DIGE Analysis of Fish Tissues.

Two-dimensional difference gel electrophoresis (2D-DIGE) appears to be especially useful in quantitative approaches, allowing the co-separation of proteins of control samples and proteins of treated/disease samples on the same gel, eliminating gel-to-gel variability. The principle of 2D-DIGE is to label proteins prior to isoelectric focusing and use three spectrally resolvable fluorescent dyes, allowing the independent labeling of control and experimental samples. This procedure makes it possible to reduce the number of gels in an experiment, allowing the accurate and reproducible quantification of multiple samples. 2D-DIGE has been found to be an excellent methodical tool in several areas of fish research, including environmental pollution and toxicology, the mechanisms of development and disorders, reproduction, nutrition, evolution, and ecology.

Application of two-dimensional difference gel electrophoresis to identify protein changes between center, margin, and adjacent non-tumor tissues obtained from non-small-cell lung cancer with adenocarcinoma or squamous cell carcinoma subtype.

Lung cancer is responsible for the most cancer-related mortality worldwide and the mechanism of its development is poorly understood. Proteomics has become a powerful tool offering vital knowledge related to cancer development. Using a two-dimensional difference gel electrophoresis (2D-DIGE) approach, we sought to compare tissue samples from non-small-cell lung cancer (NSCLC) patients taken from the tumor center and tumor margin. Two subtypes of NSCLC, adenocarcinoma (ADC) and squamous cell carcinoma (SCC) were compared. Data are available via ProteomeXchange with identifier PXD032736 and PXD032962 for ADC and SCC, respectively. For ADC proteins, 26 significant canonical pathways were identified, including Rho signaling pathways, a semaphorin neuronal repulsive signaling pathway, and epithelial adherens junction signaling. For SCC proteins, nine significant canonical pathways were identified, including hypoxia-inducible factor-1α signaling, thyroid hormone biosynthesis, and phagosome maturation. Proteins differentiating the tumor center and tumor margin were linked to cancer invasion and progression, including cell migration, adhesion and invasion, cytoskeletal structure, protein folding, anaerobic metabolism, tumor angiogenesis, EMC transition, epithelial adherens junctions, and inflammatory responses. In conclusion, we identified several proteins that are important for the better characterization of tumor development and molecular specificity of both lung cancer subtypes. We also identified proteins that may be important as biomarkers and/or targets for anticancer therapy.

Neurodevelopment vs. the immune system: Complementary contributions of maternally-inherited gene transcripts and proteins to successful embryonic development in fish.

The aim of this study was to investigate the respective contribution of maternally-inherited mRNAs and proteins to egg molecular cargo and to its developmental competence in fish using pikeperch as a model. Our study provides novel insights into the understanding of type-specific roles of maternally-inherited molecules in fish. Here we show, for the first time, that transcripts and proteins have distinct, yet complementary, functions in the egg of teleost fish. Maternally-inherited mRNAs would shape embryo neurodevelopment, while maternally-inherited proteins would rather be responsible for protecting the embryo against pathogens. Additionally, we observed that processes directly preceding ovulation may considerably affect the reproductive success by modifying expression level of genes crucial for proper embryonic development, being novel fish egg quality markers (e.g., smarca4 or h3f3a). These results are of major importance for understanding the influence of external factors on reproductive fitness in both captive and wild-type fish species.

Characteristics and Cryopreservation of Semen of Sex-Reversed Females of Salmonid Fish.

Sex reversal has been used as a breeding strategy by salmonid fish to produce genetically and phenotypically single sex populations. Production of all-female fish has great importance for the creation of monosex female triploids of salmonid fish, which are valued for their sterility, lack of female maturation, and larger commercial size. Among salmonids, the majority of rainbow trout (Oncorhynchus mykiss) production is based on all-female production with a high proportion of all-female triploid production in Europe. The main aim of this review is to present the recent knowledge regarding sex-reversed females (SRFs) of salmonid fish. We discuss the methods of sex reversal as well as their effects on the morphology and histology of the reproductive tract. We focus on the characteristics of SRF semen as well as the factors determining semen quality. The lower quality of SRF sperm compared to that of normal males has resulted in the need for the artificial maturation of semen. Most importantly, methods of semen storage-both short-term and long-term (cryopreservation)-that can improve hatchery operations are presented with the special emphasis on recent progress in development of efficient cryopreservation procedures and use of cryopreserved semen in hatchery practice. Moreover, we also address the emerging knowledge concerning the proteomic investigations of salmonid sperm, focusing primarily on the proteomic comparison of normal male and SRF testicular semen and presenting changes in SRF rainbow trout sperm proteome after in vitro incubation in artificial seminal plasma.

Domestication modulates the expression of genes involved in neurogenesis in high-quality eggs of Sander lucioperca.

Pikeperch, Sander lucioperca, is a species of high interest to the aquaculture. The expansion of its production can only be achieved by furthering domestication level. However, the mechanisms driving the domestication process in finfishes are poorly understood. Transcriptome profiling of eggs was found to be a useful tool allowing understanding of the domestication process in teleosts. In this study, using next-generation sequencing, the first pikeperch transcriptome has been generated as well as pikeperch-specific microarray comprising 35,343 unique probes. Next, we performed transcriptome profiling of eggs obtained from wild and domesticated populations. We found 710 differentially expressed genes that were linked mostly to nervous system development. These results provide new insights into processes that are directly involved in the domestication of finfishes. It can be suggested that all the identified processes were predetermined by the maternally derived set of genes contained in the unfertilized eggs. This allows us to suggest that fish behavior, along with many other processes, can be predetermined at the cellular level and may have significant implications on the adaptation of cultured fish to the natural environment. This also allows to suggest that fish behavior should be considered as a very important pikeperch aquaculture selection trait.

Identification of protein changes in the blood plasma of lung cancer patients subjected to chemotherapy using a 2D-DIGE approach.

A comparative analysis of blood samples (depleted of albumin and IgG) obtained from lung cancer patients before chemotherapy versus after a second cycle of chemotherapy was performed using two-dimensional difference gel electrophoresis (2D-DIGE). The control group consisted of eight patients with non-cancerous lung diseases, and the experimental group consisted of four adenocarcinoma (ADC) and four squamous cell carcinoma (SCC) patients. Analyses of gels revealed significant changes in proteins and/or their proteoforms between control patients and lung cancer patients, both before and after a second cycle of chemotherapy. Most of these proteins were related to inflammation, including acute phase proteins (APPs) such as forms of haptoglobin and transferrin, complement component C3, and clusterin. The variable expression of APPs can potentially be used for profiling lung cancer. The greatest changes observed after chemotherapy were in transferrin and serotransferrin, which likely reflect disturbances in iron turnover after chemotherapy-induced anaemia. Significant changes in plasma proteins between ADC and SCC patients were also revealed, suggesting use of plasma vitronectin as a potential marker of SCC.

Proteomic and metabolomic insights into the functions of the male reproductive system in fishes.

Proteomics and metabolomics are emerging and powerful tools to unravel the complex molecular mechanisms regulating reproduction in male fish. So far, numerous proteins and metabolites have been identified that provide us with valuable information to conduct a comprehensive analysis on seminal plasma and spermatozoa components and their functions. These analyses have allowed a better understanding of the blood-testis barrier functions, the molecular mechanisms underlying spermatogenesis, spermatozoa maturation, motility signaling, and competition as well as the mechanism of cryodamage to sperm structure and functions. To extend, proteins that undergo posttranslational modification, such as phosphorylation and oxidation in response to spermatozoa motility activation and cryopreservation, respectively, have been identified. Proteomic studies resulted in identification of potential proteins that can be used as biomarkers for sperm quality and freezability to enable the control of artificial reproduction, and to improve methods for long-term preservation (cryopreservation) of sperm. The different proteins expressed in the spermatozoa of neomales and normal males can also provide new insights into development of methods for separating X and Y fish sperm, and changes in the protein profiles in haploid and diploid spermatozoa will provide new perspectives to better understand the mechanism of male polyploidy. Overall, the knowledge gained by proteomic and metabolomic studies is important from basic to applied sciences for the development and/or optimisation of techniques in controlled fish reproduction.

Opportunities and challenges related to the implementation of sperm cryopreservation into breeding of salmonid fishes.

The main aim of the present review is to present the opportunities and challenges associated with the application of cryopreserved sperm, which may improve the breeding of salmonid fishes. Cryopreservation of sperm has been used as a strategy for the conservation of biodiversity of fishes populations, the preservation of sperm from the most valuable breeding individuals and facilitate transportation of genomes, and providing a biological source of sperm regardless of the synchronisation of the maturity of broodstocks. Cryopreserved sperm can be used for the genetic improvement of salmonid fishes based on the programs of individual crossing of selected males with individual females. However, these opportunities have not yet been fully implemented at the conditions of hatchery practice. Despite the significant progress concerning the standardization of cryopreservation procedures, there are still more challenges than opportunities related to the implementation of sperm cryopreservation into breeding of salmonid fishes. The main challenge concerns the scaling up of the method towards fulfilling the requirements of fishes-breeders, in particular mass production of eyed eggs and fry. The present review shows knowledge gaps that should be considered in further studies, including development of methods to obtain sufficient amounts of sperm from numerous species of salmonids, scaling up the methods towards cryopreservation of high volumes of sperm and towards thawing high number of straws, and optimizing artificial fertilization in which oocytes are fertilized with high numbers of frozen/thawed sperm. Moreover, the implementation of technologies into hatchery practice will require special consideration to counteract the risk of sperm infection and its transmission to offsprings during cryopreservation and storage in liquid nitrogen.

Foxn1 expression in keratinocytes is stimulated by hypoxia: further evidence of its role in skin wound healing.

Recent studies have shown that the transcription factor Foxn1, which is expressed in keratinocytes, is involved in the skin wound healing process, yet how Foxn1 functions remains largely unknown. Our latest data indicate that Foxn1 drives skin healing via engagement in re-epithelization and the epithelial-mesenchymal transition (EMT) process. In the present study, 2D-DIGE proteomic profiling analysis of in vitro cultured keratinocytes transfected with adenoviral vector carrying Foxn1-GFP or GFP alone (control) revealed forty proteins with differential abundance between the compared groups. Among the proteins with Foxn1-dependent expression, several enable adaptation to hypoxia. Subsequent experiments revealed that hypoxic conditions (1% O2) stimulate endogenous and exogenous (transfected Ad-Foxn1) Foxn1 expression in cultured keratinocytes. A proteomics analysis also identified proteins that can act as a factors controlling the balance between cell proliferation, differentiation and apoptosis in response to Foxn1. We also showed that in C57BL/6 keratinocytes, the stimulation of Foxn1 by hypoxia is accompanied by increases in Mmp-9 expression. These data corroborate the detected co-localization of Foxn1 and Mmp-9 expression in vivo in post-wounding skin samples of Foxn1::Egfp transgenic mice. Together, our data indicate that Foxn1 orchestrates cellular changes in keratinocytes in both physiological (self-renewal) and pathological (skin wound healing) contexts.

DIGE Analysis of Fish Tissues.

Two-dimensional difference gel electrophoresis (2D-DIGE) appears to be especially useful in quantitative approaches, allowing the co-separation of proteins of control samples from proteins of treatment/disease samples on the same gel, eliminating gel-to-gel variability. The principle of 2D-DIGE is to label proteins prior to isoelectric focusing and use three spectrally resolvable fluorescent dyes, allowing the independent labeling of control and experimental samples. This procedure makes it possible to reduce the number of gels in an experiment, allowing the accurate and reproducible quantification of multiple samples. 2D-DIGE has been found to be an excellent methodical tool in several areas of fish research, including environmental pollution and toxicology, the mechanisms of development and disorders, reproduction, nutrition, evolution, and ecology.

Purification, characterization and expression of transferrin from rainbow trout seminal plasma.

Transferrin (TF) is recognized as a multifunctional protein and has been implicated in antioxidative, antimicrobial protection, growth, differentiation and cytoprotection effects. An efficient, original three-step isolation procedure for TF consisting in hydrophobic interaction chromatography, gel filtration and preparative electrophoresis was developed. Rainbow trout TF was found to be N-glycosylated (not O-glycosylated) and phosphorylated at all serine, threonine, and tyrosine residues. The protein consists of several proteoforms with an average molecular weight of 76.9kDa and isoelectric point ranging from 5.2 to 5.7. Rainbow trout TF has two functional iron-binding sites and appears to be quite distinct from carp TF regarding glycosylation and iron-binding properties. The highest gene expression of TF was detected in liver and testis, the lowest was detected in head kidney, spleen and efferent ducts. For the first time TF was identified in the semen of several salmonid species. TF was localized within testis, mainly in spermatozoa, Sertoli, Leydig cells, as well as in both columnar secretory and basal cells within the efferent duct. This work contributes to the existing knowledge information indicating significant variations in TF structure within teleost fish. The results obtained in this study provide valuable data on the TF from trout seminal plasma and the physiological role of this protein in the reproductive tract of salmonids. The results are important for our understanding of the role of TF in the antioxidant protection and resistance to pathogenic infections of reproductive cells. The protective role of TF against environmental pollution with heavy metals, especially during prolonged storage of spermatozoa in the spermatic duct, as well as regulation of spermatogenesis and providing Fe for developing germ cells is also postulated.

Proteomic identification of rainbow trout blood plasma proteins and their relationship to seminal plasma proteins.

The characterisation of fish blood proteomes is important for comparative studies of seminal and blood proteins as well as for the analysis of fish immune mechanisms and pathways. In this study, LC-MS/MS and 2D-DIGE were applied to compare rainbow trout seminal (SP) and blood plasma (BP) proteomes. The 54 differentially abundant proteins identified in SP are involved in a variety of signalling pathways, including protein ubiquitination, liver X receptor/retinoid X receptor (LXR/RXR) and farnesoid X receptor activation, cell cycle and acute phase signalling. These findings may indicate the prevalence of acute phase signalling pathways in trout SP, and its essential role in protecting spermatozoa and reproductive tissues. Our study provides the first in-depth analysis of the trout BP proteome, with a total of 119 proteins identified. The major proteins of rainbow trout BP were recognised as acute phase proteins. Analysis of BP proteins indicated that acute phase response signalling, the complement system, liver X receptor/retinoid X receptor and farnesoid X receptor activation and the coagulation system are the top canonical pathways. This study enhances knowledge of the blood origin of trout SP proteins and understanding of fish reproductive biology. Our results provide new insight into blood proteins specifically important for fish physiology and innate immunity. The mass spectrometry data are available via ProteomeXchange with the identifier PXD005988 and https://doi.org/10.6019/PXD005988.

Potassium ions in extender differentially influence the post-thaw sperm motility of salmonid fish.

Potassium ions are known to have an inhibitory effect on the sperm motility of salmonids. For this reason, the addition of K(+) to the extender is frequently applied. However, the effect of the addition of K(+) to the extender has not yet been tested. The aim of this study was to test the influence of potassium ion supplementation of the extender on the sperm motility parameters from five Salmonidae species (rainbow trout (Oncorhynchus mykiss), sex-reversed female rainbow trout, whitefish (Coregonus lavaretus), brown trout (Salmo trutta) and brook trout (Salvelinus fontinalis)). Semen samples were diluted in extender containing 0.18 M glucose in 9% methanol (GM) supplemented with 0, 20 or 40 mM potassium chloride. After thawing sperm were stored for 30, 60, 120 and 240 min at 4 °C. Our results demonstrated that the presence of potassium ions in the extender had a negative effect on percentage of motile sperm in four of the salmonid species. In contrast, potassium ions appeared to have a positive effect on percentage of post-thaw motile sperm in whitefish semen. However, this effect could be mimicked by changing the osmolality of the extender (which was achieved by increasing the glucose concentration to 0.22 M). The addition of potassium ions turned out to have no positive effect on post-thaw storage time. Our results suggest that osmolality, rather than potassium ions, seems to be essential for cryopreservation success of salmonids sperm. Further studies should focus on the effects of small changes in osmolality on the post-thaw quality of semen.

Expression of apolipoprotein A-I and A-II in rainbow trout reproductive tract and their possible role in antibacterial defence.

Antimicrobial proteins such as apolipoproteins A (ApoA-I and ApoA-II) play an important role in the primary defence barrier in vertebrates including fish. The aims of the present study were to isolate and characterise rainbow trout seminal plasma ApoA-I and ApoA-II, to examine the mRNA expression of each apolipoprotein in testis and spermatic ducts, and to test the antibacterial properties of the apolipoproteins. Using a three-step isolation procedure consisting of ion-exchange chromatography, gel filtration and preparative SDS-PAGE, apolipoproteins were purified and identified as ApoA-I and ApoA-II. Both apolipoproteins were represented by several proteoforms. The expression of ApoA-I and ApoA-II mRNA in the reproductive tract and their antibacterial properties against Escherichia coli suggest that seminal apolipoproteins play an important role in innate immunity in the rainbow trout reproductive tract. The functions of seminal ApoA can be related to protection of sperm and reproductive tissue from microbial attack and to the maintenance of sperm membrane integrity.

Cryopreservation-induced alterations in protein composition of rainbow trout semen.

The aim of this study was to detect cryopreservation-induced alterations in the protein composition of rainbow trout semen using two independent methods 1DE SDS-PAGE prefractionation combined with LC-MS/MS and 2D difference gel electrophoresis followed by MALDI-TOF/TOF identification. Here, we show the first comprehensive dataset of changes in rainbow trout semen proteome after cryopreservation, with a total of 73 identified proteins released from sperm to extracellular fluid, including mitochondrial, cytoskeletal, nuclear, and cytosolic proteins. Our study provides new information about proteins released from sperm, their relation to sperm structure and function, and changes of metabolism of sperm cells as a result of cryopreservation. The identified proteins represent potential markers of cryoinjures of sperm structures and markers of the disturbances of particular sperm metabolic pathways. Further studies will allow to decipher the precise function of the proteins altered during rainbow trout cryopreservation and are useful for the development of extensive diagnostic tests of sperm cryoinjures and for the successful improvement of sperm cryopreservation of this economically important species.

Maturation of spermatozoa from rainbow trout (Oncorhynchus mykiss) sex-reversed females using artificial seminal plasma or glucose-methanol extender.

Masculinized females (sex-reversed females) produce only homogametic spermatozoa (X) for fertilization which is desired for the production of all-female rainbow trout populations. The milt of sex-reversed females is of low quality and must be matured through extension in maturation solutions. The aim of this study was to compare the usefulness of glucose-methanol (GM) extender with artificial seminal plasma (ASP) extender for the maturation of milt of sex-reversed female rainbow trout. Milt suspensions were incubated at 4 °C for either 15 minutes (GM extender) or 120 minutes (ASP extender). Incubation of milt diluted in either the GM or ASP extender caused a significant (P < 0.05) increase in the percentage of sperm motility to 76.1 ± 10.9% and 74.7 ± 18.6% for GM and ASP, respectively, but no differences between both the extenders were found. Incubation also increased the average path velocity, straight line velocity, and linearity values of spermatozoa diluted with the GM extender; at the same time, none of the other parameters changed for ASP suspensions. Sperm diluted with ASP was characterized by higher curvilinear velocity and lateral head displacement values. Percentage of eyed embryos produced by fertilization using milt diluted in the GM extender amounted to 63.6 ± 16.4% and 67.2 ± 11.9% for sperm-to-egg ratio of 300,000:1 or 600,000:1, respectively and was lower (P < 0.05) compared with that of ASP extender (79.5 ± 5.8% and 80.3 ± 4.7% for sperm-to-egg ratio of 300,000:1 or 600,000:1, respectively). The results of our study clearly report that the mechanism of sperm maturation by the GM extender differs from that based on ASP.

Shotgun proteomics of rainbow trout ovarian fluid.

In the present study we used a shotgun proteomic approach to identify 54 proteins of rainbow trout ovarian fluid. The study has unravelled the identity of several proteins not previously reported in fish ovarian fluid. The proteome of trout ovarian fluid consists of diverse proteins participating in lipid binding and metabolism, carbohydrate and ion transport, innate immunity, maturation and ovulation processes. Most trout ovarian fluid proteins correspond to follicular fluid proteins of higher vertebrates, but 15% of the proteins were found to be different, such as those related to the immune system (precerebellin-like protein), proteolysis (myeloid cell lineage chitinase), carbohydrate and lipid binding and metabolism (vitellogenins), cell structure and shape (vitelline envelope protein gamma) and a protein with unknown functions (UPF0762 protein C6orf58 homologue). The present study could help in the decoding of the biological function of these proteins and in the discovery of potential biomarkers of oocyte quality.

Isolation and characterization of an ovoinhibitor, a multidomain Kazal-like inhibitor from Turkey (Meleagris gallopavo) seminal plasma.

Turkey seminal plasma contains three serine proteinase inhibitors. Two of them, with low molecular masses (6 kDa), were identified as single-domain Kazal-type inhibitors responsible for regulating acrosin activity. Our experimental objective was to isolate and characterize the inhibitor with the high molecular weight from turkey seminal plasma. The inhibitor was purified using hydrophobic interaction and affinity chromatography. Pure preparations of the inhibitor were used for identification by mass spectrometry, for determination of physicochemical properties (molecular weight, pI, and content and composition of the carbohydrate component), for kinetic studies, and for antibacterial tests. Gene expression and immunohistochemical detection of the inhibitor were analyzed in the testis, epididymis, and ductus deferens. The inhibitor with a high molecular weight from turkey seminal plasma was identified as an ovoinhibitor, which was found in avian semen for the first time. The turkey seminal plasma ovoinhibitor was a six-tandem homologous Kazal-type domain serine proteinase inhibitor that targeted multiple proteases, including subtilisin, trypsin, and elastase, but not acrosin. Our results suggested that hepatocyte growth factor activator was a potential target proteinase for the ovoinhibitor in turkey seminal plasma. The presence of the ovoinhibitor within the turkey reproductive tract suggested that its role was to maintain a microenvironment for sperm in the epididymis and ductus deferens. The turkey seminal plasma ovoinhibitor appeared to play a significant role in an antibacterial semen defense against Bacillus subtilis and Staphylococcus aureus.

Proteomic identification of rainbow trout sperm proteins.

Proteomics represents a powerful tool for the analysis of fish spermatozoa, since these cells are transcriptionally inactive. The aim of the present study was to generate an inventory of the most prominent rainbow trout sperm proteins by SDS-PAGE prefractionation combined with nano-LC-MS/MS based identification. This study provides the first in-depth analysis of the rainbow trout sperm proteome, with a total of 206 identified proteins. We found that rainbow trout spermatozoa are equipped with functionally diverse proteins related to energetic metabolism, signal transduction, protein turnover, transport, cytoskeleton, oxidative injuries, and stress and reproduction. The availability of a catalog of rainbow trout sperm proteins provides a crucial tool for the understanding of fundamental molecular processes in fish spermatozoa, for the ongoing development of novel markers of sperm quality and for the optimization of short- and long-term sperm preservation procedures. The MS data are available at ProteomeXchange with the dataset identifier PXD000355 and DOI 10.6019/PXD000355.