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1. A non-invasive piTreg-related gene signature for spontaneous tolerance in renal transplantation

Author:
Di Zhang; Yang Ye; Xiaopeng Hu
Source:
Gene 2023 v.848 pp. 146901
ISSN:
0378-1119
Subject:
microarray technology,   etc   ; T-lymphocytes; biomarkers; gene expression; genes; immunosuppression; immunosuppressive agents; kidney transplant; monitoring;     Show all 9 Subjects
Abstract:
... Achieving spontaneous tolerance is the optimal goal in renal transplantation (RT). However, robust biomarkers indicating spontaneous tolerance are still lacking for RT recipients in clinics. The peripheral blood gene expression profiles of RT recipients in the state of tolerance and other conditions from four independent cohorts were collected in databases. Immune cell abundance assessment and sin ...
DOI:
10.1016/j.gene.2022.146901

2. Heteroscedasticity-Adjusted Ranking and Thresholding for Large-Scale Multiple Testing

Author:
Luella Fu; Bowen Gang; Gareth M. James; Wenguang Sun
Source:
Journal of the American Statistical Association 2022 v.117 no.538 pp. 1028-1040
ISSN:
1537-274X
Subject:
microarray technology,   etc   ; myeloma; variance;     Show all 3 Subjects
Abstract:
... Standardization has been a widely adopted practice in multiple testing, for it takes into account the variability in sampling and makes the test statistics comparable across different study units. However, despite conventional wisdom to the contrary, we show that there can be a significant loss in information from basing hypothesis tests on standardized statistics rather than the full data. We dev ...
DOI:
10.1080/01621459.2020.1840992

3. Investigating the impact of RNA integrity variation on the transcriptome of human leukemic cells

Author:
Suliman A. Alsagaby
Source:
3 Biotech 2022 v.12 no.8 pp. 160
ISSN:
2190-572X
Subject:
microarray technology,   etc   ; DNA; humans; transcriptome; transcriptomics;     Show all 5 Subjects
Abstract:
... High RNA integrity is essential for good quality of transcriptomics profiling. Nevertheless, in some cases samples with low RNA integrity is the only available material to study. This work was set to investigate the impact of thermal-induced RNA degradation on the transcriptomic profiles of human leukemic cells. DNA microarray-based transcriptomics was conducted on two groups of samples; high RNA ...
DOI:
10.1007/s13205-022-03223-1

4. Ultraviolet Photodetectors Based on Polymer Microwire Arrays toward Wearable Medical Devices

Author:
Zhen Zhang; Yue Geng; Shiqi Cao; Zheng Chen; Hanfei Gao; Xuanbo Zhu; Xuesong Zhang; Yuchen Wu
Source:
ACS applied materials & interfaces 2022 v.14 no.36 pp. 41257-41263
ISSN:
1944-8252
Subject:
microarray technology,   etc   ; durability; mice; nanomaterials; polymers;     Show all 5 Subjects
Abstract:
... Polymer micro/nanoarchitectures have attracted intense interest for wearable medical applications due to their excellent mechanical flexibility, solution processability, and tunable optoelectronic properties. Based on polymer micro/nanostructures, high-performance ultraviolet (UV) photodetectors can not only functionalize the accurate image sensing but also sustain the biocomfortable flexible devi ...
DOI:
10.1021/acsami.2c04169

5. Partial induced reorientation of 5CB in a liquid crystal microarray and a signal-on sensing assay for the detection of aflatoxin B1

Author:
Shihong Wang; Ting Huang; Jun Zhou; Qianshan Chen; Zhaoyang Wu; Ruqin Yu
Source:
Chemical communications 2022 v.58 no.32 pp. 5009-5012
ISSN:
1364-548X
Subject:
microarray technology,   etc   ; aflatoxin B1; biosensors; liquid crystals;     Show all 4 Subjects
Abstract:
... Herein, a signal-on liquid crystal microarray (LCM) sensor is designed for the first time with a micro-spectral optical sensing signal. Depending on the change of the orientation of the LC molecules in the LCM films and the intensity of the spectral peaks of the PhCs, the signal-on LCM biosensor achieves the detection of AFB1 and the Partial Response Mechanism (PSM) of the LCM films is discovered. ...
DOI:
10.1039/d2cc00988a

6. SOX2-OT induced by PAI-1 promotes triple-negative breast cancer cells metastasis by sponging miR-942-5p and activating PI3K/Akt signaling

Author:
Wenwen Zhang; Shuofei Yang; Datian Chen; Daolu Yuwen; Juan Zhang; Xiaowei Wei; Xin Han; Xiaoxiang Guan
Source:
Cellular and molecular life sciences 2022 v.79 no.1 pp. 59
ISSN:
1420-682X
Subject:
microarray technology,   etc   ; breast neoplasms; carcinogenesis; metastasis; therapeutics;     Show all 5 Subjects
Abstract:
... Triple-negative breast cancer (TNBC) has an aggressive biological behavior and poor outcome. Our published study showed that PAI-1 could induce the migration and metastasis of TNBC cells. However, the underlying mechanism by which PAI-1 regulates TNBC metastasis has not been addressed. Here, we demonstrated that PAI-1 is high expressed in TNBC and promotes TNBC cells tumorigenesis. Using microarra ...
DOI:
10.1007/s00018-021-04120-1

7. Simultaneous estimation of cluster number and feature sparsity in high‐dimensional cluster analysis

Author:
Yujia Li; Xiangrui Zeng; Chien‐Wei Lin; George C. Tseng
Source:
Biometrics 2022 v.78 no.2 pp. 574-585
ISSN:
0006-341X
Subject:
microarray technology,   etc   ; cluster analysis; data collection; sequence analysis;     Show all 4 Subjects
Abstract:
... Estimating the number of clusters (K) is a critical and often difficult task in cluster analysis. Many methods have been proposed to estimate K, including some top performers using resampling approach. When performing cluster analysis in high‐dimensional data, simultaneous clustering and feature selection is needed for improved interpretation and performance. To our knowledge, little has been stud ...
DOI:
10.1111/biom.13449

8. Long-term chronic caloric restriction alters miRNA profiles in the brain of ageing mice

Author:
Umit Ozorhan; Bilge G. Tuna; Munevver B. Cicekdal; Aysegul Kuskucu; Omer F. Bayrak; Bayram Yilmaz; Pinar B. Demirel; Margot P. Cleary; Soner Dogan
Source:
British journal of nutrition 2022 v.127 no.5 pp. 641-652
ISSN:
1475-2662
Subject:
microarray technology,   etc   ; brain; chromatin; genes; histones; low calorie diet; microRNA; neurogenesis;     Show all 8 Subjects
Abstract:
... Calorie restriction (CR) has been shown to be one of the most effective methods in alleviating the effects of ageing and age-related diseases. Although the protective effects of CR have been reported, the exact molecular mechanism still needs to be clarified. This study aims to determine differentially expressed (DE) miRNAs and altered gene pathways due to long-term chronic (CCR) and intermittent ...
DOI:
10.1017/S0007114521001239

9. MicroRNA expression in male infertility

Author:
C. F. Burgos; R. Cikutovic; M. Alarcón
Source:
Reproduction, fertility, and development 2022 v.34 no.12 pp. 805-818
ISSN:
1031-3613
Subject:
microarray technology,   etc   ; biomarkers; gene expression; male sterility; microRNA; reproduction; testes; therapeutics;     Show all 8 Subjects
Abstract:
... Male infertility is a multifactorial disorder that involves different physiopathological mechanisms and multiple genes. In this sense, we analyse the role of miRNAs in this pathology. Gene expression analysis can provide relevant information to detect biomarkers, signalling pathways, pathologic mechanisms, and potential therapeutic targets for the disease. In this review, we describe four miRNA mi ...
DOI:
10.1071/RD21131

10. Confined electrochemiluminescence imaging microarray for high-throughput biosensing of single cell-released dopamine

Author:
Ningning Wang; Hang Ao; Wencheng Xiao; Weiwei Chen; Guangming Li; Jie Wu; Huangxian Ju
Source:
Biosensors & bioelectronics 2022 v.201 pp. 113959
ISSN:
0956-5663
Subject:
microarray technology,   etc   ; biosensors; dopamine; electrochemiluminescence; electrochemistry; hypoxia; oligonucleotides; oxidation; polymers; secretion;     Show all 10 Subjects
Abstract:
... The quantitative detection of single cell secretions is always limited by their accurate collection and the heterogeneity of different cells. In this work, a confined electrochemiluminescence (ECL) imaging microarray (CEIM) chip was designed to capture single or a few cells in each cylindrical microwell for high-throughput quantitation of cell-secreted dopamine (DA). The ITO surface at the bottom ...
DOI:
10.1016/j.bios.2021.113959

11. Forensic genetic genealogy using microarrays for the identification of human remains: The need for good quality samples – A pilot study

Author:
A. Davawala; A. Stock; M. Spiden; R. Daniel; J. McBain; D. Hartman
Source:
Forensic science international 2022 v.334 pp. 111242
ISSN:
0379-0738
Subject:
microarray technology,   etc   ; DNA; databases; forensic sciences; genome; heterozygosity; homozygosity; humans; Australia;     Show all 9 Subjects
Abstract:
... The successful application of forensic genetic genealogy (FGG) to identify Jane and John Doe cases in the United States has raised the prospect of using the technique in Australia to assist in the reconciliation of unidentified human remains (UHRs) with long term missing persons. A study was conducted to explore the feasibility of FGG using whole genome array (WGA) data from both pristine control ...
DOI:
10.1016/j.forsciint.2022.111242

12. Transcriptome analysis of long non-coding RNAs reveals NR_015556 lncRNA is a novel regulator for adipocyte differentiation

Author:
Changqing Zuo; Yaqiong Pan; Dan Leng; Xiuju Chen; Fanghongniu Dong; Zhanying Lin; Zhong Dai; Zonggui Wang
Source:
Biochemical and biophysical research communications 2022 v.601 pp. 79-85
ISSN:
0006-291X
Subject:
microarray technology,   etc   ; adipocytes; gene expression regulation; lipids; research; transcription (genetics); transcriptomics;     Show all 7 Subjects
Abstract:
... Long non-coding RNAs (lncRNAs) have gained extensive attentions due to their significant roles in diverse biological process. However, the potential functions of lncRNAs participation in adipocyte differentiation have not been fully explored. In the present study, we globally profiled lncRNA expression using lncRNA microarray and identified 1745 lncRNA probes with differential expression on day 0 ...
DOI:
10.1016/j.bbrc.2022.02.069

13. Approaches in Gene Coexpression Analysis in Eukaryotes

Author:
Vasileios L. Zogopoulos; Georgia Saxami; Apostolos Malatras; Konstantinos Papadopoulos; Ioanna Tsotra; Vassiliki A. Iconomidou; Ioannis Michalopoulos
Source:
Biology 2022 v.11 no.7 pp. -
ISSN:
2079-7737
Subject:
microarray technology,   etc   ; data collection; eukaryotic cells; genes; prediction; sequence analysis; transcriptomics;     Show all 7 Subjects
Abstract:
... Gene coexpression analysis constitutes a widely used practice for gene partner identification and gene function prediction, consisting of many intricate procedures. The analysis begins with the collection of primary transcriptomic data and their preprocessing, continues with the calculation of the similarity between genes based on their expression values in the selected sample dataset and results ...
DOI:
10.3390/biology11071019

14. Development of Reference Genes for Horticultural Plants

Author:
Umair Ahmed; Qi Xie; Xueping Shi; Bo Zheng
Source:
Critical reviews in plant sciences 2022 v.41 no.3 pp. 190-208
ISSN:
1549-7836
Subject:
microarray technology,   etc   ; gene expression; horticulture; reverse transcriptase polymerase chain reaction; transcriptome;     Show all 5 Subjects
Abstract:
... Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is extensively applied technique to investigate the transcript abundance of target genes in various organisms. Selection of appropriate reference genes (RGs) for qRT-PCR normalization is a crucial prerequisite for accurately quantifying gene expression level. RGs should exhibit minimal variation in gene expression. However, the ...
DOI:
10.1080/07352689.2022.2084227

15. Dissection of the practical soybean breeding pipeline by developing ZDX1, a high-throughput functional array

Author:
Rujian Sun; Bincheng Sun; Yu Tian; Shanshan Su; Yong Zhang; Wanhai Zhang; Jingshun Wang; Ping Yu; Bingfu Guo; Huihui Li; Yanfei Li; Huawei Gao; Yongzhe Gu; Lili Yu; Yansong Ma; Erhu Su; Qiang Li; Xingguo Hu; Qi Zhang; Rongqi Guo; Shen Chai; Lei Feng; Jun Wang; Huilong Hong; Jiangyuan Xu; Xindong Yao; Jing Wen; Jiqiang Liu; Yinghui Li; Lijuan Qiu
Source:
Theoretical and applied genetics 2022 v.135 no.4 pp. 1413-1427
ISSN:
0040-5752
Subject:
microarray technology,   etc   ; alleles; artificial selection; dissection; genomics; genotyping; prediction; progeny; soybeans;     Show all 9 Subjects
Abstract:
... KEY MESSAGE: We developed the ZDX1 high-throughput functional soybean array for high accuracy evaluation and selection of both parents and progeny, which can greatly accelerate soybean breeding. Microarray technology facilitates rapid, accurate, and economical genotyping. Here, using resequencing data from 2214 representative soybean accessions, we developed the high-throughput functional array ZD ...
DOI:
10.1007/s00122-022-04043-w

16. Glycan microarrays from construction to applications

Author:
Yujun Kim; Ji Young Hyun; Injae Shin
Source:
Chemical Society reviews 2022 v.51 no.19 pp. 8276-8299
ISSN:
1460-4744
Subject:
microarray technology,   etc   ; animals; glycomics; lectins; ligands; polysaccharides; quantitative analysis; rapid methods;     Show all 8 Subjects
Abstract:
... Through their specific interactions with proteins, cellular glycans play key roles in a wide range of physiological and pathological processes. One of the main goals of research in the areas of glycobiology and glycomedicine is to understand glycan–protein interactions at the molecular level. Over the past two decades, glycan microarrays have become powerful tools for the rapid evaluation of inter ...
DOI:
10.1039/d2cs00452f

17. Proteomic assessment of humoral immune responses in smallpox vaccine recipients

Author:
Richard B. Kennedy; Inna G. Ovsyannikova; Iana H. Haralambieva; Diane E. Grill; Gregory A. Poland
Source:
Vaccine 2022 v.40 no.5 pp. 789-797
ISSN:
0264-410X
Subject:
microarray technology,   etc   ; animals; antibody formation; globulins; monitoring; proteome; proteomics; smallpox; vaccines;     Show all 9 Subjects
Abstract:
... The availability of effective smallpox vaccines was a critical element of the successful eradication of smallpox in 1980. Antibody responses play a primary role in protective immunity and neutralizing antibody is an established correlate of protection against smallpox. In this study we used a poxvirus proteome array to assess the antibody response to individual viral proteins in a cohort of 1,037 ...
DOI:
10.1016/j.vaccine.2021.12.033

18. Real-time monitoring of single-cell secretion with a high-throughput nanoplasmonic microarray

Author:
Yen-Cheng Liu; Saeid Ansaryan; Xiaokang Li; Eduardo R. Arvelo; Hatice Altug
Source:
Biosensors & bioelectronics 2022 v.202 pp. 113955
ISSN:
0956-5663
Subject:
microarray technology,   etc   ; biosensors; cell communication; interleukin-2; lymphoma; secretion; spectral analysis;     Show all 7 Subjects
Abstract:
... Proteins secreted by cells play significant roles in mediating many physiological, developmental, and pathological processes due to their functions in intra/intercellular communication and signaling. Conventional end-point methods are insufficient for understanding the temporal response in cell secretion process, which is often highly dynamic. Furthermore, cellular heterogeneity makes it essential ...
DOI:
10.1016/j.bios.2021.113955

19. IL‐ 35 enhances angiogenic effects of small extracellular vesicles in breast cancer

Author:
Jia Liu; Nana Dong; Ning Li; Hui Zhao; Yali Li; Huihui Mao; Hanxiao Ren; Yimin Feng; Jie Liu; Lutao Du; Haiting Mao
Source:
FEBS journal 2022 v.289 no.12 pp. 3489-3504
ISSN:
1742-464X
Subject:
microarray technology,   etc   ; angiogenesis; breast neoplasms; breasts; cell cycle; cell proliferation; metastasis; microvessels;     Show all 8 Subjects
Abstract:
... As an indispensable process for breast cancer metastasis, tumour angiogenesis requires a tight interaction between cancer cells and endothelial cells in tumour microenvironment. Here, we explored the participation of small extracellular vesicles (sEVs) derived from breast cancer cells in modulating angiogenesis and investigated the effect of IL‐35 in facilitating this process. Firstly, we characte ...
DOI:
10.1111/febs.16359

20. Glucosylceramide in T cells regulates the pathology of inflammatory bowel disease

Author:
Mariko Komuro; Masaki Nagane; Rikito Endo; Takashi Nakamura; Takayoshi Miyamoto; Chiaki Niwa; Tomoki Fukuyama; Hideyoshi Harashima; Naoyuki Aihara; Junichi Kamiie; Rimina Suzuki; Tadashi Yamashita
Source:
Biochemical and biophysical research communications 2022 v.599 pp. 24-30
ISSN:
0006-291X
Subject:
microarray technology,   etc   ; colitis; colon; dextran sulfate; glucosylceramides; lymph; pathogenesis; research; spleen; therapeutics;     Show all 10 Subjects
Abstract:
... Inflammatory bowel disease (IBD) is a chronic inflammatory disease in the colon characterized by excessive activation of T cells. Glycosphingolipids (GSLs) are composed of lipid rafts in cellular membranes, and their content is linked to immune cell function. In the present study, we investigated the involvement of GSLs in IBD. Microarray data showed that in IBD patients, the expression of only UD ...
DOI:
10.1016/j.bbrc.2022.02.004