Internal transcribed spacer sequence based identification and phylogenic relationship of Herba Dendrobii

Wu, Chin-Tung; Gupta, Sushim K.; Wang, Arthur Zi-Ming; Lo, Shu-Fang; Kuo, Chao‐Lin; Ko, Yu-Jen; Chen, Chung-Li; Hsieh, Chang-Chi; Tsay, Hsin‐Sheng

doi:10.38212/2224-6614.2051

Cited by 6 publications

(9 citation statements)

References 17 publications

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“…This condition may explain the low number of sperm in the light group exposed to continuous light (Figure 1). The result was found similar with the research conducted by Wu et al (2012); the chronic stress in the mice has a negative effect on female rat reproduction through a decrease in the expression of BDNF (brainderived neurotrophic factor) in antral follicles, the number of oocytes retrieved and the average formation of blastocysts [31]. The epidemiological research also reports that the stress associated with infertility influences the success of pregnancy in couples [32].…”

Section: Resultssupporting

confidence: 85%

Light Environment Effect in the Sperm and Ribonucleic Acid Quality and Body Weight of Male Mus musculus

Hanizar

Huang

Siswoyo

et al. 2021

Open Access Maced J Med Sci

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BACKGROUND: The mice are categorized as the nocturnal animal meaning that most of the activity conducted in dark environment. However, the treatment of mice as the object studied in the laboratory often experiences the lack attention especially the treat to light exposure to mice during the investigation period which potentially affect the result. AIM: The present study aims to investigate the effect of light environment in the sperm quality, RNA quality, and body weight of male Mus musculus. METHODS: We compared in the mice the desired parameter onto the sample of 16 mice which kept in light and dark cages for 6 weeks. RESULTS: The results indicated that there was a significant difference in the number of sperm, concentration, and purity of RNA between the mice exposed in dark and light environment. The average number of sperm from the ones kept in the dark was found twice as much as those in the light condition. The average RNA concentration in the dark was higher than in the light place but the RNA purity in the dark was lower than the light place. However, the motility and morphology of sperm was not showing any significancy different in both conditions. CONCLUSION: The result proved that the natural light of cages for treating the mice in the laboratory influences the amount of sperm and the quality RNA. Therefore, the control of the light room in the experimental laboratory needs to be considered, especially during the further experiment which related to the quality of sperm, RNA, and body weight of mice.

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Section: Resultssupporting

confidence: 85%

Light Environment Effect in the Sperm and Ribonucleic Acid Quality and Body Weight of Male Mus musculus

Hanizar

Huang

Siswoyo

et al. 2021

Open Access Maced J Med Sci

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“…Following, based on these alignment data, similarity or variation are investigated. This step is performed by evaluating such parameters as GC% content [27,29], genetic distance [30][31][32][33], variable sites [32,34], indel appearances [35], or monophyletic clusters [36][37][38], which can indicate typical characters of the examined sequences. These measurements vary from different studies as they depend on alignment and identification methods (Table 1).…”

Section: Common Bioinformatics Analyses In Identification Techniques Using Sequencesmentioning

confidence: 99%

“…Regardless of which method is used, the core property of the identification strategy is that all conspecific sequences should be grouped together without blending with any other species. To address this issue, the tree-based method is a simple and visualized approach that is most common in such classification studies [2,[25][26][27]29,34,[36][37][38][39]45,46,48,49,55]. Two species are completely separated when all sequences of one species are clustered in a monophyletic branch [56].…”

Section: Common Bioinformatics Analyses In Identification Techniques Using Sequencesmentioning

confidence: 99%

“…There are some problems that should be noticed to avoid errors in identification process. Small sample size [4,26,29,36,51,[57][58][59] or a wide range but less con-level of taxonomic samples [27,60,61] may lead to over-fitting [56].…”

Section: Common Bioinformatics Analyses In Identification Techniques Using Sequencesmentioning

confidence: 99%

“…However, as the trees are built based on specific DNA sequences, information from them can be used for phylogenetic investigations. Barcoding and phylogenetic relationships of species have also been studied in combination previously [28,29,36,74]. For phylogenetic relationship analyses, homologous variations at each alignment site are considered.…”

Section: Relation Between Molecular Identification and Application For Phylogenetic Studymentioning

confidence: 99%

See 2 more Smart Citations

Bioinformatics Analysis on DNA Barcode Sequences for Species Identification: A Review

2019

ARRB

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Classification of organisms is the primary step in management of biodiversity, breeding, conservation and development of populations and distinguishing adulterant objects. There are many approaches in taxonomic identification, from morphological, PCR-based to sequence-based techniques. Molecular methods give more accurate results than morphological comparisons and are independent of plant stages. PCR-based methods are low-cost but their limited information gives less reproducibility and can only distinguish samples among determined groups. In contrast, in sequence-based methods each nucleotide site is considered as genetic information hence a sequence of nucleotide represents large data, which is highly specific and more stable than PCR bands. Establishment of worldwide DNA library for barcoding is essential. There were previous reviews on screenings and applications of barcodes in different taxa. In this review we discussed common bioinformatics analyses as well as some new improved techniques relying on barcoding approaches.

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Advances in Testing for Adulteration of Food Supplements

El-Ahmady

Ashour

2016

Advances in Food Authenticity Testing

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Internal transcribed spacer sequence based identification and phylogenic relationship of Herba Dendrobii

Cited by 6 publications

References 17 publications

Light Environment Effect in the Sperm and Ribonucleic Acid Quality and Body Weight of Male Mus musculus

Light Environment Effect in the Sperm and Ribonucleic Acid Quality and Body Weight of Male Mus musculus

Bioinformatics Analysis on DNA Barcode Sequences for Species Identification: A Review

Advances in Testing for Adulteration of Food Supplements

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