Evidence map›Paper›PMID 25486443›Full record

ArticlePloS one2014

Transcriptome and expression profiling analysis of the hemocytes reveals a large number of immune-related genes in mud crab Scylla paramamosain during Vibrio parahaemolyticus infection.

Chuping Xie, Yaping Chen, Wanwei Sun, Jun Ding, Lizhen Zhou, Shasha Wang, Shuqi Wang, Yueling Zhang, Dashi Zhu, Xiaobo Wen and 2 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
0.8field-weighted citation impact, top 28% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed, 38 citations in OpenAlex.

  1. Article
  2. Review
  3. Review
  4. Article
  5. Article
  6. Enhanced Immune Protection of Mud CrabFrontiers in immunology · 2020
    Article
  7. Article
  8. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors at 2 institutions in 1 country.

Chuping XieGuangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
Yaping ChenThe CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
Wanwei SunGuangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
Jun DingGuangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
Lizhen ZhouGuangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
Shasha WangGuangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
Shuqi WangGuangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
Yueling ZhangGuangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
Dashi ZhuGuangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
Xiaobo WenGuangdong provincial key laboratory of marine biology, Shantou University, Shantou, China.
Songnian HuThe CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
Shengkang LiGuangdong provincial key laboratory of marine biology, Shantou University, Shantou, China; Marine Biology Institute, Shantou University, Shantou, China.
Shantou University · CNBeijing Institute of Genomics · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundMud crab Scylla paramamosain is an economically important marine species in China. However, frequent outbreaks of infectious diseases caused by marine bacteria, such as Vibrio parahaemolyticus, result in great economic losses. METHODOLOGY/PRINCIPAL

findingsComparative de novo transcriptome analysis of S. paramamosain infected with V. parahaemolyticus was carried out to investigate the molecular mechanisms underlying the immune response to pathogenic bacteria by using the Illumina paired-end sequencing platform. A total of 52,934,042 clean reads from the hemocytes of V. parahaemolyticus-infected mud crabs and controls were obtained and assembled into 186,193 contigs. 59,120 unigenes were identified from 81,709 consensus sequences of mud crabs and 48,934 unigenes were matched proteins in the Nr or Swissprot databases. Among these, 10,566 unigenes belong to 3 categories of Gene Ontology, 25,349 to 30 categories of KEGG, and 15,191 to 25 categories of COG database, covering almost all functional categories. By using the Solexa/Illumina's DGE platform, 1213 differentially expressed genes (P<0.05), including 538 significantly up-regulated and 675 down-regulated, were detected in V. parahaemolyticus-infected crabs as compared to that in the controls. Transcript levels of randomly-chosen genes were further measured by quantitative real-time PCR to confirm the expression profiles. Many differentially expressed genes are involved in various immune processes, including stimulation of the Toll pathway, Immune Deficiency (IMD) pathway, Ras-regulated endocytosis, and proPO-activating system. CONCLUSIONS/SIGNIFICANCE: Analysis of the expression profile of crabs under infection provides invaluable new data for biological research in S. paramamosain, such as the identification of novel genes in the hemocytes during V. parahaemolyticus infection. These results will facilitate our comprehensive understanding of the mechanisms involved in the immune response to bacterial infection and will be helpful for diseases prevention in crab aquaculture.

Indexed as

Gene Expression ProfilingAnimalsBiomarkersBrachyuraCells, CulturedGene LibraryGene OntologyHemocytesOligonucleotide Array Sequence AnalysisReal-Time Polymerase Chain ReactionReverse Transcriptase Polymerase Chain ReactionRNA, MessengerVibrio InfectionsVibrio parahaemolyticusBiomarkersRNA, Messenger

Identifiers

PMID25486443
PMCPMC4259333
OpenAlexW2086794345

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.