85 research outputs found
A Novel Strategy Based on Permanent Protein Modifications Induced by Formaldehyde for Food Safety Analysis
The illegal additions of chemicals
in food products are serious
incidents threatening current public safety. To date, ideal methods
to determine permanent traces of prohibited chemicals in foods are
still lacking. For example, formaldehyde (FA) can be added illegally
as a food preservative. However, most current methods that are dependent
on the direct detection of FA are not able to determine if FA has
ever been added once food products are rinsed completely. Herein,
we present a novel approach relying upon protein modifications induced
by FA (PMIF) to examine FA in foods. We reveal the entire catalog
of PMIFs in food products by combining mass spectrometry analysis
with unrestrictive identification of protein modifications. Consequently,
four obvious PMIFs were identified and confirmed as markers to discriminate
the addition of FA in foods. Our study demonstrates that the approach
based on PMIFs enables detecting the imprinted trace of FA even if
the food products have been washed thoroughly. Our work presents a
novel strategy for analysis of chemical additives, offering broad
potential applications in protein analysis and food safety
Additional file 4: of Identification of differentially expressed genes and pathways for intramuscular fat metabolism between breast and thigh tissues of chickens
The common DEGs involved in two pathways (ECM-receptor interaction and Focal adhesion) in this study. (XLS 40 kb
Additional file 5: of Identification of differentially expressed genes and pathways for intramuscular fat metabolism between breast and thigh tissues of chickens
The specific primers for q-PCR in this study. (XLS 57 kb
The deformed (left) and normal (right) beaks of Beijing-You chickens.
<p>The chicken with a deformed beak had problem with feeding, drinking, and preening and therefore showed lower body weight and poor mental condition.</p
Identification of Genes Related to Beak Deformity of Chickens Using Digital Gene Expression Profiling
<div><p>Frequencies of up to 3% of beak deformity (normally a crossed beak) occur in some indigenous chickens in China, such as and Beijing-You. Chickens with deformed beaks have reduced feed intake, growth rate, and abnormal behaviors. Beak deformity represents an economic as well as an animal welfare problem in the poultry industry. Because the genetic basis of beak deformity remains incompletely understood, the present study sought to identify important genes and metabolic pathways involved in this phenotype. Digital gene expression analysis was performed on deformed and normal beaks collected from Beijing-You chickens to detect global gene expression differences. A total of >11 million cDNA tags were sequenced, and 5,864,499 and 5,648,877 clean tags were obtained in the libraries of deformed and normal beaks, respectively. In total, 1,156 differentially expressed genes (DEG) were identified in the deformed beak with 409 being up-regulated and 747 down-regulated in the deformed beaks. qRT-PCR using eight genes was performed to verify the results of DGE profiling. Gene ontology (GO) analysis highlighted that genes of the keratin family on GGA25 were abundant among the DEGs. Pathway analysis showed that many DEGs were linked to the biosynthesis of unsaturated fatty acids and glycerolipid metabolism. Combining the analyses, 11 genes (<i>MUC</i>, <i>LOC426217</i>, <i>BMP4</i>, <i>ACAA1</i>, <i>LPL</i>, <i>ALDH7A1</i>, <i>GLA</i>, <i>RETSAT</i>, <i>SDR16C5</i>, <i>WWOX</i>, and <i>MOGAT1</i>) were highlighted as potential candidate genes for beak deformity in chickens. Some of these genes have been identified previously, while others have unknown function with respect to thus phenotype. To the best of our knowledge, this is the first genome-wide study to investigate the transcriptome differences in the deformed and normal beaks of chickens. The DEGs identified here are worthy of further functional characterization.</p></div
Additional file 4: of Decreased testosterone levels after caponization leads to abdominal fat deposition in chickens
The enriched pathways based on the 872 DEGs. (XLS 61ΓΒ kb
The two most significantly enriched pathways and the involved differentially expressed genes (DEG).
a<p><i>SCD5</i> β=β stearoyl-CoA desaturase 5; <i>GLG1</i> β=β golgi glycoprotein 1; <i>ELOVL6</i> β=β ELOVL family member 6; <i>PTPLB</i> β=β protein tyrosine phosphatase-like B; <i>ACAA1</i> β=β acetyl-CoA acyltransferase 1; <i>PECR</i> β=β privacy and electronic communications regulations; <i>MFSD4</i> β=β major facilitator superfamily domain containing 4; <i>DLEC1</i> β=β deleted in lung and esophageal cancer 1; <i>PTPLAD1</i> β=β protein tyrosine phosphatase-like A domain containing 1; <i>HSDL1</i> β=β hydroxysteroid dehydrogenase like gene; <i>LOC423119</i> β=β Gallus gallus fatty acid desaturase 1-like; <i>LPL</i> β=β lipoprotein lipase; <i>PNPLA2</i> β=β patatin-like phospholipase domain containing 2; <i>PPAP2A</i> β=β phosphatidic acid phosphatase 2A; <i>PPAP2B</i> β=β phosphatidic acid phosphatase 2B; <i>AGPAT6</i> β=β 1-acylglycerol-3-phosphate O-acyltransferase 6; <i>SHROOM3</i> β=β shroom family member 3; <i>ALDH7A1</i> β=β aldehyde dehydrogenase 7 family, member A1; <i>AKR1B10</i> β=β aldo-keto reductase family 1, member B10; <i>DGKD</i> β=β diacylglycerol kinase; <i>GK5</i> β=β glycerol kinase 5; <i>GLA</i> β=β galactosidase, alpha; <i>MOGAT1</i> β=β monoacylglycerol O-acyltransferase 1; <i>AR</i> β=β androgen receptor; <i>LIPG</i> β=β endothelial lipase.</p><p>The two most significantly enriched pathways and the involved differentially expressed genes (DEG).</p
Sequencing saturation analysis for RNA from the deformed (A) and normal beak (B).
<p>Sequencing saturation analysis for RNA from the deformed (A) and normal beak (B).</p
Some extremely differentially expressed genes (|log2-Ratio (deformed beak/normal beak)| β§ 9).
a<p><i>LOC426217</i> β=β claw keratin-like; <i>NPM3</i> β=β nucleophosmin/nucleoplasmin 3; <i>LPL</i> β=β lipoprotein lipase; <i>RBP7</i> β=β retinol binding protein 7 cellular; <i>NUBP2</i> β=β nucleotide binding protein 2 (MinD homolog <i>E. coli</i>); <i>ARL6IP1</i> β=β ADP-ribosylation factor-like 6 interacting protein 1; <i>ABF1 β=β activated B-cell factor 1</i>; <i>RNG213</i> β=β ring finger protein 213; <i>THOC3</i> β=β THO complex 3; <i>DGCR14</i> β=β DiGeorge syndrome critical region gene 14; <i>C3orf38</i> β=β chromosome 3 open reading frame 38; <i>KRT19</i> β=β Keratin 19; <i>SGOL1</i> β=β shugoshin-like 1; <i>sKer</i> β=β similar to Scale keratin; <i>MMP7</i> β=β matrix metalloproteinase 7; <i>MUC</i>β=β mucin protein.</p><p>Some extremely differentially expressed genes (|log2-Ratio (deformed beak/normal beak)| β§ 9).</p
qRT-PCR of 8 transcripts for validating the DGE results.
<p>The horizontal axis identifies the 8 transcripts examined by qRT-PCR; the vertical axis shows the relative gene expression level in deformed (individuals 1 and 2) versus normal (individuals 3, 4, 5, and 6) beak tissues. The 4 pairs of individuals were all full sibs. The first bar shows the value obtained from DEG using 1 and 6. <i>NPM3</i> β=β nucleophosmin/nucleoplasmin 3; <i>LPL</i> β=β lipoprotein lipase; <i>BMP4</i> β=β bone morphogenetic protein 4; <i>SGOL1</i> β=β shugoshin-like 1; <i>KRT19</i> β=β Keratin 19; <i>sKer</i> β=β similar to Scale keratin; <i>MMP7</i> β=β matrix metalloproteinase 7; <i>MUC</i> β=β mucin protein.</p
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