1,721,415 research outputs found
The uncertainty of seafood labeling in China can affect the global trade and favor frauds
No full textAdvancements in genome engineering and applications in mammalian systems
No full textIn the past three decades, we have witnessed the outbreak of technology development and applications in the field of genome engineering. From zinc finger proteins (ZFPs), to transcription activator-like effectors (TALEs), to Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), these programmable DNA targeting proteins have been successfully adapted for genome editing, loci imaging and gene regulations. In Chapter 2, I demonstrated an efficient epitope tagging approach that enabled subsequent chromatin immunoprecipitation followed by sequencing (ChIP-Seq) experiments. Specifically, I combined CRISPR-Cas9 with MMEJ (Micro-homology Mediated End Joining) to genetically engineer an endogenous transcription factor (TF) with a 3xFLAG tag in a human colorectal cancer cell line (HCT116). I genotyped modified clones to confirm the precise tag insertion. The TF binding motifs, typical peak locations and peak calling enrichment were validated from ChIP-seq results. Similar analyses and results were observed among single clones and pooled clones, suggesting colony isolation could be skipped for cell line generation. The highly scalable procedure makes this strategy ideal for ChIP-seq analysis of TFs in diverse species and cell types. In Chapter 3, I emphasized on comparing Tet Operator (TetO)/Tet Repressor (TetR) based imaging method with TALE and CRISPR-Cas9 mediated loci labeling methods. Signal to nuclear noise ratios (SNRs) were analyzed first. The high SNRs indicated all methods should be suitable for live cell imaging applications. Labeled loci positioning to nuclear speckles were found similar among these methods. Orthogonal imaging of paired loci was also confirmed by utilizing two of these methods to target genomic regions separated by 7kb. When targeting the sub-telomeric region, loci labeled by TetR showed slightly higher frequency in the form of doublets than the other methods. When targeting a typical euchromatic region, loci labeled by CRISPR-Cas9 based approach maintained much lower doublet frequency than TetR labeling. Long term live imaging was conducted to track the labeled loci by CRISPR-Cas9 during S-phase, which had approximately an hour delay in replication timing. Moreover, fewer doublets were observed from CRISPR-Cas9 labeling over the live imaging acquisition, implying a possibility that CRISPR-Cas9 perturbed sister locus separation. Generally, these imaging methodologies can efficiently label endogenous sites with high SNR and positioning specificity. CRISPR-Cas9 based method may not be the ideal for cell cycle relevant research due to its potential intervention of replication progression. In Chapters 4 and 5, I switched gear to aim at expanding gene regulation toolbox. In Chapter 4, I coupled three nuclease-deficient Cas9 orthologs from Streptococcus pyogenes (dCas9Sp), Neisseria meningitidis (dCas9Nm) and Staphylococcus aureus (dCas9Sa) with chemically inducible dimerizers GAI-GID, FKBP-FRB and ABI-PYL1 respectively. The dCas9 protein was fused with one of the dimerizers and the other dimerizer was fused with activator domain p65-HSF1. Addition of inducers enabled dimerization which resulted in the recruitment of p65-HSF1 molecules to targeted promoter regions for gene upregulation. These three platforms were tested with high induction efficiency and were able to regulate three model genes orthogonally. Spatial and temporal regulation was also executed to show the applicability of multi-pathway regulation in a time-dependent manner. In Chapter 5, I further engineered CRISPR single guide RNA (sgRNA) scaffolds by adding aptamer sequences. The RNA binding protein was fused with one of the dimerizers; while the other dimerizer was fused with p65-HSF1. Efficient gene regulations were achieved, and orthogonality of inducible gene regulation was proved. The new systems used only dCas9Sp, which had less limitation to design specific targeting sites. The induction efficiency could potentially be further improved by inserting more copies of aptamer sequences in the future work.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2023-05-01The student, Xiong Xiong, accepted the attached license on 2021-04-22 at 00:57.The student, Xiong Xiong, submitted this Dissertation for approval on 2021-04-22 at 01:09.This Dissertation was approved for publication on 2021-04-22 at 14:36.DSpace SAF Submission Ingestion Package generated from Vireo submission #16491 on 2021-09-16 at 20:13:46Made available in DSpace on 2021-09-17T04:06:50Z (GMT). No. of bitstreams: 3
XIONG-DISSERTATION-2021.pdf: 40725568 bytes, checksum: 984e14335c7e65983443cd6441b484a4 (MD5)
LICENSE.txt: 4208 bytes, checksum: 47a282b617a89847ccccffb84cc7ea82 (MD5)
Rightslink? by Copyright Clearance Center_ACS Synbio.pdf: 117240 bytes, checksum: 73268400b851a9c2bfb47f3725e87972 (MD5)
Previous issue date: 2021-04-22Embargo set by: Seth Robbins for item 118693
Lift date: 2023-09-17T04:07:01Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemAuthor requested closed access (OA after 2yrs) in Vireo ETD systemLimite
DNA barcoding reveals chaotic labeling and misrepresentation of cod (Xue) products sold on the Chinese market
Full text linkThe increasing rate of seafood frauds, especially in the case of highly priced species, highlights the need of verifying the identity of fish products. This paper describes the application of DNA barcoding to the identification of 52 products commercialized with the Chinese term 鳕 (Xue, Cod) in supermarkets (Nanjing and Shanghai) and in the online market. Considering the lack of harmonization around the definition of Cod, the mislabeling rate was assessed according to three increasingly stringent definitions: Cod meaning Gadiformes species; Cod meaning Gadus spp.; Cod not meaning any specific species, since a qualifier (“Atlantic”, “Pacific” or “Greenland”) should be added in order to refer to Gadus morhua, Gadus macrocephalus or Gadus ogac, respectively.
Results highlighted a very high mislabeling rate, which exceeded 60% even with the less stringent definition. Interestingly, only 42.3% of the samples were Gadiformes, while the others were Perciformes, Pleuronectiformes or toxic Tetraodontiformes species. Economic, ecological and health issues arising from the misuse of the term Cod are discussed in the light of the leading role of China in the seafood worldwide industry and of the increased national consumption of marine species
Fish species identification in canned pet food by BLAST and Forensically Informative Nucleotide Sequencing (FINS) analysis of short fragments of the mitochondrial 16s ribosomal RNA gene (16S rRNA)
Full text linkNowadays, pet food claiming high-valued fish among ingredients is largely available on the market. Unfortunately, the modifications induced by processing make species identification by visual inspection difficult and hinder the enforcement of the legislation on traceability. In this work, after aligning 819 sequences of Clupeidae, Engraulidae, Salangidae and Scombridae families, we developed new universal primers for the amplification and sequencing of 2 short fragments (±118 and ±213) of the mitochondrial 16s ribosomal RNA (16S rRNA) gene. Once tested on 130 DNA reference samples, these primers were used in the analysis of highly degraded DNA extracted from 43 canned cat food containing whole minnows (whitebait) (M) and tuna, or bonito or mackerel fillets (F). Three M and 2 F samples were analyzed for each can. A BLAST and a FINS analysis, the latter performed only on the 118 bp fragment, were performed separately on the sequences obtained from M and F samples. All the M samples were identified at the species or genus level by both BLAST and FINS analysis. This allowed to highlight an impressive rate of mislabeling (100%). F samples, for which FINS was less performing in species identification, resulted mislabeled in 40% of the products
The uncertainty of seafood labeling in China: A case study on Cod, Salmon and Tuna
Full text linkExotic marine fish products are increasingly appreciated in China. In this study, 100 samples of Cod, Salmon and Tuna products were collected from supermarkets in Shanghai, Nanjing and Hangzhou. First the information reported on the label were assessed in the light of the Chinese legislation, paying particular attention to the fish names and the geographical origin. Then, a comparative analysis of the official trade denominations adopted by five European countries (Italy, France, Germany, Spain and United Kingdom) for Cod, Salmon and Tuna was performed. Finally, the Chinese names of the species considered in the EU list were verified consulting the available international lists. Overall, 95% of the samples employed just generic names. In particular, 98% of Salmon and 100% of Tuna products were generically labeled while the labeling of Cod products was more diversified, even though 80% reported misleading or fake denominations. The results of this work highlighted the lack of a mandatory legislation on seafood traceability and of an official naming system. In particular, this study propose the introduction of a detailed Chinese naming system based on the Chinese Latin Dictionary for Seafood Names, following the EU approach. In fact, inaccurate labeling can have both economic and health implications for consumers as well as it may distort the true abundance of fish stocks. These drawbacks can be particularly serious considering the pivotal role of China in the global fishery industry
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Multiple fish species identified from China's roasted Xue Yu fillet products using DNA and mini-DNA barcoding: Implications on human health and marine sustainability
Full text linkRoasted Xue Yu fillet is among the most common fish products in China and the market appealing can be reflected by its high price that occasionally exceeds 300 RMB/kg in local supermarket. However, due to the lack of harmonization around the definition of Xue Yu, as well as the disability of visual inspection for transformed fish products, China's roasted Xue Yu fillet products are quite deep in the scandal of species adulteration. The objective of this study is to apply DNA and mini-DNA barcoding for the species identification of 153 roasted Xue Yu fillet products, on behalf of 30 brands, collected from 16 cities of China. The mislabeling rate was assessed according to three increasingly stringent definitions: 1) Xue Yu meaning Gadiformes species; 2) Xue Yu meaning Gadidae species; 3) Xue Yu meaning Gadus spp. Results highlighted a very high mislabeling rate, which reached 58% even with the least stringent definition. Only 42% of the samples were identified as belonging to Gadiformes, while the others were Scorpaeniformes, Tetraodontiformes and Lophiiformes. Moreover, the implications on human health and marine sustainability were also discussed, given the identification of poisonous Lagocephalus spp. from 37 samples and the China's rising consumption of marine resources
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
- …
