The Translationally Controlled Tumor Protein Is a Novel Calcium Binding Protein of the Human Placenta and Regulates Calcium Handling in Trophoblast Cells1

Screening Candidate Genes Regulating Placental Development from Trophoblast Transcriptome at Early Pregnancy in Dazu Black Goats (Capra hircus)

Simple Summary

The trophoblast is an original placental tissue whose normal proliferation, differentiation, migration, adhesion, and angiopoiesis are essential for placenta formation and fetal survival during early pregnancy. However, the key genes and molecular mechanisms involved in placenta development in goats are unknown. Herein, the morphology and histological structures of trophoblast tissues from day 20 to 30 of pregnancy were determined. RNA-sequencing was used to screen potential functional genes in common highly expressed and differentially expressed genes. RAP1 signaling pathway was used as the contact center and coordinated with other pathways to regulate placenta development. This study could provide insights into the molecular mechanisms underlying ruminant placentation.

Abstract

This study explored the trophoblast transcriptome to understand potential functional genes involved in early placental development in goats and their enriched signaling pathways. Trophoblast samples were collected from nine Dazu Black goats on days 20, 25, and 30 of pregnancy (D20, D25, and D30). As the pregnancy progressed, the morphology and histological structures showed significant growth, adhesion, and angiogenesis. A total of 23,253 commonly expressed genes (CEGs) and 4439 differently expressed genes (DEGs) were detected by RNA sequencing. The common highly expressed genes (ChEGs) (the top 100 CEGs) with the highest FPKM percentage (29.9%) of all CEGs were annotated to the ribosome pathway and maintain pregnancy. DEGs were abundant in D30 vs. D20 (3715 DEGs). Besides, the DEGs were associated with the inhibition of oxidative phosphorylation and activation of PI3K-Akt, focal adhesion, ECM–receptor interaction, Rap1, and CAM signaling pathways. The RAP1 may be a central pathway since it coordinates with others to regulate the cell proliferation, invasion, migration, and fusion of trophoblasts. qRT-PCR and Western blot analysis confirmed the transcriptional expression in IGF1, VEGFC, RAPGEF3, PIK3CA, AKT3, ITGB3, ITGA11, SPP1, NOS1, and ATP6V0B genes and protein levels in VEGF, RAPGEF3, and Akt. This is the first study of transcriptome profiling in goat placenta and provides diverse genetic resources for further research on placenta development.

Genetic dissection of reproductive performance of dairy cows under heat stress

Heat stress negatively impacts the reproductive performance of dairy cows. The main objective of this study was to dissect the genetic basis underlying dairy cow fertility under heat stress conditions. Our first goal was to estimate genetic components of cow conception across lactations considering heat stress. Our second goal was to reveal individual genes and functional gene‐sets that explain a cow’s ability to conceive under thermal stress. Data consisted of 74 221 insemination records on 13 704 Holstein cows. Multitrait linear repeatability test‐day models with random regressions on a function of temperature–humidity index values were used for the analyses. Heritability estimates for cow conception under heat stress were around 2–3%, whereas genetic correlations between general and thermotolerance additive genetic effects were negative and ranged between −0.35 and −0.82, indicating an unfavorable relationship between cows’ ability to conceive under thermo‐neutral vs. thermo‐stress conditions. Whole‐genome scans identified at least six genomic regions on BTA1, BTA10, BTA11, BTA17, BTA21 and BTA23 associated with conception under thermal stress. These regions harbor candidate genes such as BRWD1, EXD2, ADAM20, EPAS1, TAOK3, and NOS1, which are directly implicated in reproductive functions and cellular response to heat stress. The gene‐set enrichment analysis revealed functional terms related to fertilization, developmental biology, heat shock proteins and oxidative stress, among others. Overall, our findings contribute to a better understanding of the genetics underlying the reproductive performance of dairy cattle under heat stress conditions and point out novel genomic strategies for improving thermotolerance and fertility via marker‐assisted breeding.

Function of translationally controlled tumor protein (TCTP) in Eudrilus eugeniae regeneration

TCTP (Translationally Controlled Tumour Protein) is a multifunctional protein that plays a role in the development, immune system, tumour reversion, and maintenance of stem cells. The mRNA of the Tpt1 gene is over-expressed during liver regeneration. But, the function of the protein in regeneration is not known. To study the role of the protein in regeneration, the earthworm Eudrilus eugeniae was chosen. First, the full length cDNA of the Tpt1 gene was sequenced. The size of the cDNA is 504 bp and the protein has 167 amino acids. The highest level of TCTP expression was documented in the worm after three days of regeneration. The protein was found to be expressed specifically in the epithelial layer of the skin. During regeneration, the protein expression was found to be the highest at the tip of blastema. The pharmacological suppression of TCTP using nutlin-3 and TCTP RNAi experiments resulted in the failure of the regeneration process. The suppression of TCTP caused the arrest of proliferation in posterior amputated worms. The severe cell death was documented in the amputated region of nutlin-3 injected worm. The silencing of TCTP has blocked the modification of clitellar segments. The experiments confirm that TCTP has major functions in the upstream signalling of cell proliferation in the early regeneration process in E. eugeniae.

The Translational Controlled Tumour Protein TCTP: Biological Functions and Regulation

The Translational Controlled Tumour Protein TCTP (gene symbol TPT1, also called P21, P23, Q23, fortilin or histamine-releasing factor, HRF) is a highly conserved protein present in essentially all eukaryotic organisms and involved in many fundamental cell biological and disease processes. It was first discovered about 35 years ago, and it took an extended period of time for its multiple functions to be revealed, and even today we do not yet fully understand all the details. Having witnessed most of this history, in this chapter, I give a brief overview and review the current knowledge on the structure, biological functions, disease involvements and cellular regulation of this protein.TCTP is able to interact with a large number of other proteins and is therefore involved in many core cell biological processes, predominantly in the response to cellular stresses, such as oxidative stress, heat shock, genotoxic stress, imbalance of ion metabolism as well as other conditions. Mechanistically, TCTP acts as an anti-apoptotic protein, and it is involved in DNA-damage repair and in cellular autophagy. Thus, broadly speaking, TCTP can be considered a cytoprotective protein. In addition, TCTP facilitates cell division through stabilising the mitotic spindle and cell growth through modulating growth signalling pathways and through its interaction with the proteosynthetic machinery of the cell. Due to its activities, both as an anti-apoptotic protein and in promoting cell growth and division, TCTP is also essential in the early development of both animals and plants.Apart from its involvement in various biological processes at the cellular level, TCTP can also act as an extracellular protein and as such has been involved in modulating whole-body defence processes, namely in the mammalian immune system. Extracellular TCTP, typically in its dimerised form, is able to induce the release of cytokines and other signalling molecules from various types of immune cells. There are also several examples, where TCTP was shown to be involved in antiviral/antibacterial defence in lower animals. In plants, the protein appears to have a protective effect against phytotoxic stresses, such as flooding, draught, too high or low temperature, salt stress or exposure to heavy metals. The finding for the latter stress condition is corroborated by earlier reports that TCTP levels are considerably up-regulated upon exposure of earthworms to high levels of heavy metals.Given the involvement of TCTP in many biological processes aimed at maintaining cellular or whole-body homeostasis, it is not surprising that dysregulation of TCTP levels may promote a range of disease processes, foremost cancer. Indeed a large body of evidence now supports a role of TCTP in at least the most predominant types of human cancers. Typically, this can be ascribed to both the anti-apoptotic activity of the protein and to its function in promoting cell growth and division. However, TCTP also appears to be involved in the later stages of cancer progression, such as invasion and metastasis. Hence, high TCTP levels in tumour tissues are often associated with a poor patient outcome. Due to its multiple roles in cancer progression, TCTP has been proposed as a potential target for the development of new anti-cancer strategies in recent pilot studies. Apart from its role in cancer, TCTP dysregulation has been reported to contribute to certain processes in the development of diabetes, as well as in diseases associated with the cardiovascular system.Since cellular TCTP levels are highly regulated, e.g. in response to cell stress or to growth signalling, and because deregulation of this protein contributes to many disease processes, a detailed understanding of regulatory processes that impinge on TCTP levels is required. The last section of this chapter summarises our current knowledge on the mechanisms that may be involved in the regulation of TCTP levels. Essentially, expression of the TPT1 gene is regulated at both the transcriptional and the translational level, the latter being particularly advantageous when a rapid adjustment of cellular TCTP levels is required, for example in cell stress responses. Other regulatory mechanisms, such as protein stability regulation, may also contribute to the regulation of overall TCTP levels.

A translationally controlled tumor protein gene Rpf41 is required for the nodulation of Robinia pseudoacacia

Translationally controlled tumor protein (TCTP) is fundamental for the regulation of development and general growth in eukaryotes. Its multiple functions have been deduced from its involvement in several cell pathways, but its potential involvement in symbiotic nodulation of legumes cannot be suggested a priori. In the present work, we identified and characterized from the woody leguminous tree Robinia pseudoacacia a homolog of TCTP, Rpf41, which was up-regulated in the infected roots at 15 days post-inoculation but decreased in the matured nodules. Subcellular location assay showed that Rpf41 protein was located in the plasma membrane, cytoplasm, nucleus, and also maybe in cytoskeleton. Knockdown of Rpf41 via RNA interference (RNAi) resulted in the impaired development of both nodule and root hair. Compared with wild plants, the root and stem length, fresh weight and nodule number per plant was decreased dramatically in Rpf41 RNAi plants. The number of ITs or nodule primordia was also significantly reduced in the Rpf41 RNAi roots. The analyses of nodule ultrastructure showed that the infected cell development in Rpf41 RNAi nodules remained in zone II, which had fewer infected cells. Furthermore, the symbiosomes displayed noticeable shrinkage of bacteroid and peribacteroid space enlargement in the infected cells of Rpf41 RNAi nodules. In the deeper cell layers, a more remarkable aberration of the infected cell ultrastructure was observed, and electron-transparent lesions in the bacteroid cytoplasm were detected. These results identify TCTP as an important regulator of symbiotic nodulation in legume for the first time, and it may be involved in symbiotic cell differentiation and preventing premature aging of the young nodules in R. pseudoacacia.

Immunization of mice with Plasmodium TCTP delays establishment of Plasmodium infection

Translationally controlled tumour protein (TCTP) may play an important role in the establishment or maintenance of parasitemia in a malarial infection. In this study, the potential of TCTP as a malaria vaccine was investigated in two trials. In the initial vaccine trial, Plasmodium falciparum TCTP (PfTCTP) was expressed in Saccharomyces cerevisiae and used to immunize BALB/c mice. Following challenge with Plasmodium yoelii YM, parasitemia was significantly reduced during the early stages of infection. In the second vaccine trial, the TCTP from P. yoelii and P. berghei was expressed in Escherichia coli and used in several mouse malaria models. A significant reduction in parasitemia in the early stages of infection was observed in BALB/c mice challenged with P. yoelii YM. A significantly reduced parasitemia at each day leading up to a delayed and reduced peak parasitemia was also observed in BALB/c mice challenged with the nonlethal Plasmodium chabaudi (P.c.) chabaudi AS. These results suggest that TCTP has an important role for parasite establishment and may be important for pathogenesis.

Translationally controlled tumor protein in prostatic adenocarcinoma: correlation with tumor grading and treatment-related changes

Prostate cancer is the second leading cause of cancer-related death. The androgen deprivation therapy is the standard treatment for advanced stages. Unfortunately, virtually all tumors become resistant to androgen withdrawal. The progression to castration-resistance is not fully understood, although a recent paper has suggested translationally controlled tumor protein to be implicated in the process. The present study was designed to investigate the role of this protein in prostate cancer, focusing on the correlation between its expression level with tumor differentiation and response to treatment. We retrieved 292 prostatic cancer specimens; of these 153 had been treated only by radical prostatectomy and 139 had undergone radical prostatectomy after neoadjuvant treatment with combined androgen blockade therapy. Non-neoplastic controls were represented by 102 prostatic peripheral zone specimens. In untreated patients, the expression of the protein, evaluated by RT-qPCR and immunohistochemistry, was significantly higher in tumor specimens than in non-neoplastic control, increasing as Gleason pattern and score progressed. In treated prostates, the staining was correlated with the response to treatment. An association between protein expression and the main clinicopathological factors involved in prostate cancer aggressiveness was identified. These findings suggest that the protein may be a promising prognostic factor and a target for therapy.

Ligand binding reveals a role for heme in translationally-controlled tumor protein dimerization

The translationally-controlled tumor protein (TCTP) is a highly conserved, ubiquitously expressed, abundant protein that is broadly distributed among eukaryotes. Its biological function spans numerous cellular processes ranging from regulation of the cell cycle and microtubule stabilization to cell growth, transformation, and death processes. In this work, we propose a new function for TCTP as a “buffer protein” controlling cellular homeostasis. We demonstrate that binding of hemin to TCTP is mediated by a conserved His-containing motif (His⁷⁶His⁷⁷) followed by dimerization, an event that involves ligand-mediated conformational changes and that is necessary to trigger TCTP's cytokine-like activity. Mutation in both His residues to Ala prevents hemin from binding and abrogates oligomerization, suggesting that the ligand site localizes at the interface of the oligomer. Unlike heme, binding of Ca²⁺ ligand to TCTP does not alter its monomeric state; although, Ca²⁺ is able to destabilize an existing TCTP dimer created by hemin addition. In agreement with TCTP's proposed buffer function, ligand binding occurs at high concentration, allowing the “buffer” condition to be dissociated from TCTP's role as a component of signal transduction mechanisms.

cDNA cloning, genomic organization and expression analysis during somatic embryogenesis of the translationally controlled tumor protein (TCTP) gene from Japanese larch (Larix leptolepis)

A full-length cDNA and genomic sequences of a translationally controlled tumor protein (TCTP) gene were isolated from Japanese larch (Larix leptolepis) and designated LaTCTP. The length of the cDNA was 1, 043 bp and contained a 504 bp open reading frame that encodes a predicted protein of 167 amino acids, characterized by two signature sequences of the TCTP protein family. Analysis of the LaTCTP gene structure indicated four introns and five exons, and it is the largest of all currently known TCTP genes in plants. The 5'-flanking promoter region of LaTCTP was cloned using an improved TAIL-PCR technique. In this region we identified many important potential cis-acting elements, such as a Box-W1 (fungal elicitor responsive element), a CAT-box (cis-acting regulatory element related to meristem expression), a CGTCA-motif (cis-acting regulatory element involved in MeJA-responsiveness), a GT1-motif (light responsive element), a Skn-1-motif (cis-acting regulatory element required for endosperm expression) and a TGA-element (auxin-responsive element), suggesting that expression of LaTCTP is highly regulated. Expression analysis demonstrated ubiquitous localization of LaTCTP mRNA in the roots, stems and needles, high mRNA levels in the embryonal-suspensor mass (ESM), browning embryogenic cultures and mature somatic embryos, and low levels of mRNA at day five during somatic embryogenesis. We suggest that LaTCTP might participate in the regulation of somatic embryo development. These results provide a theoretical basis for understanding the molecular regulatory mechanism of LaTCTP and lay the foundation for artificial regulation of somatic embryogenesis.

Molecular cloning, expression profiles and characterization of a novel translationally controlled tumor protein in rubber tree (Hevea brasiliensis)

The translationally controlled tumor protein (TCTP) is a multi-functioning protein that carries out vital roles in various life processes. In this study, a new TCTP gene, designated as HbTCTP1, was isolated in Hevea brasiliensis. The full-length complementary DNA (cDNA) of HbTCTP1 contained a maximum open reading frame (ORF) of 507base pair (bp) encoding 168 amino acids. The sequence comparison showed that the deduced HbTCTP1 indicated high identities to plant TCTP proteins, and clustered in the dicot cluster of plant TCTPs. Although HbTCTP1 and human TCTP proteins did not parallel in overall sequence similarity, they indicated highly similar 3D structures with a nearly identical spatial organization of α-helices, β-sheets, and coil regions. Real time reverse-transcription PCR (RT-PCR) analyses showed that HbTCTP1 was expressed throughout different tissues and developmental stages of leaves. Besides being related to tapping panel dryness (TPD), the HbTCTP1 transcripts were regulated by various treatments, including drought, low temperature, high salt, ethrel (ET), wounding, H2O2, and methyl jasmonate (Me-JA) treatments. The recombinant HbTCTP1 fusion protein was shown to protect supercoiled plasmid DNA from damages induced by metal-catalyzed generation of reactive oxygen species. The (45)Ca(2+)-overlay assay showed that HbTCTP1 was a calcium-binding protein. Our results are greatly helpful in understanding the molecular characterization and expression profiles of HbTCTP1, and lay the foundation for further analyzing the function of HbTCTP1 in rubber tree.

Translationally controlled tumour protein (TCTP) is present in human cornea and increases in herpetic keratitis

BACKGROUND

Translationally controlled tumour protein is a multifunctional calcium binding protein which has an important role in apoptosis, calcium levels balance and immunological response. The aim of this study was to evaluated the presence and distribution of TCTP in healthy human corneas and to identify and characterize the presence and distribution of this protein in human normal cornea. Since recent studies suggest that apoptosis, calcium levels and immunological mechanisms play a role in the pathogenesis of herpetic stromal keratitis, we studied TCTP expression in this disease.

METHODS

We evaluated the expression of TCTP at both RNA messanger and protein level by using reverse transcriptase analysis, immunoblotting and immunohistochemistry in 10 healthy samples cornea: four obtained after penetrating keratoplasty and six from eyes enucleated for other pathologies. Finally, we analysed by immunohistochemistry ten paraffin-embedded samples of Herpes simplex virus keratitis collected at Siena Department of Human Pathology and Oncology: 5 had clinically quiescent disease and 5 had active corneal inflammation.

RESULTS

Reverse transcriptase and immunoblotting demonstrated TCTP expression in cornea as a 22,000 Da molecular weight band corresponding to the molecular weight of this protein. Immunohistochemically, all the layers of normal corneal epithelium showed TCTP cytoplasmic expression. TCTP was, also, observed in keratocytes and in the endothelium. In Herpes simplex virus keratitis samples, strong expression of TCTP was evident in stromal cells, in the inflammatory infiltrate and in neo-vessels.

CONCLUSIONS

In this preliminary study we demonstrated, for the first time, the presence of TCTP in human cornea, suggesting a potential role in the pathogenesis of herpes virus keratitis.

VIRTUAL SLIDES

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/3306813447428149.

The calcium: an early signal that initiates the formation of the nervous system during embryogenesis

The calcium (Ca(2+)) signaling pathways have crucial roles in development from fertilization through differentiation to organogenesis. In the nervous system, Ca(2+) signals are important regulators for various neuronal functions, including formation and maturation of neuronal circuits and long-term memory. However, Ca(2+) signals are also involved in the earliest steps of neurogenesis including neural induction, differentiation of neural progenitors into neurons, and the neuro-glial switch. This review examines when and how Ca(2+) signals are generated during each of these steps with examples taken from in vivo studies in vertebrate embryos and from in vitro assays using embryonic and neural stem cells (NSCs). During the early phases of neurogenesis few investigations have been performed to study the downstream targets of Ca(2+) which posses EF-hand in their structure. This opens an entire field of research. We also discuss the highly specific nature of the Ca(2+) signaling pathway and its interaction with the other signaling pathways involved in early neural development.

Expression of translationally controlled tumor protein (TCTP) in the uterus of mice of early pregnancy and its possible significance during embryo implantation

BACKGROUND

Translationally controlled tumor protein (TCTP) is a highly conserved, growth-related protein. Previous studies showed that TCTP is involved in many biological processes and it is essential for early embryo development and proliferation of embryonic stem cells. However, whether TCTP plays a role during embryo implantation remains unclear. This paper examines the expression and the role of TCTP in the uterus of mice during early pregnancy.

METHODS

The expression of TCTP in the uterus of mice during early pregnancy was examined by quantitative real-time PCR, immunohistochemistry and western blot. A functional study of TCTP in embryo implantation of mice was also performed by intrauterine injection with antisense oligodeoxynucleotides (A-ODNs) of TCTP on day 3 (D3) of pregnancy.

RESULTS

The TCTP mRNA levels were significantly upgraded from D3 to D5 of pregnancy and reached maximum levels on D5, then dramatically decreased on D6 and D7. The levels of the TCTP protein detected by western blot were consistent with those of the mRNA. Immunohistochemistry analysis showed that the TCTP protein was mainly located in the luminal and the glandular epithelium on D1 and D2 of pregnancy and reached maximum levels on D5 in the luminal and glandular epithelium and in the stromal cells. The levels of TCTP in the pseudo-pregnant uterus of mice were lower than those of pregnant mice on D4 and D6. Furthermore, inhibiting the TCTP expression by intrauterine injection with A-ODNs of TCTP on D3 of pregnancy significantly reduced the number of the implanted embryos compared with the control.

CONCLUSIONS

This study demonstrated that TCTP may play a significant role in embryo implantation in mice.

Early neural development in vertebrates is also a matter of calcium

The calcium (Ca(2+)) signaling pathways have crucial roles in development from fertilization through differentiation to organogenesis. In the nervous system, Ca(2+) signals are important regulators for various neuronal functions, including formation and maturation of neuronal circuits and long-term memory. However, Ca(2+) signals are mainly involved in the earliest steps of nervous system development including neural induction, differentiation of neural progenitors into neurons, and the neuro-glial switch. This review examines when and how Ca(2+) signals are generated during each of these steps with examples taken from in vivo studies in vertebrate embryos and from in vitro assays using embryonic and neural stem cells. Also discussed is the highly specific nature of the Ca(2+) signaling pathway and its interaction with the other signaling pathways involved in early neural development.

Identification of reference genes across physiological states for qRT-PCR through microarray meta-analysis

Background

The accuracy of quantitative real-time PCR (qRT-PCR) is highly dependent on reliable reference gene(s). Some housekeeping genes which are commonly used for normalization are widely recognized as inappropriate in many experimental conditions. This study aimed to identify reference genes for clinical studies through microarray meta-analysis of human clinical samples.

Methodology/Principal Findings

After uniform data preprocessing and data quality control, 4,804 Affymetrix HU-133A arrays performed by clinical samples were classified into four physiological states with 13 organ/tissue types. We identified a list of reference genes for each organ/tissue types which exhibited stable expression across physiological states. Furthermore, 102 genes identified as reference gene candidates in multiple organ/tissue types were selected for further analysis. These genes have been frequently identified as housekeeping genes in previous studies, and approximately 71% of them fall into Gene Expression (GO:0010467) category in Gene Ontology.

Conclusions/Significance

Based on microarray meta-analysis of human clinical sample arrays, we identified sets of reference gene candidates for various organ/tissue types and then examined the functions of these genes. Additionally, we found that many of the reference genes are functionally related to transcription, RNA processing and translation. According to our results, researchers could select single or multiple reference gene(s) for normalization of qRT-PCR in clinical studies.

Calcium signaling in placenta

The placenta sustains the developing fetus throughout gestation and its major functions include nutrition, gas and waste exchange via a variety of passive or active mechanisms. Up to 30 g of calcium (Ca(2+)) actively crosses the trophoblast layer during human pregnancy. The Ca(2+) ion not only plays an important role for skeletal development but is also an essential second messenger. This review is intended to highlight the implications of Ca(2+) signaling during reproduction and specifically placentation. Initially, a Ca(2+) wave induces fertilization of the oocyte. The intracellular Ca(2+) concentration is key for the blastocyst implantation, proper placental development and function. Current knowledge of many proteins involved in placental Ca(2+) regulation and their function in pathologic conditions is largely limited. Recent studies, however, point to alterations in Ca(2+) homeostasis in placental pathologies such as pre-eclampsia (PE) and intrauterine growth restriction (IUGR). A broader understanding of the role of Ca(2+) signaling during human reproduction may offer insight into impaired pregnancy outcomes.

Mechanics and regulation of cell shape during the cell cycle

Many cell types undergo dramatic changes in shape throughout the cell cycle. For individual cells, a tight control of cell shape is crucial during cell division, but also in interphase, for example during cell migration. Moreover, cell cycle-related cell shape changes have been shown to be important for tissue morphogenesis in a number of developmental contexts. Cell shape is the physical result of cellular mechanical properties and of the forces exerted on the cell. An understanding of the causes and repercussions of cell shape changes thus requires knowledge of both the molecular regulation of cellular mechanics and how specific changes in cell mechanics in turn effect global shape changes. In this chapter, we provide an overview of the current knowledge on the control of cell morphology, both in terms of general cell mechanics and specifically during the cell cycle.

Genome-wide expression profile of first trimester villous and extravillous human trophoblast cells

We have examined the transcriptional changes associated with differentiation from villous to extravillous trophoblast using a whole genome microarray. Villous trophoblast (VT) is in contact with maternal blood and mediates nutrient exchange whereas extravillous trophoblast (EVT) invades the decidua and remodels uterine arteries. Using highly purified first trimester trophoblast we identified over 3000 transcripts that are differentially expressed. Many of these transcripts represent novel functions and pathways that show co-ordinated up-regulation in VT or EVT. In addition we identify new players in established functions such as migration, immune modulation and cytokine or angiogenic factor secretion by EVT. The transition from VT to EVT is also characterised by alterations in transcription factors such as STAT4 and IRF9, which may co-ordinate these changes. Transcripts encoding several members of the immunoglobulin-superfamily, which are normally expressed on leukocytes, were highly transcribed in EVT but not expressed as protein, indicating specific control of translation in EVT. Interactions of trophoblast with decidual leukocytes are involved in regulating EVT invasion. We show that decidual T-cells, macrophages and NK cells express the inhibitory collagen receptor LAIR-1 and that EVT secrete LAIR-2, which can block this interaction. This represents a new mechanism by which EVT can modulate leukocyte function in the decidua. Since LAIR-2 is detectable in the urine of pregnant, but not non-pregnant women, trophoblast-derived LAIR-2 may also have systemic effects during pregnancy.

Identification and optimization of classifier genes from multi-class earthworm microarray dataset

Monitoring, assessment and prediction of environmental risks that chemicals pose demand rapid and accurate diagnostic assays. A variety of toxicological effects have been associated with explosive compounds TNT and RDX. One important goal of microarray experiments is to discover novel biomarkers for toxicity evaluation. We have developed an earthworm microarray containing 15,208 unique oligo probes and have used it to profile gene expression in 248 earthworms exposed to TNT, RDX or neither. We assembled a new machine learning pipeline consisting of several well-established feature filtering/selection and classification techniques to analyze the 248-array dataset in order to construct classifier models that can separate earthworm samples into three groups: control, TNT-treated, and RDX-treated. First, a total of 869 genes differentially expressed in response to TNT or RDX exposure were identified using a univariate statistical algorithm of class comparison. Then, decision tree-based algorithms were applied to select a subset of 354 classifier genes, which were ranked by their overall weight of significance. A multiclass support vector machine (MC-SVM) method and an unsupervised K-mean clustering method were applied to independently refine the classifier, producing a smaller subset of 39 and 30 classifier genes, separately, with 11 common genes being potential biomarkers. The combined 58 genes were considered the refined subset and used to build MC-SVM and clustering models with classification accuracy of 83.5% and 56.9%, respectively. This study demonstrates that the machine learning approach can be used to identify and optimize a small subset of classifier/biomarker genes from high dimensional datasets and generate classification models of acceptable precision for multiple classes.

Molecular cloning and expression characterization of translationally controlled tumor protein in silkworm pupae

A Bombyx mori (B. mori) cDNA was isolated from silkworm pupae cDNA library encoding a homologue of translationally controlled tumor protein (BmTCTPk). BmTCTPk was expressed in E. coli; SDS-PAGE and Western blot showed the molecular weight of recombinant and native BmTCTPk is approximately 28 and 25 kDa, respectively; they are larger than the theoretical molecular weight. Immunohistochemical studies showed that BmTCTPk is uniformly distributed throughout the cytoplasm of BmN cells. In silkworm pupae, BmTCTPk is expressed in the midgut wall, the midgut cavity, and some fat body tissues lying between the midgut wall and body wall. Western blot and ELISAs performed on total protein extracts isolated from silkworm pupae at different development stages showed that, although BmTCTPk is expressed during all pupae stages, its expression level increases dramatically during late pupae stages, suggesting that BmTCTPk may play an important role during the developmental transition from pupa to imago.

Highly sensitive saturation labeling reveals changes in abundance of cell cycle-associated proteins and redox enzyme variants during oocyte maturation in vitro

Oocyte maturation is a complex process and a critical issue in assisted reproduction techniques (ART) in humans and other mammals. We used a sensitive 2-D DIGE saturation labeling approach including an internal pooled standard for quantitative proteome profiling of immature versus in vitro matured bovine oocytes in six independent samples. The study comprised 48 2D gel images representing 24 DIGE experiments. From 250 ng sample analyzed per gel, quantitative analysis revealed an average of 2244 spots in pH 4-7 images and 1291 spots in pH 6-9 images. Thirty-eight spots with different intensities were detected in total. Spots of a preparative gel from 2200 oocytes were identified by nano-LC-MS/MS analysis. The ten spots which could be unambiguously identified include the Ca2+-binding protein translationally controlled tumor protein, enzymes of the Krebs and pentose phosphate cycles, clusterin, 14-3-3 epsilon, elongation factor-1 gamma, and redox enzymes such as polymorphic forms of GST Mu 5 and peroxiredoxin-3. The cellular distribution of two proteins was determined by confocal laser scanning microscopy. The interesting protein candidates identified by this study may help to improve the in vitro maturation process in order to increase the rate of successful in vitro fertilization and other ART in cattle and other mammals.

Complex relationship between TCTP, microtubules and actin microfilaments regulates cell shape in normal and cancer cells

Translationally controlled tumor-associated protein (TCTP) is a ubiquitous and highly conserved protein implicated in cancers. Here, we demonstrate that interactions of TCTP with microtubules (MTs) are functionally important but indirect, and we reveal novel interaction of TCTP with the actin cytoskeleton. Firstly, immunofluorescence in Xenopus XL2 cells revealed cytoplasmic fibers stained with TCTP but not with tubulin antibodies, as well as MTs free of TCTP. Furthermore, TCTP localized to a subset of actin-rich fibers in migrating cells. Secondly, Xenopus laevis TCTP did not affect in vitro assembly/disassembly of MTs and lacked MT-binding affinity both in pull-down assays and in cell-free extracts. Although TCTP also failed to bind to purified filamentous actin (F-actin), it was associated with microfilaments in cell-free extracts. Thirdly, TCTP concentrated in mitotic spindle did not colocalize with MTs and was easily dissociated from these structures except at the poles. Finally, RNA interference knockdown of TCTP in XL2 and HeLa cells provoked drastic, MT-dependent shape change. These data show that although TCTP interacts with MTs, it does not behave as classic MT-associated protein. Our evidence for an association of TCTP with F-actin structures, and for an involvement in cell shape regulation, implicates this protein in integrating cytoskeletal interactions both in interphase and mitosis providing a new avenue to fully understand the role of TCTP.

Identification of defense-related genes in rice responding to challenge by Rhizoctonia solani

Rice sheath blight, caused by Rhizoctonia solani is one of the major diseases of rice. The pathogen infects rice plants directly through stomata or using lobate appressoria and hyphal masses called infection cushions. The infection structures were normally found at 36 h post-inoculation. During infection, the pathogenesis-related genes, PR1b and PBZ1 were induced in rice plants. To identify rice genes induced early in the defense response, suppression subtractive hybridization (SSH) was used to generate a cDNA library enriched for transcripts differentially expressed during infection by R. solani. After differential screening by membrane-based hybridization and subsequent confirmation by reverse Northern blot analysis, selected clones were sequenced. Fifty unique cDNA clones were found and assigned to five different functional categories. Most of the genes were not previously identified as being induced in response to pathogens. We examined expression of 100 rice genes induced by infection with Magnaporthe grisea, Xanthomonas oryzae pv. oryze (Xoo) and X. oryzae pv. oryzicola (Xooc). Twenty-five of them were found to be differentially expressed after the sheath blight infection, suggesting overlap of defense responses to different fungal and bacterial pathogens infection.

Solution structure and mapping of a very weak calcium-binding site of human translationally controlled tumor protein by NMR

Human translationally controlled tumor protein (TCTP) is a growth-related, calcium-binding protein. We determined the solution structure and backbone dynamics of human TCTP, and identified the calcium-binding site of human TCTP using multi-dimensional NMR spectroscopy. The overall structure of human TCTP has a rather rigid well-folded core and a very flexible long loop connected by a short two-strand beta-sheet, which shows a conserved fold in the TCTP family. The C-terminal portions of loop L(alpha3beta8) and strand beta9 and the N-terminal region of strand beta8 may form a calcium-binding site in the human TCTP structure, which is largely conserved in the sequence alignment of TCTPs. The K(d) value for the calcium binding is 0.022-0.025 M indicating a very weak calcium-binding site.

Proteome Changes in Bovine Longissimus Thoracis Muscle During the Early Postmortem Storage Period

Postmortem changes in protein composition up to 24 h in bovine longissimus thoracis muscle were investigated by two-dimensional gel electrophoresis and MALDI-TOF MS/MS. A total of 47 spots were significantly changed the first 24 h postmortem. The 39 identified proteins can be divided into five groups: metabolic enzymes, defense and stress proteins, structural proteins, proteolytic enzymes, and unclassified proteins. The identified metabolic enzymes are all associated with ATP-generating pathways, either the glycolytic pathway or energy metabolism. In addition, several defense and stress proteins were changed in abundance in this study. These findings contribute to a better understanding of the biochemical processes during postmortem storage of meat.

The expression of AmphiTCTP, a TCTP orthologous gene in amphioxus related to the development of notochord and somites

The translationally controlled tumor protein (TCTP) is highly conserved and has been widely found in eukaryotic organisms. Here, we report the phylogenetic analysis and developmental expression of AmphiTCTP, a TCTP homologous gene in cephalochordate amphioxus. Phylogenetic analysis indicates that the putative protein of AmphiTCTP is close to its vertebrate orthologs. The mRNA of AmphiTCTP is found in fertilized eggs, early cleavage embryo and most of the early developmental stages by in situ hybridization and RT-PCR, but its expression is not detectable from late cleavage stage to mid-gastrula. The expression of AmphiTCTP in zygotes and early cleavage stages shows that AmphiTCTP may be a maternal gene. From the early neurula stage onward, AmphiTCTP transcript is localized in the presumptive notochord, presomitic mesoderm, and nascent somites. However, its expression is gradually down-regulated after the notochord and somites have been formed. The expression pattern of AmphiTCTP thus coincides with the differentiation of the notochord and somites, this suggests that AmphiTCTP may not be a housekeeping gene and may play an important role in mesoderm development.

Calcium Homeostasis in Human Placenta: Role of Calcium‐Handling Proteins

The human placenta is a transitory organ, representing during pregnancy the unique connection between the mother and her fetus. The syncytiotrophoblast represents the specialized unit in the placenta that is directly involved in fetal nutrition, mainly involving essential nutrients, such as lipids, amino acids, and calcium. This ion is of particular interest since it is actively transported by the placenta throughout pregnancy and is associated with many roles during intrauterine life. At term, the human fetus has accumulated about 25-30 g of calcium. This transfer allows adequate fetal growth and development, since calcium is vital for fetal skeleton mineralization and many cellular functions, such as signal transduction, neurotransmitter release, and cellular growth. Thus, there are many proteins involved in calcium homeostasis in the human placenta.