xia Wang / Baojun Zhang / Youji Ma

    PeerJ, Vol 9, p e

    2021  Volume 11295

    Abstract: To date, utilization of feed grains is increasing, which competes for human food. It is imperative to develop and utilize unconventional feed materials. Broussonetia papyrifera L. (B. papyrifera) is a good feeding material with high crude protein, crude ... ...

    Abstract To date, utilization of feed grains is increasing, which competes for human food. It is imperative to develop and utilize unconventional feed materials. Broussonetia papyrifera L. (B. papyrifera) is a good feeding material with high crude protein, crude fat, and low crude fiber, which is widely distributed in China. In this study, 12 Dorper ♂×Hu ♀ crossbred weaned male lambs were seleted into four groups based on the feed that ratio of the B. papyrifera fermented feed in the total mixed diet (0%, 6%, 18%, and 100%), to character the lambs’ longissimus dorsi (LD) fatty acids, morphology and transcriptome. Results showed that the muscle fiber’s diameter and area were the smallest in the 100% group. The highest content of beneficial fatty acids and the lowest content of harmful fatty acids in group 18%. RNA-seq identified 443 differentially expressed genes (DEGs) in the LD of lambs from 4 groups. Among these genes, 169 (38.1%) were up-regulated and 274 (61.9%) were down-regulated. The DEGs were mostly enriched in in fatty acid metabolism, arginine and proline metabolism, and PPAR signaling pathways. Our results provide knowledge to understand effect of different ratios of B. papyrifera fermented feed on sheep meat quality traits, also a basis for understanding of the molecular regulation mechanism of B. papyrifera fermented feed affecting on sheep meat quality.
    Keywords B. papyrifera fermented feed ; Sheep ; Meat quality ; Transcriptome ; Medicine ; R ; Biology (General) ; QH301-705.5
    Subject code 630
    Language English
    Publishing date 2021-04-01T00:00:00Z
    Publisher PeerJ Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: The synergistic potential of biochar and nanoparticles in phytoremediation and enhancing cadmium tolerance in plants.

    Yasin, Muhammad Umair / Haider, Zulqarnain / Munir, Raheel / Zulfiqar, Usman / Rehman, Muhammad / Javaid, Muhammad Haseeb / Ahmad, Irshan / Nana, Chen / Saeed, Muhammad Sulaman / Ali, Bahar / Gan, Yinbo

    Chemosphere

    2024  Volume 354, Page(s) 141672

    Abstract: Cadmium (Cd) is classified as a heavy metal (HM) and is found into the environment through both natural processes and intensified anthropogenic activities such as industrial operations, mining, disposal of metal-laden waste like batteries, as well as ... ...

    Abstract Cadmium (Cd) is classified as a heavy metal (HM) and is found into the environment through both natural processes and intensified anthropogenic activities such as industrial operations, mining, disposal of metal-laden waste like batteries, as well as sludge disposal, excessive fertilizer application, and Cd-related product usage. This rising Cd disposal into the environment carries substantial risks to the food chain and human well-being. Inadequate regulatory measures have led to Cd bio-accumulation in plants, which is increasing in an alarming rate and further jeopardizing higher trophic organisms, including humans. In response, an effective Cd decontamination strategy such as phytoremediation emerges as a potent solution, with innovations in nanotechnology like biochar (BC) and nanoparticles (NPs) further augmenting its effectiveness for Cd phytoremediation. BC, derived from biomass pyrolysis, and a variety of NPs, both natural and less toxic, actively engage in Cd removal during phytoremediation, mitigating plant toxicity and associated hazards. This review scrutinizes the application of BC and NPs in Cd phytoremediation, assessing their synergistic mechanism in influencing plant growth, genetic regulations, structural transformations, and phytohormone dynamics. Additionally, the review also underscores the adoption of this sustainable and environmentally friendly strategies for future research in employing BC-NP microaggregates to ameliorate Cd phytoremediation from soil, thereby curbing ecological damage due to Cd toxicity.
    MeSH term(s) Humans ; Cadmium/analysis ; Biodegradation, Environmental ; Metals, Heavy/analysis ; Plants ; Soil/chemistry ; Nanoparticles ; Soil Pollutants/toxicity ; Soil Pollutants/analysis ; Charcoal
    Chemical Substances Cadmium (00BH33GNGH) ; biochar ; Metals, Heavy ; Soil ; Soil Pollutants ; Charcoal (16291-96-6)
    Language English
    Publishing date 2024-03-11
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 120089-6
    ISSN 1879-1298 ; 0045-6535 ; 0366-7111
    ISSN (online) 1879-1298
    ISSN 0045-6535 ; 0366-7111
    DOI 10.1016/j.chemosphere.2024.141672
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Oleylamine-Mediated Hydrothermal Growth of Millimeter-Long Cu Nanowires and Their Electrocatalytic Activity for Reduction of Nitrate

    Yifan Zheng / Nana Chen / Chunxiao Wang / Xiaoping Zhang / Zongjian Liu

    Nanomaterials, Vol 8, Iss 4, p

    2018  Volume 192

    Abstract: While high-aspect-ratio metal nanowires are essential for producing nanowire-based electrodes of good performance used in electronics and electrocatalysis, the synthesis of millimeter-long Cu nanowires remains a challenge. This work demonstrates an ... ...

    Abstract While high-aspect-ratio metal nanowires are essential for producing nanowire-based electrodes of good performance used in electronics and electrocatalysis, the synthesis of millimeter-long Cu nanowires remains a challenge. This work demonstrates an oleylamine-mediated hydrothermal method for synthesis of Cu nanowires with an average diameter of ~80 nm and a length up to several millimeters. An investigation on the role of oleylamine in nanowire formation by mass spectroscopy, small angle X-ray diffraction and transmission electron microscopy reveals that oleylamine serves as a mild reducing agent for slow reduction of Cu(II) to Cu, a complexing agent to form Cu(II)-oleylamine complex for guiding the nanowire growth, as well as a surfactant to generate lamellar phase structure for the formation of nanowire bundles. The growth mechanism of these millimeter-long Cu nanowire bundles is proposed based on the experimental observations. Electrochemical measurements by linear sweep voltammetry indicate that the self-supported nanowire electrode prepared from as-formed Cu nanowire bundles shows high catalytic activity for electroreduction of nitrate in water.
    Keywords Cu nanowires ; hydrothermal method ; oleylamine ; nitrate ; electroreduction ; Chemistry ; QD1-999
    Subject code 540
    Language English
    Publishing date 2018-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Cathelicidin-WA Protects Against LPS-Induced Gut Damage Through Enhancing Survival and Function of Intestinal Stem Cells

    Sisi Wang / Lixia Kai / Luoyi Zhu / Bocheng Xu / Nana Chen / Teresa G. Valencak / Yizhen Wang / Tizhong Shan

    Frontiers in Cell and Developmental Biology, Vol

    2021  Volume 9

    Abstract: Preservation of intestinal stem cells (ISCs) plays a critical role in initiating epithelial regeneration after intestinal injury. Cathelicidin peptides have been shown to participate in regulating intestinal damage repair. However, it is not known how ... ...

    Abstract Preservation of intestinal stem cells (ISCs) plays a critical role in initiating epithelial regeneration after intestinal injury. Cathelicidin peptides have been shown to participate in regulating intestinal damage repair. However, it is not known how exactly Cathelicidin-WA (CWA) exert its function after tissue damage. Using a gut injury model in mice involving Lipopolysaccharide (LPS), we observed that CWA administration significantly improved intestinal barrier function, preserved ISCs survival, and augmented ISCs viability within the small intestine (SI) under LPS treatment. In addition, CWA administration effectively prevented proliferation stops and promoted the growth of isolated crypts. Mechanistically, our results show that the appearance of γH2AX was accompanied by weakened expression of SETDB1, a gene that has been reported to safeguard genome stability. Notably, we found that CWA significantly rescued the decreased expression of SETDB1 and reduced DNA damage after LPS treatment. Taken together, CWA could protect against LPS-induced gut damage through enhancing ISCs survival and function. Our results suggest that CWA may become an effective therapeutic regulator to treat intestinal diseases and infections.
    Keywords CWA ; intestinal stem cell ; intestinal barrier ; intestinal disease ; regeneration ; Biology (General) ; QH301-705.5
    Subject code 610
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Melatonin alleviated cadmium accumulation and toxicity by modulating phytohormonal balance and antioxidant metabolism in rice.

    Munir, Raheel / Yasin, Muhammad Umair / Afzal, Muhammad / Jan, Mehmood / Muhammad, Sajid / Jan, Nazia / Nana, Chen / Munir, Faisal / Iqbal, Hamza / Tawab, Faiza / Gan, Yinbo

    Chemosphere

    2023  Volume 346, Page(s) 140590

    Abstract: Cadmium (Cd) contamination is an eminent dilemma that jeopardizes global food safety and security, especially through its phytotoxicity in rice; one of the most edible crops. Melatonin (MET) has emerged as a protective phytohormone in stress conditions, ... ...

    Abstract Cadmium (Cd) contamination is an eminent dilemma that jeopardizes global food safety and security, especially through its phytotoxicity in rice; one of the most edible crops. Melatonin (MET) has emerged as a protective phytohormone in stress conditions, but the defensive role and underlying mechanisms of MET against Cd toxicity in rice still remain unclear. To fulfill this knowledge gap, the present study is to uncover the key mechanisms for MET-mediated Cd-stress tolerance in rice. Cd toxicity significantly reduced growth by hindering the process of photosynthesis, cellular redox homeostasis, phytohormonal imbalance, and ultrastructural damages. Contrarily, MET supplementation considerably improved growth attributes, photosynthetic efficiency, and cellular ultrastructure as measured by gas exchange elements, chlorophyll content, reduced Cd accumulation, and ultrastructural analysis via transmission electron microscopy (TEM). MET treatment significantly reduced Cd accumulation (39.25%/31.58%), MDA (25.87%/19.45%), H
    MeSH term(s) Antioxidants/pharmacology ; Antioxidants/metabolism ; Cadmium/metabolism ; Plant Growth Regulators/metabolism ; Melatonin/metabolism ; Oryza/metabolism ; Hydrogen Peroxide/metabolism ; Oxidative Stress ; Superoxide Dismutase/metabolism
    Chemical Substances Antioxidants ; Cadmium (00BH33GNGH) ; Plant Growth Regulators ; Melatonin (JL5DK93RCL) ; Hydrogen Peroxide (BBX060AN9V) ; Superoxide Dismutase (EC 1.15.1.1)
    Language English
    Publishing date 2023-10-31
    Publishing country England
    Document type Journal Article
    ZDB-ID 120089-6
    ISSN 1879-1298 ; 0045-6535 ; 0366-7111
    ISSN (online) 1879-1298
    ISSN 0045-6535 ; 0366-7111
    DOI 10.1016/j.chemosphere.2023.140590
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Cloning, Molecular Characterization and Expression Patterns of DMRTC2 Implicated in Germ Cell Development of Male Tibetan Sheep

    Taotao Li / Hongyu Zhang / Xia Wang / De′en Yin / Nana Chen / Lingyun Kang / Xingxu Zhao / Youji Ma

    International Journal of Molecular Sciences, Vol 21, Iss 2448, p

    2020  Volume 2448

    Abstract: The double sex and mab-3-related transcription factors like family C2 ( DMRTC2 ) gene is indispensable for mammalian testicular function and spermatogenesis. Despite its importance, what expression and roles of DMRTC2 possesses and how it regulates the ... ...

    Abstract The double sex and mab-3-related transcription factors like family C2 ( DMRTC2 ) gene is indispensable for mammalian testicular function and spermatogenesis. Despite its importance, what expression and roles of DMRTC2 possesses and how it regulates the testicular development and spermatogenesis in sheep, especially in Tibetan sheep, remains largely unknown. In this study, DMRTC2 cDNA from testes of Tibetan sheep was firstly cloned by the RT-PCR method, and its molecular characterization was identified. Subsequently, the expression and localization patterns of DMRTC2 were evaluated by quantitative real-time PCR (qPCR), Western blot, and immunofluorescence. The cloning and sequence analysis showed that the Tibetan sheep DMRTC2 cDNA fragment contained 1113 bp open reading frame (ORF) capable of encoding 370 amino acids, and displayed high identities with some other mammals, which shared an identical DM domain sequence of 47 amino acids ranged from residues 38 to 84. qPCR and Western blot results showed that DMRTC2 was expressed in testes throughout the development stages while not in epididymides (caput, corpus, and cauda), with higher mRNA and protein abundance in Tibetan sheep testes of one- and three-year-old (post-puberty) compared with that of three-month-old (pre-puberty). Immunofluorescence results revealed that immune staining for DMRTC2 protein was observed in spermatids and spermatogonia from post-puberty Tibetan sheep testes, and gonocytes from pre-puberty Tibetan sheep testes. Together, these results demonstrated, for the first time, in sheep, that DMRTC2 , as a highly conserved gene in mammals, is essential for sheep spermatogenesis by regulating the proliferation or differentiation of gonocytes and development of spermatids in ram testes at different stages of maturity.
    Keywords Tibetan sheep ; DMRTC2 ; cloning ; testis ; spermatogenesis ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 630
    Language English
    Publishing date 2020-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: YAP1 maintains active chromatin state in head and neck squamous cell carcinomas that promotes tumorigenesis through cooperation with BRD4

    Nana Chen / Gabriel Golczer / Subhoshree Ghose / Brian Lin / Adam Langenbucher / Jason Webb / Haymanti Bhanot / Nicholas B. Abt / Derrick Lin / Mark Varvares / Martin Sattler / Ann Marie Egloff / Richard Joh / Ravindra Uppaluri / Kevin S. Emerick / Michael S. Lawrence / Srinivas Vinod Saladi

    Cell Reports, Vol 39, Iss 11, Pp 110970- (2022)

    2022  

    Abstract: Summary: Analysis of The Cancer Genome Atlas and other published data of head and neck squamous cell carcinoma (HNSCC) reveals somatic alterations of the Hippo-YAP pathway in approximately 50% of HNSCC. Better strategies to target the YAP1 ... ...

    Abstract Summary: Analysis of The Cancer Genome Atlas and other published data of head and neck squamous cell carcinoma (HNSCC) reveals somatic alterations of the Hippo-YAP pathway in approximately 50% of HNSCC. Better strategies to target the YAP1 transcriptional complex are sought. Here, we show that FAT1, an upstream inhibitor of YAP1, is mutated either by missense or by truncating mutation in 29% of HNSCC. Comprehensive proteomic and drug-screening studies across pan-cancer models confirm that FAT1-mutant HNSCC exhibits selective and higher sensitivity to BRD4 inhibition by JQ1. Epigenomic analysis reveals an active chromatin state in FAT1-mutant HNSCC cells that is driven by the YAP/TAZ transcriptional complex through recruitment of BRD4 to deposit active histone marks, thereby maintaining an oncogenic transcriptional state. This study reveals a detailed cooperative mechanism between YAP1 and BRD4 in HNSCC and suggests a specific therapeutic opportunity for the treatment of this subset of head and neck cancer patients.
    Keywords CP: Cancer ; CP: Molecular biology ; Biology (General) ; QH301-705.5
    Subject code 004
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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