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Article ; Online: Compound Kushen injection reduces severity of radiation-induced gastrointestinal mucositis in rats

Yuka Harata-Lee / Zhipeng Qu / Emma Bateman / Xi Xiao / Marianne D. Keller / Joanne Bowen / Wei Wang / David L. Adelson

Frontiers in Oncology, Vol

2022 Volume 12

Abstract: Mucositis, or damage/injury to mucous membranes of the alimentary, respiratory, or genitourinary tract, is the major side effect associated with anticancer radiotherapies. Because there is no effective treatment for mucositis at present, this is a ... ...

Abstract	Mucositis, or damage/injury to mucous membranes of the alimentary, respiratory, or genitourinary tract, is the major side effect associated with anticancer radiotherapies. Because there is no effective treatment for mucositis at present, this is a particular issue as it limits the dose of therapy in cancer patients and significantly affects their quality of life. Gastrointestinal mucositis (GIM) occurs in patients receiving radiotherapies to treat cancers of the stomach, abdomen, and pelvis. It involves inflammation and ulceration of the gastrointestinal (GI) tract causing diarrhea, nausea and vomiting, abdominal pain, and bloating. However, there is currently no effective treatment for this debilitating condition. In this study, we investigated the potential of a type of traditional Chinese medicine (TCM), compound Kushen injection (CKI), as a treatment for GIM. It has previously been shown that major groups of chemical compounds found in CKI have anti-inflammatory effects and are capable of inhibiting the expression of pro-inflammatory cytokines. Intraperitoneal administration of CKI to Sprague Dawley (SD) rats that concurrently received abdominal irradiation over five fractions resulted in reduced severity of GIM symptoms compared to rats administered a vehicle control. Histological examination of the intestinal tissues revealed significantly less damaged villus epithelium in CKI-administered rats that had reduced numbers of apoptotic cells in the crypts. Furthermore, it was also found that CKI treatment led to decreased levels of inflammatory factors including lower levels of interleukin (IL)-1β and IL-6 as well as myeloperoxidase (MPO)-producing cells in the intestinal mucosa. Together, our data indicate a novel effect of CKI to reduce the symptoms of radiation-induced GIM by inhibiting inflammation in the mucosa and apoptosis of epithelial cells.
Keywords	Compound Kushen injection ; gastrointestinal mucositis ; radiation injury ; traditional Chinese medicine ; inflammatory markers ; Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282
Subject code	610
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Fast Self-Adaptive Digital Camouflage Design Method Based on Deep Learning

Houdi Xiao / Zhipeng Qu / Mingyun Lv / Yi Jiang / Chuanzhi Wang / Ruiru Qin

Applied Sciences, Vol 10, Iss 5284, p

2020 Volume 5284

Abstract: Traditional digital camouflage is mainly designed for a single background and state. Its camouflage performance is appealing in the specified time and place, but with the change of place, season, and time, its camouflage performance is greatly weakened. ... ...

Abstract	Traditional digital camouflage is mainly designed for a single background and state. Its camouflage performance is appealing in the specified time and place, but with the change of place, season, and time, its camouflage performance is greatly weakened. Therefore, camouflage technology, which can change with the environment in real-time, is the inevitable development direction of the military camouflage field in the future. In this paper, a fast-self-adaptive digital camouflage design method based on deep learning is proposed for the new generation of adaptive optical camouflage. Firstly, we trained a YOLOv3 model that could identify four typical military targets with mean average precision (mAP) of 91.55%. Secondly, a pre-trained deepfillv1 model was used to design the preliminary camouflage texture. Finally, the preliminary camouflage texture was standardized by the k-means algorithm. The experimental results show that the camouflage pattern designed by our proposed method is consistent with the background in texture and semantics, and has excellent camouflage performance in optical camouflage. Meanwhile, the whole pattern generation process takes a short time, less than 0.4 s, which meets the camouflage design requirements of the near-real-time camouflage in the future.
Keywords	adaptive camouflage ; convolutional neural network (CNN) ; k-means ; object detection ; image completion ; machine learning ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	006
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Distribution, contamination and accumulation of heavy metals in water, sediments, and freshwater shellfish from Liuyang River, Southern China

Jia, Yuyu / Lin Wang / Zhipeng Qu / Zhaoguang Yang

Environmental science and pollution research international. 2018 Mar., v. 25, no. 7

2018

Abstract: Heavy metal distributions in water, sediments, and freshwater shellfish collected from Liuyang River in China have been investigated. The concentrations of heavy metals including Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Cd, and Pb were determined by ICP-MS. The ... ...

Abstract	Heavy metal distributions in water, sediments, and freshwater shellfish collected from Liuyang River in China have been investigated. The concentrations of heavy metals including Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Cd, and Pb were determined by ICP-MS. The distribution pattern of heavy metals in sediments was different from that in water. Large coefficients of variation of heavy metal concentrations were observed in water due to the susceptibility to discharge fluctuation and seasonal variation. Multivariate statistical analysis such as Pearson’s correlation analysis, hierarchical cluster analysis (HCA), and principal component analysis (PCA) were employed to identify the possible sources of heavy metals in sediments. These heavy metals were categorized into three distinct groups, one was derived from natural existence and two were associated with anthropogenic activities. Five shellfish species including three species of gastropod mollusks (Parafossarulus eximius, Semisulcospira cancellata, and Pomacea canaliculata) and two species of bivalve mollusks (Corbicula fluminea and Anodonta woodiana) were collected and investigated. The distribution pattern of heavy metals in shellfish species was visualized by the nonmetric multidimensional scaling (NMDS) plot. The metal pollution index (MPI) values for the shellfish species were in the descending order of C. fluminea > A. woodiana > S. cancellata > P. eximius > P. canaliculata.
Keywords	Anodonta woodiana ; Corbicula fluminea ; Pomacea canaliculata ; anthropogenic activities ; arsenic ; cadmium ; chromium ; cobalt ; copper ; correlation ; freshwater ; heavy metals ; iron ; lead ; manganese ; molluscs ; multidimensional scaling ; multivariate analysis ; nickel ; pollution ; principal component analysis ; rivers ; seasonal variation ; sediments ; shellfish ; zinc ; China
Language	English
Dates of publication	2018-03
Size	p. 7012-7020.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-017-1068-x
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Bovine ncRNAs are abundant, primarily intergenic, conserved and associated with regulatory genes.

Zhipeng Qu / David L Adelson

PLoS ONE, Vol 7, Iss 8, p e

2012 Volume 42638

Abstract: It is apparent that non-coding transcripts are a common feature of higher organisms and encode uncharacterized layers of genetic regulation and information. We used public bovine EST data from many developmental stages and tissues, and developed a ... ...

Abstract	It is apparent that non-coding transcripts are a common feature of higher organisms and encode uncharacterized layers of genetic regulation and information. We used public bovine EST data from many developmental stages and tissues, and developed a pipeline for the genome wide identification and annotation of non-coding RNAs (ncRNAs). We have predicted 23,060 bovine ncRNAs, 99% of which are un-annotated, based on known ncRNA databases. Intergenic transcripts accounted for the majority (57%) of the predicted ncRNAs and the occurrence of ncRNAs and genes were only moderately correlated (r = 0.55, p-value<2.2e-16). Many of these intergenic non-coding RNAs mapped close to the 3' or 5' end of thousands of genes and many of these were transcribed from the opposite strand with respect to the closest gene, particularly regulatory-related genes. Conservation analyses showed that these ncRNAs were evolutionarily conserved, and many intergenic ncRNAs proximate to genes contained sequence-specific motifs. Correlation analysis of expression between these intergenic ncRNAs and protein-coding genes using RNA-seq data from a variety of tissues showed significant correlations with many transcripts. These results support the hypothesis that ncRNAs are common, transcribed in a regulated fashion and have regulatory functions.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2012-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification and comparative analysis of ncRNAs in human, mouse and zebrafish indicate a conserved role in regulation of genes expressed in brain.

Zhipeng Qu / David L Adelson

PLoS ONE, Vol 7, Iss 12, p e

2012 Volume 52275

Abstract: ncRNAs (non-coding RNAs), in particular long ncRNAs, represent a significant proportion of the vertebrate transcriptome and probably regulate many biological processes. We used publically available ESTs (Expressed Sequence Tags) from human, mouse and ... ...

Abstract	ncRNAs (non-coding RNAs), in particular long ncRNAs, represent a significant proportion of the vertebrate transcriptome and probably regulate many biological processes. We used publically available ESTs (Expressed Sequence Tags) from human, mouse and zebrafish and a previously published analysis pipeline to annotate and analyze the vertebrate non-protein-coding transcriptome. Comparative analysis confirmed some previously described features of intergenic ncRNAs, such as a positionally biased distribution with respect to regulatory or development related protein-coding genes, and weak but clear sequence conservation across species. Significantly, comparative analysis of developmental and regulatory genes proximate to long ncRNAs indicated that the only conserved relationship of these genes to neighbor long ncRNAs was with respect to genes expressed in human brain, suggesting a conserved, ncRNA cis-regulatory network in vertebrate nervous system development. Most of the relationships between long ncRNAs and proximate coding genes were not conserved, providing evidence for the rapid evolution of species-specific gene associated long ncRNAs. We have reconstructed and annotated over 130,000 long ncRNAs in these three species, providing a significantly expanded number of candidates for functional testing by the research community.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2012-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The effect of compound kushen injection on cancer cells

Jian Cui / Zhipeng Qu / Yuka Harata-Lee / Hanyuan Shen / Thazin Nwe Aung / Wei Wang / R Daniel Kortschak / David L Adelson

PLoS ONE, Vol 15, Iss 7, p e

Integrated identification of candidate molecular mechanisms.

2020 Volume 0236395

Abstract: Traditional Chinese Medicine (TCM) preparations are often extracts of single or multiple herbs containing hundreds of compounds, and hence it has been difficult to study their mechanisms of action. Compound Kushen Injection (CKI) is a complex mixture of ... ...

Abstract	Traditional Chinese Medicine (TCM) preparations are often extracts of single or multiple herbs containing hundreds of compounds, and hence it has been difficult to study their mechanisms of action. Compound Kushen Injection (CKI) is a complex mixture of compounds extracted from two medicinal plants and has been used in Chinese hospitals to treat cancer for over twenty years. To demonstrate that a systematic analysis of molecular changes resulting from complex mixtures of bioactives from TCM can identify a core set of differentially expressed (DE) genes and a reproducible set of candidate pathways. We used in vitro cancer models to measure the effect of CKI on cell cycle phases and apoptosis, and correlated those phenotypes with CKI induced changes in gene expression. We treated two cancer cell lines with or without CKI and assessed the resulting phenotypes by employing cell viability and proliferation assays. Based on these results, we carried out high-throughput transcriptome data analysis to identify genes and candidate pathways perturbed by CKI. We integrated these differential gene expression results with previously reported results and carried out validation of selected differentially expressed genes. CKI induced cell-cycle arrest and apoptosis in the cancer cell lines tested. In these cells CKI also altered the expression of 363 core candidate genes associated with cell cycle, apoptosis, DNA replication/repair, and various cancer pathways. Of these, 7 are clinically relevant to cancer diagnosis or therapy, 14 are cell cycle regulators, and most of these 21 candidates are downregulated by CKI. Comparison of our core candidate genes to a database of plant medicinal compounds and their effects on gene expression identified one-to-one, one-to-many and many-to-many regulatory relationships between compounds in CKI and DE genes. By identifying genes and promising candidate pathways associated with CKI treatment based on our transcriptome-based analysis, we have shown that this approach is useful for the ...
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Understanding the Effectiveness of Natural Compound Mixtures in Cancer through Their Molecular Mode of Action

Thazin Nwe Aung / Zhipeng Qu / R. Daniel Kortschak / David L. Adelson

International Journal of Molecular Sciences, Vol 18, Iss 3, p

2017 Volume 656

Abstract: Many approaches to cancer management are often ineffective due to adverse reactions, drug resistance, or inadequate target specificity of single anti-cancer agents. In contrast, a combinatorial approach with the application of two or more anti-cancer ... ...

Abstract	Many approaches to cancer management are often ineffective due to adverse reactions, drug resistance, or inadequate target specificity of single anti-cancer agents. In contrast, a combinatorial approach with the application of two or more anti-cancer agents at their respective effective dosages can achieve a synergistic effect that boosts cytotoxicity to cancer cells. In cancer, aberrant apoptotic pathways allow cells that should be killed to survive with genetic abnormalities, leading to cancer progression. Mutations in apoptotic mechanism arising during the treatment of cancer through cancer progression can consequently lead to chemoresistance. Natural compound mixtures that are believed to have multiple specific targets with minimal acceptable side-effects are now of interest to many researchers due to their cytotoxic and chemosensitizing activities. Synergistic interactions within a drug mixture enhance the search for potential molecular targets in cancer cells. Nonetheless, biased/flawed scientific evidence from natural products can suggest false positive therapeutic benefits during drug screening. In this review, we have taken these factors into consideration when discussing the evidence for these compounds and their synergistic therapeutic benefits in cancer. While there is limited evidence for clinical efficacy for these mixtures, in vitro data suggest that these preparations merit further investigation, both in vitro and in vivo.
Keywords	cancer ; apoptosis ; chemosensitization ; microRNA ; natural compound mixtures ; metal derivatized natural compounds ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	610
Language	English
Publishing date	2017-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A New Strategy for Identifying Mechanisms of Drug-drug Interaction Using Transcriptome Analysis

Hanyuan Shen / Zhipeng Qu / Yuka Harata-Lee / Jian Cui / Thazin Nwe Aung / Wei Wang / R. Daniel Kortschak / David L. Adelson

Scientific Reports, Vol 9, Iss 1, Pp 1-

Compound Kushen Injection as a Proof of Principle

2019 Volume 12

Abstract: Abstract Drug-drug interactions (DDIs), especially with herbal medicines, are complex, making it difficult to identify potential molecular mechanisms and targets. We introduce a workflow to carry out DDI research using transcriptome analysis and ... ...

Abstract	Abstract Drug-drug interactions (DDIs), especially with herbal medicines, are complex, making it difficult to identify potential molecular mechanisms and targets. We introduce a workflow to carry out DDI research using transcriptome analysis and interactions of a complex herbal mixture, Compound Kushen Injection (CKI), with cancer chemotherapy drugs, as a proof of principle. Using CKI combined with doxorubicin or 5-Fu on cancer cells as a model, we found that CKI enhanced the cytotoxic effects of doxorubicin on A431 cells while protecting MDA-MB-231 cells treated with 5-Fu. We generated and analysed transcriptome data from cells treated with single treatments or combined treatments and our analysis showed that opposite directions of regulation for pathways related to DNA synthesis and metabolism which appeared to be the main reason for different effects of CKI when used in combination with chemotherapy drugs. We also found that pathways related to organic biosynthetic and metabolic processes might be potential targets for CKI when interacting with doxorubicin and 5-Fu. Through co-expression analysis correlated with phenotype results, we selected the MYD88 gene as a candidate major regulator for validation as a proof of concept for our approach. Inhibition of MYD88 reduced antagonistic cytotoxic effects between CKI and 5-Fu, indicating that MYD88 is an important gene in the DDI mechanism between CKI and chemotherapy drugs. These findings demonstrate that our pipeline is effective for the application of transcriptome analysis to the study of DDIs in order to identify candidate mechanisms and potential targets.
Keywords	Medicine ; R ; Science ; Q
Subject code	004
Language	English
Publishing date	2019-11-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Understanding the Mechanistic Contribution of Herbal Extracts in Compound Kushen Injection With Transcriptome Analysis

Hanyuan Shen / Zhipeng Qu / Yuka Harata-Lee / Thazin Nwe Aung / Jian Cui / Wei Wang / R. Daniel Kortschak / David L. Adelson

Frontiers in Oncology, Vol

2019 Volume 9

Abstract: Herbal compatibility is the knowledge of which herbs to combine in traditional Chinese medicine (TCM) formulations. The lack of understanding of herbal compatibility is one of the key problems for the application and popularization of TCM in western ... ...

Abstract	Herbal compatibility is the knowledge of which herbs to combine in traditional Chinese medicine (TCM) formulations. The lack of understanding of herbal compatibility is one of the key problems for the application and popularization of TCM in western society. Because of the chemical complexity of herbal medicines, it is simpler to begin to conduct compatibility research based on herbs rather than component plant secondary metabolites. We have used transcriptome analysis to explore the effects and interactions of two plant extracts (Kushen and Baituling) combined in Compound Kushen Injection (CKI). Based on shared chemical compounds and in vitro cytotoxicity comparisons, we found that both the major compounds in CKI, and the cytotoxicity effects of CKI were mainly derived from the extract of Kushen (Sophorae flavescentis). We generated and analyzed transcriptome data from MDA-MB-231 cells treated with single-herb extracts or CKI and results showed that Kushen contributed to the perturbation of the majority of cytotoxicity/cancer related pathways in CKI such as cell cycle and DNA replication. We also found that Baituling (Heterosmilax yunnanensis Gagnep) could not only enhance the cytotoxic effects of Kushen in CKI, but also activate immune-related pathways. Our analyses predicted that IL-1β gene expression was upregulated by Baituling in CKI and we confirmed that IL-1β protein expression was increased using an ELISA assay. Altogether, these findings help to explain the rationale for combining Kushen and Baituling in CKI, and show that transcriptome analysis using single herb extracts is an effective method for understanding herbal compatibility in TCM.
Keywords	transcriptome ; herb combination ; traditional Chinese medicine ; cancer treatment ; Compound Kushen Injection ; Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282
Subject code	500
Language	English
Publishing date	2019-07-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Contribution of filamentous fungi to the musty odorant 2,4,6-trichloroanisole in water supply reservoirs and associated drinking water treatment plants

Bai, Xiuzhi / Haipu Li / Ting Zhang / Zhaoguang Yang / Zhipeng Qu

Chemosphere. 2017,

2017

Abstract: In this study, the distribution of 2,4,6-trichloroanisole (2,4,6-TCA) in two water supply reservoirs and four associated drinking water treatment plants (DWTPs) were investigated. The 2,4,6-TCA concentrations were in the range of 1.53â2.36Â ngÂ Lâ1 ... ...

Abstract	In this study, the distribution of 2,4,6-trichloroanisole (2,4,6-TCA) in two water supply reservoirs and four associated drinking water treatment plants (DWTPs) were investigated. The 2,4,6-TCA concentrations were in the range of 1.53â2.36Â ngÂ Lâ1 in water supply reservoirs and 0.76â6.58Â ngÂ Lâ1 at DWTPs. To determine the contribution of filamentous fungi to 2,4,6-TCA in a full-scale treatment process, the concentrations of 2,4,6-TCA in raw water, settled water, post-filtration water, and finished water were measured. The results showed that 2,4,6-TCA levels continuously increased until chlorination, suggesting that 2,4,6-TCA could form without a chlorination reaction and fungi might be the major contributor to the 2,4,6-TCA formation. Meanwhile, twenty-nine fungal strains were isolated and identified by morphological and molecular biological methods. Of the seventeen isolated fungal species, eleven showed the capability to convert 2,4,6-trichlorophenol (2,4,6-TCP) to 2,4,6-TCA. The highest level of 2,4,6-TCA formation was carried out by Aspergillus versicolor voucher BJ1-3: 40.5% of the original 2,4,6-TCP was converted to 2,4,6-TCA. There was a significant variation in the capability of different species to generate 2,4,6-TCA. The results from the proportions of cell-free, cell-attached, and cell-bound 2,4,6-TCA suggested that 2,4,6-TCA generated by fungi was mainly distributed in their extracellular environment. In addition to 2,4,6-TCA, five putative volatile by-products were also identified by gas chromatography and mass spectrometry. These findings increase our understanding on the mechanisms involved in the formation of 2,4,6-TCA and provide insights into managing and controlling 2,4,6-TCA-related problems in drinking water.
Keywords	Aspergillus versicolor ; byproducts ; chlorination ; drinking water ; fungi ; gas chromatography ; mass spectrometry ; odor compounds ; water supply ; water treatment
Language	English
Size	p. .
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
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.2017.04.138
Database	NAL-Catalogue (AGRICOLA)

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