• Journal of Animal Reproduction and Biotechnology
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• v.36 no.1
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• pp.35-44
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• 2021

A pregnancy diagnosis is an important standard for control of livestock's reproduction in paricular dairy cattle. High reproductive performance in dairy animals is a essential condition to realize of high life-time production. Pregnancy diagnosis is crucial to shortening the calving interval by enabling the farmer to identify open animals so as to treat or re-breed them at the earliest opportunity. MicroRNAs are short RNA molecules which are critically involved in regulating gene expression during both health and disease. This study is sought to establish the feasible of circulating miRNAs as biomarkers of early pregnancy in cattle. We applied Illumina small-RNA sequencing to profile miRNAs in plasma samples collected from 12 non-pregnant cows ("open" cows: samples were collected before insemination (non-pregnant state) and after pregnancy check at the indicated time points) on weeks 0, 4, 8, 12 and 16. Using small RNA sequencing we identified a total of 115 miRNAs that were differentially expressed weeks 16 relative to non-pregnancy ("open" cows). Weeks 8, 12 and 16 of pregnancy commonly showed a distinct increase in circulating levels of miR-221 and miR-320a. Through genome-wide analyses we have successfully profiled plasma miRNA populations associated with pregnancy in cattle. Their application in the field of reproductive biology has opened up opportunities for research communities to look for pregnancy biomarker molecules in dairy cattle.

• Genomics & Informatics
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• v.20 no.3
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• pp.26.1-26.19
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• 2022

Diabetes and its related complications are associated with long term damage and failure of various organ systems. The microvascular complications of diabetes considered in this study are diabetic retinopathy, diabetic neuropathy, and diabetic nephropathy. The aim is to identify the weighted co-expressed and differentially expressed genes (DEGs), major pathways, and their miRNA, transcription factors (TFs) and drugs interacting in all the three conditions. The primary goal is to identify vital DEGs in all the three conditions. The overlapped five genes (AKT1, NFKB1, MAPK3, PDPK1, and TNF) from the DEGs and the co-expressed genes were defined as key genes, which differentially expressed in all the three cases. Then the protein-protein interaction network and gene set linkage analysis (GSLA) of key genes was performed. GSLA, gene ontology, and pathway enrichment analysis of the key genes elucidates nine major pathways in diabetes. Subsequently, we constructed the miRNA-gene and transcription factor-gene regulatory network of the five gene of interest in the nine major pathways were studied. hsa-mir-34a-5p, a major miRNA that interacted with all the five genes. RELA, FOXO3, PDX1, and SREBF1 were the TFs interacting with the major five gene of interest. Finally, drug-gene interaction network elucidates five potential drugs to treat the genes of interest. This research reveals biomarker genes, miRNA, TFs, and therapeutic drugs in the key signaling pathways, which may help us, understand the processes of all three secondary microvascular problems and aid in disease detection and management.

• Journal of Biomedical Engineering Research
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• v.43 no.4
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• pp.185-192
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• 2022

Early detection of mild cognitive impairment can help prevent the progression of dementia. The purpose of this study was to design and validate a machine learning model that automatically differential diagnosed patients with mild cognitive impairment and identified cognitive decline characteristics compared to a control group with normal cognition using resting-state quantitative electroencephalogram (qEEG) with eyes closed. In the first step, a rectified signal was obtained through a preprocessing process that receives a quantitative EEG signal as an input and removes noise through a filter and independent component analysis (ICA). Frequency analysis and non-linear features were extracted from the rectified signal, and the 3067 extracted features were used as input of a linear support vector machine (SVM), a representative algorithm among machine learning algorithms, and classified into mild cognitive impairment patients and normal cognitive adults. As a result of classification analysis of 58 normal cognitive group and 80 patients in mild cognitive impairment, the accuracy of SVM was 86.2%. In patients with mild cognitive impairment, alpha band power was decreased in the frontal lobe, and high beta band power was increased in the frontal lobe compared to the normal cognitive group. Also, the gamma band power of the occipital-parietal lobe was decreased in mild cognitive impairment. These results represented that quantitative EEG can be used as a meaningful biomarker to discriminate cognitive decline.

• Molecules and Cells
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• v.43 no.11
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• pp.909-920
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• 2020

Cytosolic Ca²⁺ levels ([Ca²⁺]_c) change dynamically in response to inducers, repressors, and physiological conditions, and aberrant [Ca²⁺]_c concentration regulation is associated with cancer, heart failure, and diabetes. Therefore, [Ca²⁺]_c is considered as a good indicator of physiological and pathological cellular responses, and is a crucial biomarker for drug discovery. A genetically encoded calcium indicator (GECI) was recently developed to measure [Ca²⁺]_c in single cells and animal models. GECI have some advantages over chemically synthesized indicators, although they also have some drawbacks such as poor signal-to-noise ratio (SNR), low positive signal, delayed response, artifactual responses due to protein overexpression, and expensive detection equipment. Here, we developed an indicator based on interactions between Ca²⁺-loaded calmodulin and target proteins, and generated an innovative GECI sensor using split nano-luciferase (Nluc) fragments to detect changes in [Ca²⁺]_c. Stimulation-dependent luciferase activities were optimized by combining large and small subunits of Nluc binary technology (NanoBiT, LgBiT:SmBiT) fusion proteins and regulating the receptor expression levels. We constructed the binary [Ca²⁺]_c sensors using a multicistronic expression system in a single vector linked via the internal ribosome entry site (IRES), and examined the detection efficiencies. Promoter optimization studies indicated that promoter-dependent protein expression levels were crucial to optimize SNR and sensitivity. This novel [Ca²⁺]_c assay has high SNR and sensitivity, is easy to use, suitable for high-throughput assays, and may be useful to detect [Ca²⁺]_c in single cells and animal models.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.12
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• pp.7635-7638
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• 2013

Background: Sperm-associated antigen 9 (SPAG9) has been recently proposed as a novel biomarker for early diagnosis of several human tumors, including ovarian, cervical and breast cancers. Its clinical value remains to be clarified for endometrial cancer (EC). In this study, we investigated the utility of serum SPAG9 levels in diagnosis of EC and its association with important clinicopathological parameters. Materials and Methods: This cross-sectional study was performed at a tertiary women's referral center in Ankara, Turkey. Preoperative serum samples were collected from patients surgically treated for endometrial cancer between June 2012-April 2013. Similar aged women with a biopsy proven benign endometrium were used as controls. Serum SPAG9 levels were measured with an enzyme-linked immunosorbent assay (ELISA) method and assessed for links with clinicopathological factors. Receiver operating characteristic (ROC) curve analysis was performed to assess power of SPAG9 levels for EC prediction. P values less than 0.05 were considered statistically significant. Results: A total of 63 women with EC and 27 with benign endometrium were included in the study. Mean age in the EC group was $58.7{\pm}1.1$. Median SPAG9 levels in the EC and control groups were 18.3 (range, 12.7-53.8) and 14.1 (range, 4.3-65.3), respectively (p<0.001). A cut-off value of 17 ng/ml for SPAG9 predicted presence of malignant endometrium with 74% sensitivity and 83% specificity [Area under curve (AUC)=0.82, p<0.001]. SPAG9 levels did not demonstrate any significant association with histological type, FIGO stage, tumor grade, size, myometrial invasion, lymphovascular space invasion, cervical involvement, adnexal involvement, peritoneal cytology or lymph node status (all p>0.05). Conclusions: Testing for SPAG9 may be useful for early detection of EC in asymptomatic high-risk women. Its role in post-treatment follow-up and early detection of recurrence should be assessed in future trials.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.4
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• pp.1657-1663
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• 2015

Background: Early diagnosis of hepatocellular carcinoma (HCC) is the most important step in successful treatment. However, it is usually rare due to the lack of a highly sensitive specific biomarker so that the HCC is usually fatal within few months after diagnosis. The aim of this work was to study the role of plasma nuclear factor kappa B (NF-${\kappa}B$) and serum peroxiredoxin 3 (PRDX3) as diagnostic biomarkers for early detection of HCC in a high-risk population. Materials and Methods: Plasma nuclear factor kappa B level (NF-${\kappa}B$) and serum peroxiredoxin 3 (PRDX3) levels were measured using enzyme linked immunosorbent assay (ELISA), in addition to alpha-fetoprotein (AFP) in 72 cirrhotic patients, 64 patients with HCC and 29 healthy controls. Results: NF-${\kappa}B$ and PRDX3 were significantly elevated in the HCC group in relation to the others. Higher area under curve (AUC) of 0.854 (for PRDX3) and 0.825 (for NF-${\kappa}B$) with sensitivity of 86.3% and 84.4% and specificity of 75.8% and 75.4% respectively, were found compared to AUC of alpha-fetoprotein (AFP) (0.65) with sensitivity of 72.4% and specificity of 64.3%. Conclusions: NF-${\kappa}B$ and PRDX3 may serve as early and sensitive biomarkers for early detection of HCC facilitating improved management. The role of nuclear factor kappa B (NF-${\kappa}B$) as a target for treatment of liver fibrosis and HCC must be widely evaluated.

• Korean Journal of Environmental Biology
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• v.26 no.4
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• pp.330-342
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• 2008

A comprehensive quality survey for PCDDs/PCDFs and coplanar PCBs as well as heavy metals (Cu, Zn, Cd and Pb) in sediments has been investigated in August 2006, Korea. Monitoring was undertaken at five streams representing different surrounding environments throughout Juwang and Gapyeong streams (reference sites), Jungrang stream (dense population site), Ansan stream (mixed small population and industrial site), and Siheung stream (heavy industrial site). The levels of heavy metal in samples were found to be significantly higher in sediment from Siheung stream compared to those of other stream sites. The heavy metal concentrations (dry weight basis) in sediment from Siheung stream were as follows; Cd (3.7 ${\mu}g$/g), Pb (1,295 ${\mu}g$/g), Cu (713.4 ${\mu}g$/g) and Zn (358.1 ${\mu}g$/g). Among 12 coplanar PCBs and 17 PCDDs/PCDFs selected as target compounds in this study, PCB (IUPAC no. 118) and OCDD were the most abundant congeners found in all sediment samples, followed by 1,2,3,4,6,7,8-HpCDD, OCDF and 1,2,3,4,6,7,8HpCDF as well as PCB (IUPAC no. 105). These results were shown to be in the same trend as the sediment samples of other countries. The levels of PCDDs/PCDFs/coplanar PCBs in sediment samples were expressed as concentrations and WHO- TEQ values. The PCDDs/PCDFs/coplanar PCBs concentrations and their WHO-TEQ values in sediment from Siheung stream were remarkably high. The levels detected were 788.16 pg/g and 36.080 pg WHO-TEQ/g dry weight for PCDDs/ PCDFs and 314 pg/g and 0.4189 pg WHO-TEQ/g dry weight for coplanar PCBs, respectively, beyond the safety level of sediment value 20 pg WHO-TEQ/g. Sediment samples of the five streams were also monitored by sensitive biomarkers using insect immune responses: hemocyte-spreading behavior and immune-associated enzyme activities of phospholipase A$_2$ (PLA$_2$) and phenoloxidase. Organic extracts of Siheung and Jungrang sediments significantly interfered with the hemocytespreading behavior, whereas those of Ansan, Gapyeong, and Juwang did not. These organic extracts did not inhibit the PLA$_2$ and phenoloxidase activities. However, phenoloxidase was highly susceptible to exposure to aqueous extracts in all site sediments. In comparison, PLA$_2$ activities of the hemocytes were significantly inhibited only by aqueous extracts of Siheung, Jungrang, and Gapyeong sediments, but not by those of Ansan and Juwang. Despite some disparity between bioand chemical monitoring results, the biomarkers can be recommended as a device warning the contamination of biohazard environmental chemicals because of a fast and inexpensive detection method.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.9
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• pp.4469-4475
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• 2012

Background: The potential use of hypomethylation of Long INterspersed Element 1 (LINE-1) and Alu elements (Alu) as a biomarker has been comprehensively assessed in several cancers, including head and neck squamous cell carcinoma (HNSCC). Failure to detect occult metastatic head and neck tumors on radical neck lymph node dissection can affect the therapeutic measures taken. Objective: The aim of this study was to investigate the LINE-1 and Alu methylation status and determine whether it can be applied for detection of occult metastatic tumors in HNSCC cases. Methods: We used the Combine Bisulfite Restriction Analysis (COBRA) technique to analyse LINE-1 and Alu methylation status. In addition to the methylation level, LINE-1 and Alu loci were classified based on the methylation statuses of two CpG dinucleotides in each allele as follows: hypermethylation ($^mC^mC$), hypomethylation ($^uC^uC$), and 2 forms of partial methylation ($^mC^uC$ and $^uC^mC$). Sixty-one lymph nodes were divided into 3 groups: 1) non-metastatic head and neck cancer (NM), 2) histologically negative for tumor cells of cases with metastatic head and neck cancer (LN), and 3) histologically positive for tumor cells (LP). Results: Alu methylation change was not significant. However, LINE-1 methylation of both LN and LP was altered, as demonstrated by the lower LINE-1 methylation levels (p<0.001), higher percentage of $^mC^uC$ (p<0.01), lower percentage of $^uC^mC$ (p<0.001) and higher percentage of $^uC^uC$ (p<0.001). Using receiver operating characteristic (ROC) curve analysis, $%^uC^mC$ and $%^mC^uC$ values revealed a high level of AUC at 0.806 and 0.716, respectively, in distinguishing LN from NM. Conclusion: The LINE-1 methylation changes in LN have the same pattern as that in LP. This epigenomic change may be due to the presence of occult metastatic tumor in LN cases.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.6
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• pp.3931-3936
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• 2013

Background: Iran is a country with very high incidences of stomach cancer, especially in Northern parts. Here we assessed prognostic value of serum screening biomarkers among people >50 years old for early detection of precancerous lesions in a hot spot for gastric carcinoma in Guilan Province, North Iran. Methods: A cross-sectional population-based survey was conducted on 1,390 residents of Lashtenasha city with the mean age (SD) of 61.8 (9.02) years old (50.8% females) to assess the association of gastrin and the pepsinogen (PG) I/II ratio with premalignant gastric lesions. Blood samples were taken for CBC, blood group, and serologic exams (PGI, PGII, and gastrin 17) from each subject. Expert gastroenterologists performed upper GI endoscopy and ROC curves were generated to determine appropriate cutoff points. Results: Mean values of PGI, PGII, PGI/PGII and gastrin were significantly different between patients with and without atrophy or metaplasia (P<0.05). To diagnose atrophy and intestinal metaplasia, a significantly higher AUC was observed for the PGI/PGII ratio (70 and 72%, respectively) compared to the PGI (56, 55%), PGII (63, 64%) and gastrin (59, 61%) (all p<0.001). Conclusions: Biomarker tests such as the PGI/II ratio can be used in the screening and diagnosis of subjects at high gastric cancer risk in our region.

• Analytical Science and Technology
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• v.25 no.6
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• pp.460-466
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• 2012

An environmentally friendly, so-called green, high performance liquid chromatography method was developed and validated for the determination of trans, trans-muconic acid (t,t-MA) in human urine as a biomarker of benzene exposure. After urinary t,t-MA was extracted and enriched using solid-phase extraction, a MF-Ph1 SG80 ($150mm{\times}2.0mm$ I.D., 5 ${\mu}m$) column with a mobile phase of 10 mM $KH_2PO_4$ containing 0.1% $H_3PO_4$ was used for isocratic separation of t,t-MA with UV detection at 259 nm. The calibration curve was constructed in the range of 0.1-5.0 mg/L with good linearity ($r^2$=0.9992). The intra-day and inter-day precision (as RSD) were 0.9-8.5% and 3.1-4.5%, respectively. The average recovery ranged from 97.5% to 101.7%. The green sample preparation and separation with no organic solvents were successfully achieved. The validated method would be suitable for the routine biological monitoring of benzene exposure in the occupational settings.