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Applied Biosystems 3730
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Description
instrument, automatic sequencer, instrument, automated sequencer, sequencer
This model was found at
4310 locations
The model is used in
77 countries
Usage per year (up to 2020)
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189 related research fields
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About the Applied Biosystems 3730

The model Applied Biosystems 3730 was found in 4310 unique locations in 77 countries where it was mentioned from 2004 until recentlyIt is used by scientists in various research fields such as Genetics, General Medicine, Genetics (clinical), Molecular Biology, and Ecology, Evolution, Behavior and Systematics. The model is also used in Microbiology, Infectious Diseases, Cancer Research, Microbiology (medical), Oncology, Plant Science, Biotechnology, General Biochemistry, Genetics and Molecular Biology, Parasitology, Virology, Molecular Medicine, Immunology, Biochemistry, Animal Science and Zoology, Cell Biology, Immunology and Allergy, General Veterinary, General Agricultural and Biological Sciences, Organic Chemistry, Physical and Theoretical Chemistry, General Immunology and Microbiology, Neurology (clinical), Computer Science Applications, Pharmacology, and Aquatic Science.
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Research that uses the Applied Biosystems 3730

Adeyinka Abiola Adetula, Xiaolei Liu, Liubin Yang, Chengchi Fang, Hui Yu, Hua Li, Shijun Li, Archives Animal Breeding, 63, 231-239 (2), 2020
Abstract. A genome-wide association study (GWAS) was performed on a resource family consisting of white and colored chickens for identification of genes related to plumage coloration using the Fixed and random model Circulating Probability Unification (FarmCPU) package. GWAS identified three chromosomal single-nucleotide polymorphisms (SNPs), demonstrating the polygenic basis of plumage phenotypes. Herein, retinoic acid-induced protein 14 (RAI14), a developmentally regulated gene that encodes a protein containing many ankyrin repeats, was identified as a candidate gene involved in plumage color. In this study, mRNA expression profiles of chicken RAI14 were determined, indel (insertion–deletion) variants were identified, and their association was analyzed in white and colored chickens. RA114 mRNA was expressed in all tissues tested (brain, spleen, liver, heart, oviduct, kidney, lung, pituitary gland, ovary, muscle, feather bulb, and skin). A relatively high RAI14 expression in white feather bulb compared to colored feather bulb (P<0.01) indicated a potential association with plumage color. Additionally, statistical analysis revealed that a 4 bp indel genetic variation in RAI14 was associated with plumage phenotypes (P<0.01). Together, our analysis of the identification of the RAI14 gene will enable us to understand the genetic mechanisms behind chicken pigmentation.
Guangsen Hou, Yong Tang, Luping Ren, Yunpeng Guan, Xiaoyu Hou, Guangyao Song, International Journal of Endocrinology, 2020, 1-8, 2020
Background. Our aim was to investigate the association between the genetics of the angiopoietin protein-like 8 (ANGPTL8) rs2278426 (C/T) polymorphism with prediabetes (pre-DM) and type 2 diabetes (T2DM) in a Han Chinese population in Hebei Province, China. Methods. We enrolled 1,460 participants into this case-control study: healthy controls, n = 524; pre-DM, n = 460; and T2DM: n = 460. Ligase assays on blood samples from all participants were used to identify polymorphisms. Differences in genotype and allele distributions were compared by the chi-square test and one-way analysis of variance, and a post hoc pairwise analysis was performed using the Bonferroni test. The logistic regression technique was adjusted for age, sex, and body mass index. Results. The frequency of the TT (10.9%) genotype was significantly higher in pre-DM patients than in controls (odds ratio [OR] = 1.696, 95% confidence interval [CI] = 1.026–2.802, P = 0.039 ). In the T2DM group, the CT (48%) and TT (15%) genotypes were significantly higher compared with those in the control group (CT : OR = 1.384, 95% CI = 1.013–1.890, P = 0.041 ; TT : OR = 2.530, 95% CI = 1.476–4.334, P = 0.001 ). The frequency of the T allele was significantly higher in the pre-DM (32.8%) and T2DM (39%) groups compared with the control group (26.9%) and was significantly associated with an increased risk of pre-DM (OR = 1.253, 95% CI = 1.017–1.544, P = 0.034 ) and T2DM (OR = 1.518, 95% CI = 1.214–1.897, P = 0.001 ). Furthermore, insulin levels in the pre-DM and T2DM groups were significantly decreased in those with the TT genotype compared with the CC and CT genotypes. Conclusion. ANGPTL8 rs2278426 may be involved in the mechanism of insulin secretion and could lead to an increased risk of pre-DM and T2DM.
Sha-Sha Tao, Yi-Lin Dan, Guo-Cui Wu, Qin Zhang, Tian-Ping Zhang, Yin-Guang Fan, Hai-Feng Pan, BioMed Research International, 2020, 1-7, 2020
Background. Recently, increasing studies have revealed that leptin is involved in the development of rheumatoid arthritis (RA). This study is aimed at exploring the association of leptin gene single nucleotide polymorphisms (SNPs) with susceptibility to RA in a Chinese population. Methods. We recruited 600 RA patients and 600 healthy controls from a Chinese population and analyzed their three leptin SNPs (rs10244329, rs2071045, and rs2167270) using the improved Multiplex Ligase Detection Reaction (iMLDR) assays. The associations of these SNPs with clinical manifestations of RA were also analyzed. Enzyme-linked immunosorbent assay (ELISA) was performed for plasma leptin determination. Results. No significant difference in either allele or genotype frequencies of these three SNPs between RA patients and healthy controls was observed (all P > 0.05 ). Association between the genotype effects of dominant, recessive models was also not found (all P > 0.05 ). No significant difference in plasma leptin levels was detected between RA patients and controls ( P > 0.05 ). Conclusion. Leptin gene (rs10244329, rs2071045, and rs2167270) polymorphisms are not associated with RA genetic susceptibility and its clinical features in the Chinese population.
Theint Theint Win, Sikandar Khan, PengCheng Fu, Journal of Nanotechnology, 2020, 1-9, 2020
The scientific consensus is now on developing a biocontrol agent that can cause cellular metabolic reprogramming against agricultural pathogens. Biosynthesis of silver nanoparticles was performed by using phytopathogenic fungi (Alternaria sp.) isolated from banana cultivated soil. Alternaria sp. can grow very fast and produce high enough bioactive compounds. This study aims to biosynthesize silver nanoparticles (AgNPs) using fungal Alternaria sp.’s metabolites as a safe antifungal agent against plant pathogenic fungi (Fusarium spp. and Alternaria sp.). To visualize the formation of AgNPs, analytical instruments were used, such as ultraviolet-visible (UV-Vis) spectroscopy, Fourier-transform infrared (FTIR) spectroscopy, scanning transmission electron microscopy (STEM), energy dispersive X-ray (EDX), and elemental mapping. The UV-visible spectra showed a peak at 435 nm. Analysis of scanning transmission electron microscopy (STEM) micrographs evidenced that the size of synthesized silver nanoparticles ranged between 3 and 10 nm. The resulting AgNPs showed distinct antifungal activity against selected plant pathogenic fungi. Synthesized AgNPs have demonstrated remarkable potential for the use of antifungal compounds to combat plant diseases.
Mahasen Mohamed Ahmed Ebaya, Mohammed El-Mowafy, Mohamed Mohamed Adel El-Sokkary, Ramadan Hassan, International Journal of Microbiology, 2020, 1-11, 2020
Dextranase is a useful enzyme that catalyzes the degradation of dextran to low-molecular-weight fractions, which have many critical commercial and clinical applications. Endophytic fungi represent a source of both high heat-stable and pH-stable enzymes. In this study, from Delonix regia bark by plate assay, out of 12 isolated fungal strains, hyaline zones were detected in only one strain. By using the standard ITS rDNA sequencing analysis, the isolated strain was identified as Talaromyces sp. In the case of carbon source, in a medium containing 1% dextran T2000 as the sole carbon source, the maximum dextranase activity reached approximately 120 U/ml after incubation of 2 days where the optimum pH was 7.4. Peptone addition to the production medium as a sole nitrogen source was accompanied by a significant increase in the dextranase production. Similarly, some metal ions, such as Fe2+ and Zn2+, increased significantly enzyme production. However, there was no significant difference resulting from the addition of Cu2+. The crude dextranase was purified by ammonium sulfate fractionation, followed by Sephadex G100 chromatography with 28-fold purification. The produced dextranase was 45 kDa with an optimum activity at 37°C and a pH of 7. Moreover, the presence of MgSO4, FeSO4, and NH4SO4 increased the purified dextranase activity; however, SDS and EDTA decreased it. Interestingly, the produced dextranase expressed remarkable pH stability, temperature stability, and biofilm inhibition activity, reducing old-established biofilm by 86% and biofilm formation by 6%.
Xiulin Zhang, Yang He, Wei Zhang, Yining Wang, Xinmeng Liu, Aique Cui, Yidi Gong, Jing Lu, Xin Liu, Xueyun Huo, Jianyi Lv, Meng Guo, Xiaoyan Du, Lingxia Han, Hongyan Chen, Jilan Chen, Changlong Li, Zhenwen Chen, BioMed Research International, 2021, 1-14, 2021
Poultries including chickens, ducks, geese, and pigeons are widely used in the biological and medical research in many aspects. The genetic quality of experimental poultries directly affects the results of the research. In this study, following electrophoresis analysis and short tandem repeat (STR) scanning, we screened out the microsatellite loci for determining the genetic characteristics of Chinese experimental chickens, ducks, geese, and pigeons. The panels of loci selected in our research provide a good choice for genetic monitoring of the population genetic diversity of Chinese native experimental chickens, ducks, geese, and ducks.
Li-Li Wang, Li Ding, Peng Zhao, Jing-Jing Guan, Xiao-Bin Ji, Xiao-Li Zhou, Shi-Hong Shao, Yu-Wei Zou, Wei-Wei Fu, Dong-Liang Lin, Disease Markers, 2021, 1-10, 2021
Background. Morule-like component (MLC) was a rare structure in primary lung adenocarcinoma. We aimed to reveal the clinicopathological, radiological, immunohistochemical, and molecular features of lung adenocarcinoma with MLCs. Methods. Twenty lung adenocarcinomas with MLCs were collected, and computed tomographic and histological documents were reviewed. Immunohistochemistry, targeted next-generation sequencing, and Sanger sequencing for β-catenin gene were performed. Results. There were 9 lepidic adenocarcinomas, 8 acinar adenocarcinomas, 2 papillary adenocarcinomas, and 1 minimally invasive adenocarcinoma. Most patients (16/17) were shown a pure solid nodule, and 1 patient was shown a partly solid nodule on chest computed tomography (CT). Nine cases were accompanied with micropapillary components, and 3 were with cribriform components in which 2 suffered a worse prognosis. No significant association was found between the MCLs and the overall survival of lung adenocarcinoma ( P = 0.109 ). The MLCs were often arranged in whorled or streaming patterns. The cells in MLCs showed syncytial and mild appearance. The MLCs were positive for E-cadherin, CK7, TTF-1, napsin-A, vimentin, and β-catenin (membrane), and negative for CK5/6, p40, p63, Synaptophysin, chromogranin A, and Cdx-2. EGFR mutation, ALK-EML4 fusion, HER2 amplification, and PIK3CA mutation were detected in 16 cases, 2 cases, 1 case, and 1 case, respectively. EGFR mutation was more frequent in adenocarcinomas with MLCs than those without MLCs ( P = 0.040 ). β-catenin gene mutation was not detected in any patients. Conclusions. MLC is often observed in the background of acinar, lepidic, and papillary adenocarcinomas. Lung adenocarcinomas with MLCs tend to appear as a solid mass on CT and harbor EGFR gene mutations. The micropapillary components and cribriform components may cause poor prognosis of lung adenocarcinomas with MLCs. Vimentin is always positive in MLCs, and it is a useful marker for the identification of MLCs.
Jean-Lou Justine, Delphine Gey, Jessica Thévenot, Romain Gastineau, Hugh D. Jones, PeerJ, 8, e10098, 2020
Background The land flatworm Amaga expatria Jones & Sterrer, 2005 (Geoplanidae) was described from two specimens collected in Bermuda in 1963 and 1988 and not recorded since. Methods On the basis of a citizen science project, we received observations in the field, photographs and specimens from non-professionals and local scientists in Martinique and Guadeloupe. We barcoded (COI) specimens from both islands and studied the histology of the reproductive organs of one specimen. Based on Next Generation Sequencing, we obtained the complete mitogenome of A. expatria and some information on its prey from contaminating DNA. Results We add records from 2006 to 2019 in two French islands of the Caribbean arc, Guadeloupe (six records) and Martinique (14 records), based on photographs obtained from citizen science and specimens examined. A specimen from Martinique was studied for histology of the copulatory organs and barcoded for the COI gene; its anatomy was similar to the holotype, therefore confirming species identification. The COI gene was identical for several specimens from Martinique and Guadeloupe and differed from the closest species by more than 10%; molecular characterisation of the species is thus possible by standard molecular barcoding techniques. The mitogenome is 14,962 bp in length and contains 12 protein coding genes, two rRNA genes and 22 tRNA genes; for two protein genes it was not possible to determine the start codon. The mitogenome was compared with the few available mitogenomes from geoplanids and the most similar was Obama nungara, a species from South America. An analysis of contaminating DNA in the digestive system suggests that A. expatria preys on terrestrial molluscs, and citizen science observations in the field suggest that prey include molluscs and earthworms; the species thus could be a threat to biodiversity of soil animals in the Caribbean.
Irene Martín-Rodríguez, Adrián Escudero, Alfredo García-Fernández, PeerJ, 9, e10533, 2021
BackgroundGypsum ecosystems are edaphic islands surrounded by a matrix that is inhospitable to gypsum soil plant specialists. These naturally fragmented landscapes are currently exacerbated due to man-made disturbances, jeopardising their valuable biodiversity. Concomitant action of other fragmentation drivers such as linear infrastructures may increase the already high threat to these specialists. Although some evidence suggest that gypsophytes are not evolutionary dead-ends and can respond to fragmentation by means of phenotypic plasticity, the simultaneous action of barriers to genetic flow can pose a severe hazard to their viability. Here, we evaluated the effect of a highway with heavy traffic on the genetic flow and diversity in the speciesLepidium subulatum, a dominant Iberian shrubby gypsophyte.MethodsWe tested the possible existence of bottlenecks, and estimated the genetic diversity, gene flow and genetic structure in the remnant populations, exploring in detail the effect of a highway as a possible barrier.ResultsResults showed variability in genetic diversity, migrants and structure. The highway had a low impact on the species since populations can retain high levels of genetic diversity and genetic parameter, likeFSTandFIS, did not seem to be affected. The presence of some level of genetic flow in both sides along the highway could explain the relatively high genetic diversity in the habitat remnants.DiscussionNatural fragmentation and their exacerbation by agriculture and linear infrastructures seem to be negligible for this species and do not limit its viability. The biological features, demographic dynamics and population structures of gypsum species seem to be a valuable, adaptive pre-requisite to be a soil specialist and to maintain its competitiveness with other species in such adverse stressful conditions.
Siyu Wang, Hongbo Guo, JiaJia Li, Wei Li, Qin Wang, Xiaodan Yu, PeerJ, 7, e7307, 2019
Background Distinguishing among species in the genus Lepista is difficult because of their similar morphologies. Methods To identify a suitable DNA barcode for identification of Lepista species, we assessed the following five regions: internal transcribed spacer (ITS), the intergenic spacer (IGS), nuclear ribosomal RNA subunit, mitochondrial small subunit rDNA, and tef1. A total of 134 sequences from 34 samples belong to eight Lepista species were analyzed. The utility of each region as a DNA barcode was assessed based on the success rates of its PCR amplification and sequencing, and on its intra- and inter-specific variations. Results The results indicated that the ITS region could distinguish all species tested. We therefore propose that the ITS region can be used as a DNA barcode for the genus Lepista. In addition, a phylogenetic tree based on the ITS region showed that the tested eight Lepista species, including two unrecognized species, formed eight separate and well-supported clades.
Yukino Mizutani, Tetsushi Mori, Taeko Miyazaki, Satoshi Fukuzaki, Reiji Tanaka, PeerJ, 8, e9326, 2020
Gills are important organs for aquatic invertebrates because they harbor chemosynthetic bacteria, which fix inorganic carbon and/or nitrogen and provide their hosts with organic compounds. Nevertheless, in contrast to the intensive researches related to the gut microbiota, much is still needed to further understand the microbiota within the gills of invertebrates. Using abalones as a model, we investigated the community structure of microbes associated with the gills of these invertebrates using next-generation sequencing. Molecular identification of representative bacterial sequences was performed using cloning, nested PCR and fluorescence in situ hybridization (FISH) analysis with specific primers or probes. We examined three abalone species, namely Haliotis gigantea, H. discus and H. diversicolor using seawater and stones as controls. Microbiome analysis suggested that the gills of all three abalones had the unclassified Spirochaetaceae (one OTU, 15.7 ± 0.04%) and Mycoplasma sp. (one OTU, 9.1 ± 0.03%) as the core microbes. In most libraries from the gills of H. gigantea, however, a previously unknown epsilonproteobacterium species (one OTU) was considered as the dominant bacterium, which accounted for 62.2% of the relative abundance. The epsilonproteobacterium was only detected in the gills of H. diversicolor at 0.2% and not in H. discus suggesting that it may be unique to H. gigantea. Phylogenetic analysis performed using a near full-length 16S rRNA gene placed the uncultured epsilonproteobacterium species at the root of the family Helicobacteraceae. Interestingly, the uncultured epsilonproteobacterium was commonly detected from gill tissue rather than from the gut and foot tissues using a nested PCR assay with uncultured epsilonproteobacterium-specific primers. FISH analysis with the uncultured epsilonproteobacterium-specific probe revealed that probe-reactive cells in H. gigantea had a coccus-like morphology and formed microcolonies on gill tissue. This is the first report to show that epsilonproteobacterium has the potential to be a dominant species in the gills of the coastal gastropod, H. gigantea.
Jessica Briggs, Alison Kuchta, Max Murphy, Sofonias Tessema, Emmanuel Arinaitwe, John Rek, Anna Chen, Joaniter I Nankabirwa, Chris Drakeley, David Smith, Teun Bousema, Moses Kamya, Isabel Rodriguez-Barraquer, Sarah Staedke, Grant Dorsey, Philip J Rosenthal, Bryan Greenhouse, 2020
Abstract Background: Evaluation of genetic relatedness of malaria parasites is a useful tool for understanding transmission patterns, but patterns are not easily detectable in areas with moderate to high malaria transmission. To evaluate the feasibility of detecting genetic relatedness in a moderate malaria transmission setting, we measured relatedness of Plasmodium falciparum infections in cohort participants from randomly selected households in the Kihihi sub-county of Uganda (annual entomological inoculation rate of 27 infectious bites per person). Methods: All infections detected via microscopy or Plasmodium-specific loop mediated isothermal amplification from passive and active case detection during August 2011-March 2012 were genotyped at 26 microsatellite loci, providing data for 349 samples from 230 participants living in 80 households. Pairwise genetic relatedness was calculated using identity by state (IBS).Results: As expected, genetic diversity was high (mean heterozygosity [He]=0.73), and the majority (76.5%) of samples were polyclonal. Despite the high genetic diversity, fine-scale population structure was detectable, with significant spatiotemporal clustering of highly related infections. Although the difference in malaria incidence between households at higher (mean 1127 meters) vs. lower elevation (mean 1015 meters) was modest (1.4 malaria cases per person-year versus 1.9 per person-year, respectively), we found a significant difference in multiplicity of infection (2.2 versus 2.6, p = 0.008) and, more strikingly, a higher proportion of highly related infections within households (6.3% vs 0.9%, p = 0.0005) at higher elevation compared to lower elevation. Conclusions: Genetic data from a relatively small number of diverse, multiallelic loci reflected fine scale patterns of malaria transmission. Given the increasing interest in applying genetic data to augment malaria surveillance, our study provides evidence that genetic data can be used to inform transmission patterns at local spatial scales even in moderate transmission areas.
Satoshi Fujito, Turgut Yigit Akyol, Takuya Mukae, Tadayuki Wako, Ken-ichiro Yamashita, Hikaru Tsukazaki, Hideki Hirakawa, Keisuke Tanaka, Yoko Mine, Shusei Sato, Masayoshi Shigyo, 2020
Abstract BackgroundGenomic information for Allium cepa L. is limited as it is heterozygous and its genome is very large. To elucidate potential SNP markers obtained by NGS, we used a complete set of A. fistulosum L.-A. cepa monosomic addition lines (MALs) and doubled haploids (DHs). These were the parental lines of an A. cepa mapping population for transcriptome-based SNP genotyping.ResultsWe mapped the transcriptome sequence reads from a series of A. fistulosum-A. cepa MALs onto the unigene sequence of the doubled haploid shallot A. cepa Aggregatum group (DHA) and compared the MAL genotype call for parental bunching onion and shallot transcriptome mapping data. We identified SNP sites with at least four reads on 25,462 unigenes. They were anchored on eight A. cepa chromosomes. A single SNP site was identified on 3,278 unigenes and multiple SNPs were identified on 22,184 unigenes. The chromosome marker information was made public via the web database Allium TDB (http://alliumtdb.kazusa.or.jp/). To map these markers, we gathered RNA sequence data from 96 lines of a DHA × doubled haploid bulb onion A. cepa common onion group (DHC) mapping population. After selecting co-dominant SNP sites, 16,872 SNPs were identified in 5,339 unigenes. Of these, at least two SNPs with identical genotypes were found in 1,435 unigenes. We developed a linkage map using genotype information from these unigenes. All unigene markers mapped onto the eight chromosomes and graphical genotyping was conducted based on the unigene order information. Another 2,963 unigenes were allocated onto the eight chromosomes. To confirm the accuracy of this transcriptome-based genetic linkage map, conventional PCR-based markers were used for linkage analysis. All SNP - and PCR-based markers were mapped onto the expected linkage groups and no inconsistency was found among these chromosomal locations.ConclusionsEffective transcriptome analysis with unique Allium resources successfully associated numerous chromosome markers with unigene information and an ultrahigh-density A. cepa linkage map. The information on these unigene markers is valuable in genome sequencing and useful trait detection in Allium.
Binbin Chen, Xiaoning Yu, Xin Zhang, Hao Yang, Yilei Cui, Xingchao Shentu, 2020
Abstract BACKGROUND Keratoconus (KC) is characterized by bilateral progressive corneal thinning and ectasia. The prevalence of KC is approximately 8.8 to 54.4 per 100,000 individuals across the globe. Genetic factors have been shown to contribute to the pathogenesis of KC. This study will identify new mutations in the susceptibility gene of keratoconus (KC) in the Chinese Han population. METHODS A total of fifty-two patients with primary KC were recruited. Blood samples were collected, and genomic DNA was isolated from peripheral blood leukocytes. The entire coding region, intron–exon junctions, and promoter regions of sixteen known KC susceptibility genes were screened with next-generation sequencing technology, and all identified variants were further confirmed using the Sanger sequencing technology. The Sorting Intolerant from Tolerant (SIFT), Mutation Taster and PolyPhen 2 programs were used to predict the effect of amino acid substitution on protein. RESULTS After removing twelve known SNPs (single nucleotide polymorphisms) and three variants predicted to be harmless, nine novel mutations were identified in eight of the fifty-two patients, including c.455C > T:p.P152L in FNDC3B, c.3636_3637del:p.R1212fs in COL4A4, c.5015G > T:p.R1672L, c.3798dupA:p.P1267fs and c.28G > A:p.A10T in MPDZ, c.1940C > T:p.P647L in DOCK9, c.127_128insGGC:p.Q43delinsRQ in POLG, c.3019G > A:p.V1007I in IPO5, and c.624 + 7->A in TGFBI. All nine mutations in the patients with KC were heterozygote. CONCLUSION This study enlarged the gene profile of KC and should be further confirmed by well-powered, genome-wide association studies (GWAS) of Han Chinese patients.
Fahmi Fahmi, Ian Tibbetts, Mike Bennett, Chris Dudgeon, 2020
Abstract BackgroundDelimiting cryptic species in elasmobranchs is a major challenge in modern taxonomy due the lack of available phenotypic features. Employing stand-alone genetics in splitting a cryptic species may prove problematic for further studies and for implementing conservation management. In this study, we examined mitochondrial DNA and genome-wide nuclear single nucleotide polymorphisms (SNPs) in the brown-banded bambooshark, Chiloscyllium punctatum to evaluate potential cryptic species and the species-population boundary in the group.ResultsOur results found four operational taxonomic units (OTUs) within C. punctatum from the Indo-Australian region. Each OTU can be interpreted differently depending on available supporting information. Similarly, we confirmed that comprehensive sampling over the species' geographic distribution was essential to determine the boundary between population and cryptic species.ConclusionWe provide suggestions about what should be considered prior to split cryptic species and the designation of new species.
Yuanmei Wang, Liying Liu, Min Li, Lili Lin, Pengcheng Su, Hui Tang, Xinzhong Fan, Xianyao LI, 2020
Abstract Background: Salmonella enterica serovar Enteritidis (SE) is one of the pathogenic bacteria, which affects poultry production and poses severe threat to public health. Chicken meat and egg are the main source of SE. DNA methylation, an important epigenetic modification, involves in regulatory processes including gene expression, chromatin structure and genomic imprinting. To understand the methylation regulation in response to SE inoculation in chicken, the genome-wide DNA methylation profile following SE inoculation was analyzed through whole genome bisulfite sequencing in the current study. Results: There were 185,362,463 clean reads and 126,098,724 unique reads in the control group, and 180,530,750 clean Reads, 126,782,896 unique reads in the inoculated group. We found that the methylation density in gene body was higher than that in the upstream and downstream regions of gene. There were 8,946 differentially methylated genes (3,639 hypo-methylated genes, 5,307 hyper-methylated genes) obtained between inoculated and control groups. Methylated genes were mainly enriched in immune-related Gene Ontology (GO) terms and metabolic process terms. Cytokine-cytokine receptor interaction, TGF-beta signaling pathway, FoxO signaling pathway, Wnt signaling pathway and several metabolism-related pathways were significantly enriched. The density of differentially methylated cytosines in miRNAs was the highest. HOX genes were widely methylated and mainly distributed in Chr2 and 7. Conclusions: We firstly analyzed the genome-wide DNA methylation in the response to SE inoculation in chicken. SE inoculation promoted the DNA methylation in chicken cecum and caused methylation alteration in immune- and metabolic- related genes. Wnt signal pathway, miRNAs and HOX gene family may play a crucial role in the methylation regulation of SE infection in chicken. The findings herein will deepen the understanding of epigenetic regulation in the response to SE inoculation in chicken.
Kevin Tak-Pan NG, Oscar Wai-Ho Yeung, Yin Fan Lam, Jiang Liu, Hui Liu, Li Pang, Xin Xiang Yang, Ji Ye Zhu, Wei yi Zhang, Matthew YH Lau, Wen Qi Qiu, Hoi Chung Shiu, Man Kit Lai, Chung Mau Lo, Kwan Man, 2020
Abstract BackgroundAn inevitable hepatic injury at the early phase after liver transplantation vitally affects the late phase hepatocellular carcinoma (HCC) recurrence. However, their linkage and underlying risk factors of HCC recurrence are unclear. This study aimed to clarify the clinical impact and functional roles of glutathione S-transferase A2 (GSTA2) in affecting HCC recurrence after liver transplantation.MethodsExpression significance and prognostic value of hepatic and circulating GSTA2 in HCC recipients were examined. The polymorphism of GSTA2 transcript was analysed by Sanger sequencing. The functions and molecular mechanisms of GSTA2 in the proliferation and metastasis of HCC were characterized by molecular, cellular and animal experiments. ResultsThe GSTA2 expression was significantly correlated with the early phase hepatic and systemic injury and reactive oxygen species (ROS) level after liver transplantation. Importantly, the level of the early phase circulating GSTA2 protein was a significant predictor of HCC recurrence and survival of HCC recipients. Heterogeneous single nucleotide polymorphism at G335C of GSTA2 was significantly associated with poor survival of HCC recipients. The GSTA2 expression was positively correlated with the aggressiveness of HCCs. Overexpression of GSTA2, by endogenous or exogenous approaches, could enhance the proliferation and invasion of HCCs through activating epithelial-mesenchymal-transition promoting proteins. Targeted inhibition of GSTA2 remarkably suppressed the proliferation and metastasis of HCCs. Increased level of GSTA2 could compensate the H2O2-induced ROS stress and therefore protect the HCC cells from damage. Alteration of GSTA2 expression in HCC cells could influence the activation of ROS-associated JNK and AKT signaling pathways and the expression of ROS-associated genes in responding to the H2O2 condition. ConclusionsOur research discovered GSTA2 to be the significant risk factor of HCC recurrence via providing a favorable ROS environment for HCC to survival and progress. This study presents a novel functional biomarker for combating HCC recurrence after liver transplantation.
Yuehui Li, Nana Li, Long Chen, Yueyuan Li, Zaiping Xiong, Yuanman Hu, Animals, 10, 1135 (7), 2020
It is necessary to estimate the population abundance of deer for managing their populations. However, most estimates are from high-density populations inhabiting the forests of North America or Europe; there is currently a lack of necessary knowledge regarding low-density deer populations in different forest habitats. In this article, we used fecal DNA based on the capture-mark-recapture method to estimate the population abundance of Siberian roe deer (Capreolus pygargus) in Liangshui National Nature Reserve in the Lesser Xing’an Mountains, northeast China, where the deer population was found to be of a low density by limited studies. We used a robust survey design to collect 422 fecal pellet groups in 2016 and extracted DNA from those samples, generating 265 different genotypes; we thus identified 77 deer individuals based on six microsatellite markers (Roe1, Roe8, Roe9, BM757, MB25 and OarFCB304). With capture and recapture records of these 77 individuals, the abundance of roe deer was estimated to be 87 deer (80–112, 95% CI) using the Program CAPTURE. Using an effective sampling area which resulted from the mean maximum recapture distance (MMRD), we converted the population abundance to a density of 2.9 deer/km2 (2.7–3.7, 95% CI). Our study estimated the roe deer population abundance by a feces-based capture-mark-recapture approach in northeast China, successfully demonstrating the applicability of non-invasive genetic sampling in monitoring populations of deer in this area, which contributes to the development of low-density deer population ecology and management.
Dimitrios Chatziplis, Stavroula Oikonomou, Dimitrios Loukovitis, Dimitrios Tsiokos, Athanasios Samaras, Arkadios Dimitroglou, Lefteris Kottaras, Kantham Papanna, Leonidas Papaharisis, Costas Tsigenopoulos, Michail Pavlidis, Animals, 10, 1668 (9), 2020
There is a growing interest in selective breeding in European sea bass (Dicentrarchus labrax), especially regarding family selection based on growth performance. In particular, quantitative trait loci (QTL) identification in sea bass enhances the application of marker-assisted breeding for the genetic improvement of the production traits. The aims of the study were to identify potential QTL affecting stress and immunological indicators, body weight, and mortality after vibriosis injection in sea bass as well as to estimate heritability and genetic/phenotypic correlations for the aforementioned traits. To this end, stress test was performed on 960 offspring and a sub-group of them (420) was selected to explore the mortality after vibrio injection. Selective genotyping was performed in 620 offspring for 35 microsatellite markers and distributed into 6 linkage groups. The length of the genetic linkage map was 283.6 cM and the mean distance between the markers was 8.1 cM. QTL affecting body weight in three different growth periods detected on linkage groups LG1, LG4, LG6, and LG14. A QTL associated with weight in early growth stages (290–306 days post-hatching) was also identified on LG3. QTL analysis confirmed the existence of QTL affecting cortisol levels, on LG3 and LG14. Moreover, new QTL affecting only cortisol and glucose levels were detected on LG1 and LG23. No QTL affecting hormonal or biochemical marks was found on LG4 and LG6. Heritability of cortisol, lysozyme levels, and mortality were high (0.36, 0.55, and 0.38, respectively).
Adrienne E. Crosier, Julie Lamy, Priya Bapodra, Suzi Rapp, Morgan Maly, Randy Junge, Holly Haefele, Jason Ahistus, Jenny Santiestevan, Pierre Comizzoli, Animals, 10, 1811 (10), 2020
Approximately 30% of the Association of Zoos and Aquariums cheetah population (~350 total animals) is unlikely to breed naturally due to advanced age, health, or behavioral issues. Aging cheetah females (≥9 y old) are unlikely to become pregnant via natural breeding if they are nulliparous. We previously demonstrated that oocytes recovered from aged females were of similar quality compared with those recovered from younger females (2–8 y old). We hypothesize that transfer of 4–8 cell embryos produced by in vitro fertilization with oocytes from old donors could result in pregnancy after transfer into younger recipients. Female cheetahs (n = 3 aging donors and n = 3 young recipients) received 300 IU equine Chorionic Gonadotropin (eCG) and 3000 IU Luteinizing Hormone (LH) while fecal metabolites of estrogens and progestogens were closely monitored. At 28 h post-LH injection, oocytes were aspirated laparoscopically from donors and inseminated in vitro with cryopreserved sperm. After 48 h of in vitro culture, resulting embryos (4–8 cells) were transferred into the oviducts of recipient females. Pregnancy was confirmed in one recipient via ultrasound 32 days after transfer and by radiograph 62 days after transfer. Two cubs were born naturally after 90 days of gestation, representing the first cheetah births resulting from transfer of embryos produced in vitro.
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