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101. Biol Lett. 2013 Feb 27;9(2):20130044. doi: 10.1098/rsbl.2013.0044. Print 2013 Apr



Absence of major histocompatibility complex class II mediated immunity in

pipefish, Syngnathus typhle: evidence from deep transcriptome sequencing.


Haase D(1), Roth O, Kalbe M, Schmiedeskamp G, Scharsack JP, Rosenstiel P, Reusch



Author information:

(1)Evolutionary Ecology of Marine Fishes, Helmholtz-Centre for Ocean Research

Kiel (GEOMAR), 24105 Kiel, Germany.


The major histocompatibility complex (MHC)-mediated adaptive immune system is the

hallmark of gnathostome immune defence. Recent work suggests that cod-like fishes

(Gadidae) lack important components of the MHC class II mediated immunity. Here,

we report a putative independent loss of functionality of this pathway in another

species, the pipefish Syngnathus typhle, that belongs to a distantly related fish

family (Syngnathidae). In a deep transcriptome sequencing approach comprising

several independent normalized and non-normalized expressed sequence tag (EST)

libraries with approximately 7.5 × 10(8) reads, sequenced with two next

generation platforms (454 and Illumina), we were unable to identify MHC class

IIα/β genes as well as genes encoding associated receptors. Along with the recent

findings in cod, our results suggest that immune systems of the Euteleosts may be

more variable than previously assumed.


DOI: 10.1098/rsbl.2013.0044

PMCID: PMC3639783

PMID: 23445951  [PubMed - indexed for MEDLINE]



102. Appl Environ Microbiol. 2013 Oct;79(19):5830-43. doi: 10.1128/AEM.00538-13. Epub

2013 Jul 19.


Characterization of the Burkholderia thailandensis SOS response by using

whole-transcriptome shotgun sequencing.


Ulrich RL(1), Deshazer D, Kenny TA, Ulrich MP, Moravusova A, Opperman T, Bavari

S, Bowlin TL, Moir DT, Panchal RG.


Author information:

(1)Integrated Toxicology Division, United States Army Medical Research Institute

of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, USA.


The bacterial SOS response is a well-characterized regulatory network encoded by

most prokaryotic bacterial species and is involved in DNA repair. In addition to

nucleic acid repair, the SOS response is involved in pathogenicity,

stress-induced mutagenesis, and the emergence and dissemination of antibiotic

resistance. Using high-throughput sequencing technology (SOLiD RNA-Seq), we

analyzed the Burkholderia thailandensis global SOS response to the

fluoroquinolone antibiotic, ciprofloxacin (CIP), and the DNA-damaging chemical,

mitomycin C (MMC). We demonstrate that a B. thailandensis recA mutant (RU0643) is

∼4-fold more sensitive to CIP in contrast to the parental strain B. thailandensis

DW503. Our RNA-Seq results show that CIP and MMC treatment (P < 0.01) resulted in

the differential expression of 344 genes in B. thailandensis and 210 genes in

RU0643. Several genes associated with the SOS response were induced and include

lexA, uvrA, dnaE, dinB, recX, and recA. At the genome-wide level, we found an

overall decrease in gene expression, especially for genes involved in amino acid

and carbohydrate transport and metabolism, following both CIP and MMC exposure.

Interestingly, we observed the upregulation of several genes involved in

bacterial motility and enhanced transcription of a B. thailandensis genomic

island encoding a Siphoviridae bacteriophage designated E264. Using B.

thailandensis plaque assays and PCR with B. mallei ATCC 23344 as the host, we

demonstrate that CIP and MMC exposure in B. thailandensis DW503 induces the

transcription and translation of viable bacteriophage in a RecA-dependent manner.

This is the first report of the SOS response in Burkholderia spp. to DNA-damaging

agents. We have identified both common and unique adaptive responses of B.

thailandensis to chemical stress and DNA damage.


DOI: 10.1128/AEM.00538-13

PMCID: PMC3811356

PMID: 23872555  [PubMed - indexed for MEDLINE]



103. Fish Shellfish Immunol. 2015 Nov;47(1):130-40. doi: 10.1016/j.fsi.2015.08.035.

Epub 2015 Sep 2.


Embryonic gene expression of Coregonus palaea (whitefish) under pathogen stress

as analyzed by high-throughput RNA-sequencing.


Wilkins LG(1), Clark ES(2), Farinelli L(3), Wedekind C(2), Fumagalli L(2).


Author information:

(1)Department of Ecology and Evolution, Biophore, University of Lausanne, 1015

Lausanne, Switzerland. Electronic address: laetitia.wilkins@unil.ch.

(2)Department of Ecology and Evolution, Biophore, University of Lausanne, 1015

Lausanne, Switzerland. (3)Fasteris SA, 1228 Plan-les-Ouates, Switzerland.


Most fishes produce free-living embryos that are exposed to environmental

stressors immediately following fertilization, including pathogenic

microorganisms. Initial immune protection of embryos involves the chorion, as a

protective barrier, and maternally-allocated antimicrobial compounds. At later

developmental stages, host-genetic effects influence susceptibility and

tolerance, suggesting a direct interaction between embryo genes and pathogens. So

far, only a few host genes could be identified that correlate with embryonic

survival under pathogen stress in salmonids. Here, we utilized high-throughput

RNA-sequencing in order to describe the transcriptional response of a non-model

fish, the Alpine whitefish Coregonus palaea, to infection, both in terms of host

genes that are likely manipulated by the pathogen, and those involved in an early

putative immune response. Embryos were produced in vitro, raised individually,

and exposed at the late-eyed stage to a virulent strain of the opportunistic fish

pathogen Pseudomonas fluorescens. The pseudomonad increased embryonic mortality

and affected gene expression substantially. For example, essential, upregulated

metabolic pathways in embryos under pathogen stress included ion binding

pathways, aminoacyl-tRNA-biosynthesis, and the production of arginine and

proline, most probably mediated by the pathogen for its proliferation. Most

prominently downregulated transcripts comprised the biosynthesis of unsaturated

fatty acids, the citrate cycle, and various isoforms of b-cell transcription

factors. These factors have been shown to play a significant role in host blood

cell differentiation and renewal. With regard to specific immune functions,

differentially expressed transcripts mapped to the complement cascade, MHC class

I and II, TNF-alpha, and T-cell differentiation proteins. The results of this

study reveal insights into how P. fluorescens impairs the development of

whitefish embryos and set a foundation for future studies investigating host

pathogen interactions in fish embryos.


Copyright © 2015 Elsevier Ltd. All rights reserved.


DOI: 10.1016/j.fsi.2015.08.035

PMID: 26340848  [PubMed - indexed for MEDLINE]



104. DNA Res. 2014 Feb;21(1):1-13. doi: 10.1093/dnares/dst035. Epub 2013 Aug 13.


Comprehensive transcriptome profiling and functional analysis of the frog

(Bombina maxima) immune system.


Zhao F(1), Yan C, Wang X, Yang Y, Wang G, Lee W, Xiang Y, Zhang Y.


Author information:

(1)1Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese

Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese

Academy of Sciences, Kunming, Yunnan 650223, China.


Amphibians occupy a key phylogenetic position in vertebrates and evolution of the

immune system. But, the resources of its transcriptome or genome are still little

now. Bombina maxima possess strong ability to survival in very harsh environment

with a more mature immune system. We obtained a comprehensive transcriptome by

RNA-sequencing technology. 14.3% of transcripts were identified to be

skin-specific genes, most of which were not isolated from skin secretion in

previous works or novel non-coding RNAs. 27.9% of transcripts were mapped into

242 predicted KEGG pathways and 6.16% of transcripts related to human disease and

cancer. Of 39 448 transcripts with the coding sequence, at least 1501 transcripts

(570 genes) related to the immune system process. The molecules of immune

signalling pathway were almost presented, several transcripts with high

expression in skin and stomach. Experiments showed that lipopolysaccharide or

bacteria challenge stimulated pro-inflammatory cytokine production and activation

of pro-inflammatory caspase-1. These frog's data can remarkably expand the

existing genome or transcriptome resources of amphibians, especially immunity

data. The entity of the data provides a valuable platform for further

investigation on more detailed immune response in B. maxima and a comparative

study with other amphibians.


DOI: 10.1093/dnares/dst035

PMCID: PMC3925390

PMID: 23942912  [PubMed - indexed for MEDLINE]