Differential expression of duplicated genes for prothymosin alpha during zebrafish development

Cross-species Data Classification by Domain Adaptation via Discriminative Heterogeneous Maximum Mean Discrepancy

Cross-species or Cross-platform data classification is a challenging problem in the field of bioinformatics, which aims to classify data samples in one species/platform by using labeled data samples in another species/platform. Traditional classification methods can not be used in this case, since the samples from two species/platforms may have different feature spaces, or follow different statistical distributions. Domain adaptation is a new strategy which could be used to deal with this problem. A big challenge in domain adaptation is how to reduce the difference and correct the drift between the source and the target domains in the heterogeneous case, when the feature spaces of the two domains are different. It has been shown theoretically that probability divergences between the two domains such as maximum mean discrepancy (MMD) play an important role in the generalization bound for domain adaptation. However, they are rarely used for heterogeneous domain adaptation due to the different feature spaces of the domains. In this work, we propose a heterogeneous domain adaptation approach by making use of MMD, which measures the probability divergence in an embedded low-dimensional common subspace. Our proposed discriminative heterogeneous MMD approach (DMMD) aims to find new representations of the samples in a common subspace by minimizing the domain probability divergence with preserving the known discriminative information. A conjugate gradient algorithm on a Grassmann manifold is applied to solve the nonlinear DMMD model. Our experiments on both simulation and benchmark machine learning datasets show that our approaches outperform other state-of-the-art approaches for heterogeneous domain adaptation. We finally apply our approach to a cross-platform dataset and a cross-species dataset, and the results show the effectiveness of our approach.

Comparison of the organic matrix found in intestinal CaCO3 precipitates produced by several marine teleost species

Marine bony fish poses the unique ability to hydrate from imbibed seawater. They accomplish this, in part, by the precipitation of inorganic carbonate mineral in their intestine, which lowers luminal osmotic pressure and allows for water uptake. It has recently been described that in the Gulf toadfish (Opsanus beta) this Ca(Mg)CO₃ precipitation occurs under the regulation of an organic matrix. To date no investigations have aimed to determine if this phenomenon applies more generally to marine fish. Here, intestinally derived precipitates were collected from gray snapper (Lutjanus griseus), white grunt (Haemulon plumieri), European flounder (Platichthys flesus), as well as Gulf toadfish, and their matrices were extracted. The ability of these matrices to regulate CaCO₃ production was determined using an in vitro calcification assay, which revealed that the matrix derived from each of the tested species increased precipitation at low concentrations, while inhibiting it at higher concentrations in full agreement with the earlier studies on toadfish. Matrix extracted from European flounder precipitates was then analyzed by mass spectrometry, leading to the identification of over 50 unique proteins. When the identities of these proteins were compared to previous investigation of toadfish precipitate matrix, nearly 35% were found to overlap between the flounder and toadfish analyses, suggesting conserved mechanisms of precipitation control. The effects of using different sodium hypochlorite (NaOCl) solutions during precipitate purification on the resulting organic matrix are also discussed.

Prothymosin alpha expression in the vertebrate testis: a comparative review

Prothymosin alpha (PTMA) is a highly acidic, intrinsically disordered protein that was first extracted from rat thymus and characterized as an immunogenic factor but soon detected in a variety of mammalian tissues. The presence of a nuclear localization signal and the adoption of a peculiar random-coil conformation are among the reasons behind its interaction with several molecular partners, hence at this time PTMA is known to be a very conserved and widely expressed molecule, involved in numerous and diverse biological processes. Only few studies have tried to weigh its possible involvement in reproduction, specifically in male gametogenesis: first reports have suggested that PTMA might be associated with the proliferative and early-meiotic phases of mammal spermatogenesis. Some years later, a comparative project on vertebrate spermatogenesis reported the isolation, for the first time, of prothymosin in a non-mammalian species, the amphibian Pelophylax esculentus. PTMA transcript and protein are localized in the germinal compartment, from spermatocytes to spermatozoa. A congruent pattern has been highlighted in studies on the fish Torpedo marmorata and Danio rerio, and in the mammal Rattus norvegicus, in which the expression of PTMA has been found in meiotic and post-meiotic germ cells inside testicular cysts and tubules. Moreover, its presence has been confirmed in rat and human spermatozoa (associated with the acrosome); its retention in the apical region of the head after the acrosome reaction revealed a striking conservation of the pattern during phylogenesis and suggested a possible role for the protein in gametogenesis and in fertilization.

Subcellular dissemination of prothymosin alpha at normal physiology: immunohistochemical vis-a-vis western blotting perspective

BACKGROUND

The cell type, cell status and specific localization of Prothymosin α (PTMA) within cells seemingly determine its function. PTMA undergoes 2 types of protease proteolytic modifications that are useful in elucidating its interactions with other molecules; a factor that typifies its roles. Preferably a nuclear protein, PTMA has been shown to function in the cytoplasm and extracellularly with much evidence leaning on pathognomonic status. As such, determination of its cellular distribution under normal physiological context while utilizing varied techniques is key to illuminating prospective validation of its distinct functions in different tissues. Differential distribution insights at normal physiology would also portent better basis for further clarification of its interactions and proteolytic modifications under pathological conditions like numerous cancer, ischemic stroke and immunomodulation. We therefore raised an antibody against the C terminal of PTMA to use in tandem with available antibody against the N terminal in a murine model to explicate the differences in its distribution in brain cell types and major peripheral organs through western blotting and immunohistochemical approaches.

RESULTS

The newly generated antibody was applied against the N-terminal antibody to distinguish truncated versions of PTMA or deduce possible masking of the protein by other interacting molecules. Western blot analysis indicated presence of a truncated form of the protein only in the thymus, while immunohistochemical analysis showed that in brain hippocampus the full-length PTMA was stained prominently in the nucleus whereas in the stomach full-length PTMA staining was not observed in the nucleus but in the cytoplasm.

CONCLUSION

Truncated PTMA could not be detected by western blotting when both antibodies were applied in all tissues examined except the thymus. However, immunohistochemistry revealed differential staining by these antibodies suggesting possible masking of epitopes by interacting molecules. The differential localization patterns observed in the context of nucleic versus cytoplasmic presence as well as punctate versus diffuse pattern in tissues and cell types, warrant further investigations as to the forms of PTMA interacting partners.

Tongue sole (Cynoglossus semilaevis) prothymosin alpha: Cytokine-like activities associated with the intact protein and the C-terminal region that lead to antiviral immunity via Myd88-dependent and -independent pathways respectively

Prothymosin alpha (ProTα) is a small protein that in mammals is known to participate in diverse biological processes including immunomodulation. In teleost, the immunological function of ProTα is unknown. In the current study, we investigated the expression and function of the ProTα (named CsProTα) from the teleost fish tongue sole (Cynoglossus semilaevis). We found that CsProTα expression was abundant in immune relevant tissues and upregulated by megalocytivirus infection. Immunoblot detected secretion of CsProTα by peripheral blood leukocytes. Recombinant CsProTα (rCsProTα) as well as the C-terminal 11-residue (Ct11) were able to bind head kidney monocytes (HKM) and induce immune gene expression; however, the induction patterns caused by rCsProTα and Ct11 differed considerably. When introduced in vivo, rCsProTα and Ct11 significantly reduced megalocytivirus infection in fish tissues, whereas rCsProTα antibody significantly promoted viral replication. Blocking of Myd88 activity abolished the virus-inhibitory effect of rCsProTα but not Ct11. Taken together, these results demonstrate for the first time that both the intact protein and the C-terminal segment of a teleost ProTα can act like cytokines and induce antiviral immunity via, however, distinct signaling pathways that differ in the requirement of Myd88.

Prothymosin alpha expression and localization during the spermatogenesis ofDanio rerio

Prothymosin α (PTMA) is a highly acidic, intrinsically disordered protein, which is widely expressed and conserved throughout evolution; its uncommon features are reflected by its involvement in a variety of processes, including chromatin remodelling, transcriptional regulation, cell proliferation and death, immunity. PTMA has also been implicated in spermatogenesis: during vertebrate germ cell progression in the testis the protein is expressed in meiotic and post-meiotic stages, and it is associated with the acrosome system of the differentiating spermatids in mammals. Then, it finally localizes on the inner acrosomal membrane of the mature spermatozoa, suggesting its possible role in both the maturation and function of the gametes. In the present work we studied PTMA expression during the spermatogenesis of the adult zebrafish, a species in which two paralogs have been described. Our data show thatptmatranscripts are expressed in the testis, and localize in meiotic and post-meiotic germ cells, namely spermatocytes and spermatids. Consistently, the protein is expressed in spermatocytes, spermatids, and spermatozoa: its initial perinuclear distribution is extended to the chromatin region during cell division and, in haploid phases, to the cytoplasm of the developing and final gametes. The nuclear localization in the acrosome-lacking spermatozoa suggests a role for PTMA in chromatin remodelling during gamete differentiation. These data further provide a compelling starting point for the study of PTMA functions during vertebrate fertilization.

Characterization of two thymosins as immune-related genes in common carp (Cyprinus carpio L.)

Prothymosin alpha (ProTα) and thymosin beta (Tβ) belong to thymosin family, which consists of a series of highly conserved peptides involved in stimulating immune responses. ProTα b and Tβ are still poorly studied in teleost. Here, the full-length cDNAs of ProTα b and Tβ-like (Tβ-l) were cloned and identified in common carp (Cyprinus carpio L.). The expressions of carp ProTα b and Tβ-l exhibited rise-fall pattern and then trended to be stable during early development. After spring viraemia of carp virus (SVCV) infection, the carp ProTα b and Tβ-l transcripts were significantly up-regulated in some immune-related organs. When transiently over-expressed carp ProTα b and Tβ-l in zebrafish, these two proteins up-regulated the expressions of T lymphocytes-related genes (Rag 1, TCR-γ, CD4 and CD8α). These results suggest that carp ProTα b and Tβ may ultimately enhance the immune response during viral infection and modulate the development of T lymphocytes in teleost.

Expression analysis of five zebrafish RXFP3 homologues reveals evolutionary conservation of gene expression pattern

Relaxin peptides exert different functions in reproduction and neuroendocrine processes via interaction with two evolutionarily unrelated groups of receptors: RXFP1 and RXFP2 on one hand, RXFP3 and RXFP4 on the other hand. Evolution of receptor genes after splitting of tetrapods and teleost lineage led to a different retention rate between mammals and fish, with the latter having more gene copies compared to the former. In order to improve our knowledge on the evolution of the relaxin ligands/receptors system and have insights on their function in early stages of life, in the present paper we analyzed the expression pattern of five zebrafish RXFP3 homologue genes during embryonic development. In our analysis, we show that only two of the five genes are expressed during embryogenesis and that their transcripts are present in all the developmental stages. Spatial localization analysis of these transcripts revealed that the gene expression is restricted in specific territories starting from early pharyngula stage. Both genes are expressed in the brain but in different cell clusters and in extra-neural territories, one gene in the interrenal gland and the other in the pancreas. These two genes share expression territories with the homologue mammalian counterpart, highlighting a general conservation of gene expression regulatory processes and their putative function during evolution that are established early in vertebrate embryogenesis.

Knockdown of prothymosin α leads to apoptosis and developmental defects in zebrafish embryos

Prothymosin alpha (ProTα) is an abundant nuclear protein involved in cellular processes intricately linked to development, such as cell proliferation and apoptosis. Although it is known that ProTα inhibits the formation of apoptosome and blocks caspase-3 activity, its mechanism of function in the apoptotic machinery is still under investigation. We have studied the cellular role of ProTα by knocking down its expression in HeLa cells with small hairpin RNA (shRNA) in the absence of apoptotic stimuli. Flow cytometric analysis showed that the live cell population was significantly decreased with a concomitant increase of the apoptotic populations. To understand the physiological role of ProTα within the context of embryonic development, we knocked down the Ptmab zebrafish ortholog using 2 specific morpholino oligonucleotides. Ptmab morphants exhibited growth retardation, bended trunks, and curly tails. The frequency of occurrence of the phenotypic defects was increased in a morpholino dose-dependent manner. Co-injection of ptmaa mRNA with ptmab morpholino partially rescued the morphological defects. Immunostaining with the anti-phospho-histone H3 (pH3) antibody suggested that the abnormalities of Ptmab morphants could be due to defective cell proliferation that results in growth imbalances. TUNEL fluorescent labelling and Acridine Orange staining of the morphants showed high rates of cell death in the head and tail regions. Concomitantly, the active form of caspase-3 was detected in Ptmab morphants. Our data suggest a conserved anti-apoptotic role of ProTα between zebrafish and humans, and provide the first evidence that ProTα is important for early embryogenesis.

Transgenic expression of prothymosin alpha on zebrafish epidermal cells promotes proliferation and attenuates UVB-induced apoptosis

This study generated a transgenic zebrafish line Tg(k18:Ptmaa-RFP) with overexpression of Prothymosin alpha type a (Ptmaa) in the skin epidermis. Red fluorescence first appears very weakly in the early stage, become stronger and mainly restricted in the nuclei of the epithelial cells from 3 dpf-larvae to adult fish. However, no evident morphological abnormalities were observed. Thus, overexpression of Ptmaa alone is not sufficient to cause disorganized growths or even cancer in zebrafish skin. Molecular and histological evidences showed that Tg(k18:Ptmaa-RFP) embryos have more proliferating cells in the pelvic fins [WT: 3.92 +/- 7.15; Tg(k18:Ptmaa-RFP): 38.00 +/- 10.87] and thicker skin [WT: 10.98 +/- 1.41 mum; Tg(k18:Ptmaa-RFP): 14.02 +/- 1.32 mum], indicating that overexpression of Ptmaa can promote proliferation. On the other hand, fewer apoptotic signals were found when Tg(k18:Ptmaa-RFP) embryos were exposed to UVB. Together with quantitative RT-PCR data, we suggest that UVB-induced epidermal cell apoptosis of zebrafish larvae can be attenuated by overexpression of Ptmaa through the enhancement of transcriptions of bcl2 mRNAs. Taken together, we conclude that overexpression of Ptmaa in zebrafish epidermal cells promotes proliferation and attenuates UVB-induced apoptosis but does not cause skin cancer.

Expression of Prothymosin alpha during the spermatogenesis of the spotted ray Torpedo marmorata

In this study, we show that Prothymosin alpha (Ptma), a small, unfolded, negatively charged protein, is present in the cartilaginous fish Torpedo marmorata. The ptma gene is functional and peculiarly controlled during the male spermatogenesis of T. marmorata, as revealed by in situ hybridization and by immunocytochemistry studies. The data show that the ptma transcript is present in stage-specific germ cells, i.e. spermatocytes II and round spermatids. The Ptma protein is detectable in spermatocytes II, in round and elongated spermatids as well as in spermatozoa before their release from cysts, while it is not evident in spermatozoa located in male genital tracts. The ptma transcript and protein are also evident in some Leydig cells, located among maturing cysts containing meiotic and differentiating male cells. No expression for ptma is observed within Sertoli cells. Furthermore, immunolocalization procedures demonstrate that the protein is preferentially localized in the cytoplasm, whereas a nuclear localization is observed in round and elongated spermatids. The possibility that Ptma is involved in testis activity is discussed.

Gene duplication, transfer, and evolution in the chloroplast genome

In addition to the nuclear genome, organisms have organelle genomes. Most of the DNA present in eukaryotic organisms is located in the cell nucleus. Chloroplasts have independent genomes which are inherited from the mother. Duplicated genes are common in the genomes of all organisms. It is believed that gene duplication is the most important step for the origin of genetic variation, leading to the creation of new genes and new gene functions. Despite the fact that extensive gene duplications are rare among the chloroplast genome, gene duplication in the chloroplast genome is an essential source of new genetic functions and a mechanism of neo-evolution. The events of gene transfer between the chloroplast genome and nuclear genome via duplication and subsequent recombination are important processes in evolution. The duplicated gene or genome in the nucleus has been the subject of several recent reviews. In this review, we will briefly summarize gene duplication and evolution in the chloroplast genome. Also, we will provide an overview of gene transfer events between chloroplast and nuclear genomes.