Survey of genetic structure of geese using novel microsatellite markers

Fang-Yu Lai,Po-An Tu,Shih-Torng Ding,Min-Jung Lin,Shen-Chang Chang,En-Chung Lin,Ling-Ling Lo,Pei-Hwa Wang 아세아·태평양축산학회 2018 Animal Bioscience Vol.31 No.2

Objective: The aim of this study was to create a set of microsatellite markers with high polymorphism for the genetic monitoring and genetic structure analysis of local goose populations. Methods: Novel microsatellite markers were isolated from the genomic DNA of white Roman geese using short tandem repeated probes. The DNA segments, including short tandem repeats, were tested for their variability among four populations of geese from the Changhua Animal Propagation Station (CAPS). The selected microsatellite markers could then be used to monitor genetic variability and study the genetic structures of geese from local geese farms. Results: 14 novel microsatellite loci were isolated. In addition to seven known loci, two multiplex sets were constructed for the detection of genetic variations in geese populations. The average of allele number, the effective number of alleles, the observed heterozygosity, the expected heterozygosity, and the polymorphism information content were 11.09, 5.145, 0.499, 0.745, and 0.705, respectively. The results of analysis of molecular variance and principal component analysis indicated a contracting white Roman cluster and a spreading Chinese cluster. In white Roman populations, the CAPS populations were depleted to roughly two clusters when K was set equal to 6 in the Bayesian cluster analysis. The founders of private farm populations had a similar genetic structure. Among the Chinese geese populations, the CAPS populations and private populations represented different clads of the phylogenetic tree and individuals from the private populations had uneven genetic characteristics according to various analyses. Conclusion: Based on this study’s analyses, we suggest that the CAPS should institute a proper breeding strategy for white Roman geese to avoid further clustering. In addition, for preservation and stable quality, the Chinese geese in the CAPS and the aforementioned proper breeding scheme should be introduced to geese breeders.

Development of novel microsatellite markers to analyze the genetic structure of dog populations in Taiwan

Lai Fang-Yu,Lin Yu-Chen,Ding Shih-Torng,Chang Chi-Sheng,Chao Wi-Lin,Wang Pei-Hwa 아세아·태평양축산학회 2022 Animal Bioscience Vol.35 No.9

Objective: Alongside the rise of animal-protection awareness in Taiwan, the public has been paying more attention to dog genetic deficiencies due to inbreeding in the pet market. The goal of this study was to isolate novel microsatellite markers for monitoring the genetic structure of domestic dog populations in Taiwan. Methods: A total of 113 DNA samples from three dog breeds—beagles (BEs), bichons (BIs), and schnauzers (SCs)—were used in subsequent polymorphic tests applying the 14 novel microsatellite markers that were isolated in this study. Results: The results showed that the high level of genetic diversity observed in these novel microsatellite markers provided strong discriminatory power. The estimated probability of identity (P(ID)) and the probability of identity among sibs (P(ID)sib) for the 14 novel microsatellite markers were 1.7×10–12 and 1.6×10–5, respectively. Furthermore, the power of exclusion for the 14 novel microsatellite markers was 99.98%. The neighbor-joining trees constructed among the three breeds indicated that the 14 sets of novel microsatellite markers were sufficient to correctly cluster the BEs, BIs, and SCs. The principal coordinate analysis plot showed that the dogs could be accurately separated by these 14 loci based on different breeds; moreover, the Beagles from different sources were also distinguished. The first, the second, and the third principal coordinates could be used to explain 44.15%, 26.35%, and 19.97% of the genetic variation. Conclusion: The results of this study could enable powerful monitoring of the genetic structure of domestic dog populations in Taiwan. Objective: Alongside the rise of animal-protection awareness in Taiwan, the public has been paying more attention to dog genetic deficiencies due to inbreeding in the pet market. The goal of this study was to isolate novel microsatellite markers for monitoring the genetic structure of domestic dog populations in Taiwan.Methods: A total of 113 DNA samples from three dog breeds—beagles (BEs), bichons (BIs), and schnauzers (SCs)—were used in subsequent polymorphic tests applying the 14 novel microsatellite markers that were isolated in this study.Results: The results showed that the high level of genetic diversity observed in these novel microsatellite markers provided strong discriminatory power. The estimated probability of identity (P(ID)) and the probability of identity among sibs (P(ID)sib) for the 14 novel microsatellite markers were 1.7×10–12 and 1.6×10–5, respectively. Furthermore, the power of exclusion for the 14 novel microsatellite markers was 99.98%. The neighbor-joining trees constructed among the three breeds indicated that the 14 sets of novel microsatellite markers were sufficient to correctly cluster the BEs, BIs, and SCs. The principal coordinate analysis plot showed that the dogs could be accurately separated by these 14 loci based on different breeds; moreover, the Beagles from different sources were also distinguished. The first, the second, and the third principal coordinates could be used to explain 44.15%, 26.35%, and 19.97% of the genetic variation.Conclusion: The results of this study could enable powerful monitoring of the genetic structure of domestic dog populations in Taiwan.

Monitoring of genetically close Tsaiya duck populations using novel microsatellite markers with high polymorphism

Lai, Fang-Yu,Chang, Yi-Ying,Chen, Yi-Chen,Lin, En-Chung,Liu, Hsiu-Chou,Huang, Jeng-Fang,Ding, Shih-Torng,Wang, Pei-Hwa Asian Australasian Association of Animal Productio 2020 Animal Bioscience Vol.33 No.6

Objective: A set of microsatellite markers with high polymorphism from Tsaiya duck were used for the genetic monitoring and genetic structure analysis of Brown and White Tsaiya duck populations in Taiwan. Methods: The synthetic short tandem repeated probes were used to isolate new microsatellite markers from the genomic DNA of Tsaiya ducks. Eight populations, a total of 566 samples, sourced from Ilan Branch, Livestock Research Institute were genotyped through novel and known markers. The population genetic variables were calculated using optional programs in order to describe and monitor the genetic variability and the genetic structures of these Tsaiya duck populations. Results: In total 24 primer pairs, including 17 novel microsatellite loci from this study and seven previously known loci, were constructed for the detection of genetic variations in duck populations. The average values for the allele number, the effective number of alleles, the observed heterozygosity, the expected heterozygosity, and the polymorphism information content were 11.29, 5.370, 0.591, 0.746, and 0.708, respectively. The results of analysis of molecular variance and principal component analysis indicated a contracting Brown Tsaiya duck cluster and a spreading White Tsaiya duck cluster. The Brown Tsaiya ducks and the White Tsaiya ducks with Pekin ducks were just split to six clusters and three clusters when K was set equal to 6 and 3 in the Bayesian cluster analysis. The individual phylogenetic tree revealed eight taxa, and each individual was assigned to its own population. Conclusion: According to our study, the 24 novel microsatellite markers exhibited a high capacity to analyze relationships of inter- and intra-population in those populations with a relatively limited degree of genetic diversity. We suggest that duck farms in Taiwan could use the new (novel) microsatellite set to monitor the genetic characteristics and structures of their Tsaiya duck populations at various intervals in order to ensure quality breeding and conservation strategies.

Analysis of genetic diversity among different geographic populations of Athetis lepigone using ISSR molecular markers

Fang Chen,Tofael Ahmeda,Yu-juan Liu,Kang-lai He,Zhen-yingWang 한국응용곤충학회 2014 Journal of Asia-Pacific Entomology Vol.17 No.4

Athetis lepigone (Möschler) is an invasive insect pest that feeds on corn seedlings in the summer corn region ofChina. Inter-simple sequence repeat (ISSR) markers were used to determine genotype of A. lepigone collectedfrom 15 geographic locations in North China. Data from seven primers resulted in a total of 183 bands thatwere scored, 174 (95.08%) of which were polymorphic. Genetic distance estimates among the 15 populationsof A. lepigone ranged from 0.0133 to 0.0595. At species level, Nei's genetic diversity index was 0.3537 andShannon information index was 0.5288. Genetic differentiation among the 15 populations was estimated at0.0747 and historical mean number of migrants (Nm) was 6.19. Clustering analysis revealed no correlationbetween genetic diversity and geographic proximity among the A. lepigone populations. This lack of significantgenetic diversity or correlation with geographic location suggests that gene flow may be high among the15 A. lepigone populations or homogenization may be a result of recent range expansion. These data provide importantpreliminary estimates of A. lepigone population dynamics which may help in evaluating local scales requiredfor control of this insect.

Implementation of Obstacle Avoidance and Target Following based on Machine Learning for Unmanned Aerial Vehicle At Low Altitude

( Yu-hung Lin ),( Tzu-fang Lai ),( Po-yen Lin ),( Tse-min Chen ) 한국농업기계학회 2018 한국농업기계학회 학술발표논문집 Vol.23 No.1

This research developed an integrated system that consist of orientation sensing, balance control, machine vision recognition and shape sorting and avoidance of obstacle with which the UVA will meet the requirement of a low altitude shuttle in orchards and forest. This research also focused on employing machine learning as the main control core to achieve the performances of target following and obstacle avoidance for unmanned aerial vehicle (UAV). In order to keep the balance of a quadcopter, the orientation data from gyroscope and accelerometer will be the inputs of a double loop PID controller. Target is recognized by machine vision. Distances and shapes of obstacles are defined by a laser rangefinder that mounted on the vehicle. The control of UAV depending on the shape of the obstacle, execute different obstacle avoidance strategies. The results of experiment indicated that the complementary filter can compensate the defects of the gyroscope and accelerometer since it fixes steady-state error of gyroscope and oscillation in high frequency of accelerometer. Double-loop PID controller is more stable than single-loop PID controller is. Due to the stability of control board and safety of operators in target following and obstacle avoidance experiment, a three wheels omni robot was employed to conduct the performance evaluation. The final results validate that the novel UAV is equipped with the ability of shuttling among orchards in low-altitude, target following, classification of obstacle shape and obstacle avoidance.

Expression, Purification and Properties of Shikimate Dehydrogenasefrom Mycobacterium Tuberculosis

Xuhui Lai,Honghai Wang,Xuelian Zhang,Shunbao Zhang,Fang Hao,Haidong Yu,Yishu Huang 한국생화학분자생물학회 2005 BMB Reports Vol.38 No.5

The assessment of host and bacterial proteins in sputum from active pulmonary tuberculosis

Hsin-Chih Lai,Yu-Tze Horng,Pen-Fang Yeh,Jann-Yuan Wang,Chin-Chung Shu,Chia-Chen Lu,Jang-Jih Lu,Jen-Jyh Lee,Po-Chi Soo 한국미생물학회 2016 The journal of microbiology Vol.54 No.11

Pulmonary tuberculosis (TB) is caused by Mycobacterium tuberculosis. The protein composition of sputum may reflect the immune status of the lung. This study aimed to evaluate the protein profiles in spontaneous sputum samples from patients with active pulmonary TB. Sputum samples were collected from patients with pulmonary TB and healthy controls. Western blotting was used to analyze the amount of interleukin 10 (IL-10), interferon-gamma (IFN-γ), IL-25, IL- 17, perforin-1, urease, albumin, transferrin, lactoferrin, adenosine deaminase (also known as adenosine aminohydrolase, or ADA), ADA-2, granzyme B, granulysin, and caspase- 1 in sputum. Results of detection of IL-10, IFN-γ, perforin- 1, urease, ADA2, and caspase-1, showed relatively high specificity in distinguishing patients with TB from healthy controls, although sensitivities varied from 13.3% to 66.1%. By defining a positive result as the detection of any two proteins in sputum samples, combined use of transferrin and urease as markers increased sensitivity to 73.2% and specificity to 71.1%. Furthermore, we observed that the concentration of transferrin was proportional to the number of acidfast bacilli detected in sputum specimens. Detection of sputum transferrin and urease was highly associated with pulmonary TB infection. In addition, a high concentration of transferrin detected in sputum might correlate with active TB infection. This data on sputum proteins in patients with TB may aid in the development of biomarkers to assess the severity of pulmonary TB.

Retrospective study of the medical status of 34 Formosan sika deer (Cervus nippon taiouanu) at the Taipei Zoo from 2003 to 2014

Kang, Chu-Lin,Yu, Jane-Fang,Lai, Hsueh,Guo, Jun-Cheng,Wang, Lih-Chiann The Korean Society of Veterinary Science 2015 大韓獸醫學會誌 Vol.55 No.3

The Formosan sika deer (Cervus nippon taiouanus) is an endemic subspecies in Taiwan. The original wild deer has been extinct since the late 1960s. The largest captive population is located at the Taipei Zoo. Except for infectious disease outbreaks, no systemic medical research has been reported for this subspecies. This study was conducted to analyze the medical status of the captive Formosan sika deer population, including the hematological and serum chemistry characteristics. To accomplish this, medical records for 34 Formosan sika deer from January 2003 to January 2014 were acquired and analyzed. The most common illness and cause of death was trauma, followed by gastrointestinal and respiratory disease, respectively. The hematologic and serum chemical values of healthy adults were quite different from those of sika deer (Cervus nippon yesoensis). This study provides a closer medical understanding of this subspecies and the results will facilitate its management.

Expression, Purification and Properties of Shikimate Dehydrogenase from Mycobacterium Tuberculosis

Zhang, Xuelian,Zhang, Shunbao,Hao, Fang,Lai, Xuhui,Yu, Haidong,Huang, Yishu,Wang, Honghai Korean Society for Biochemistry and Molecular Biol 2005 Journal of biochemistry and molecular biology Vol.38 No.5

Tuberculosis, caused by Mycobacterium tuberculosis, continues to be one of the main diseases to mankind. It is urgent to discover novel drug targets for appropriate antimicrobial agents against this human pathogen. The shikimate pathway is onsidered as an attractive target for the discovery of novel antibiotics for its essentiality in bacteria and absence in mammalian cells. The Mycobacterium tuberculosis aroE-encoded shikimate dehydrogenase was cloned, expressed and purified. Sequence alignment analysis shows that shikimate dehydrogenase of Mycobacterium tuberculosis exhibit the pattern of G-X-(N/S)-V-(T/S)-X-PX-K, which is highly conserved within the shikimate dehydrogenase family. The recombinant shikimate dehydrogenase spectrum determined by CD spectroscopy showed that the percentages for $\alpha$-helix, $\beta$-sheet, $\beta$-turn, and random coil were 29.2%, 9.3%, 32.7%, and 28.8%, respectively. The enzymatic characterization demonstrates that it appears to be fully active at pH from 9.0 to 12, and temperature $63^{\circ}C$. The apparent Michaelis constant for shikimic acid and $NADP^+$ were calculated to be about $29.5\;{\mu}M$ and $63\;{\mu}M$. The recombinant shikimate dehydrogenase catalyzes the substrate in the presence of $NADP^+$ with an enzyme turnover number of $399\;s^{-1}$. Zymological studies suggest that the cloned shikimate dehydrogenase from M. tuberculosis has a pretty activity, and the work should help in the discovery of enzyme inhibitors and further of possible antimicrobial agents against Mycobacterium tuberculosis.

Cardioprotective effect of ginsenoside Rb1 via regulating metabolomics profiling and AMP-activated protein kinase-dependent mitophagy

Jingui Hu,Ling Zhang,Fei Fu,Qiong Lai,Lu Zhang,Tao Liu,Boyang Yu,Junping Kou,Fang Li 고려인삼학회 2022 Journal of Ginseng Research Vol.46 No.2

Background: Ginsenoside Rb1, a bioactive component isolated from the Panax ginseng, acts as a remedy to prevent myocardial injury. However, it is obscure whether the cardioprotective functions of Rb1 are related to the regulation of endogenous metabolites, and its potential molecular mechanism still needs further clarification, especially from a comprehensive metabolomics profiling perspective. Methods: The mice model of acute myocardial ischemia (AMI) and oxygen glucose deprivation (OGD)-induced cardiomyocytes injury were applied to explore the protective effect and mechanism of Rb1. Meanwhile, the comprehensive metabolomics profiling was conducted by high-performance liquid chromatography and quadrupole time-of-flight mass spectrometry (HPLC-Q/TOF-MS) and a tandem liquid chromatography and mass spectrometry (LC-MS). Results: Rb1 treatment profoundly reduced the infarct size and attenuated myocardial injury. The metabolic network map of 65 differential endogenous metabolites was constructed and provided a new inspiration for the treatment of AMI by Rb1, which was mainly associated with mitophagy. In vivo and in vitro experiments, Rb1 was found to improve mitochondrial morphology, mitochondrial function and promote mitophagy. Interestingly, the mitophagy inhibitor partly attenuated the cardioprotective effect of Rb1. Additionally, Rb1 markedly facilitated the phosphorylation of AMP-activated protein kinase a (AMPKa), and AMPK inhibition partially weakened the role of Rb1 in promoting mitophagy. Conclusions: Ginsenoside Rb1 protects acute myocardial ischemia injury through promoting mitophagy via AMPKa phosphorylation, which might lay the foundation for the further application of Rb1 in cardiovascular diseases.