Nucleobindin is produced by bone cells and secreted into the osteoid, with a potential role as a modulator of matrix maturation

The impact of maceration on the 'Osteo-ome'; a pilot investigation

The bone proteome, i.e., the 'osteo-ome', is a rich source of information for forensic studies. There have been advances in the study of biomolecule biomarkers for age-at-death (AAD) and post-mortem interval (PMI) estimations, by looking at changes in protein abundance and post-translational modifications (PTMs) at the peptide level. However, the extent to which other post-mortem factors alter the proteome, including 'maceration' procedures adopted in human taphonomy facilities (HTFs) to clean bones for osteological collections, is poorly understood. This pilot study aimed to characterise the impact of these 'cleaning' methods for de-fleshing skeletons on bone biomolecules, and therefore, what further impact this may have on putative biomarkers in future investigations. Three specific maceration procedures, varying in submersion time (one week or two days) and water temperature (55 °C or 87 °C) were conducted on six bovid tibiae from three individual bovines; the proteome of fresh and macerated bones of each individual was compared. The maceration at 87 °C for two days had the greatest proteomic impact, decreasing protein relative abundances and inducing specific PTMs. Overall, these results suggest that routinely-employed maceration procedures are harsh, variable and potentially threaten the viability of discovering new forensic biomarkers in macerated skeletal remains. SIGNIFICANCE: For the first time, the application of bone proteomics in understanding maceration procedures was conducted to help address the risks for experimental confounding associated with this post-mortem cleaning technique. This pilot study demonstrates that recent advances in biomarker discovery for post-mortem interval and age-at-death estimation using bone proteomics has potential for confounding by differing and destructive bone-cleaning methods.

Zinc-binding proteins in stallion seminal plasma as potential sperm function regulators

Sperm functions may be influenced by seminal plasma (SP) proteins with affinity to zinc ions. The aim of the study was to isolate and characterise zinc-binding proteins (ZnBPs) from stallion SP using proteomic tools. Zinc-binding proteins were isolated from the SP of eight stallions by zinc-affinity chromatography. They were analysed in the SDS-PAGE system, and peptide extracts were prepared. Samples of ZnBPs isolated from stallion SP were injected onto the nLC-1000 nanoflow HPLC system coupled via a nano-electrospray ion source to the Orbitrap Elite FTMS mass spectrometer (Thermo Fisher Scientific). Raw MS data were analysed using MaxQuant software with label-free quantification (LFQ). Protein sequences were obtained from the UniProt database. Forty-seven proteins in ZnBPs were annotated in a gene ontology (GO) analysis. The LFQ intensity analysis of individual proteins revealed that ZnBPs comprised mainly clusterin (CLU, 27%), serin protease inhibitor F1 (SERPINF1, 13%), actin, cytoplasmic 1 (ACTB, 9%), nucleobindin 2 (NUCB2, 8%) and polymeric immunoglobulin receptor (PIGR, 6%). This is the first proteomic study to analyse ZnBPs in stallion SP. The present findings show that ZnBPs in stallion SP could play an important role in the regulation of sperm function.

The Influence of Nesfatin-1 on Bone Metabolism Markers Concentration, Densitometric, Tomographic and Mechanical Parameters of Skeletal System of Rats in the Conditions of Established Osteopenia

Simple Summary

Nesfatin-1 is an adipokine with little known effect on the skeletal system. In this study, we examined the effect of 8-wk administration of nesfatin-1 on densitometric, tomographic, and mechanical parameters of bones, as well as the concentration of bone metabolism markers in rats with experimentally induced established osteopenia.

Abstract

Our study aimed to evaluate the impact of nesfatin-1 administration on bone metabolism and properties in established osteopenia in ovariectomized female rats. In total, 21 female Wistar rats were assigned to two groups: sham-operated (SHAM, n = 7) and ovariectomized (OVA, n = 14). After 12 weeks of osteopenia induction in the OVA females, the animals were given i.p. physiological saline (OVA, n = 7) or 2 µg/kg body weight of nesfatin-1(NES, n = 7) for the next 8 weeks. The SHAM animals received physiological saline at the same time. Final body weight, total bone mineral density and content of the skeleton were estimated. Then, isolated femora and tibias were subjected to densitometric, tomographic, and mechanical tests. Bone metabolism markers, i.e., osteocalcin, bone specific alkaline phosphatase (bALP), and crosslinked N-terminal telopeptide of type I collagen (NTx) were determined in serum using an ELISA kit. Ovariectomy led to negative changes in bone metabolism associated with increased resorption, thus diminishing the densitometric, tomographic, and mechanical parameters. In turn, the administration of nesfatin-1 led to an increase in the value of the majority of the tested parameters of bones. The lowest bALP concentration and the highest NTx concentration were found in the OVA females. The bALP concentration was significantly higher after nesfatin-1 administration in comparison to the OVA rats. In conclusion, the results indicate that nesfatin-1 treatment limits bone loss, preserves bone architecture, and increases bone strength in condition of established osteopenia.

Effect of Nesfatin-1 on Rat Humerus Mechanical Properties under Quasi-Static and Impact Loading Conditions

The investigations on the response of bone tissue under different loading conditions are important from clinical and engineering points of view. In this paper, the influence of nesfatin-1 administration on rat humerus mechanical properties was analyzed. The classical three-point bending and impact tests were carried out for three rat bone groups: control (SHO), the humerus of animals under the conditions of established osteopenia (OVX), and bones of rats receiving nesfatin-1 after ovariectomy (NES). The experiments proved that the bone strength parameters measured under various mechanical loading conditions increased after the nesfatin-1 administration. The OVX bones were most susceptible to deformation and had the smallest fracture toughness. The SEM images of humerus fracture surface in this group showed that ovariectomized rats had a much looser bone structure compared to the SHO and NES females. Loosening of the bone structure was also confirmed by the densitometric and qualitative EDS analysis, showing a decrease in the OVX bones’ mineral content. The samples of the NES group were characterized by the largest values of maximum force obtained under both quasi-static and impact conditions. The energies absorbed during the impact and the critical energy for fracture (from the three-point bending test) were similar for the SHO and NES groups. Statistically significant differences were observed between the mean F_{i max} values of all analyzed sample groups. The obtained results suggest that the impact test was more sensitive than the classical quasi-static three-point bending one. Hence, F_{i max} could be used as a parameter to predict bone fracture toughness.

Nesfatin-1-like peptide suppresses hypothalamo-pituitary-gonadal mRNAs, gonadal steroidogenesis, and oocyte maturation in fish†

Nucleobindin (Nucb)-1 and Nucb2 are DNA and Ca2+ binding proteins with multiple functions in vertebrates. Prohormone convertase-mediated processing of Nucb2 results in the production of biologically active nesfatin-1. Nesfatin-1 is involved in the regulation of reproduction in many vertebrates, including fish. Our lab originally reported a nesfatin-1-like peptide (Nlp) encoded in Nucb1 that exhibits nesfatin-1-like metabolic effects. We hypothesized that Nlp has a suppressive role in the reproductive physiology of fish. In this research, whether Nlp regulates reproductive hormones and oocyte maturation in fish were determined. Single intraperitoneal (IP) injection of goldfish Nlp (50 ng/g body weight) suppressed salmon and chicken gonadotropin-releasing hormone (sgnrh and cgnrh2), gonadotropin-inhibiting hormone (gnih) and its receptor (gnihr), and kisspeptin and brain aromatase mRNA expression in the hypothalamus of both male and female goldfish. In the pituitary, Nlp decreased mRNAs encoding lhb, fshb and kisspeptin and its receptor, while a significant increase in gnih and gnihr was observed. In the gonads, lh (only in male fish) and fsh receptor mRNAs were also significantly downregulated in Nlp-injected fish. Sex-specific modulation of gnih, gnihr, and kisspeptin system in the gonads was also observed. Nlp decreased sex steroidogenic enzyme encoding mRNAs and circulating levels of testosterone and estradiol. In addition, incubation of zebrafish ovarian follicles with Nlp resulted in a reduction in oocyte maturation. These results provide evidence for a robust role for Nlp in regulating reproductive hormones in goldfish and oocyte maturation in zebrafish, and these effects resemble that of nesfatin-1.

Cross comparison of seminal plasma proteins from cattle and buffalo (Bubalus bubalis)

The objective of this study was to evaluate seminal plasma proteins from cattle and buffalo (Bubalus bubalis), to identify differences between related species. Sixteen buffaloes and 16 cattle between 30 and 60 months of age were used. Semen collection was performed by electroejaculation, followed by macroscopic and microscopic subjective analyses. After analysis, the samples were centrifuged at 800 g for 10 min, and the supernatant (seminal plasma) was recentrifuged at 10,000 g for 30 min at 4°C. The total protein concentration was determined by the Bradford method, and the proteins were digested in solution for mass spectrometry (nLC-MS/MS). Multivariate statistical analysis was used to evaluate the proteomics results by non-hierarchical clustering the considering exponentially modified protein abundance index (emPAI). Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were used for clustering. Proteomics identified 78 proteins, and multivariate analysis showed 4 that were over-expressed in buffaloes (cystatin C, prosaposin, peptide YY and keratin type II cytoskeletal 5) and 9 in cattle (spermadhesin-1, seminal plasma protein PDC-109, ribonuclease 4, metalloproteinase inhibitor 2, acrosin inhibitor 1, seminal ribonuclease, C-type natriuretic peptide, angiogenin-1 and osteopontin). Among the proteins identified in seminal plasma, the C-type natriuretic peptide and metalloproteinase inhibitors were described for the first time in buffaloes. Some protease inhibitors were found over-expressed in buffaloes, and important proteins in seminal plasma of cattle were not identified or were found at lower expression levels in buffaloes, which can contribute to reproductive performance in this species.

Neurotensin Broadly Recruits Inhibition via White Matter Neurons in the Mouse Cerebral Cortex: Synaptic Mechanisms for Decorrelation

The neuropeptide, neurotensin (NT), inhibits UP state generation in the cerebral cortex and temporally restricts the response to thalamic input, likely by a generalized increase in inhibition. To investigate the cellular and circuit substrate(s) for how a neuropeptide can shift the balance between cortical excitation and inhibition, we performed whole-cell recordings on slice preparations from mice expressing enhanced green fluorescent protein under control of the promoter for the homeobox gene, lhx6 (lhx6-EGFP mice). These mice identify the 2 largest classes of cortical interneurons; FS and low-threshold-spiking inhibitory neurons. In the presence of NT, both types of lhx6-EGFP neurons were excited through a direct, Na+-dependent depolarization, and through an increase in synaptic excitation. Paired recordings identified cortical white matter (WM) neurons as a source of this excitatory input, which was strengthened in the presence of NT. NT-driven increased synaptic input caused a functional decorrelation of gap junction transmission between lhx6-EGFP neuron pairs. Finally, the synaptic transmission between pyramidal cells and lhx6-EGFP neurons was modulated by addition of NT in favor of stronger inhibition and weaker excitation. These findings demonstrate the existence and functional consequences of an intracortical WM neuron projection, and suggest mechanisms underlying NT-induced promotion of wakefulness.

Nesfatin-1-like peptide is a novel metabolic factor that suppresses feeding, and regulates whole-body energy homeostasis in male Wistar rats

Nucleobindin-1 has high sequence similarity to nucleobindin-2, which encodes the anorectic and metabolic peptide, nesfatin-1. We previously reported a nesfatin-1-like peptide (NLP), anorectic in fish and insulinotropic in mice islet beta-like cells. The main objective of this research was to determine whether NLP is a metabolic regulator in male Wistar rats. A single intraperitoneal (IP) injection of NLP (100 μg/kg BW) decreased food intake and increased ambulatory movement, without causing any change in total activity or energy expenditure when compared to saline-treated rats. Continuous subcutaneous infusion of NLP (100 μg/kg BW) using osmotic mini-pumps for 7 days caused a reduction in food intake on days 3 and 4. Similarly, water intake was also reduced for two days (days 3 and 4) with the effect being observed during the dark phase. This was accompanied by an increased RER and energy expenditure. However, decreased whole-body fat oxidation, and total activity were observed during the long-term treatment (7 days). Body weight gain was not significantly different between control and NLP infused rats. The expression of mRNAs encoding adiponectin, resistin, ghrelin, cholecystokinin and uncoupling protein 1 (UCP1) were significantly upregulated, while leptin and peptide YY mRNA expression was downregulated in NLP-treated rats. These findings indicate that administration of NLP at 100 μg/kg BW reduces food intake and modulates whole body energy balance. In summary, NLP is a novel metabolic peptide in rats.

Nucleobindin 1 (NUCB1) is a Golgi-resident marker of neurons

Nucleobindin 1 (NUCB1; also known as CALNUC or NUC) is a putative DNA- and calcium-binding protein and exhibits significant structural homology with the protein nucleobindin 2 (NUCB2; also known as nesfatin). While NUCB2 has been mapped in detail in the brain and implicated in the hypothalamic control of energy metabolism, no study has to date addressed the presence of NUCB1 in the central nervous system. Here we have explored the expression and distribution of NUCB1 in the rat brain and spinal cord, using RT-PCR, immunofluorescence and in situ hybridization. NUCB1 mRNA and protein was found to be present in all brain regions, extending to the spinal cord and dorsal root ganglia. Double-staining for NUCB1 and NeuN, glial fibrillary acidic protein and myelin basic protein revealed that NUCB1 is exclusively found in neurons, and not in glial or ependymal cells. Notably, NUCB1-immunoreactivity was observed in all neurons examined, making no distinction between previously identified glutamatergic and GABAergic populations, including those that are known not to stain for NeuN. This included the markedly more restricted population of NUCB2-expressing neurons in the brain. The protein was detected in cell somata and proximal dendrites, but not in axons or terminal structures. Further examination of the subcellular distribution of NUCB1 using organelle-specific markers revealed its consistent presence in the Golgi apparatus. These findings identify NUCB1 as a novel pan-neuronal marker. Along with the recent demonstration of broad expression of the protein in endocrine cells, the present results suggest that NUCB1 may play a role in spatiotemporal calcium handling in signaling cells.

The novel pro-osteogenic activity of NUCB2(1-83.)

NUCB2^1–83 has been recently reported as an anorexigenic and anti-hyperglycemic peptide. Here we report that NUCB2^1–83 promotes osteogenesis. It was found after two months of once-a-day intravenous injection of NUCB2^1–83, bone mineral density of femora and lumbar vertebrae were increased in ovariectomized rats. NUCB2^1–83 also increased the alkaline phosphatase activity and promoted mineralization in mouse MC3T3-E1 preosteoblastic cell line. When either both Arg⁶⁰ and Arg⁶³ or Ser⁷² were mutated to Ala, the pro-osteogenic activity was completely lost, indicating that these residues are structurally important for its biological function. Furthermore, it encumbered osteoclastic differentiation of RAW 264.7 macrophage. It also excluded any possibility of the effect caused by contaminants or experimental faults, and demonstrated that the pro-osteogenic activity observed was a specific effect of NUCB2^1–83 itself. These findings warranted that further studies on NUCB2^1–83 would be valuable for the treatment of bone metabolic diseases especially for osteoporosis.

Nucleobindins: bioactive precursor proteins encoding putative endocrine factors?

The nucleobindins, nucleobindin 1 (NUCB1) and nucleobindin 2 (NUCB2), are homologous multidomain calcium and DNA binding proteins. NUCB1 is a well-characterized Golgi protein found within the rat pituitary, liver and kidney with functions related to immunity, calcium homeostasis and G protein signaling. NUCB2 is found both in the hypothalamus and brain stem centers, as well as peripherally in the digestive tract. Renewed interest in the nucleobindins has been sparked by the recent discovery of nesfatin-1, an endocrine factor post-translationally processed from the N-terminal of NUCB2. Nesfatin-1 has quickly established itself as a novel regulator of appetite, insulin secretion, energy homeostasis and reproduction with important consequences to the etiology of metabolic diseases including diabetes and obesity. The discovery of nesfatin-1 and it endocrine functions attracted more attention to the nucleobindins that are already known to have important intracellular functions. From the sequence information available, it is possible that nucelobindins itself or nesfatin-1 like peptides within the NUCB1 could also elicit nesfatin-1-like biological functions. The research on nesfatin-1 in last 5years further adds to the importance of nucleobindins as potential endocrine precursors. This review aims to summarize some of the most recent findings on the functional significance of NUCB1, NUCB2, as well as encoded proteins and highlights the questions that remain unanswered.

Organellar calcium buffers

Ca(2+) is an important intracellular messenger affecting many diverse processes. In eukaryotic cells, Ca(2+) storage is achieved within specific intracellular organelles, especially the endoplasmic/sarcoplasmic reticulum, in which Ca(2+) is buffered by specific proteins known as Ca(2+) buffers. Ca(2+) buffers are a diverse group of proteins, varying in their affinities and capacities for Ca(2+), but they typically also carry out other functions within the cell. The wide range of organelles containing Ca(2+) and the evidence supporting cross-talk between these organelles suggest the existence of a dynamic network of organellar Ca(2+) signaling, mediated by a variety of organellar Ca(2+) buffers.

Extracellular proteomes of M-CSF (CSF-1) and GM-CSF-dependent macrophages

Macrophage colony-stimulating factor (M-CSF) (also known as CSF-1) and granulocyte-macrophage colony-stimulating factor (GM-CSF) have distinct effects on macrophage lineage populations, which are likely to be contributing to their functional heterogeneity. A comparative proteomic analysis of proteins released into culture media from such populations after M-CSF and GM-CSF exposure was carried out. Adherent macrophage populations, termed bone marrow-derived macrophage (BMM) and GM-BMM, were generated after treatment of murine bone marrow precursors with M-CSF and GM-CSF, respectively. Proteins in 16-h serum-free conditioned media (CM) were identified by two-dimensional gel electrophoresis and mass spectrometry. Respective protein profiles from BMM and GM-BMM CM were distinct and there was the suggestion of a switch from primarily signal peptide-driven secretion to non-classical secretion pathways from BMM to GM-BMM. Extracellular expression of cathepsins (lysosomal proteases) and their inhibitors seems to be a characteristic difference between these macrophage cell types with higher levels usually observed in BMM-CM. Furthermore, we have identified a number of proteins in BMM-CM and GM-BMM-CM that could be involved in various tissue regeneration and inflammatory (immune) processes, respectively. The uncharacterized protein C19orf10, a protein found at high levels in the synovial fluid of arthritis patients, was also differentially regulated; its extracellular levels were upregulated in the presence of GM-CSF.

Early over expression of messenger RNA for multiple genes, including insulin, in the Pancreatic Lymph Nodes of NOD mice is associated with Islet Autoimmunity

BACKGROUND

Autoimmune diabetes (T1D) onset is preceded by a long inflammatory process directed against the insulin-secreting beta cells of the pancreas. Deciphering the early autoimmune mechanisms represents a challenge due to the absence of clinical signs at early disease stages. The aim of this study was to identify genes implicated in the early steps of the autoimmune process, prior to inflammation, in T1D. We have previously established that insulin autoantibodies (E-IAA) predict early diabetes onset delineating an early phenotypic check point (window 1) in disease pathogenesis. We used this sub-phenotype and applied differential gene expression analysis in the pancreatic lymph nodes (PLN) of 5 weeks old Non Obese Diabetic (NOD) mice differing solely upon the presence or absence of E-IAA. Analysis of gene expression profiles has the potential to provide a global understanding of the disease and to generate novel hypothesis concerning the initiation of the autoimmune process.

METHODS

Animals have been screened weekly for the presence of E-IAA between 3 and 5 weeks of age. E-IAA positive or negative NOD mice at least twice were selected and RNAs isolated from the PLN were used for microarray analysis. Comparison of transcriptional profiles between positive and negative animals and functional annotations of the resulting differentially expressed genes, using software together with manual literature data mining, have been performed.

RESULTS

The expression of 165 genes was modulated between E-IAA positive and negative PLN. In particular, genes coding for insulin and for proteins known to be implicated in tissue remodelling and Th1 immunity have been found to be highly differentially expressed. Forty one genes showed over 5 fold differences between the two sets of samples and 30 code for extracellular proteins. This class of proteins represents potential diagnostic markers and drug targets for T1D.

CONCLUSION

Our data strongly suggest that the immune related mechanisms taking place at this early age in the PLN, correlate with homeostatic changes influencing tissue integrity of the adjacent pancreatic tissue. Functional analysis of the identified genes suggested that similar mechanisms might be operating during pre-inflammatory processes deployed in tissues i) hosting parasitic microorganisms and ii) experiencing unrestricted invasion by tumour cells.

A novel endoplasmic reticulum export signal: proline at the +2-position from the signal peptide cleavage site

NUCB1 (nucleobindin 1) is a Golgi-localized soluble protein with a signal peptide and multiple functional domains. We reported recently that NUCB1 is a negative regulator of the unfolded protein response that activates various endoplasmic reticulum (ER)-originating signaling pathways. In that report, we also showed that Golgi localization of NUCB1 was essential to regulate the unfolded protein response. However, the localization mechanism of NUCB1 is still unknown. Here, we report that the proline residue at the +2-position (Pro(+2)) from the signal peptide cleavage site is the determinant of NUCB1 protein export from the ER and subsequent transport to the Golgi. Fusion of the N-terminal amino acids 1-35 peptide region, including both signal peptide (amino acids 1-26) and Pro(+2), was sufficient for enhanced green fluorescent protein to localize in the Golgi, whereas single amino acid mutation of Pro(+2) resulted in defective export from the ER without affecting the protein maturation process. Furthermore, we demonstrated that Pro(+2) was important for the enhanced green fluorescent protein fusion protein to concentrate at a transport vesicle formation site within the ER, often termed the ER exit site. Interestingly, such a Pro(+2) has also been functionally conserved in other Golgi-localized soluble proteins, Cab45 (Ca(2+)-binding protein of 45 kDa), reticulocalbin 1, and calumenin. Our findings indicate that Pro(+2) can function as a novel ER export signal of some Golgi proteins.

Nucleobindin co-localizes and associates with cyclooxygenase (COX)-2 in human neutrophils

The inducible cyclooxygenase isoform (COX-2) is associated with inflammation, tumorigenesis, as well as with physiological events. Despite efforts deployed in order to understand the biology of this multi-faceted enzyme, much remains to be understood. Nucleobindin (Nuc), a ubiquitous Ca²⁺-binding protein, possesses a putative COX-binding domain. In this study, we investigated its expression and subcellular localization in human neutrophils, its affinity for COX-2 as well as its possible impact on PGE₂ biosynthesis. Complementary subcellular localization approaches including nitrogen cavitation coupled to Percoll fractionation, immunofluorescence, confocal and electron microscopy collectively placed Nuc, COX-2, and all of the main enzymes involved in prostanoid synthesis, in the Golgi apparatus and endoplasmic reticulum of human neutrophils. Immunoprecipitation experiments indicated a high affinity between Nuc and COX-2. Addition of human recombinant (hr) Nuc to purified hrCOX-2 dose-dependently caused an increase in PGE₂ biosynthesis in response to arachidonic acid. Co-incubation of Nuc with COX-2-expressing neutrophil lysates also increased their capacity to produce PGE₂. Moreover, neutrophil transfection with hrNuc specifically enhanced PGE₂ biosynthesis. Together, these results identify a COX-2-associated protein which may have an impact in prostanoid biosynthesis.

Nucleobindin 1 Controls the Unfolded Protein Response by Inhibiting ATF6 Activation

In response to endoplasmic reticulum (ER) stress, activating transcription factor 6 (ATF6), an ER membrane-anchored transcription factor, is transported to the Golgi apparatus and cleaved by site-1 protease (S1P) to activate the unfolded protein response (UPR). Here, we identified nucleobindin 1 (NUCB1) as a novel repressor of the S1P-mediated ATF6 activation. NUCB1 is an ER stress-inducible gene with the promoter region having functional cis-elements for transcriptional activation by ATF6. Overexpression of NUCB1 inhibits S1P-mediated ATF6 cleavage without affecting ER-to-Golgi transport of ATF6, whereas knock-down of NUCB1 by siRNA accelerates ATF6 cleavage during ER stress. NUCB1 protein localizes in the Golgi apparatus, and disruption of the Golgi localization results in loss of the ATF6-inhibitiory activity. Consistent with these observations, NUCB1 can suppress physical interaction of S1P-ATF6 during ER stress. Together, our results demonstrate that NUCB1 is the first-identified, Golgi-localized negative feedback regulator in the ATF6-mediated branch of the UPR.

Screening for genes regulated by gamma aminobutyric acid in hepatic stellate cells using suppression subtractive hybridization

AIM: To screen for genes regulated by gamma aminobutyric acid (GABA) in hepatic stellate cells (HSC) using suppression subtractive hybridization (SSH), and to investigate the biological function of GABA in the liver.

METHODS: The hepatic stellate cell line HSC-T6 was co-cultured with 10 μmol/L GABA for 24 h, after which mRNA was extracted and reverse transcribed into cDNA. HSC-T6 cells co-cultured with phosphate buffer saline (PBS) were used as controls. mRNAs upregulated by GABA were identified by SSH. Thirty one randomly selected clones were sequenced and analyzed bioinformatically.

RESULTS: Fifteen genes were found to be significantly up-regulated, including genes involved in DNA synthesis, apoptosis, mitochondrial function and tumor suppression. These results showed that GABA might promote HSC-T6 cell proliferation and inhibit apoptosis.

CONCLUSION: SSH technology successfully enabled the identification of genes that are differentially expressed in the presence and absence of GABA, demonstrating that GABA can affect the gene expression profiles of HSCs.

Calnuc binds to Alzheimer's beta-amyloid precursor protein and affects its biogenesis

Calnuc, a Golgi calcium binding protein, plays a key role in the constitution of calcium storage. Abnormal calcium homeostasis has been linked to Alzheimer's disease (AD). Excessive production and/or accumulation of beta-amyloid (Abeta) peptides that are proteolytically derived from the beta-amyloid precursor protein (APP) have been linked to the pathogenesis of AD. APP has also been indicated to play multiple physiological functions. In this study, we demonstrate that calnuc interacts with APP through direct binding to the carboxyl-terminal region of APP, possibly in a calcium-sensitive manner. Immunofluorescence study revealed that the two proteins co-localize in the Golgi in both cultured cells and mouse brains. Over-expression of calnuc in neuroblastoma cells significantly reduces the level of endogenous APP. Conversely, down-regulation of calnuc by siRNA increases cellular levels of APP. Additionally, we show that over-expression of calnuc down-regulates the APP mRNA level and inhibits APP biosynthesis, which in turn results in a parallel reduction of APP proteolytic metabolites, sAPP, CTFs and Abeta. Furthermore, we found that the level of calnuc was significantly decreased in the brain of AD patients as compared with that of age-matched non-AD controls. Our results suggest a novel function of calnuc in modulating the levels of APP and its proteolytic metabolites, which may further affect the patho/physiological functions of APP including AD pathogenesis.

Genes with greater up-regulation in the fracture callus of older rats with delayed healing

The rate of bone formation to bridge a fracture gap slows with age. To explore potential pathogenic mechanisms and possible negative-feedback responses by the skeleton to this reduced rate of healing, mRNA transcripts up-regulated more and/or longer were studied in older rats with delayed healing. Female rats at 6 (young), 26 (adult), and 52 (old) weeks of age received unilateral diaphyseal femoral fractures with intramedullary rod stabilization. At 0, 0.4, 1, 2, 4, and 6 weeks after fracture, the fracture site was harvested. Total RNA was extracted, cRNA was prepared, and the cRNA was hybridized to 54 Affymetrix U34A microarrays (three arrays/age/time point). Transcripts for 180 genes were identified as up-regulated more and/or longer in old rats with delayed fracture healing. Of these, 60 were selected for more intense review. Significantly more and/or longer expression was seen in genes related to myofibroblasts, cell proliferation, calcification inhibition, TGF-beta activity, lipid metabolism, cell adhesion, and the cytoskeleton. Further study is needed to determine if these up-regulated transcripts are related to the pathological processes which slow healing or are related to attempts by the fracture tissue to stimulate bone to bridge the fracture gap.

Proteomic analysis of cisplatin-induced cochlear damage: Methods and early changes in protein expression

To identify early changes in protein expression associated with cisplatin ototoxicity, we used two dimensional-difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption-time-of-flight (MALDI-TOF) mass spectrometry to analyze proteins from P3 rat cochleae that were cultured for 3h with or without 1mM cisplatin. Replicate analysis of fluorescent images from six gels revealed significant (p<0.01) cisplatin-induced changes (greater than 1.5-fold) in expression of 22 cochlear proteins. These include increases in the expression of five proteins, four of which were identified as nucleobindin 1, a nuclear calcium signaling and homeostasis protein (2.1-fold), heterogeneous nuclear ribonucleoprotein C, an RNA processing protein (1.8-fold), a 55 kDa protein that is either endothelial differentiation-related factor 1 or alpha-6 tubulin (1.7-fold), and calreticulin, a calcium binding chaperone of the endoplasmic reticulum (ER, 1.6-fold). The expression of 17 proteins was significantly (p<0.01) decreased by greater than 1.5-fold. These include ribonuclease/angiogenin inhibitor 1 (1.6-fold), RAS-like, family 12 (predicted), ras association (RalGDS/AF-6) domain family 5 (4.5-fold), homologous the RAS family of GTPase signaling proteins (2.4-fold), and Protein tyrosine phosphatase domain containing 1 (predicted, 6.1-fold). We identified seven cochlear proteins with either smaller (1.2-1.5-fold) or less significant (p<0.05) cisplatin-induced changes in expression. Notably, heat shock 70 kDa protein 5 (Hspa5, Grp78, and BiP), an ER chaperone protein involved in stress response, decreased 1.7-fold. We observed changes consistent with phosphorylation in the level of isoforms of another ER stress-induced protein, glucose-regulated protein Grp58. Changes in cisplatin-induced protein expression are discussed with respect to known or hypothesized functions of the identified proteins.

A comprehensive proteomic analysis of the accessory sex gland fluid from mature Holstein bulls

The expression of proteins in accessory sex gland fluid (AGF) of proven, high use mature Holstein bulls was evaluated. Thirty-seven bulls with documented fertility based on their non-return rates were studied. AGF was obtained by artificial vagina after bulls were surgically equipped with cannulae in the vasa deferentia. Samples of AGF were evaluated by two-dimensional SDS-PAGE, gels stained with Coomassie blue and polypeptide maps analyzed by PDQuest software. A master gel generated by the software representing the best pattern of spots in the AGF polypeptide maps was used as a reference for protein identification. Proteins were identified by Western blots and capillary liquid chromatography-nanoelectrospray ionization tandem-mass spectrometry (CapLC-MS/MS). The product ion spectra were processed using Protein Lynx Global Server 2.1 prior to database search with both PLGS and MASCOT (Matrix Science) software. The entire NCBI database was considered for mass fingerprint matching. An average of 52+/-5 spots was detected in the AGF 2D gels, which corresponded to proteins potentially involved in capacitation (bovine seminal plasma protein-BSP-A1/A2 and A3, BSP 30 kDa, albumin); sperm membrane protection, prevention of oxidative stress, complement-mediated sperm destruction and anti-microbial activity (albumin, clusterin, acidic seminal fluid protein--aSFP, 5'-nucleotidase--5'-NT, phospholipase A2--PLA2); acrosome reaction and sperm-oocyte interaction (PLA2, osteopontin); interaction with the extracellular matrix (tissue inhibitor of metalloproteinase 2, clusterin) and sperm motility (aSFP, spermadhesin Z13, 5'-NT). The 20 spots distinguished in all gels were matched to proteins associated with these functions. Proteins identified by tandem mass spectrometry as ecto-ADP-ribosyltransferase 5 and nucleobindin, never described before in the accessory sex gland secretions, were also detected. In summary, we identified a diverse range of components in the accessory sex gland fluid of a select group of Holstein bulls with documented fertility. Known characteristics of these proteins suggest that they play important roles in sperm physiology after ejaculation.

Phosphoproteins of the chicken eggshell calcified layer

The chicken eggshell matrix is a complex mixture of proteins and proteoglycans. It also contains phosphoproteins that are thought to affect mineralization of the matrix. Several of the matrix phosphoproteins, such as the major component osteopontin, have already been identified as phosphoproteins in other tissues, but the phosphorylation status of the eggshell matrix forms was unknown. The phosphopeptides, obtained after cleavage of the matrix proteins with several different cleavage methods, were enriched by anion-exchange chromatography and reversible binding to titanium oxide and identified by LC-MS(n) or pseudo-MS(n) analysis following neutral loss scanning. Altogether we identified 39 phosphorylated matrix proteins, 22 of which were not known to be phosphorylated before. Eight of the proteins were identified as eggshell matrix components for the first time. Together these proteins contained more than 150 different phosphorylation sites, 103 of which were determined with high confidence. Among the major phosphorylated proteins of the chicken eggshell matrix were osteopontin and the eggshell-specific proteins ovocleidin-17, ovocleidin-116, and ovocalyxin-32.

Proteins of the accessory sex glands associated with the oocyte-penetrating capacity of cauda epididymal sperm from holstein bulls of documented fertility

We previously reported that accessory sex gland fluid (AGF) from high fertility (HF) bulls influenced the oocyte-penetrating capacity of cauda epididymal sperm from low fertility (LF) bulls, based on in vitro fertilization (IVF) assays. The present study determined if AGF proteins were associated with these effects. Nineteen IVF assays with 12 bulls were grouped as follows. Group I (n = 8): assays where sperm from LF bulls exposed to AGF from HF bulls had greater oocyte penetration than exposed to homologous AGF. Group II (n = 7): sperm from LF bulls to AGF from HF bulls versus homologous AGF showed no significant differences. Group III (n = 4): sperm from LF bulls treated with homologous AGF had greater fertility than sperm treated with AGF from HF bulls. Sire fertility was based on nonreturn rates (NNR) and AGF collected by artificial vagina from bulls with cannulated vasa deferentia. Two-dimensional SDS-PAGE maps of AGF were analyzed by PDQuest and proteins identified by tandem mass spectrometry and Western blots. Differences in spot intensity between AGF of HF and LF bulls were compared across groups of IVF assays (P < 0.05). The expression of BSP A1/A2 and A3, BSP 30 kDa, clusterin, albumin, phospholipase A(2) (PLA(2)), and osteopontin was greater in the AGF of HF bulls in Group I as compared to Groups II and III. Conversely, there was less nucleobindin in the AGF of HF bulls in Group I than in Groups II and III. This is the first report of nucleobindin (58 kDa/pI 5.6) in male reproductive fluids, using both immunoblots and mass spectrometry. Thus, the effect of AGF from HF bulls on epididymal sperm is likely the result of specific proteins expressed in the AGF.

A proteomic analysis of protein variations during differentiation of v-myb-transformed monoblasts

v-myb oncogene of avian myeloblastosis virus (AMV) transforms myelomonocytic cells in vitro and induces acute monoblastic leukemia in vivo. The transforming effect of the v-myb can be suppressed using phorbol ester (TPA) or histone deacetylase inhibitor trichostatin A (TSA), the inducers of cell differentiation that are in clinical trials. In this study, we used proteomics-based approach to identify proteins with variable expression in differentiated BM2 cells. Proteome variations induced by TPA and TSA were compared to examine the mechanism of differentiation-promoting effects of these drugs. We found that expression of several proteins participating in cell cytoskeleton rearrangement, heat shock response, proteosynthesis and cell signaling was altered in TPA- or TSA-treated cells. We present here the first comparative proteome analysis of v-myb-transformed monoblasts BM2 focused on identification of proteins involved in their terminal differentiation.

Proteomic analysis of the acid-soluble organic matrix of the chicken calcified eggshell layer

The major difference between inorganic minerals and biominerals is the presence of an organic matrix consisting of proteins, glycoproteins, proteoglycans, and polysaccharides, which is synthesized by specialized cells under genetic control before or during mineralization. The organic matrix is thought to play a major role in the assembly of the biomineral and determination of its mechanical properties. The recent elucidation of the chicken genome provided an opportunity to explore the matrix proteome of a biomineral using up-to-date MS-based technology. We identified 520 proteins in this matrix including the ten matrix proteins already known before. The identified proteins were divided into three abundance groups using the exponentially modified protein abundance index described recently which was roughly calibrated with the few known data on protein yield derived from Edman sequence analysis. A small group of 32 highly abundant proteins contained the presently known eggshell-specific proteins and all of the other known eggshell matrix constituents identified before with much less sensitive conventional methods. The present study, which is the first comprehensive proteomic study of a vertebrate biomineral, is intended as a starting point for the detailed molecular characterization of eggshell matrix proteins, their interactions in the matrix network and functional studies.

Identification of nesfatin-1 as a satiety molecule in the hypothalamus

The brain hypothalamus contains certain secreted molecules that are important in regulating feeding behaviour. Here we show that nesfatin, corresponding to NEFA/nucleobindin2 (NUCB2), a secreted protein of unknown function, is expressed in the appetite-control hypothalamic nuclei in rats. Intracerebroventricular (i.c.v.) injection of NUCB2 reduces feeding. Rat cerebrospinal fluid contains nesfatin-1, an amino-terminal fragment derived from NUCB2, and its expression is decreased in the hypothalamic paraventricular nucleus under starved conditions. I.c.v. injection of nesfatin-1 decreases food intake in a dose-dependent manner, whereas injection of an antibody neutralizing nesfatin-1 stimulates appetite. In contrast, i.c.v. injection of other possible fragments processed from NUCB2 does not promote satiety, and conversion of NUCB2 to nesfatin-1 is necessary to induce feeding suppression. Chronic i.c.v. injection of nesfatin-1 reduces body weight, whereas rats gain body weight after chronic i.c.v. injection of antisense morpholino oligonucleotide against the gene encoding NUCB2. Nesfatin-1-induced anorexia occurs in Zucker rats with a leptin receptor mutation, and an anti-nesfatin-1 antibody does not block leptin-induced anorexia. In contrast, central injection of alpha-melanocyte-stimulating hormone elevates NUCB2 gene expression in the paraventricular nucleus, and satiety by nesfatin-1 is abolished by an antagonist of the melanocortin-3/4 receptor. We identify nesfatin-1 as a satiety molecule that is associated with melanocortin signalling in the hypothalamus.

Definition and spatial annotation of the dynamic secretome during early kidney development

The term "secretome" has been defined as a set of secreted proteins (Grimmond et al. [2003] Genome Res 13:1350-1359). The term "secreted protein" encompasses all proteins exported from the cell including growth factors, extracellular proteinases, morphogens, and extracellular matrix molecules. Defining the genes encoding secreted proteins that change in expression during organogenesis, the dynamic secretome, is likely to point to key drivers of morphogenesis. Such secreted proteins are involved in the reciprocal interactions between the ureteric bud (UB) and the metanephric mesenchyme (MM) that occur during organogenesis of the metanephros. Some key metanephric secreted proteins have been identified, but many remain to be determined. In this study, microarray expression profiling of E10.5, E11.5, and E13.5 kidney and consensus bioinformatic analysis were used to define a dynamic secretome of early metanephric development. In situ hybridisation was used to confirm microarray results and clarify spatial expression patterns for these genes. Forty-one secreted factors were dynamically expressed between the E10.5 and E13.5 timeframe profiled, and 25 of these factors had not previously been implicated in kidney development. A text-based anatomical ontology was used to spatially annotate the expression pattern of these genes in cultured metanephric explants.

Heat-induced retrieval of immunogold labeling for nucleobindin and osteoadherin from Lowicryl sections of bone

The main purpose of this study was to examine whether antigens can be retrieved by heating Lowicryl sections of paraformaldehyde-fixed (PFF) tissues. Thus the intensity of the immunogold signal for two bone proteins (Nucleobindin (Nuc) and osteoadherin (OSAD)) was compared in retrieved and non-retrieved sections of PFF rat bone. As an additional experiment, the effect of antigen retrieval (for Nuc) in sections of tissue primary stabilized by high pressure freezing with subsequent freeze substitution (HPF-FS) was studied. Finally, the tissue distribution patterns of Nuc labeling were compared in non-retrieved HPF-FS sections to that of retrieved and non-retrieved PFF sections. Antigen retrieval in Lowicryl sections of PFF tissues showed significantly enhanced labeling intensity for both proteins in all compartments where they are known to occur. Retrieved PFF Lowicryl sections showed only minor ultrastructural differences compared to non-retrieved ones. Retrieval of HPF-FS sections exhibited no enhancement of labeling but rather a slight reduction, which was significant in the cytoplasm and in cartilage. Furthermore, striking ultrastructural differences were observed in retrieved HPF-FS sections compared to non-retrieved ones with loss of coherence and structure in sections subjected to heating. Comparison of the distribution patterns of Nuc in the sections of PFF and HPF-FS tissues showed discrepancy in most compartments. Antigen retrieval by heating Lowicryl sections of PFF tissues significantly enhances immunogold labeling in all cell compartments where the bone proteins are known to occur. However, the procedure may distort the tissue distribution pattern of bone proteins.